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

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
✓ ✓

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. 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 benzene 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 – benzene/napthalene
Right click – Computation – Optimize structure
Measure C – C – C bond angle
Press 3D Optimization before measurement
Get structure from
PDB and MOL
Right click to get console
Measure
distance/angle
Model kit to
design molecule
To create ESP - Insert benzene 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

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
Chemical viewer 3D structure (Avogadro)
Click here for pdb files
Click here download Avogadro
File – open benzene.sdf file
Extension – Optimize geometry
Select measure bond angle
Obtain file from any site as sdf/xml
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
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 benzene pdb file
Surface – Quick plot ESP
Click here download Arguslab
Red – Oxygen region
(High electron density)
Quantitative
measurement
3

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 benzene
Uses molecular modelling
2
3
Look for benzene from PubChem
Down load 3D as sdf . 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
Organic softwarefor 3D model (ACD Lab)
Click here download ACD Lab
Finish product in 3D viewer
Uses molecular modelling
1
Draw benzene
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 napthalene
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

8. Possible ResearchQuestion
DataCollection 3D modelling (Benzene/Napthalene)
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD Click here Avagrado
Are aromatic moleculeplanar/flat
Do fused aromatic ring undergo delocalization
Do they obey Huckel rule
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
How ESP shown in aromatic ring
Click here chem axon Click here NIST data
CRC database
Chem spider.
Benzene ACD Pymol Jmol Avogadro Mean
Planar/flat Flat Flat Flat Flat Flat
ESP Planar Planar Planar Planar Planar
Bond length 140 139 139 140 139
Bond angle 120.02 120.01 120.05 120.03 120.2
DataCollectionDatabase (Benzene/Napthalene)
Napthalene ACD Pymol Jmol Avogadro Mean
Planar/flat Flat Flat Flat Flat Flat
ESP Planar Planar Planar Planar Planar
Bond length 136/140 138/141 139/140 137/140 138/140
Bond angle 120.04 120.02 120.01 120.01 120.2
Benzene NIST CRC Chemspi Chemaxon Mean
Bond length 139 139 139 140 139
Bond angle 120.01 120.01 120.02 120.01 120.1
napthalene
benzene
Benzene NIST CRC Chemspi Chemaxon Mean
Bond length 136
141
137
140
137
141
137
141
137
141
Bond angle 120.01 120.01 120.02 120.01 120.1
How planarity and delocalization affect aromaticity?
Huckel rule = 4n + 2
n = 1 = 6π electron
n= 2 = 10 π electron
n = 3 = 14 π electron 6π 10π 14π

9. How planarity and delocalization affect aromaticity?
Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD Click here Avagrado
Are aromatic moleculeplanar/flat
Do fused aromatic ring undergo delocalization
Do they obey Huckel rule
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
How ESP shown in aromatic ring
Click here chem axon Click here NIST data
CRC database
Chem spider.
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?

10. 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!!!!!
Possible ResearchQuestion – How planarityand delocalizationaffect aromaticity?
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!!

11. 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
Possible ResearchQuestion – How planarityand delocalizationaffect aromaticity?
Aromatic can be heterocyclic if contain
non-carbon, with oxy, nitrogen, or sulfur They do not obey Huckel rule
Why ?

12. 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
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)
Benzene/aromatic – sp2 – 120o – no angle strain
Possible ResearchQuestion –How planarityand delocalizationaffect aromaticity?
They do not obey Huckel rule
Why ?
Aromatic can be heterocyclic if contain
non-carbon, with oxy, nitrogen, or sulfur

13. 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

14. 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

15. Resonance structure methanoate
resonance structure 1 resonance structure 2
• All CO bond are identical in length/strength
• Hybrid of 2 resonance structure
• NO C-O (single) or C=O (double) bond
• Only C ----- O bond
• Intermediate character bet single and double bond
• Bond Order = 1.5
Methanoate ion

HCOO
Click here to view
resonance hybrid
Click here to view
Resonance structureethanoate
Ethanoate ion

COOCH3
resonance structure 1 resonance structure 2
resonance hybrid
HH
CH3
Delocalizationof electron
Resonance
• Describing delocalizationof 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

16. Delocalizationof electron
Resonance structurecarbonateion
2
3CO
resonance structure 1 resonance structure 2 resonance structure 3
Resonance hybrid
• All bond CO3
2-
are identical in length /strength
• Hybrid of 3 resonance structure
• Negative charge equally distributed over all oxy
• No O-O (single) or O=O (double) bond.
• Only O ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.3
Carbonate Ion
Charge 2- delocalized into 2/3-
Lower charge – more stable
Click here on video carbonate
C
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 than2 nuclei
• π electron are shared/spread– more stable

17. Resonance structurenitrate ion

3NO
resonance structure 1 resonance structure 2 resonance structure 3
resonance hybrid
• All bond NO3
-
are identical in length/strength
• Hybrid of 3 resonance structure
• Negative charge equally distributed over all oxy
• No N-O (single) or N=O (double) bond
• Only N ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.3
Nitrate Ion
Charge 1- delocalized into 1/3-
Lower charge – more stable
Click here to view video
1/3
1/31/3
Delocalizationof electron
Resonance
• Describing delocalizationof 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

18. Resonance structurenitrite ion

2NO
resonance structure 1 resonance structure 2
resonance hybrid
• All bonds NO2
-
are identical in length and strength
• Hybrid of 2 resonance structures
• Negative charge equally distributed over all oxygen
• NO N-O (single) or N=O (double) bonds found
• Only N ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.5
Nitrite Ion
charge 1- delocalized into 1/2-
Lower charge – more stable
Click here video nitrite
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

19. Resonance structuresulfur dioxide
2SO
resonance structure 1 resonance structure 2
• All SO2 bond are identical in length/strength
• Hybrid of 2 resonance structure
• Negative charge equally distributed over all oxy
• NO S-O (single) or S=O (double) bond
• Only S ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 1.5
Sulfur Dioxide
Click here to view
S
resonance hybrid
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