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

✓ ✓

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

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

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

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 benzene pdb 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 (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 benzene

Uses molecular modelling

2

3

Look for benzene from PubChem Down load 3D as sdf . 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

Organic software for 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 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 napthalene 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

Possible Research Question

Data Collection 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 molecule planar/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

Data Collection Database (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

How planarity and delocalization affect aromaticity?

Possible Research Question Data Collection using 3D modelling

Data Collection using Database

Click here Jmol Click here PyMol

Click here ACD Click here Avagrado

Are aromatic molecule planar/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.

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?

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!!!!!

Possible Research Question – How planarity and delocalization affect 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!!

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

Possible Research Question – How planarity and delocalization affect aromaticity?

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

Why ?

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 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)

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

Possible Research Question –How planarity and delocalization affect aromaticity?

They do not obey Huckel rule Why ?

Aromatic can be heterocyclic if contain non-carbon, with oxy, nitrogen, or sulfur

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

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 structure ethanoate

Ethanoate ion COOCH3

resonance structure 1 resonance structure 2

resonance hybrid

H H

CH3

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

Delocalization of electron

Resonance structure carbonate ion

2

3CO

resonance structure 1 resonance structure 2 resonance structure 3

Resonance hybrid

• All bond CO32- 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 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 nitrate 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

1/3 1/3

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 nitrite 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

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 sulfur 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

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