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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