IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal Assessment

1. Measure number H2 bonds
Measure bond length/angle
Measure bond strength
Similarity/diff in enzyme/DNA structure diff (species)
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
Click here crystallography database.
✓ ✓ ✓

2. Measure number H2 bonds
Measure bond length/angle
Measure bond strength
Similarity/diff in enzyme/DNA structure diff (species)
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Click here J mol protein video
Type PDB code – 1BOU
Right click – select console
Select all
Colour gray
Select 39-46
Colour blue
Right click
Select proteins – by residue name – cyc
Right click – Style – scheme –ball stick
Right click – Select all
Zoom in
Measure distanceusing ruler bet cyc
Chemical viewer 3D structure (Jmol)
Uses molecular modelling
1
J mol executable file
Console
Type in above
Measure distance
final product
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
4
3
4
Click here J mol download

3. Measure number H2 bonds
Measure bond length/angle
Measure bond strength
Similarity/diff in enzyme/DNA structure diff (species)
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
J mol executable file
Type -PDB ID - 4 letter code to J mol
Protein Data Bank
Protein database key in - PDB 4 letter code
Click here - List all pdb source
Click here J mol tutorial
Minimise structure– (most stable form)
Model kit – press minimise
Click here J mol download
1
2
3
Click here - List all pdb insulin
H bonds
Bond length/angle
Uses molecular modelling
Model kit to
design molecule
Measure
distance/angle
4
Get structure from
PDB and MOL
Right click to get console
1
2
3
Chemical viewer 3D structure (Jmol)
Click here for pdb files
4

4. Measure number H2 bonds
Measure bond length/angle
Measure bond strength
Similarity/diff in enzyme/DNA structure diff (species)
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 file – open your download pdb file
from Protein Data bank
Get to command term – Type fetch 3CSY
H - Hide – S - Show cartoon – C – Type by ss
Distance bet 2 atoms
Click here for pdb files
2
Press S – sequence at bottom screen.
Right click – zoom in
Select amino acid 1 – 60 by dragging
Look 3CSY – H – hide everything
Look sele – S – Show stick
Wizard – Measure – select 2 atom measure distance – done
Look sele – A – action – find polar contact to any atom – yellow bond
4
Uses molecular modelling
2
3

5. Measure number H2 bonds
Measure bond length/angle
Measure bond strength
Similarity/diff in enzyme/DNA structure diff (species)
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Organic softwarefor 3D model (Rasmol)
Click here resources Rasmol
Click here download Rasmol
RasMol - exploring structure of molecules.
Stored in a PDB. (Protein Data Bank) file
Go to File > Open, look PDB file you want
download pdb file text
3
1
4
Click on file – open your download pdb file
from Protein Data bank - (3B6F)
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Open file – 3B6F
Command term – type - restrict dna – colour blue
Select – setting – pick distance – measure distance bet 2 atoms
Rasmol command term
Click here to view command terms
6
Click here - Protein Data Bank
Protein database key in - PDB 3B6F
2
Press setting – pick bond distance and angle
Zoom in – press shift and left click
Select distance atoms and angles to measure
Command term – type hbonds 50 – colour red
Uses molecular modelling
3
Click here for pdb files

6. Measure number H2 bonds
Measure bond length/angle
Measure bond strength
Similarity/diff in enzyme/DNA structure diff (species)
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 chloromethane
Press copy to 3D or press 3D viewer
Measure C – CI bond length/ H – C – CI 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 H - C - CI
Measure distance Measure distanceSelect atom
1
Draw chlorobenzene
Press copy to 3D or press 3D viewer
Measure C – CI 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
33

7. Measure number H2 bonds
Measure bond length/angle
Measure bond strength
Similarity/diff in enzyme/DNA structure diff (species)
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Click here download ACD Lab
Finish product in 3D viewer
Uses molecular modelling
1
Select tools
Generate structurefrom
SMILES and InChI
Paste it from Protein databank
Measure distance Measure bond angleSelect tools – generate structure from SMILES/InChI
Draw chlorobenzene
Press copy to 3D or press 3D viewer
Measure C – CI 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
Structure from SMILES
Structure from InChI
Click here to get in Protein Databank
Select tools
Calculateall properties
2
3
Generate 3D view
Press 3D Optimization bef measure bond length
1
Organic softwarefor 3D model (ACD Lab)
2
3

8. Possible ResearchQuestion
Measuring distance using 3D modelling (A=T)/(G≡C)
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
- Is H2 bond distance(A=T)/(G≡C) the same across diff species
(Archaea/Eubacteria/Eukaryotic)
- Is H2 bond distance (A=T)/(G≡C) the same in diff cell types
Is distance H2 bond (A=T)/(G≡C) always the same bet base pair in diff cell types
How H2 bond length change with changing temperature
Is distance of H2 bond bet bases always the same across diff DNA species
How number H2 bond affect stability of alpha helix/beta pleated protein
Is H2 bond distance (A-T)/(G-C) the same in all diff cell type (liver, kidney, brain)
Is H2 bond distance the same across diff species (Archaea/Eubacteria/Eukaryotic)
Is H2 bond length in ice and liq water the same? If not how big is the variation?
N6 –H6 ----------- O4
N1 ------------H3–N3
H2 bonding between
Click here NCBI
Click here UCSC
Click here Ensembl
Hydrogen Bonding
AdenineThymine
66 4
3
cytosineguanine
4
22
O6 ----------------H4–N4
N1 - H1 ---------- N3
N2 - H2 ---------- O2
H2 bonding between
H2 bond distance

9. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
- Is H2 bond distance(A=T)/(G≡C) the same across diff species
(Archaea/Eubacteria/Eukaryotic)
- Is H2 bond distance (A=T)/(G≡C) the same in diff cell types
Click here NCBI
Click here UCSC
Click here Ensembl
Hydrogen Bonding
DataCollection from 3D modelling (A=T)/(G≡C)
in diff cell type (liver/kidney/brain)
DataCollection from Database(A=T)/(G≡C)
in diff cell type (liver/kidney/brain)
Bond length Jmol Pymol Rasmol Average
A=T (N6 – H6 ----O4) 2.83 2.84 2.82 2.82
A=T (N1 ------H3- N3) 2.81 2.82 2.82 2.81
G≡C (O6 ---H4 – N4) 2.78 2.77 2.75 2.76
G≡C (N1 – H1 --- N3) 2.87 2.88 2.87 2.87
G≡C (N2 – H2----O2) 2.87 2.87 2.88 2.87
Bond length NCBI UCSC Esemble Average
A=T (N6 – H6 ----O4) 2.85 2.84 2.84 2.84
A=T (N1 ------H3- N3) 2.80 2.80 2.82 2.80
G≡C (O6 ---H4 – N4) 2.77 2.78 2.77 2.77
G≡C (N1 – H1 --- N3) 2.88 2.88 2.87 2.88
G≡C (N2 – H2----O2) 2.89 2.90 2.90 2.90
Is distance H2 bond (A=T)/(G≡C) always the same bet base pair in diff cell types
How H2 bond length change with changing temperature
Is distance of H2 bond bet bases always the same across diff DNA species
How number H2 bond affect stability of alpha helix/beta pleated protein
Is H2 bond distance (A-T)/(G-C) the same in all diff cell type (liver, kidney, brain)
Is H2 bond distance the same across diff species (Archaea/Eubacteria/Eukaryotic)
Is H2 bond length in ice and liq water the same? If not how big is the variation?

10. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
- Is H2 bond distance(A=T)/(G≡C) the same across diff species
(Archaea/Eubacteria/Eukaryotic)
- Is H2 bond distance (A=T)/(G≡C) the same in diff cell types
Click here NCBI
Click here UCSC
Click here Ensembl
Hydrogen Bonding
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?
Is distance H2 bond (A=T)/(G≡C) always the same bet base pair in diff cell types
How H2 bond length change with changing temperature
Is distance of H2 bond bet bases always the same across diff DNA species
How number H2 bond affect stability of alpha helix/beta pleated protein
Is H2 bond distance (A-T)/(G-C) the same in all diff cell type (liver, kidney, brain)
Is H2 bond distance the same across diff species (Archaea/Eubacteria/Eukaryotic)
Is H2 bond length in ice and liq water the same? If not how big is the variation?

11. Permanent dipole
Polar
Non Polar
Temporary dipole
(instantaneously induced dipole)
London dispersion forces
Van Der Waals’ Forces attraction
Polar molecule (dipole – dipole attraction)
Polar molecules due to diff in EN values
Dipole/dipole interaction
Electrostatic forces attraction bet molecules
Dipole/dipole attraction Dipole/dipole attraction
Hydrogen bonding (dipole – dipole attraction)
H atom bond to electronegative atom, N, O, F
Partial H+ attract to lone pair electron on N, O, F
Electrostatic force attraction bet molecules involve H
Intermolecular force bet molecule (IMF)
Non Polar molecule (Induced dipole attraction)
Random movement /distribution of electron
Instantaneous negative charge on atom
Induced a temporary dipole separation
Electrostatic forces attraction bet molecules
Non polar molecules
Polar molecules
Polar molecules
Forces bet molecule
Molecules

12. Hydrogen bonding (dipole – dipole attraction)
H atom bond to electronegative atom, N, O, F
Partial H+ attract to lone pair electron on N, O, F
Electrostatic force attraction bet molecules involve H
Permanent dipole
Polar
Non Polar
Temporary dipole
(instantaneously induced dipole)
London dispersion forces
Van Der Waals’ Forces attraction
Polar molecule
Polar molecules due to diff in EN values
Dipole/dipole interaction
Electrostatic forces attraction bet molecules
Dipole/dipole attraction Dipole/dipole attraction
Molecules
Non Polar molecule (Induced dipole attraction)
Random movement /distribution of electron
Instantaneous negative charge on atom
Induced a temporary dipole separation
Instantaneous dipole in one atom
induce a dipole in its neighbor
Electrostatic forces attraction bet molecules
Non polar molecules
Polar molecules
Polar molecules
Requirement for H bonding
•H atom bond to N, O, F
•N, O, F - Highly electronegative/small size
•Attract electron close to itself – Polarised H+
•N---H, O—H, F—H bonds VERY POLAR
•Very polar H+ attract closely to lone pair on N, O, F
N ---- H O ---- H F ---- H
δ- δ- δ-δ+ δ-+ δ+

13. Types of forces/Bonding
Factors affecting VDF forcesIntermolecular force bet molecule (IMF)
Interaction Strength Boiling
Point/C
Covalent Strongest High
Ionic Strong High
Ion dipole Strong HIgh
Dipole- dipole
(H bond)
Moderate High
Dipole – dipole Weak Low
Temporary induce dipole
(London dispersion)
Weakest Low
Dipole – dipole attraction Induced – dipole attraction
London dispersion forces
Polar Non Polar
All molecules have London dispersion forces due to uneven distribution of electron cloud
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
δ+δ-
London dispersion forces
RMM/Size Surface Area
London dispersion forces
Van Der Waals’ Forces attraction
N N
F F RMM – 38
RMM – 28
Size/ RMM increase
Number electrons increase
Temporary induced dipole increase
Van Der Waal bet molecule increase
RMM same
Surface area increase
Temporary induced dipole increase
Van Der Waal bet molecule increase
RMM –72
RMM– 72
Pentane (C5H12)
Factor affecting b/p of molecules
Temporary dipole attraction
London dispersion force
Permanent dipole attraction
Dipole/dipole attraction
Hydrogen bonding

14. Factors affecting VDF forcesFactor affecting b/p of molecules
RMM/Size Surface Area
N N
F F RMM – 38
RMM – 28
Size/ RMM increase
Number electrons increase
Temporary induced dipole increase
Van Der Waals bet molecule increase
RMM same
Surface area increase
Temporary induced dipole increase
Van Der Waals bet molecules increase
Temporary dipole attraction
London dispersion force
Permanent dipole attraction
Dipole/dipole attraction
Hydrogen bonding
H2 N2 CI2 H2O
RMM 2 28 71 18
Boiling
Point/C
-252 -196 -34 100
Forces London force London force London force London force
Dipole/dipole
Hydrogen bonding
-
-
--
--
H2
London forces
N2
London forces
CI2
London forces
H2O
London forces
Dipole/dipole
Hydrogen bond
RMM increase  - London force/VDF increase  – boiling point increase 
-
-
-
-
--
-
-
--
-
-
-
-
-
-
Hydrogen bondingHydrogen bonding
RMM lowest  - boiling point highest  - due to hydrogen bonding
Pentane (C5H12)
RMM –72
RMM– 72

15. HCI HBr HI HF
RMM 36.5 81 128 20
Boiling
Point/C
-85 -66 -35 19.5
Forces London
force/VDF
London
force/VDF
London
force/VDF
London
force/VDF
Dipole/dipole
Hydrogen bond
RMM increase  - London force/VDF increase  – boiling point increase 
Which liquid has higher boiling point?
H H
H
H
H
H
DNA
Br Br
Br
I I
I
Hydrogen bonding
RMM lowest  - boiling point highest  - due to hydrogen bonding
Br2 ICI
RMM 162 162
B/p/C 58 97
Forces London
force/VDF
London
force/VDF
Dipole/dipole
Which liquid has higher boiling point?
-
-
-
-
-
-
Br2
London forces bet molecules
Br Br Br Br I I ICI CI CI+
+ +- - -
ICI
London forces + Dipole –dipole attraction
Hydrogen Bond bet
nitrogenous base