IB Chemistry on ICT, 3D software, Avogadro, Jmol, Swiss PDB, Pymol for Internal Assessment on Fullerenes and Buckyballs

1. 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 softwarefor 3D model
Click here download Rasmol Click here download PyMolClick 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

2. Electrostatic Potential (ESP)
Measure polarization
Electron Map density
Electron distribution
Dipole Moment
Measure bond length/angle
Measure bond strength
Organic softwarefor 3D model
Click here download Rasmol
Click here download PyMolClick 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

3. Organic softwarefor 3D model
Click here download software
fullerenes/nanotube pdb file
1
File – open bucky ball file
3
Tools – recalculatebonds
4
Display bond angle
2
Organic softwarefor 3D model
Click here download software
fullerenes/nanotube pdb files
1
2
3
Measure conductivity Click here – bucky ball
Select type bucky ball

4. 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
1
2
3
Uses molecular modelling
1
2
Chemicalviewer 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

5. 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
Chemicalviewer 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

6. 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 softwarefor 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 tutorialClick 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

7. 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
Chemicalviewer 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

8. 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 softwarefor 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 Optimizationbefore measurement
Compareit to J mol
Compareit to CRC Data booklet
Compareit to Chem EDDL
Compute the average bond length /angle C - C - C
Measure distance Measure distanceSelect atom
1
Draw fullerene
Press copy to 3D or press 3D viewer
Measure C – C bond length/ bond angle
Press optimizationbefore measurement
Compareit to J mol
Compareit to CRC Data booklet
Compareit to Chem EDDL
Compute the average bond length /angle
Finish product in 3D viewer
22
3
3

9. Files resources for Fullerenes
Diff bucky balls
Bucky ball C60 - containpentagonal and hexagonal ring
No two pentagons share an edge (pentalene).
C60 is truncatedicosahedron - 20 hexagons and 12 pentagons
C60 avoid having double bond in pentagonal ring, which make
electron delocalizationpoor
C60 not "superaromatic".C60 - like electrondeficient alkene
React with electron rich species – addition rxn
ResearchQuestion – 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
Electrondensity – higher in 6 carbon ring than in 5 carbon ring
Undergo addition rather than substitutionrxn
Small degree – aromatic character
Still have localized C =C and single C – C bond
Super alkene ratherthan 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

10. Possible ResearchQuestion
DataCollection 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/shapeaffect 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

11. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD Click here Avagrado
How diff fullerenes/shapeaffect 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
Evaluationand Limitationusing 3D modelling
Must use a variety of sources/programmeto verify/validatethe validity and reliability of data collected
Average is computedfrom diff software and checked with databaseto confirm.
Check on methodological limitationusing 3D model. (MUST perform 3D Optimization to most stable form structure.
Criticaland skeptical of result produced by computationalchemistry.
Major limitationof computation,they assume non-interactingmolecule. (Ideal situation, ex molecule in vacuum or isolated state)
Most appropriatemolecule are those whose coordinates are not theoreticalbut derive from experimentalstructuraldetermination
(using X ray diffraction)
Be carefulof predicted arrangement from simulation /3D model
Datasources are supported using diff method/3D model/database
Certain databaselike NIST and CRC are more reliable source
Check if there is a good agreement bet CRC, diff databases and 3D model predictionbefore making conclusion
Computation programmeis always based on approximationand we cannot conclusive prove anything
Reflect of validity and reliability of data
Is model a true representation of reality?

12. 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 viewClick 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

13. Allotropes of Carbon
Diamond Fullerene, C60GrapheneGraphite
Electricalconductivity
Special property
Electricalconductivity Electricalconductivity Electricalconductivity
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✓✗
- Surfacesphere, not planar
- ElectronsCANNOT 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
Transparentconducting
electrode
Click here uses graphene
Drug in graphene
Element exist in different form/physical state

14. Allotropes of Carbon
Fullerene, C60Graphene
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
Macroscopicproperties
• 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
• Conductivethan copper
• Flexible/Transparent/lighterthan 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)

15. Uses of Carbon Allotropes
• Conduct current/heatvery well
• Conduct current at speed of light
• Electron delocalized above/belowplane
• 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

16. Click here ring strain (wiki)
Click here angle strain (master organic)
Angle strain – smaller angle (higher angle strain)
– more energeticbond
– 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!!
ResearchQuestion – How diff fullerene affect aromaticity,,delocalization and conductivity ?

17. Aromatic ring/fuse benzene ring/ heterocyclic Huckel rule
- 4n+2 electronundergo delocalization
- conjugated p-orbitalcloud
- molecule is planar/cyclic
- atom in ring participatein delocalizing e
by having p-orbital/unsharedelectron.
- 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 ?
ResearchQuestion – How diff fullerene affect aromaticity,,delocalization and conductivity ?

18. Delocalizationof electron
Resonance
• Describing delocalizationof electron within a molecule/polyatomic ion
where bonding cant be express by ONE single Lewis structure
•Delocalizationof π bond – π electron spread over more than 2 nuclei
•π electron are shared/spread – more stable
Resonance structurebenzene
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
Delocalizedelectrons
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

19. Resonance/DelocalizationEnergy
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 unsaturatedC=C
✓
Addition rxn
Substitution rxn
NO double bond
- 360χ
- 240
- 150
H H Br Br
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
C = C + Br2 → H – C – C – H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
3 Evidence for Benzene structure