88
Chapter 3: Atmosphere chemistry application 61 3.2 Series of papers

Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

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Page 1: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 3 Atmosphere chemistry application

61

32 Series of papers

Chapter 3 Atmosphere chemistry application

62

321 A computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates

Presentation of the article

TitleA computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates

Authors Sarrami F Mackenzie Rae FA and Karton A

Journal International Journal of Quantum Chemistry 2018 118 e25599

DOI httpsdxdoiorg 101002qua25599 Date of Publication February 2018

Graphical TOC

63

58

59

60

61

62

63

64

65

Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

68

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

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Page 2: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 3 Atmosphere chemistry application

62

321 A computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates

Presentation of the article

TitleA computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates

Authors Sarrami F Mackenzie Rae FA and Karton A

Journal International Journal of Quantum Chemistry 2018 118 e25599

DOI httpsdxdoiorg 101002qua25599 Date of Publication February 2018

Graphical TOC

63

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59

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62

63

64

65

Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

68

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

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818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

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M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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Page 3: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

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Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

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Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

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Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

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J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 4: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

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Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

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Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

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Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 5: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

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Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

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Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

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2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 6: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

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Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

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Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

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Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

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2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

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Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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Page 7: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

61

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Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

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74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

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86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

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Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

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Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

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Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

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MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

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2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

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Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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Page 8: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

62

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Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

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74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

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Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

References

132

24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 9: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

63

64

65

Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

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73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

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83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

References

132

24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

References

133

49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 10: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

64

65

Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

68

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

References

132

24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

References

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

References

134

69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 11: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

65

Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

68

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

2018 71 238

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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 12: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 3 Atmosphere chemistry application

66

322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Presentation of the article

Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol

Authors Sarrami F Yu LJ Wan W and Karton A

Journal Chemical Physics Letter 2017 675 27-34

DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017

Graphical TOC

67

68

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

References

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

2018 71 238

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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 13: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

67

68

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991

94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

2018 71 238

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137

131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 14: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

68

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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138

151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 15: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

69

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

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Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 16: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

70

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 17: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

71

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 18: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

72

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 19: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

73

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 20: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

74

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 21: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

75

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction

Boron like carbon forms stable covalently bonded molecular frameworks

through self-bonding a typical example being polyhedral cluster structures

possessing a unique stereochemistry Polyhedral heteroboranes have been the subject

of intense research for over 55 years 231232233234235 A subset of this extensive class

of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes

(an abbreviation of the IPUAC name carbaboranes) having the general formula

C2B10H12

Carborane clusters were first reported in the 1960s and since then this area has

experienced enormous growth Many new synthetic procedures have been

developed236237238239240241 The synthetic advances bonding theories of boron

clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy

and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion

extraction super acid chemistry 245 conducting organic polymers coordination

polymers and others

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 22: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

76

411 Introduction to Thermochemistry of icosahedral

closo-dicarboranes

Highest members of this class of compounds are dicarba-closo-dodecaboranes

commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)

having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)

para isomers which differ in the relative positions of the carbon atoms in the cluster

The structures of the three isomers for carborane are shown in Figure 41 The clusters

have nearly icosahedral geometry in which each of the carbon and boron atoms are

hexacoordinate

Figure 41 ortho (1) meta (2) and (3) para-Carborane

The synthesis of ortho-carborane was first reported in 1963 by two groups246247

Ortho-carboranes are prepared by the reaction of acetylenes including both mono and

substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a

weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are

prepared by thermal isomerization of ortho-carborane under an inert atmosphere At

400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to

the para-isomer between 600ndash700degC The mechanism of isomerization has been the

subject of considerable interest248249250251252 The structural properties of such species

are still not clearly understood especially for systems comprising large clusters which

are not always amenable from direct structural investigations such as those utilizing X-

ray and electron diffraction techniques There have been only a small number of

correlated ab initio investigations of their thermochemical properties

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

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Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 23: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

77

One of the goals of the present paper was to re-evaluate the stability of the

icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH

and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol

W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic

CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles

and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1

range for molecules that have wave functions dominated by dynamical correlation We

obtained heats of formation (

isomerization energies ionization potentials and CndashH and BndashH bond dissociation

energies for the carborane isomers using the high-level ab initio W1ndashF12

thermochemical protocol To the best of our knowledge the thermochemical properties

of the carboranes have not been previously studied at the CCSD(T)CBS level of theory

Thus this investigation provides the most accurate thermochemical values that are

presently available for these compounds Our best W1ndashF12 heats of formation

According to these W1ndashF12 values the meta isomer is less stable than the para isomer

by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865

kcal molndash1 These isomerization energies are in reasonably good agreement with

previous theoretical values obtained at much lower levels of theory Finally we

evaluated the performance of a range of lower cost Gn and CBS composite ab initio

procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance

ratio with an overall RMSD of only 027 kcal molndash1

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

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Page 24: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 4 Thermochemistry of icosahedral closo-dicarboranes

78

412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Presentation of the article

Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective

Authors Sarrami F Yu LJ and Karton A

Journal Canadian Journal of Chemistry 2016 94 1082-1089

DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

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13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

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Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

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2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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Page 25: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

79

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

References

132

24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

References

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

References

134

69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 26: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

80

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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138

151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

References

139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 27: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

82

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

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DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

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141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 28: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

83

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 29: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

84

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

References

132

24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

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13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 30: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

85

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 31: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

86

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 32: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

87

Chapter 5 Summary and Conclusions

This thesis examined the applications of high-level computational methods for a

range of important thermochemical and kinetic properties in organic and

biochemistry The dissertation has covered various theoretical procedures (eg ab

initio methods DFT methods and composite methods) to study specific reaction

mechanism based on 1) antioxidant activity of carnosine and vitamin E and

designing more effective candidates 2) catalytic reaction related to the atmosphere

and 3) calculation of thermochemical and kinetic properties (eg different type of

data set for isomerization energies reaction energies and their barrier heights) This

combination of these approaches gives a more in-depth understanding of the

application of high-level computational methods in chemistry biochemistry and

atmospheric chemistry A brief summary for the research presented along is

provided

Computational anti-oxidant design based on carnosin was the first project we

investigated by studying the reaction of intramolecular Br+ shift in carnosine that

from the imidazole ring and primary amine moieties The Br+ transfer is found to be

the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-

energy conformation of N-brominated carnosine Based on that results we started to

design new candidates by first) increasing the length of the β-alanyl-glycyl side-

chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring

with some electron donator and acceptor groups for both the Cl+ and Br+ shifts

(electronic effect) In addition we showed that combination of structural and

electronic effects leads to the most effective candidate For example a derivative of

carnosine in which the length of the β-alanyl-glycyl side chain is increased by one

carbon and the imidazole ring situated with a strong electron-donating group results

in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 33: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

88

In another project we investigated the mechanism for the intramolecular ring-

opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of

vitamin E) using DHDFT method The uncatalysed reaction is associated with a

high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water

catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1

respectively This catalytic efficiency can be rationalised by (i) the reduction in

strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water

catalysed and (ii) improved trajectories for the proton transfers from the

hydroxyl group to the heterocyclic oxygen This catalytic effect can be

explained by reducing the strain energy from uncatalyst to 2-water catalysed

which improves the proton transfer from hydroxyl group to heterocyclic oxygen

Based on proposed mechanism we continued to explore new potential candidate

by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen

by sulfur atom Our results showed that reducing the size of the heterocyclic ring

of the a-tocopherone to a four-membered ring not only reduces the barrier for

the ring-opening reaction but also significantly increases the thermodynamic

driving force for the overall reaction In particular for the four-membered ring

analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873

kJ mol-1 for the reactions catalysed by one and two water molecules

respectively We hope that our computational investigation will inspire further

experimental investigations of the antioxidant activity of the proposed antioxidants

In the second part of this thesis we investigated the application of high-level

computational methods for two important catalytic atmospheric reaction mechanisms

including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee

intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from

glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab

initio theoretical procedure sulphuric acid was found to effectively catalyse 14

hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived

CIs These products formed through this channel are likely to directly contribute to

organic aerosol production Conversely water was found to exhibit only a minor

catalytic effect for these 14 H-shift reactions The reaction barrier heights for the

sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

2018 71 238

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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 34: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

89

(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the

uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ

molndash1 of respectively Therefore the computational findings presented here suggest

the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee

intermediates containing a β-hydrogen resulting in the formation of vinyl

hydroperoxide Reaction with sulphuric acid is therefore likely an important

removal process for stabilized CIs in regions of high H2SO4 concentrations

In the second project of this chapter we used the high-level (G4(MP2)

composite ab initio procedure to investigate the uncatalysed water-catalysed

ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal

with two consecutive ethanol molecules to form a hemiacetal in the first step and a

dihemiacetal in the second step Introduction of a water molecule reduces the

reaction barrier for the first step by converting the strained 4-membered cyclic TS to

less strained 6-membered cyclic TS In particular we obtained an activation energy

of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid

catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This

significant reduction in the activation enthalpy is attributed to the conversion of the

6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces

the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the

activation enthalpy is attributed to the further reduction in strain energy associated

with moving from a first-row central atom to a larger second-row central atom in the

oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular

proton transfer that is coupled with the formation of a covalent CndashO bond These

findings may have significant consequences for atmospheric models since the

conversion of glyoxal to hemiacetal in the atmosphere may have important

consequences for secondary organic aerosol formation under atmospheric conditions

In the last part of my thesis we obtained heats of formation isomerization

energies ionization potentials and CndashH and BndashH bond dissociation energies for the

carborane isomers using the high-level W1ndashF12 thermochemical protocol To the

best of our knowledge the thermochemical properties of the carboranes have not

been previously studied at the CCSD(T)CBS level of theory Our best heats of

formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991

94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

References

138

151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

References

139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 35: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

90

(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash

F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1

whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1

These isomerization energies are in reasonably good agreement with previous

theoretical values obtained at much lower levels of theory These values agree with

the experimental values adopted by the NIST Chemistry Web Book to within

overlapping uncertainties however they suggest that the experimental IPs represent

underestimations Finally we evaluated the performance of a range of lower cost Gn

and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure

offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal

molndash1 for the isomerization ionization and bond dissociation energies However the

more recent G4-type procedures provide relatively poor performance with RMSDs

of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash

6X)

Although the high-level computational methods in this thesis are highly accurate

there are some limitations that have to be mentioned

1) When modelling biological systems (Chapter 2) we use simplified models in

which solvent and pH effects are treated in an approximate way (for example

with a continuum solvent model) In future work it would be good to

perform extensive Molecular Dynamic (MD) simulation to model these

effects more accurately

2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction

barrier heights and the catalytic enhancements are calculated using classical

transition state theory and tunneling effects are completely neglected In

future work it would be good to convert our accurate reaction barrier heights

into reaction rates using master equation and RRKM methods with explicit

account of tunneling effects

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 36: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

91

Chapter 6 Appendices

61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-

dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F

Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089

62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of

hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and

Karton A Chemical Physics Letters 2017 675 27-34

63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired

carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A

Journal of computer-aided molecular design 2017 31 905-913

64 Appendix D Online Supplementary Information for ldquo A computational investigation of the

sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by

Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry

2018 118 25599

65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-

catalysed ring-opening reaction of vitamin E by means of double-hybrid density

functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical

Physics Letters 2018 708 123

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

References

136

115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991

94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

2018 71 238

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137

131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

References

138

151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

References

139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 37: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

92

66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for

π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A

and OrsquoReilly RJ Molecular Physics 2015113 1284-1296

67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for

cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab

initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical

Physics 2015 458 1-8

68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all

aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ

Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33

69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and

physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen

storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari

M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426

610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel

auto-combustion synthesis characterization and joint experimental and

computational structural analysis for electrochemical hydrogen storage

performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T

Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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134

69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

References

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991

94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 38: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

93

611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of

hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated

graphene oxide using density functional theory molecular dynamics simulation and

experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K

Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

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Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

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Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

References

139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 39: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

94

61 Appendix A Electronic Supplementary Information

Thermochemistry of icosahedral closo-

dicarboranes A composite ab initio quantum-

chemical perspective

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

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Page 40: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

95

Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main

text)a

aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for

further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)

TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12

para 15 19 C2B10H12 meta 15 19

ortho 16 20 para 18 22

C2B10H12+ meta 17 21

ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20

C2B10H12bull meta B9bulld 16 20 meta Cbulld

16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

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DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

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141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 41: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

96

Table S2 Deviations and overall error statistics from W1-F12 values of

isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies

for carboranes obtained by standard ab initio methods (kcal molndash1)

QCISD(T)

CCSD(T) SCF SCF

6-31G(d) 6-31G(d) 6-31G(d) VTQZa

Isomerization meta 021 021 -030 -040

ortho 064 065 183 163

Ionization para -488 -445 -1748 -1484

meta -548 -577 -1938 -1790

ortho -522 -547 -1446 -1748

CndashH BDE para 020 032 -1602 -1590

meta 005 019 -1584 -1566

ortho 007 023 -1506 -1493

BndashH BDE para -058 -058 -1539 -1560

meta B2ndashHb -071 -071 -1541 -1555

meta B4ndashHb -064 -064 -1539 -1560

meta B5ndashHb -053 -053 -1535 -1561

meta B9ndashHb -056 -054 -1532 -1556

ortho B3ndashHb -072 -072 -1542 -1562

ortho B4ndashHb -060 -058 -1521 -1542

ortho B8ndashHb -054 -052 -1524 -1550

ortho B9ndashHb -048 -047 -1526 -1555

Error statisticsc RMSD 223 226 1484 1485

MAD 130 133 1402 1404

MSD -116 -114 -1380 -1385

LD -548 -577 -1938 -1790

aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

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Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem

Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem

Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 42: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

97

Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)

procedures (kcal molndash1)

G3(MP2) G4(MP2)

Isomerization meta 0 0

ortho 0 0

Ionization para 302 -048

meta 302 -048

ortho 302 -048

CndashH BDE para 175 -180

meta 175 -180

ortho 175 -180

BndashH BDE para 175 -180

meta B2ndashHa 175 -180

meta B4ndashHa 175 -180

meta B5ndashHa 175 -180

meta B9ndashHa 175 -180

ortho B3ndashHa 175 -180

ortho B4ndashHa 175 -180

ortho B8ndashHa 175 -180

ortho B9ndashHa 175 -180

aBxndashH indicates on which BndashH bond is being broken (see Figure 1)

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Page 43: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

98

Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 44: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

99

62 Appendix BElectronic Supplementary Information

Sulphuric acid-catalysed formation of hemiacetal

from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

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Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 45: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

100

Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid

Specie

Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD

Uncatalysed 157 1726 -117 23 1591 NA -203

Water 455 1482 102 364 1273 56 -203

Ethanol 400 1350 89 165 1148 07 -203

Formic acid 74 574 -180 151 598 -140 -203

Sulphuric acid 86 386 -171 179 312 -173 -203

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 46: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

101

Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

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Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

Phys 1989 90 5622

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94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 47: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

102

63 Appendix C Electronic Supplementary Information

Computational design of bio-inspired carnosine-

based HOBr antioxidants

Farzaneh Sarrami Li-Juan Yu and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia

Supplementary Data

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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134

69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka

GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys

Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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Phys

2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem

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313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 48: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

103

Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in

Table 1

Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide

atom in the REAC and INT2 (see Figure S1 for atom numbering)

APT charges

REAC

Cl+ INT2

REAC

Br+ INT2

N1 ndash0691 ndash0725 ndash0709 ndash0734

N2 ndash0002 0008 ndash0122 ndash0114

C1 0291 0282 0300 0285

C2 0015 ndash0032 0017 ndash0035

C3 0135 0188 0135 0191

H1 0123 0204 0119 0198

H2 0150 0181 0148 0173

H3 Nil 0904 Nil 0919

Imidazole ringa 0019 1011 ndash0111 0882

X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

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Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem

Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J

Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G

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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

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Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

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Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

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Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

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Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 49: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

104

Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+

transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and

Br)

Cl+ Br+

Ra N2ndashX (Aring) N2ndashX (Aring)

NO2 (078) 1764 1875

CHO (042) 1782 1890

H (00) 1790b 1893

OH (ndash037) 1804 1896

NH2 (ndash066) 1816 1900 a

p constants are given in parenthesis b

Values taken from reference 37

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

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2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 50: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

105

Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide

atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of

carnosine shown in Figure 5 of the main text (X = Cl and Br)

ap constants are given in parenthesis

Cl+ Br+

Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)

NO2 (078) +065 +063

CHO (042) +059 +055

H (00) +023 +021

OH (ndash037) ndash004 ndash006

NH2 (ndash066) ndash014 ndash016

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

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Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 51: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

106

64 Appendix D Electronic Supplementary Information

A computational investigation of sulphuric

acid-catalysed 14-hydrogen transfer in higher

Criegee intermediates

Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA 6009

Australia

Supplementary Data

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

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Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem

Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

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Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 52: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

107

Figure S1 Optimized transition structures for the uncatalysed water-catalysed and

sulphuric acid-catalysed 14 H-shift reactions in methyl CI

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

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C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 53: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

108

Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed

(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)

reactions for the 14 H-shifts of isoprene CI

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 54: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

109

Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI1

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 55: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

110

Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black

line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions

for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 56: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

111

Table S2 Full details for reference 59 (Gaussian 09)

[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

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II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 57: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

112

65 Appendix E Electronic Supplementary Information

Mechanistic insights into the water-catalysed

ring-opening reaction of vitamin E by means of

double-hybrid density functional theory

Farzaneh Sarrami Asja A Krorger and Amir Karton

School of Molecular Sciences The University of Western Australia Perth WA

6009 Australia

Supplementary Data

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

References

133

49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

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Page 58: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

113

Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

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Page 59: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

114

Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

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M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

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Page 60: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

115

Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

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Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

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Page 61: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

116

Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)

for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed

(blue line) rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

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Page 62: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

117

Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the

uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)

rearrangement reaction of candidate 2 to the related quinone

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

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Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 63: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

118

Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol

ndash1are given relative to the free reactants

Intermediate ∆G298

A ndash713 B ndash2317 C ndash2587 D ndash2283

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

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13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

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Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

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Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 64: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

119

66 Appendix F Presentation of the article

Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones

Authors Yu LJ Sarrami F Karton A

Journal Molecular Physics 113(11) 1284-1296

DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

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Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

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Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

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Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

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Page 65: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

120

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

References

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

Activity Relationship 2002 21 73

References

133

49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

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Page 66: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

121

67 Appendix G

Presentation of the article

Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo

Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal Chemical Physics 2015 458 1-8

DOI httpsdxdoiorg101016jchemphys201507005

Date of Publication September 2015

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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Page 67: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

122

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

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Page 68: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

123

68 Appendix H

Presentation of the article

Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions

Author

Yu LJ Sarrami F OrsquoReilly RJ and Karton A

Journal

Renewable Energy 2017 114 1419-1426

DOI httpsdxdoiorg1010800026897620151081418

Date of Publication

September 2015

124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

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818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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124

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

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Page 70: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

125

69 Appendix I

Presentation of the article

Title

Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory

AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A

Journal Renewable Energy 2017 114 1419-1426

DOI

httpsdxdoiorg101016jrenene201707119

Date of Publication

December 2017

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

References

131

References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik

1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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Page 71: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

126

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

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amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys

Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem

C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011

13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272

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Page 72: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

Chapter 6 Appendices

127

610 Appendix J

Presentation of the article

Title

Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances

AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton

Journal Journal of Alloys and Compounds 2018 744 574-582

DOI

httpsdxdoiorg101016jjallcom201802117

Date of Publication

May 2018

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

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Page 73: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

128

Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

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Chapter 6 Appendices

129

611 Appendix K

Presentation of the article

Title

Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods

Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton

Journal Journal of Molecular Liquids 2018 262 204-217

DOI

httpsdxdoiorg101016jmolliq201804089

Date of Publication

July 2018

130

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Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part

I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical

Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part

II Some results and discussion In Mathematical Proceedings of the Cambridge

Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson

Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced

electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991

95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51

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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139

134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am

Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980

72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ

and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett

1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure

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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy

of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD

Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo

Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature

Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci

2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A

Collection of Peer-Reviewed Research and Review Articles from Nature Publishing

Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley

amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I

J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput

2007 3(2) 407

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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

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MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

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M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

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J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 81: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991

94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997

106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999

110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem

Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999

313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem

Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000

112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys

2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo

E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam

2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem

Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991

94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem

Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem

2018 71 238

References

137

131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38

2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett

1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan

J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME

Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed

Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-

Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S

Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)

502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM

Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim

Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal

2009 11 2899

References

138

151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

References

139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 83: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

References

138

151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327

487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009

11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal

2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1

810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990

Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys

Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change

1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini

MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E

Atmos Chem Phys 2005 5(4) 1053

References

139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 84: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

References

139

173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett

2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science

Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC

Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP

and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D

Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo

PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys

Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16

1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem

Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K

Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345

1596

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 85: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

References

140

193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C

Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew

Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V

Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001

105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys

Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten

T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass

DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem

Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O

Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald

A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J

M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem

Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13

13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D

Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 86: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

References

141

209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H

Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B

G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30

2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M

Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett

2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina

MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze

J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich

MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34

L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech

2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE

Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43

818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 87: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

References

142

228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-

metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry

Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem

Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC

Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman

M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2

111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89

4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48

729

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218

Page 88: Chapter 3: Atmosphere chemistry application · Chapter 3: Atmosphere chemistry application 66 3.2.2 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol Presentation

References

143

251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218