Chemistry and Materials with the ADF modeling suite

Workshop GWU, August 12 © SCM

Chemistry & Materials with the ADF modeling suite

workshop GWUScientific Computing & Modelling NVFedor Goumans [email protected] Carstensen [email protected]

mailto:[email protected]



Outline• Background

• ADF– Spectroscopic properties– Bonding analysis

• BAND: periodic DFT

• DFTB: approximate DFT

• ReaxFF: reactive molecular dynamics

• COSMO-RS/SAC: fluid thermodynamics (logP, pKa, solubility, …)

• GUI demonstration, getting started


Amsterdam Density Functional development

• Baerends group VU, Amsterdam (>1973) • Ziegler group, Calgary (>1975)• SCM: Spin-off company (1995)

• Currently 12 people (8 senior PhD’s) + EU fellows

• Many academic collaborators / EU networks

• Development, testing, debugging, optimizing, porting, documentation, support, ..– Implement what users want– New features from academia Tom Ziegler

(1945-2015)

Evert-Jan Baerends


ADF modeling suite authors 2014E.J. Baerends, T. Ziegler, J. Autschbach, D. Bashford, A. Bérces, J.A. Berger, F.M. Bickelhaupt, C. Bo, P.L. de Boeij, P.M. Boerrigter, S. Borini, R. E. Bulo, L. Cavallo, D.P. Chong, L. Deng, R.M. Dickson, A. C. T. van Duin, D.E. Ellis, M. van Faassen, L. Fan, T.H. Fischer, C. Fonseca Guerra, M. Franchini, A. Ghysels, A. Giammona, S.J.A. van Gisbergen, M. Gorbani Asl, A.W. Götz, J.A. Groeneveld, O.V. Gritsenko, M. Grüning, S. Gusarov, F.E. Harris, T. Heine, P. van den Hoek, C.R. Jacob, H. Jacobsen, L. Jensen, E.S. Kadantsev, J.W. Kaminski, G. van Kessel, R. Klooster, F. Kootstra, A. Kovalenko, M.V. Krykunov, E. van Lenthe, J.N. Louwen, D.A. McCormack, E. S. McGarrity, A. Michalak, M. Mitoraj, S.M. Morton, J. Neugebauer, V.P. Nicu, L. Noodleman, V. P. Osinga, S. Patchkovskii, M. Pavanello, P.H.T. Philipsen, D. Post, C.C. Pye, W. Ravenek, M. de Reus, J.I. Rodríguez, P. Romaniello, P. Ros, R. Rüger, P.R.T. Schipper, H. van Schoot, G. Schreckenbach, J.S. Seldenthuis, M. Seth, D.G. Skachkov, J.G. Snijders, M. Solà, M. Swart, D. Swerhone, G. te Velde, P. Vernooijs, L. Versluis, L. Visscher, O. Visser, F. Wang, T.A. Wesolowski, E.M. van Wezenbeek, G. Wiesenekker, S.K. Wolff, T.K. Woo, A.L. Yakovlev


Dr. Olivier Visser Dr. Erik van Lenthe Dr. Alexei Yakovlev Dr. Pier PhilipsenGUI, general ADF, ZORA, COSMO ADF, ReaxFF, DFTB BAND, periodic DFTB

MSc. Hans van Schoot MSc. Mirko Franchini Dr. Ole Carstensen ReaxFF, MD, GPUs ADF, BAND technical GUI, scripting, ReaxFF

SCM software development staffVac

ancy


Dr. Stan van Gisbergen Dr. Fedor Goumans Dr. Sergio Lopez Lopez General Management Business Development Scientific Partner Manager Sales, Legal, Signatures Marketing, Technical Sales EU projects, collaborations

Mrs. Frieda Vansina Mrs. Kitty Kleinlein Office Manager Office ManagerLicense files, user interactions Bookkeeping, special projects

SCM staff – office / management / business


ADF – molecular DFT


ADF: strong points• User-friendly

– Easy install, integrated GUI, great support

• Accurate & Efficient– Slater orbitals, all-electron, all elements– heavy elements & transition metals: relativistic effects (ZORA)

• Spectroscopy– Many properties: NMR, IR, Raman, UV/Vis, X-Ray, EPR, (V)CD, ROA, ….– Advanced environment effects: FDE, RISM, (QM/MM – FlexMD)

• Chemical analysis– Energy decomposition, ETS-NOCV, charges, density properties, …

• Active developers worldwide– latest functionals, newest developments, user input


User-friendly

"The support at SCM is truly top notch." Dr. K. Skinner, Top-10 US chemical company

"... I was very impressed by the quality of the support and their efficiency..." Mr. R. David, Director HPC, University of Strasbourg

Out-of-the-box parallel binariesMac, Windows, Linux/Unix

Integrated GUI for all modulesExpert support team


ADFJobsJob type: double click to open input

Queue name

Job name

New input/Analyze output

Job status

The Graphical User Interface: key to usability


Switch between codes Calculation options & details

Search

Molecule & periodic system building tools

ADFInput



Properties



Many Spectroscopic Properties• IR frequencies and intensities, VCD

–analytical and numerical• Time-Dependent DFT (+gradients and vibronic effects)

–Closed or open shell, spin-orbit coupled (also perturbatively)–Frequency dependent (hyper-) polarizabilities (NLO)–UV/Vis, X-ray absorption (NEXAFS/XANES)– (resonance) Raman, SE(H)RS, V(R)ROA –Circular dichroism (CD), optical rotation (ORD)–Core excitations, state-selected excitations–Lifetime effects, dispersion coefficients

• NMR – chemical shifts, spin-spin couplings, finite nucleus, paramagnetic, hybrids, SOC

• ESR–G-tensor, hyperfine interaction, D-tensor (SO part) – MCD

• Nuclear-quadrupole interaction (EFG: Q-tensors, NRVS)


Insights in dinuclear metalloradical: VIS/NIR, EPR

E. F. van der Eide, P. Yang, E. D. Walter, T. Liu, and R. M. Bullock, Angew. Chem. Int. Ed. 51, 8361 (2012)

EPR


Accurate NMR: all-electron, STOs, and ZORA

L. A. Truflandier, E. Brendler, J. Wagler, J. Autschbach, 29Si DFT/NMR Observation of Spin-Orbit Effect in Metallasilatrane Sheds Some Light on the Strength of the Metal→Silicon Interaction Alkyl Complexes Angew. Chem. Int. Ed. 50, 255 (2011)

29Si

- Heavy Atom effect on Light Atom Pt→Si

- Only Spin-Orbit Couplinggets NMR spectrum right

- NBO: dative, not covalent

http://dx.doi.org/10.1002/anie.201005431

http://dx.doi.org/10.1002/anie.201005431


129Xe NMR: very sensitive probe

Bagno, Saielli (et al.) Chem. Eur. J. 18, 7341-7345 (2012); PNAS 109, 12393-12397 (2012)

Very strong deshielding by cryptophaneΔδobs = 277 ppm, Δδcalc = 281 ppm

1st spin-spin coupling via vdWJXe-H = -2.7 ± 0.6 Hz, calc. = -3.2 Hz


Recent pNMR paper: Direct Detection of 17O in Gd(DOTA)] by NMR Spectroscopy, Chem. Eur. J. 21, 1955-1960 (2015)

http://dx.doi.org/10.1002/chem.201405092




∆E = ∆Eprep + ∆Eint

∆Velstat + ∆EPauli + ∆Eoi

Analysis: Bond energy decomposition

Rev. Comput. Chem. 2000, 15, 1

Transition states/reaction pathways - activation strain theory (Bickelhaupt)

Extension: ETS-NOCV – orbital interactions + deformation densityM. Mitoraj, A. Michalak and T. Ziegler, J. Chem. Theor. Comput. 5, 962 (2009)

Periodic extension (Raupach, Tonner): molecule-surface interactions

http://www.scm.com/ChemicalAnalysis


ETS-NOCV analysis of bonding interactionsAdenine-Thymine

kcal/mol,(BP86/TZ2P)

A-T

Etotal-exp. -12.1

Etotal -other theor. -13.2

Etotal -13.0

Eorb -22.0

EPauli 38.7

Eprep 2.1

Eelstat -31.9Eorb=-22.0

R. Kurczab, M. P. Mitoraj, A. Michalak,T. Ziegler

J. Phys. Chem. A,2010, 114, 8581.

Ns*(H-N)Os*(H-N)

See ETS-NOCV Webinar (Mitoraj)

Related: L. Guillaumes, S. Simon, and C. Fonseca Guerra, The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine–Thymine (AT) Base Pairs and Their Mimics, Chemistry Open, 4, 318-327 (2015)

http://www.scm.com/Videos/Webinars/ETS-NOCV.webm



http://dx.doi.org/10.1002/open.201402132




Modeling Organic Electronics with ADF

1) OLEDs: phosphorescence2) Charge mobility (e.g. OFETs)3) PVs/DSSC: singlet fission, excitation, e- injection, regenerationpublished papers & unpublished calcs by Mr. Mori, Ryoka Inc.

http://www.scm.com/OrganicElectronics

http://www.scm.com/Products/Capabilities/OrganicElectronics.html


Hartmut YersinHartmut YersinHartmut Yersin

Y. Suzuri et al., Sci. Technol. Adv. Mater. 15 (2014) 054202. doi:10.1088/1468-6996/15/5/054202

Organic Light-Emitting Diodes

Challenges:• Optimize triplet phosphorescence rate• Minimize triplet-triplet annihilation and triplet-polaron quenching• Optimize properties of host material (higher T energy)• Optimize mobility in electron / hole transport layers• Optimize out-coupling


Phosphorescent OLED emitters: SOC-TDDFT with solvation compares well with Expt.

K. Mori, T. P. M. Goumans, E. van Lenthe, F. Wang, Phys. Chem. Chem. Phys. 16, 14523 (2014)

http://dx.doi.org/10.1039/C3CP55438D




Intersystem crossing through spin-orbit coupling in Os(II) complexes

Elise Yu-Tzu Li*, Tzung-Ying Jiang, Yun Chi and Pi-Tai Chou*. Semi-Quantitative Assessment of Intersystem Crossing Rate: An Extension of El-Sayed Rule to the Emissive Transition Metal Complexes. Phys. Chem. Chem. Phys. 16, 26184-26192 (2014)

lexc-dependent quantum yieldSOCME negligible for S1-Tn

ISC from higher Sn states

El-Sayed for organometallics: SOC is largest when:• both S (1dπ*) and T (3d’π*) are MLCT• different d-orbitals are involved (d ≠ d’).

http://pubs.rsc.org/en/content/articlelanding/2014/cp/c4cp03540b




Vibronic fine structure OLED phosphor Pt complex: vibrational progression from T1 → S0 emission

Courtesy of Mr. Kento Mori, Ryoka, unpublished results

unpublished calcs by Mr. Mori, Ryoka Inc. on TSUBAME2.0, JACI


h+

Methods to calculate charge mobilities • Hopping transport:

– Charge transfer integrals + other elements, directly printed– Electronic couplings from frozen-density embedding

• Band transport: effective mass tensors in BAND

• Non-equilibrium Green’s Function (NEGF)– transmission probabilities for single-molecule junctions– quick calculation: wide-band limit– also in BAND (periodic structures) and in DFTB (large systems) Q


Hole / electron mobilities• Ordered crystals (low T) => band-like transport

• Amorphous materials: incoherent hopping

• Accoustic deformation potential

1 me

kk

m

k2

21 1

ii

ii k

kP

mc: the effective mass along the direction of transportmd: the density of states mass, (ma mb)1/2

ac: the acoustic deformation potential, V dEvbm/dVB: the elastic modulusLeff: the length of the p-bonded core of the molecule

dcBac

eff

mmTkBLe

2

3


Effective transfer integral Jeff = electronic coupling V

• Definition of fragments • Matrix elements from ADF

C2HOMOks

C1HOMORP hJ

C2HOMO

C1HOMORP S

C1HOMOks

C1HOMORR hH

C2HOMOks

C2HOMOPP hH

extract dimer

Fragment C1

Fragment C2

Molecular crystal of pentacene

(a) “transfer integral”

(b) spatial overlap

(c) site energy

2RP

PPRRRPRP

12/

SHHSJV

orthogonalization


Anisotropic hole mobilities in pentacene

S.-H. Wen et al., J. Phys. Chem. B 113, 8813 (2009)

Anisotropic mobility：


Electronic couplings + environment with FDE:charge transfer, exciton, charge separation

Excitons: J. Chem. Phys. 138, 034104 (2013) Long range charge separation: J. Chem. Phys. 140, 164103 (2014) Charge transfer: J. Chem. Theory Comput. 10, 2546−2556 (2014)

Linear scaling, environment response, constrain charge/excitation/spin, ...

CDFT in trunk, to be extended to excited states (similar to CV-DFT)


Exciton couplings with frozen-density embedding

C. König et al., Direct determination of exciton couplings from subsystem time-dependent density-functional theory within the Tamm-Dancoff approximation, J. Chem. Phys. 138, 034104 (2013).

C. König and J. Neugebauer, Exciton Coupling Mechanisms Analyzed with Subsystem TDDFT: Direct vs. Pseudo Exchange Effects, J. Phys. Chem. B 117, 3480 (2013).

Under development in DFTB: FDE-TDDFBT (Hernandez, Visser)

http://dx.doi.org/10.1063/1.4774117

http://dx.doi.org/10.1063/1.4774117

http://dx.doi.org/10.1063/1.4774117

http://dx.doi.org/10.1021/jp3105419




Mechanism of DSSCs N3: Most typical dye

Three steps – all treated with ADF：1. Photoexcitation of dye

2. Electron injection from dye to TiO2

3. Dye regeneration


Spin-orbit coupling increases dye efficiency

SOC-TDDFT: Incident photon to current efficiency (IPCE) of Ru sensitizer DX1 increased due to spectral broadening because of SOC

S. Fantacci, E. Ronca, and F. de Angelis, Impact of Spin–Orbit Coupling on Photocurrent Generation in Ruthenium Dye-Sensitized Solar Cells, J. Phys. Chem. Lett., 5, 375-380 (2014)

http://dx.doi.org/10.1021/jz402544r






Spin-orbit coupling increases dye efficiency

SOC indispensible to describe low-energy absorption bands of Os dyes

E. Ronca, F. de Angelis, and S. Fantacci, TDDFT Modeling of Spin-Orbit Coupling in Ru and Os Solar Cell Sensitizers, J. Phys. Chem. C, just accepted

[Os(dcbpy)2(SCN)2]4-

expSR-TDDFT

SOC-TDDFT

http://dx.doi.org/10.1021/jp500869r


Rational design of dyes for p-type DSSCLight-harvesting efficiency = 1 - 10-f

Charge-separation efficiency => increase hole-e- separation

Hole-injection efficiency, Koopman’s approximation:ERP = EHOMO(dye) - E(VB)(electrode)

J. Wang et al. J. Phys. Chem. C 117, 2245−2251 (2013)


Rational design of dyes for p-type DSSC

J. Phys. Chem. C 117, 2245−2251 (2013)

Large separation e- - electrode

Alkyne-spaced-ligands (4,6) also have high f => high Light Harvesting EfficiencyHole-injection efficiency large for all ligands


Other modules in the ADF modeling Suite

• Easy to learn / install:– Same GUI– Same binary– Re-use results

• BAND: Periodic DFT• DFTB: approximate DFT• ReaxFF: reactive MD• COSMO-RS: liquid properties


BAND – periodic DFT


BAND geometries, 1-, 2, and 3-dimensional

October 2010

N3 on TiO2 - surface

Solid - PyPySPyPy – OLED material - 584 atoms in unit cell

Nanotube- chain

Zeolite - solid


BAND vs. Plane Wave codes• Atom centered basis functions, STO or NAO

– Compare cluster with periodic– No pseudopotentials, core spectrosopy– Easy (orbital) analysis– Fast for empty (1D, 2D, porous), slow for dense metallic

• True 2D surfaces:– No artifacts from 3D repetition (dipole across surface)– Continuum solvation above surface (COSMO, SM12…)– Homogeneous electric field (no sawtooth potential)– (2D-TDDFT – work in progress)


Relativity makes your car start

R. Ahuja, A. Blomqvist, P. Larsson, P. Pyykkö, and P. Zaleski-Ejgierd, Phys. Rev. Lett. 106, 018301 (2011)

- Total and partial density of states (DOS) of lead in Lead (IV) oxide

- Strong relativistic shift inboth occupied and unoccupied Pb 6s states.

- Without relativity, 12V battery would be 2.4V!

Orange = lead 6s states, Green = lead 6p states.NR = nonrelativistic, SR = scalar relativistic, SOC = 2c spin orbit coupling

SOC


Closing 2D band gaps in MoWSeS monolayers

3 eV/Å

Electron transport in MoWSeS monolayers in the presence of an external electric field, Phys. Chem. Chem. Phys. (2014)

http://dx.doi.org/10.1039/c4cp00966e

http://dx.doi.org/10.1039/c4cp00966e


DFT-D3 XC functionals in ADF&BAND

S.Grimme, J. Antony, S. Ehrlich, and H. Krieg: J. Chem. Phys. 132, 154104 (2010).

- Less empirical than earlier DFT-D-

- Asymptotically correct

- Available for elements Z = 1-94

- Dispersion coefficients and cutoff radii computed explicitly

- Dispersion coefficients independent of connectivity

- Similar or better accuracy for light elements, better for heavy ones


CH4 and H2 dissociation on Ni/γ-Al2O3

• Dissociation at interface preferred: polarization• Aluminum acts as electron donor

Li, Croiset, Ricardez-Sandoval, J. Phys. Chem. C 2013, 117, 16907


Visualization ELF• Electron Localization Function

CO on Cu(100)


STM visualization with/without bias• STM images (Tersoff-Hamann): LDOS

bias = 0.1bias = 0 Pt Ge(100)


Smooth band structure with interpolation points


Kohn-Sham gap ≠ fundamental gap => DFT underestimates band gap- underlying problem: integer derivative discontinuity in vxc

- Egap = I – A + Δxc

Possible ‘solutions’- many-body perturbation (GW) - (screened) hybrids- LDA/GGA + U (localize d, f electrons in TMO)- OEP-like exchange:

- TB-mBJ (fitted to band gaps)- GLLB-sc (includes explicit Δxc)

Fixing the band gap ‘problem’ in DFT


Accurate Band Gaps of Semiconductors and Insulators with a Semilocal Exchange-Correlation Potential Phys. Rev. Lett. 102, 226401

(2009).

Tran & Blaha’s modified Becke-Johnson (TB-mBJ)


Kohn-Sham potential with discontinuity for band gap materials M. Kuisma, J. Ojanen, J. Enkovaara, & T. T. Rantala Phys. Rev. B 82, 115106 (2010)

GLLB-sc: good band gaps for the ‘right reason’?

GLLB-sc can also be applied to 2D, 1D


PBE 1.898GLLB-sc 3.201 (Δxc = 0.92)

TB-mBJ 3.296

Non-relativistic:TB-mBJ/NR 3.494GLLB-sc/NR 3.487

Smaller basis:GLLB-sc/TZP 3.253

Exp: 3.2 eV

Fixing the GaN band gap with model potentials

(SR-TZ2P-AE, k=5 (75 k-points), acc=5)

Experimental gap


Approximate Quantum-based methods

51

DFTB ReaxFF

COSMO-RS


Density-functional Based Tight-Binding (DFTB)Fast, approximate DFT => ideal for large systems• dynamics (limited to a few elements)• electronic properties


DFTB: current capabilities• Second-order or third-order self-consistent charges (SCC, DFTB3)• Molecules, polymers, surfaces, bulk• Geometry and transition state optimization• IR, UV/VIS, phonons, (P)DOS, band structure, Mulliken analysis• Molecular Dynamics: velocity Verlet, Scaling or Berendsen thermostat• Fully integrated in GUI (pre-optimization/Hessian re-use ADF/BAND)


Time-dependent DFTB: excitation of a protein

Rüger, R., van Lenthe, E., Lu, Y., Frenzel, J., Heine, T. and Visscher, L., Efficient Calculation of Electronic Absorption Spectra by Means of Intensity-Selected Time-Dependent Density Functional Tight Binding, J. Chem. Theory Comput. 11, 157−167 (2015)

http://dx.doi.org/10.1021/ct500838h








DFTB EU projects: Propagate, MoWSeS• PROPAGATE:

– 3 PhD students Bremen-VU-SCM– MD for ground & excited states– QM/MM, QM/QM’ development– Excited state gradients (FCFs)

• MoWSeS: multi-partner ITN, 2 post-docs @ SCM– 2D systems: charge transport & optical properties

S1 (v)→S0 (v’)


Semi-automated electronic DFTB parameters

SCM & Jacobs U, J. Chem. Theory Comput. 9, 4006−4017 (2013)

Repulsive parameters in progress…

GeSi (zinc blende)- DFT (PBE/TZP)●-DFTB


Repulsive DFTB parameters (single-atom exp.)

Oliveira et al., JCTC, submittedMore repulsive parameters in progress…


Other fast approximate methods with our GUI• MOPAC: Stewart’s semi-empirical AM1, PM3, PM6, PM6-DH, …

• molecules, periodic systems (gamma point only)• 70 atoms parametrized (up to Bi, lanthanides with ‘Sparkles’)• MOPAC2012: PM7 (more accurate, esp. for solids)

• UFF: Universal Force Field: all elements; molecules & periodic


ReaxFF


Engineering challenges….

- Higher efficiency- Lower exhaust- Higher combustion

temperature - Need new

materials that can sustain higher temperatures and oxidation chemistry

- Higher efficiency- Longer lifetime- Cheaper- Need new, cheap

catalyst materials that are resistant to poisoning

Coal power plantPre-oxidized Al-tube with ethylene/O2/ozone mixture

…require atomistic-scale solutions

Ni-particle reacting with propene at T=1500KFuel cell


Force field methods

©2005 Markus Buehler, MIT

b

- Empirical, we need to derive values for the force field parameters (intuition, compare to experiment, compare to QM)

- MUCH faster than QM; can be applied to bigger systems


0

15

30

1.25 1.5 1.75

DFT

ReaxFF

Harmonic

0

100

200

1 1.5 2 2.5 3 3.5 4

DFT

ReaxFF

Harmonic

C-C bond length (Å)

Ene

rgy

(kca

l/mol

)

C-C bond stretching in Ethane

Around the equilibrium bond length Full dissociation curve

C-C bond length (Å)- ReaxFF employs a bond length/bond order relationship- All connectivty-dependent-parameters bond-length dependent

Failure of the harmonic model


ReaxFF Computational expense

0.01

0.1

1

10

100

1000

10000

100000

1000000

0 100 200 300 400

ReaxFF

QM (DFT)

Nr. of atoms

Tim

e/ite

ratio

n (s

econ

ds)

x 1000,000

- ReaxFF allows for reactive MD-simulations on systems containing more than 1000 atoms

- ReaxFF is 10-50 times slower than non-reactive force fields

- Better scaling than most QM-methods (NlogN for ReaxFF, N3 or worse for many QM)

- (linear scaling for DFT, too)


ReaxFF integration into ADF with GUI

Integration team:Olivier Visser, Alexei Yakovlev (SCM)- Mike Russo, Kaushik Joshi (Penn State)

Collaboration van Duin group – SCM• Serial speed-ups• Parallelization• Remove bottle-

necks


Examples of parallel ADF/ReaxFF simulations

Pyrolysis of an Illinois coal sample (Combustion & Flame 2012)

Coal combustion on MoNi slab (Vasenkov et al., J. Appl Phys. 2012)

Hexane cracking on a Fe/H-ZSM5 catalyst (Fe/O: Aryanpour et al., JPC-A 2010)

Water onTiO2 surfaces(J. Phys. Chem. C 2013)


TiO2 nanoparticle aggregation

Temperature- 1100KBox size- 125 Å x 325 Å x 125 ÅNumber of atoms- 10904Number of Water molecules- 1800ADF/ReaxFF

Time=0 ns

NVT simulation at 1100KNanoparticles and water molecules are placed randomly, no bias or restraints

Nano Lett. 14, 1836−1842 (2014)


Anatase (112) to Anatase (112)

Time=93.75 psTime=125 ps

Time = 187.5ps

Time=250 ps


Teflon coating reduces Li-S battery electrolyte decomposition

M. M. Islam, V. S. Bryantsev, and A. C. T. van Duin, ReaxFF Reactive Force Field Simulations on the Influence of Teflon on Electrolyte Decomposition during Li/SWCNT Anode Discharge in Lithium-Sulfur Batteries, J. Electrochem. Soc. 161, E3009-E3014 (2014).

Teflon coating acts as buffer, reducing thermal electrolyte decomposition

Temperature profile at 10ps after discharge from Li-SWCNT electrode(blue 60 K, red >1000 K).

http://dx.doi.org/10.1149/2.005408jes






ReaxFF: Reactions in large, dynamical systems

Large part of periodic table covered, including metalsEnables dynamics studies of reactions in material science & biochemistry

Adri van Duin, Goddard, and coworkers (expanding network)Work in progress: semi-automated optimization (genetic algorithms, MMC)RxFF_consulting: spin-off Adri

not currently described by ReaxFF


Semi-automatic parametrization: MMC-SA

E. Iype, M. Hutter, A. P. J. Jansen, S. V. Nedea, C. C. M. Rindt, J. Comp. Chem. 34, 1143–1154 (2013)

Caveat: training set is important!


COSMO-RS


COSMO-RS (COnductor-like Screening Model for Realistic Solvents)

• Quantum-based (post-SCF) thermodynamic properties liquids• Original: Dr. Klamt (J. Phys. Chem. A 102 (1998) 5074; book)• ADF: reparametrized by Pye, Ziegler, van Lenthe, Louwen

• 216 molecules against 642 exp. data:• vapor p: ~0.2 log, partition coeff.: ~0.35 log, hydration ~0.37 kcal/mol

• Instantaneous prediction of thermodynamic properties of mixed liquids:• activity coefficients, solvent free energies• excess energies for mixing GE, HE, TSE

• solubilities, partition coefficients (log P), VLE, LLE, boiling points• pKa

• Database of 1892 precalculated molecules, including many solvents• Easy to calculate more compounds with ADF• Database and COSMO-RS GUI included in license • Also implemented COSMO-SAC (Sandler) and COSMO-SAC-3D (Delft,

DSM, to be published)


COSMO-RSConductor-like Screening Model for Real Solvents

Calculation of the chemical potentials-profile: charge density on COSMO ( = ) surfacepair-wise interaction between moleculesstatistical thermodynamics


s-profiles

charge density averaged over rav

red curve: waterblue curve: methanolgreen curve: benzene


Solvation energies, activity coefficients, solubility

Water is the solventExperimental values taken from: • A. Klamt et al., J. Phys. Chem. A 102 (1998) 5074• J. Li et al., Analytical Chemistry 65 (1993), 3212• Wikipedia


Partition coefficients (log P)log PA/B = log {[solute]A/[solute]B}

Experimental values taken from: A. Klamt et al., J. Phys. Chem. A 102 (1998) 5074

Octanol/water Hexane, Benzene, Ethoxyethane/water


pKa values(acid) AH (aq) + H2O (l) → H3O+ (aq) + A- (aq) (base) BH+ (aq) + H2O (l) → H3O+ (aq) + B (aq)

Empirical fitting as in [1], different parameters used for ADF COSMO-RSFitting calculated Δgdiss against experimental pKa

(acid) pKa = 0.62 ΔGdiss/(RT ln(10)) + 2.10

(base) pKa = 0.67 ΔGdiss/(RT ln(10)) - 2.00

Experimental values taken from[1] F. Eckert, M. Diedenhofen,A. Klamt, Mol. Phys. 108 (2010) 229


Vapor pressure ternary mixture Methanol, Acetone. Chloroform at 330K

VLE data can be much improved by exp. Antoine parameters (DIPPR)


COSMO-RS: Gas solubility in ionic liquids

Z. Lei, C. Dai, and B. Chen, Gas Solubility in Ionic Liquids, Chem. Rev., 114, 1289−1326 (2014).

• Prediction beyond parametrization (opposed to UNIFAC)

• Works well for SO2 solubilities• Improvements needed for CO2

http://dx.doi.org/10.1021/cr300497a




• ADF & BAND: all-electron, relativistic, spectroscopy, analysis• BAND unique: Proper 2D: COSMO, E-field

• Approximate Quantum-based methods:• DFTB: larger systems, ReaxFF: reactive molecular dynamics

limited by parameters - work in progress to automate further development of analysis tools and integration into suite• COSMO-RS/SAC: VLE, LLE, logP, …

Summary


• Download binary (www.scm.com/Downloads/2014)user name: u17253 password: 73!Yp76a• Install • Run ADFJobs, enter password details to get license

Suggested exercises:• www.scm.com/Workshops/GWUWorkshop.html• Feel free to try out your own examples and ask usSupport after today: [email protected]

Try out ADF on Crunchyard (cloud)? email [email protected] to enter 2000-h prize draw

Getting started

http://www.scm.com/Workshops/GWUWorkshop.html



Science

Chemistry and Materials with the ADF modeling suite