IB Chemistry on ICT, 3D software, Avogadro, AngusLab, Swiss PDB Viewer for Internal Assessment on Electrostatic potential and Polarity

1. Click here download Rasmol
Click here download PyMolClick here download Jmol
Click here Chem EDDL
Click here chemical search.
Modelling and 3D representation
Quick Chemistry DatabaseCheck
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 softwarefor 3D model
Electrostatic Potential (ESP)
Measure polarization
Electron Map density
Electron distribution
Dipole Moment
Measure bond length/angle
Measure bond strength

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 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

3. 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

4. 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

5. 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

6. Electrostatic Potential (ESP)
Measure polarization
Electron Map density
Electron distribution
Dipole Moment
Measure bond length/angle
Measure bond strength
Organic softwarefor 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 – calculateElectrostatic Potential
Go to web server
Key in 4 pdb code – 4INS
Click visualize see result (Firefox)
control panel
- surfaceon
- colour amino acid
- ball stick
3 diff option
Click here Pymol ESP tutorial
Right click to zoom back

7. 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
Chemicalviewer 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

8. CH3CH2CI Angus Pymol Jmol Avogadro Mean
Dipole m 2.07 2.05 2.05 2.06 2.06
ESP Low Low Low Low Low
Bond length 177 176 176 177 177
Bond angle 109.04 109.03 109.04 109.03 109.03
Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Effect of halogen on electrostatic potential and polarity/ dipole moment
CRC database Chem spider.
How diff number/type of halogen affect ESP, polarity/dipole
moment bond angle/length of molecule?
Click here NIST data
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H F
Data Collection from 3D modelling
CH3CH2F Angus Pymol Jmol Avogadro Mean
Dipole m 2.09 2.08 2.09 2.08 2.08
ESP High High High High High
Bond length 137 136 136 137 137
Bond angle 109.02 109.01 109.04 109.03 109.02
Data Collection from Database
Effect of halogen on polarity, dipole moment and electrostatic potential
Effect of func gp, OH/COO/NH2/CO has on polarity and electrostatic potential
Effect of halogen gp on polarity and dissociation constant of organic acid COOH
How diff halogen gp affect the electron distribution and reactivity
Click here chem axon
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H CI
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H Br
H F
‫׀‬ ‫׀‬
H - C – C – F
‫׀‬ ‫׀‬
H F
H CI
‫׀‬ ‫׀‬
H - C – C – CI
‫׀‬ ‫׀‬
H CI
H Br
‫׀‬ ‫׀‬
H - C – C – Br
‫׀‬ ‫׀‬
H Br
Click here download Avogadro
Click here download Arguslab
type
number
CH3CH2F CRC NIST Chem axon Chem spi Mean
Dipole m 2.10 2.09 2.09 2.09 2.09
Bond length 136 136 137 137 136
Bond angle 109.01 109.04 109.02 109.03 109.02
CH3CH2CI CRC NIST Chem axon Chem spi Mean
Dipole m 2.06 2.07 2.05 2.05 2.05
Bond length 176 176 176 177 176
Bond angle 109.04 109.05 109.04 109.04 109.04
vs
vs

9. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here NIST data
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H F
Click here chem axon
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H CI
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H Br
H F
‫׀‬ ‫׀‬
H - C – C – F
‫׀‬ ‫׀‬
H F
H CI
‫׀‬ ‫׀‬
H - C – C – CI
‫׀‬ ‫׀‬
H CI
H Br
‫׀‬ ‫׀‬
H - C – C – Br
‫׀‬ ‫׀‬
H Br
Click here download Avogadro Click here download Arguslab
type
number
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?
Effect of halogen on electrostatic potential and polarity/ dipole moment
How diff number/type of halogen affect ESP, polarity/dipole
moment bond angle/length of molecule?
Evaluationand Limitationusing 3D modelling
Click here video chem axon
Click here NIST expt dipole
Effect of halogen on polarity, dipole moment and electrostatic potential
Effect of func gp, OH/COO/NH2/CO has on polarity and electrostatic potential
Effect of halogen gp on polarity and dissociation constant of organic acid COOH
How diff halogen gp affect the electron distribution and reactivity

10. ChemicalBond
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 polarIonic
EN – 3
Diff = (3 – 2.1 ) = 0.9
Na+
CI-
EN – 3
Sharing of electron
bet non metal atoms

11. 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
✓✗

12. ✗
Separation of charges
Unequal distribution electron due to diff EN value
shared electron closer to Oshared electron closer to F
Covalent Bond
Polar covalent Bonds Non Polar covalent Bond
Equal sharing electronUnequal 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 DistancePolar 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

13. Polarity
Shape
Asymmetrical
Polar bond
↓
Polaritydont cancel
↓
(ASYMMETRICAL)
↓
Net dipolemoment
↓
MoleculePOLAR
Polar bond
↓
Polaritycancel
↓
(SYMMETRICAL)
↓
NO dipolemoment
↓
MoleculeNON 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
↓
Polaritydont cancel
↓
(ASYMMETRICAL)
↓
Net dipolemoment
↓
MoleculePOLAR
δ- δ-
Polar bonds
Bond polarity cancel
No Net Dipole moment
Polar bond
↓
Polaritycancel
↓
(SYMMETRICAL)
↓
NO dipolemoment
↓
MoleculeNON POLAR
✗ ✗✓
✓
I