Click here download Rasmol

Click here download PyMol Click here download Jmol

Click here Chem EDDL

Click here chemical search.

Modelling and 3D representation

Quick Chemistry Database Check

Click here down Swiss PDB

Modelling and 3D representation

✓ ✓

Click here NIST data

✓ Click here download Arguslab

Click here chemaxon quick chem check

Click here download Avagrado

Click here chem EdDL

Click here for Visualization/3D sources

Click here download Marvin Sketch

Click here quick chemical check

Click here quick chemical check

Organic software for 3D model

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

Dipole Moment Measure bond length/angle

Measure bond strength

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 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 crystallography database.

✓ ✓

Click here NIST data

✓ Click here download Arguslab

Click here chem axon

Click here download Avagrado

Click here chem EdDL

Type -PDB ID – 1GCN – save pdb file type

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

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

Dipole Moment Measure bond length/angle

Measure bond strength

File – open acetic acid pdb file

Click here download Arguslab

Red – Oxygen region (High electron density)

Quantitative measurement

3

Calculation – Optimize geometry Optimize/clean geometry Surface – Quick plot ESP

Type -PDB ID - 4 letter code to J mol

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

Click here Avogadro tutorial

1

2

3

Uses molecular modelling

Save file type as. Mol2 type

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

4

1

2

Chemical viewer 3D structure (Avogadro)

Click here for pdb files

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

Dipole Moment Measure bond length/angle

Measure bond strength

Click here download Avogadro

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

Insert file. Mol2 file to Jmol or Pymol to view Right click – Surface – Molecular Surface Potential

J mol (View) Red – Oxygen region (High electron density) White – Hydrogen (Low electron density)

File – open acetic acid pdb file Obtain file from any site as sdf/xml from Chempub Select Optimization tool – press start

Click here J mol protein video

Look file – Get Mol Type – acetic acid

Chemical viewer 3D structure (Jmol)

Uses molecular modelling

1

J mol executable file

Measure distance

final product

J mol executable file

1

Designing CH3COOH 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 length C = O Measure bond length C - O

Model kit to design molecule

Click here J mol tutorial

2 2

3 3

Click here J mol download

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

Dipole Moment Measure bond length/angle

Measure bond strength

Red – oxygen (electron dense region) White – hydrogen (electron poor region)

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

J mol (View) Red – Oxygen region (High electron density) White – Hydrogen (Low electron density)

Click here J mol ESP video

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

Dipole Moment Measure bond length/angle

Measure bond strength

Organic software for 3D model (Pymol/APBS)

download pdb file text

1 1

Click here - Protein Data Bank Protein database – look for insulin – 4INS

3

Click here download PyMol

Click here Pymol video tutorial

2 Uses molecular modelling

2

Click here APBS Server

APBS – calculate Electrostatic Potential Go to web server Key in 4 pdb code – 4INS Click visualize see result (Firefox)

control panel - surface on - colour amino acid - ball stick

3 diff option

Click here Pymol ESP tutorial

Right click to zoom back

Type -PDB ID – 1GCN – save pdb file type

Click here Swiss PDB tutorial

1

2

Uses molecular modelling

White – Hydrogen (Low electron density)

1

2

Chemical viewer 3D structure (Swiss PDB)

Click here for pdb files

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

Dipole Moment Measure bond length/angle

Measure bond strength

File – open glucagon pdb file (1GCN)

Tool- Compute Electrostatic Potential

Click here down Swiss PDB

Chemical viewer 3D structure (Chem EDDL)

Red – Oxygen region (High electron density)

Click here chem Ed DL

1

Check on ESP Van Der Waals surface

1

Type- acetic acid (file name) Check – Molecular Electrostatic potential

Chemical viewer 3D structure (Gaussian)

Click here Gaussian tutorial

Click here download Gaussian

1 1

2

Br O ‖ ׀ Br -C - C - OH ׀ Br

Possible Research Question Data Collection using 3D modelling

Data Collection using Database

Click here Jmol Click here PyMol

Investigate relationship bet ESP and dissociation constant/strength acid

CRC database Chem spider.

How diff number/type of halogen affect ESP and dissociation constant,pKa of acid?

Click here NIST data

Data Collection from 3D modelling

ESP Angus Pymol Jmol Avogadro Mean

CH3FCOOH High High High High High

CH3CICOOH Ave Ave Ave Ave Ave

CH3BrCOOH Low Low Low Low Low

Data Collection from Database

Investigate relationship bet ESP and dissociation constant/strength acid Effect of halogen on polarity and dissociation constant of organic acid COOH How diff halogen affect electron distribution and reactivity How diif alkyl gp affect pKa of acid (Positive/Negative inductive effect) Effect of halogen on polarity, dipole moment and electrostatic potential Effect of func gp, OH/COO/NH2/CO has on polarity and electrostatic potential

Click here chem axon

Click here download Avogadro

Click here download Arguslab

type

number

H O ‖ ׀ H - C - C - OH ׀ F

F O ‖ ׀ F - C - C - OH ׀ F

H O ‖ ׀ H - C - C - OH ׀ CI

H O ‖ ׀ H - C - C - OH ׀ Br

CI O ‖ ׀ CI - C - C - OH ׀ CI

ESP Angus Pymol Jmol Avogadro Mean

CF3COOH v.High v.High v.High v.High v.High

CCI3COOH Ave Ave Ave Ave Ave

CBr3COOH Low Low Low Low Low

pKa CRC NIST Chemaxon Chemspi Mean

CH3FCOOH 2.59 2.51 2.42 2.35 2.40

CH3CICOOH 2.87 2.88 2.86 2.85 2.85

CH3BrCOOH 2.90 2.90 2.91 2.90 2.90

pKa CRC NIST Chemaxon Chemspi Mean

CF3COOH 0.52 0.51 0.51 0.52 0.52

CCI3COOH 0.66 0.67 0.65 0.67 0.66

CBr3COOH 0.74 0.72 0.73 0.73 0.73

Br O ‖ ׀ Br -C - C - OH ׀ Br

Possible Research Question Data Collection using 3D modelling

Data Collection using Database

Click here Jmol Click here PyMol

Investigate relationship bet ESP and dissociation constant/strength acid

CRC database Chem spider.

How diff number/type of halogen affect ESP and dissociation constant,pKa of acid?

Click here NIST data

Investigate relationship bet ESP and dissociation constant/strength acid Effect of halogen on polarity and dissociation constant of organic acid COOH How diff halogen affect electron distribution and reactivity How diif alkyl gp affect pKa of acid (Positive/Negative inductive effect) Effect of halogen on polarity, dipole moment and electrostatic potential Effect of func gp, OH/COO/NH2/CO has on polarity and electrostatic potential

Click here chem axon

Click here download Avogadro

Click here download Arguslab

type

number

H O ‖ ׀ H - C - C - OH ׀ F

F O ‖ ׀ F - C - C - OH ׀ F

H O ‖ ׀ H - C - C - OH ׀ CI

H O ‖ ׀ H - C - C - OH ׀ Br

CI O ‖ ׀ CI - C - C - OH ׀ CI

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?

Chemical Bond

Ionic Bond

Transfer of electron from metal to non metal

Metal donate e Non Metal accept e

Positive ion (cation)

Negative ion (anion)

Ionic compound

Covalent Bond

Equal sharing electron

+ - electrostatic forces

attraction

4 0.4 0 Difference in electronegativity

2

EN - 0.9 EN – 3

Diff = (3 – 3 ) = 0

H

EN – 2.1

Diff = 3 – 0.9 = 2.1

Polar covalent Bonds Non Polar covalent Bonds

Unequal sharing electron

Covalent Polar Non polar

CI CI

EN – 3

Covalent Non polar

CI

Covalent polar Ionic

EN – 3

Diff = (3 – 2.1 ) = 0.9

Na+ CI-

EN – 3

Sharing of electron bet non metal atoms

Shared electron cloud closer to O

Electronegativity

Electronegativity (EN) • Tendency of atom to attract/pull shared/bonding electron to itself • EN value higher – pull/attract electron higher (EN value from 0.7 – 4)

Electronegativity • EN increase up a Group • EN increase across a Period

H 2.2

Li Be B C N O F

CI

Br

I

1 1.6 2 2.6 3 3.4 4

Electronegativity values

N, O, F have high EN value

3.2

3

2.7

Molecule Diff in EN Polarity

H - F (4.0 – 2.2) = 1.8 Most polar

H - CI (3.2 – 2.2) = 1

H - Br (3.0 – 2.2) = 0.8

H - I (2.7 – 2.2) = 0.5 Least polar

Polarity

Shape Diff in EN

Symmetrical Asymmetrical

Bond polarity cancel out each other

Polar bonds – molecule NON POLAR

Bond polarity cancel out each other

Polar bonds – molecule POLAR

Lewis structure

VSEPR

Geometry

1

4 ECC

3 bond pair

1 lone pair

.. N

H H

H

Polarity

2

3

4

Polar

✓ ✗

✗

Separation of charges

Unequal distribution electron due to diff EN value

shared electron closer to O shared electron closer to F

Covalent Bond

Polar covalent Bonds Non Polar covalent Bond

Equal sharing electron Unequal sharing electron

Sharing of electron

Formation electric dipole

Partial +/-

Dipole moment

towards O

Partial + ( δ+)

Partial – (δ−)

Net dipole moment

Molecule polar (dipole)

Net Dipole moment

Measured in Debye

Turning force/Dipole moment =Force x Distance Polar covalent Bond

+ - O

III

C δ+

δ-

Turning force – dipole moment

+ -

O

II

C

II

O

δ+

δ-

δ-

No Turning force – No dipole moment

✓

Molecule polar ✓

O

O

In presence of electric field

Polarity

Shape

Asymmetrical

Polar bond ↓

Polarity dont cancel ↓

(ASYMMETRICAL) ↓

Net dipole moment ↓

Molecule POLAR

Polar bond ↓

Polarity cancel ↓

(SYMMETRICAL) ↓

NO dipole moment ↓

Molecule NON POLAR

Shape

Symmetrical

Polar bonds

CI Polar bonds

δ-

δ+ δ+

δ+

δ-

δ-

δ-

δ-

δ-

δ-

Bond polarity

don’t cancel

Bond polarity

cancel

H

Net Dipole moment No Net Dipole moment

✗

Asymmetrical Symmetrical

δ- δ+

Polar bonds

Bond polarity

don’t cancel

Net Dipole moment

C O

Polar bond ↓

Polarity dont cancel ↓

(ASYMMETRICAL) ↓

Net dipole moment ↓

Molecule POLAR

δ- δ-

Polar bonds

Bond polarity cancel

No Net Dipole moment

Polar bond ↓

Polarity cancel ↓

(SYMMETRICAL) ↓

NO dipole moment ↓

Molecule NON POLAR

✗ ✗ ✓ ✓

I