Measure bond length/angle Measure number H2 bonds

Measure bond strength Protein 1, 2 , 3O structure

Presence of disulfide bond Presence alpha and beta pleated sheet

Organic software for 3D model

Click here download Rasmol Click here download PyMol Click here download ACD Click here download Jmol Click here Chem EDDL

Click here ChemDraw editor

Click here download(Accelrys)

Click here chemical search. Click here CRC database Click here RSC Databooklet

Modelling and 3D representation

Chemistry Database

Click here Spectra database(OhioState) Click here Spectra database(NIST)

Click here chem finder.

Spectroscopic Database

Click here download Swiss PDB Viewer

Modelling and 3D representation

✓ ✓

Click here download nano modeller Click here download nano modeller fullerene library

Electrostatic Potential (ESP) Measure polarization Electron Map density Electron distribution

Dipole Moment Measure bond length/angle

Measure bond strength

Organic software for 3D model

Click here download Rasmol

Click here download PyMol Click here download Jmol

Click here Chem EDDL

Click here chemical search. Click here CRC database

Modelling and 3D representation

Chemistry Database

Click here Spectra database(OhioState) Click here Spectra database (NIST)

Click here chem finder.

Spectroscopic Database

Click here down Swiss PDB

Modelling and 3D representation

✓ ✓

Click here NIST data

✓ Click here download Arguslab

Click here chem axon

Click here download Avagrado

Click here chem EdDL

Organic software for 3D model

Click here download software fullerenes/nanotube pdb file

1

File – open bucky ball file

3

Tools – recalculate bonds

4

Display bond angle

2

Organic software for 3D model

Click here download software fullerenes/nanotube pdb files

1

2

3

Measure conductivity Click here – bucky ball

Select type bucky ball

Measure bond length/angle Measure number H2 bonds

Measure bond strength Protein 1, 2 , 3O structure

Presence of disulfide bond Presence alpha and beta pleated sheet

Type -PDB ID - 4 letter code to J mol

Protein Data Bank Protein database key in - PDB 4 letter code

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2

3

Uses molecular modelling

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2

Chemical viewer 3D structure (Avogadro)

Click here for pdb files

Click here download Avogadro

File – open C60. xyz or pdb file

Extension – Optimize geometry Select measure bond angle

Obtain file from any site as xyz/pdb

Select measure measure bond angle

Select E Optimize geometry

View – Bond angle

View – Bond angle

4

Extension – Create surface Type – Van Der Waals - Electrostatic potential - Calculate

5

Save file type as. Mol2 type

Electrostatic Potential Red – Oxygen region (High electron density) White – Hydrogen (Low electron density)

Insert file. mol2 to Jmol Right click – Surface – Molecular Surface Potential

Measure bond length/angle Measure number H2 bonds

Measure bond strength Protein 1, 2 , 3O structure

Presence of disulfide bond Presence alpha and beta pleated sheet

Chemical viewer 3D structure (Jmol)

Uses molecular modelling

1

J mol executable file

final product

J mol executable file

1

Designing C60 molecule Open model kit Drag to bond – choose carbon Drag to bond – choose oxygen Choose double bond – cursor center Model kit – Minimize structure Choose ruler for measurement Measure bond angle CCC Measure bond length C – C

Click here J mol tutorial

2 2

3

File – Get MOL – type – C60 Save file type as Mol2 in Avogadro – transfer to Jmol Right click – Computation – Optimize structure Press 3D Optimization before measurement Measure C – C bond length/angle

Get structure from PDB and MOL

Right click to get console

Measure distance/angle

Model kit to design molecule

To create ESP - Insert C60 file type . mol2 to Jmol Right click – Surface – Molecular Surface Potential

3 Electrostatic Potential Red – Oxygen region (High electron density) White – Hydrogen (Low electron density)

Click here J mol download

Measure bond length/angle Measure number H2 bonds

Measure bond strength Protein 1, 2 , 3O structure

Presence of disulfide bond Presence alpha and beta pleated sheet

Organic software for 3D model (Pymol)

download pdb file text

1 1

Click here - Protein Data Bank Protein database key in - PDB 4 letter code

3

Click here download PyMol

Click here Pymol video tutorial Click here Pymol video tutorial

Click here for pdb files

2

Wizard – measurement - measure bond angle/length C60

Uses molecular modelling

2

3

Look for C60 from PubChem Download as sdf /pdb/xyz file type File – open from Pymol

Measure bond length/angle Measure number H2 bonds

Measure bond strength Protein 1, 2 , 3O structure

Presence of disulfide bond Presence alpha and beta pleated sheet

Protein Data Bank Protein database key in - PDB 4 letter code

1

2

Uses molecular modelling

White – Hydrogen (Low electron density)

1

2

Chemical viewer 3D structure (Argus Lab)

Click here for pdb files

File – open C60 pdb/xyz file

Surface – Quick plot ESP

Click here download Arguslab

Red – Oxygen region (High electron density)

Quantitative measurement

3

Measure bond length/angle Measure number H2 bonds

Measure bond strength Protein 1, 2 , 3O structure

Presence of disulfide bond Presence alpha and beta pleated sheet

Organic software for 3D model (ACD Lab)

Click here download ACD Lab

Finish product in 3D viewer

Uses molecular modelling

1

Draw C60

Press copy to 3D or press 3D viewer Measure C – C bond length/ C – C – C bond angle Press 3D Optimization before measurement Compare it to J mol Compare it to CRC Data booklet Compare it to Chem EDDL Compute the average bond length /angle C - C - C

Measure distance Measure distance Select atom

1

Draw fullerene Press copy to 3D or press 3D viewer Measure C – C bond length/ bond angle Press optimization before measurement Compare it to J mol Compare it to CRC Data booklet Compare it to Chem EDDL Compute the average bond length /angle

Finish product in 3D viewer

2 2

3 3

Files resources for Fullerenes

Diff bucky balls

Bucky ball C 60 - contain pentagonal and hexagonal ring No two pentagons share an edge (pentalene). C60 is truncated icosahedron - 20 hexagons and 12 pentagons C60 avoid having double bond in pentagonal ring, which make electron delocalization poor C60 not "superaromatic".C60 - like electron deficient alkene React with electron rich species – addition rxn

Research Question – How diff fullerene affect aromaticity,, delocalization and conductivity ?

6:6 ring (bet two hexagon) - double bond - shorter 6:5 ring (bet hexagon and pentagon) - longer Average bond length is 1.4A Electron density – higher in 6 carbon ring than in 5 carbon ring Undergo addition rather than substitution rxn Small degree – aromatic character Still have localized C =C and single C – C bond Super alkene rather than aromatic compound

6:6 ring (C=C)

6:5 ring (C- C)

Fullerene, n carbon atoms has n pi elec, free to delocalize over whole molecule. Smallest spherical fullerene – C20

Most common – C60

They exist as - C70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90

C20 C60 C70 C80 C90

Click here view excellent fullerene xyz file Click here view excellent fullerene pdb file Click here fullerene pdb file

Possible Research Question

Data Collection 3D modelling

Data Collection using 3D modelling

Data Collection using Database

Click here Jmol Click here PyMol

Click here ACD Click here Avagrado

How diff fullerenes/shape affect aromaticity Are they still aromatic and is Huckel rule obey How shape fullerene affect conductivity/delocalization Are their angle of 120o

Are their bond length the same Is there single/double bond present What is their bond length/angle Are all c in ring – sp2 hybrid

Click here chem axon Click here NIST data

CRC database Chem spider.

C60 ACD Pymol Jmol Avogadro Mean

Bond angle Hexagon Pentagon

< 120 < 118

< 120 < 117

< 120 < 115

< 120 < 114

< 120 < 115

Bond length C = C C – C

139 142

141 144

141 143

139 143

139 142

Data Collection Database

How diff fullerenes affect aromaticity, delocalization and conductivity ?

C60

6:6 ring (C=C) 6:5 ring (C- C)

Graphene ACD Pymol Jmol Avogadro Mean

Bond angle Hexagon

120 120 120 120 120

Bond length C - C

143 142

143 142 142

C60 NIST CRC Chemaxo Chemspi Mean

Bond angle Hexagon Pentagon

< 120 < 113

< 120 < 117

< 120 < 115

< 120 < 114

< 120 < 116

Bond length C = C C – C

140 143

142 144

141 143

141 143

140 143

Graphene

Graphene NIST CRC Chemaxo Chenspi Mean

Bond angle Hexagon

120 120 120 120 120

Bond length C - C

142 142

143 142 142

Graphene C60 Nanotubes

Possible Research Question Data Collection using 3D modelling

Data Collection using Database

Click here Jmol Click here PyMol

Click here ACD Click here Avagrado

How diff fullerenes/shape affect aromaticity Are they still aromatic and is Huckel rule obey How shape fullerene affect conductivity/delocalization Are their angle of 120o

Are their bond length the same Is there single/double bond present What is their bond length/angle Are all c in ring – sp2 hybrid

Click here chem axon Click here NIST data

CRC database Chem spider.

How diff fullerenes affect aromaticity, delocalization and conductivity ?

Graphene C60 Nanotubes

Evaluation and Limitation using 3D modelling

Must use a variety of sources/programme to verify/validate the validity and reliability of data collected Average is computed from diff software and checked with database to confirm. Check on methodological limitation using 3D model. (MUST perform 3D Optimization to most stable form structure. Critical and skeptical of result produced by computational chemistry. Major limitation of computation, they assume non-interacting molecule. (Ideal situation, ex molecule in vacuum or isolated state) Most appropriate molecule are those whose coordinates are not theoretical but derive from experimental structural determination (using X ray diffraction) Be careful of predicted arrangement from simulation /3D model Data sources are supported using diff method/3D model/database Certain database like NIST and CRC are more reliable source Check if there is a good agreement bet CRC, diff databases and 3D model prediction before making conclusion Computation programme is always based on approximation and we cannot conclusive prove anything Reflect of validity and reliability of data Is model a true representation of reality?

Allotropes of Carbon

Diamond Fullerene, C60

• Carbon- sp2 hybridization • Bonded in geodesic shape • 60 carbon spherical - 20 hexagon/12 pentagon • 1 π electron free to delocalized. • Surface is not planar, but sphere • Electrons NOT able to flow easily.

Graphene

• Carbon- sp2 hybridization • Carbon bond to 3 others form hexagon (120o) • Exist chicken wire/honeycomb- 1 layer

Click here to view Click here to view Click here to view

• Carbon- sp3 hybridization • Bonded tetrahedrally • Strong hard covalent network

• Carbon- sp2 hybridization • Bonded Trigonal planar (layers) • Giant covalent structure (2D) • Strong covalent network within layers • Weak Van Der Waals force bet layers

Giant covalent structure (3D)

Giant covalent structure (2D)

Molecular structure

✓

✓ ✓

Giant covalent structure (2D) ✓

Uses of graphene

Graphite

Bond to 4 C atoms

Bond to 3 C atoms

Bond to 3 C atoms

…

Element exist in different form/physical state

Allotropes of Carbon

Diamond Fullerene, C60 Graphene Graphite

Electrical conductivity

Special property

Electrical conductivity Electrical conductivity Electrical conductivity

Special property

Good

- Within layer, C sp2 hybridized - ONE free delocalized π electron

Very Good

- Within layer, C sp2 hybridized - ONE free delocalized π electron moving across the layer easily

Poor

- C sp3 hybridized - No free moving electron

Semiconductor ✓ ✗

- Surface sphere, not planar - Electrons CANNOT flow easily. - Lower electron mobility

- Soft, layer slide across each other

- Hardest substance - Jewellery

Special property

graphite lubricant electrode

Lightest/strongest material replacing silicon in photovoltaic cell

Drug delivery Transistor/Electronic Transparent conducting electrode

Click here uses graphene Drug in graphene

Element exist in different form/physical state

Allotropes of Carbon

Fullerene, C60 Graphene

Click here to view touch screen

Electron in hexagonal rings dont delocalized over whole molecule.

6:6 bond shorter than 6:5

6:5 bond bet hexagon and pentagon

Macroscopic properties • High tensile strength • High electrical/heat conductivity • High ductility and chemical inactivity

Potential medicinal use • Trap/bind drug inside/outside cage • Target cancer cells

Drug inside Drug bind outside

• sp2 hybridization • Exist as 2D/chicken wire/honeycomb • Stronger than diamond, x200 stronger steel • Conductive than copper • Flexible/Transparent/lighter than rubber • Solar cell and batteries

Graphene touch screen and photovoltaic cell

Click here for application of graphene

Single sheet conductor Rool into conductive nanotubes

Electrical contact

photovoltaic cell

Lightest and strongest replacing silicon in photovoltaic cell

6:6 bond length bet two hexagon

Double bond Single bond

Element exist in different form/physical state

60 carbon in spherical (20 hexagon/12 pentagon)

Uses of Carbon Allotropes

• Conduct current/heat very well • Conduct current at speed of light • Electron delocalized above/below plane • High electron mobility

Click here discovery graphene Click here CNT Click here to view

sp2 hybridization

graphene

rool into rool into

Carbon Nanotube (CNT)

CNT- fullerene family of carbon allotropes. Hollow cylindrical molecule Rolling single or multiple layers of graphene sheet. Single-wall SWNT/ multi-wall MWCNT High tensile, stable, unreactive

Single wall Nanotube (SWNT) Multi wall Nanotubes (MWNT)

Click here TEDtalk graphene

1 layer thick

Uses of CNT

Strong tubes as space elevator

Filter off salt (desalination)

Drug delivery to body Attachment drug therapeutics

Click here ring strain (wiki) Click here angle strain (master organic) Angle strain – smaller angle (higher angle strain) – more energetic bond – more unstable/reactive

Angle strain destabilize molecule - higher reactivity Angle strain leads to elevated heat of combustion. Max bond strength result from effective overlap of atomic orbital. Angle strain and torsional strain combine to create ring strain Both affect stability of cyclic molecules

Angle strain- deviation from ideal angle

Ideal angle = 109o Angle = 60o 49o deviate from 109o

(angle/torsional strain)

Angle = 90o 49o deviate from 109o

(angle/torsional strain)

Angle = 108o 1o deviate from 109o

(angle/torsional strain)

Angle = 120o 11o deviate from 109o

(angle/torsional strain)

Molecule is NOT FLAT!!!!!

Aromatic ring/fuse benzene ring/ heterocyclic

Benzene/aromatic – sp2 – 120 – no angle strain

Angle = 120o NO deviate from 120o

(No angle strain)

Molecule is FLAT!!

Research Question – How diff fullerene affect aromaticity,, delocalization and conductivity ?

Aromatic ring/fuse benzene ring/ heterocyclic Huckel rule

- 4n+2 electron undergo delocalization - conjugated p-orbital cloud - molecule is planar/cyclic - atom in ring participate in delocalizing e by having p-orbital/unshared electron. - 4n+2 electrons → n = 1 → C6H6 (Benzene)

Are these molecule planar/flat Do they obey Huckel rule Do they have angle of 120o

Are their bond length the same Is there single/double bond present What is their bond length/angle Are all c in ring – sp2 hybrid How are ESP shown in ring

Benzene/aromatic – sp2 – 120o – no angle strain

Furan thiphene pyrrole pyridine pyran

oxazine thiazine pyrimidine piperazine thipyran

Aromatic can be heterocyclic if contain non-carbon, with oxy, nitrogen, or sulfur They do not obey Huckel rule

Why ?

Research Question – How diff fullerene affect aromaticity,, delocalization and conductivity ?

Delocalization of electron

Resonance • Describing delocalization of electron within a molecule/polyatomic ion where bonding cant be express by ONE single Lewis structure •Delocalization of π bond – π electron spread over more than 2 nuclei •π electron are shared/spread – more stable

Resonance structure benzene

Benzene 6HC6

resonance structure 1 resonance structure 2

Resonance hybrid

• All bond C6H6 identical in length/strength • Hybrid of 2 resonance structures • No C-C (single) or C=C (double) bond • Only C ----- C bond • Intermediate character bet single/double bond • Bond Order = 1.5

• Unhybridised p orbital • Delocalization electron above below plane • sp2 hybridization on carbon center

Click here to view

Delocalized electrons

Kekulé structure

Cyclohexa- 1,3,5 triene

χ ✓

Benzene

Hexagonal, planar

Resonance Hybrid more stable than any of resonance structure ✓

Click here to view

Kekule

Resonance/Delocalization Energy

ΔH cyclohexene = -120 kJmol-1

ΔH cyclohexa 1,3 diene = -240 kJmol-1

ΔH cyclohexa 1,3,5 triene = -360 kJmol-1

ΔH Benzene = -208 kJmol-1

Enthalpy change hydrogenation

✓

✓

……

• Benzene lower in energy by 150 kJ • More stable due to delocalization of π electron

150kJ

C-C Single bond

C=C Double bond

C=C Benzene

Bond length/pm 154 134 140

Bond enthalpy/kJmol-1

346 614 507

1

2

• X ray hit benzene crystal • Interact with electron (electron density map) • X ray diffraction produced • Bond length measured

X ray crystallography

NO single/double bond detected ✓

✓

3 Addition rxn for unsaturated C=C

✓ Addition rxn

Substitution rxn

NO double bond

- 360 χ - 240

- 150

H H Br Br

׀ ׀ ׀ ׀

C = C + Br2 → H – C – C – H

׀ ׀ ׀ ׀

H H H H

3 Evidence for Benzene structure