IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol 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)
5
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
Data Collection from 3D modelling (4ECC)
Bond angle Jmol Pymol Rasmol ACD Lab Average
∠CF4 109.013 109.011 109.021 109.021 109.012
∠CCI4 109.011 109.032 109.022 109.031 109.021
∠CBr4 109.021 109.011 109.021 109.021 109.013
∠CI4 109.011 109.021 109.011 109.011 109.110
Data Collection from Database (4ECC)
Bond angle CRC RSC Chemspi Chemfind Average
∠CF4 109.011 109.012 109.023 109.012 109.011
∠CCI4 109.011 109.012 109.012 109.031 109.013
∠CBr4 109.011 109.012 109.011 109.024 109.011
∠CI4 109.011 109.022 109.012 109.011 109.120
vs
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
How element with diff EN affect bond angle/length
How double bond C=O affect bond angle/length
Will size/EN of substituted gp affect bond angle
Will diff/bulky alkyl substituted gp affect bond angle
How lone pair electron affect bond angle
VSEPR
- Factoraffectingbond angle for 3/4/5/6 electron charged center
- How EN/size/type alkyl gp substituent, double bond
or number lone pair electrons (1 or 2) affect bond angle
..
ECC = 3
ECC = 4
..
..
..
..
ECC = 5
..
Bond angle Jmol Pymol Rasmol ACD Lab Average
∠F2O 103.013 103.011 103.021 103.021 103.012
∠CI2O 110.011 110.032 110.022 110.031 110.021
∠Br2O 111.021 111.011 111.021 111.021 111.013
∠I2O 111.011 111.021 112.011 112.011 112.111
Bond angle CRC RSC Chemspi Chemfind Average
∠F2O 103.011 103.010 103.011 103.022 103.011
∠CI2O 110.021 110.022 110.022 110.031 110.022
∠Br2O 111.011 111.012 111.011 111.012 111.012
∠I2O 111.012 111.011 112.012 112.012 112.102
F
‫׀‬
F - C – F
‫׀‬
F
O
F F
CI
‫׀‬
CI - C – CI
‫׀‬
CI
O
CI CI

9. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
How element with diff EN affect bond angle/length
How double bond C=O affect bond angle/length
Will size/EN of substituted gp affect bond angle
Will diff/bulky alkyl substituted gp affect bond angle
How lone pair electron affect bond angle
..
ECC = 3
ECC = 4
..
..
..
..
ECC = 5
..
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?
VSEPR
- Factoraffectingbond angle for 3/4/5/6 electron charged center
- How EN/size/type alkyl gp substituent, double bond
or number lone pair electrons (1 or 2) affect bond angle

10. Bond angle
104.5°
B C SO
F
F
F
H
H O O
O
C
O
O
O
B X
F
F
F
C
H
H
x
x
O S
O O
C
O
x
x
O
2-
2-
O
x
x
:
||
BF3 CH2O SO3 CO3
2-
= =
ECC = 3
3 bond pair
Bond angle
120° Trigonal
planar
✓
E
L
E
C
T
R
O
N
C
H
A
R
G
E
C
E
N
T
E
R
O3
O
O O
:
O
O
:
O
NO2

N
OO

N
OO
NO2
-
N
OO
:
N
OO
:
SO2
OO
-
-
S
:
S
OO :
ECC = 3
2 bond pair
1 lone pair
Bent ✓
Equal repulsion
Electron
Distribution
(TRIGONAL PLANAR)
Unequal repulsion
Electron
Distribution
(TRIGONAL PLANAR)
How element with diff EN affect bond angle/length
How double bond C=O affect bond angle/length
Will size/EN of substituted gp affect bond angle
Will diff/bulky alkyl substituted gp affect bond angle
How lone pair electron affect bond angle
Possible ResearchQuestion (VSEPR)
Factoraffecting bond angle for 3 electroncharged center?
Is it EN/size/type alkyl gp substituent, double bond or number lone pair electrons (1 or 2)
:

11. How element with diff EN affect bond angle/length
How double bond C=O affect bond angle/length
Will size/EN of substituted gp affect bond angle
Will diff/bulky alkyl substituted gp affect bond angle
How lone pair electron affect bond angle
Bond angle
109.5°
Bond angle
104.5°
O
Bond angle
107°
Tetrahedral
Trigonal
Pyrimidal
N
H
N
:
O
SO3
2-PH3NH3
O
HH
H2O
O
F2O
F F
S
CICI
SCI2
N
H H
NH2
- -
Bent
CIO3
-
H H
P
H H H
H
H
H
P
H
H
H
:
O O
S
O
S
O
:
O
2-
2-
CI
O
OO
CI
:
O
O
-
:
CH4
C
H
NH4
+ BH4
- PCI4
+
H
H
H
H
C
H
H
H

N
H
H H
H
H
N
H
H
H

H
B
HH H
H
B
H

H
H
CI
CI
CI
CI
P
CI
CI
CI
P

CI
-
-
+
+
+
+
::
:
::
::
: :
::
:
:
:
:
:
Lone
Pair
Bonding
Pair
E
L
E
C
T
R
O
N
C
H
A
R
G
E
C
E
N
T
E
R
2 bond pair
2 lone pair
ECC = 4
3 bond pair
1 lone pair
✓
ECC = 4
4 bond pair
✓
-
✓
Unequal repulsion
Unequal repulsion
Electron
Distribution
(TETRAHEDRAL)
Equal repulsion
Electron
Distribution
(TETRAHEDRAL)
Factoraffecting bond angle for 4 electroncharged center?
Is it EN/size/type alkyl gp substituent, double bond or number lone pair electrons (1 or 2)
:

12. 
Bond angle
180° Linear
Bond angle
<90°
T shape
Bond angle
< 90° , < 120°
Trigonal
Bipyrimidal
Bond angle
90° , 120°
P CI
CI
CI
CI
CI

S
F
F
F
F
Te
CI
CI
CI
CI
CI
F
F
F
CI
F

F
F

I
CI
CI
CI
CI
I


CI

CI
I
F
F
F
F
Xe
F
F
O
O
+


I
I
I


Xe
CI
CI
I

F
F

:
::
:
::
:
::
::
:
::
:
::
:
::
::
::
::
::
::
::
::
::
: : :
BrF
F
F
Br
F


F
F
: :
:
: :
:
::
:
-
PCI5
SF4 TeCI4 (IF4)+ XeO2F2
(I3)-
(ICI2)- XeF2
-
Bonding
Pair
Lone
Pair
E
L
E
C
T
R
O
N
C
H
A
R
G
E
C
E
N
T
E
R
:
:
:
:
ECC = 5
5 bond pair
✓
ECC = 5
4 bond pair
1 lone pair
Seesaw ✓
ECC = 5
3 bond pair
2 lone pair
✓
ECC = 5
2 bond pair
3 lone pair
F
F Xe
F
F
Xe
 F
F
::
:
::
::
::
+
+
✓
Equal repulsion
Unequal repulsion
Unequal repulsion
Electron Distribution
(TRIGONAL BIPYRIMIDAL)
Electron Distribution
(TRIGONAL BIPYRIMIDAL)
How element with diff EN affect bond angle/length
How double bond C=O affect bond angle/length
Will size/EN of substituted gp affect bond angle
Will diff/bulky alkyl substituted gp affect bond angle
How lone pair electron affect bond angle
Factoraffecting bond angle for 5 electroncharged center?
Is it EN/size/type alkyl gp substituent, double bond or number lone pair electrons (1 or 2)
:

13. Linear
Square planar
F
S
SF6
F
F
F
F
F
PCI6
-
P
CI
CI
CI
CI
CI
CI
IF5O
I
O
||
F
F
F
F
F
Square pyrimidal
CI
Sb
CI
CICI
CI
(SbCI5)2- BrF5
Xe
F
FF
F
Xe
XeF4
F
F
F
Br
F
FF
F
O
Xe
|| F
FF
F
F
Te
F
FF
F
XeOF4 (TeF5)-
-
CICI
I
CICI
(ICI4)- -
2-
:
-
Lone
Pair
Bonding
Pair
::
::
:
::::
::::
:
: :
:
:
:
:
:
:
:
::
::
:
(XeF3) -
F
(XeF2)2-
F
F
Xe
E
L
E
C
T
R
O
N
C
H
A
R
G
E
C
E
N
T
E
R
Lone pair in equatorial first, then axial
Lone pair in equatorial first, then axial
:
:
:
:
-
2-
Minimise repulsion
Minimise repulsion
ECC = 6
6 bond pair
Bond angle
90° Octahedral ✓
ECC = 6
5 bond pair
1 lone pair
Bond angle
< 90° ✓
4 bond pair
2 lone pair
✓
3 bond pair
3 lone pair
T shape ✓
2 bond pair
4 lone pair
Bond angle
180°
✓
Equal repulsion
Unequal repulsion
Bond angle
90°
Electron Distribution
(OCTAHEDRAL)
Electron Distribution
(OCTAHEDRAL)
Unequal repulsion
Electron Distribution
(OCTAHEDRAL)
Factoraffecting bond angle for 6 electroncharged center?
Is it EN/size/type alkyl gp substituent, double bond or number lone pair electrons (1 or 2)
How element with diff EN affect bond angle/length
How double bond C=O affect bond angle/length
Will size/EN of substituted gp affect bond angle
Will diff/bulky alkyl substituted gp affect bond angle
How lone pair electron affect bond angle
Bond angle
< 90°
:
:

14. Valence Shell Electron Pair Repulsion
Predict molecular shape/geometry Shape determine by electron pair/
electron charge centers/ECC
Bonding/lone pair – repel each other
Bonding/lone pair arrangethemselves as far as possible
(minimise repulsion)
Valence
Shell
Electron
Pair
Repulsion
N
H
HH
..
Principles of VSEPR
Shape of molecule
Determinenumber valence e around centralatom1
2 Single, double, triple bond , lone pair act as ECC
3
4 Lone pair-lonepair > Lone pair-bondingpair >
bonding pair- bonding pair repulsion
5
6 ECC or electron pair position in equatorialfirst, then axial
Lewis structure
VSEPR
..
N
H
H
H
Geometry
4 ECC
3 bonding pair
1 lone pair
Trigonal pyrimidal
1
2
3
Bond pair electron
• Occupy smaller region
space bet nuclei
• Repulsion less
Lone pair electron
nucleus
>
Bonding pair electron
Concept Map
nuclei
Lone pair electron
• Electron pair occupy
greater space
• Repel any bonding pair nearby
• Lone pair repulsion > bonding pair repulsion
Double bond
•Repulsion greater
•Angle smaller, 111.4°
B
F
F
F
Single bond
•Equal repulsion
•Angle 120°
120°
120°
120°
space occupy
by electron
space occupy
by electron

15. ValenceShell Electron Pair Repulsion
Bonding/lone pair arrangethemselves as far as possible
(minimise repulsion)
Principles of VSEPR
Determinenumber valence e around centralatom1
2 Single, double, triple bond , lone pair act as ECC
3 Bonding/lone pair repel each other
Lone /lone pair > Lone /bond pair > bond/bond pair repulsion
4
5
For 5/6 ECC: lone pair in equatorial first, then axial
..
N
HHH
3 bonding pair
1 lone pair
4 ECCN – central atom
3 ECC
C
H
=O
H
2 ECC
O
H H
4 ECC
> >
1 lone pair2 lone pair 0 lone pair
Repulsion greater - Bond angle smaller
Repulsion
greater
Repulsion
greater
✓
ECC far apart – Bond angle greatest – minimise repulsion
6
Lone pair need more space
Multiple bonds more space
Unequal repulsionEqual repulsion
90°
120°
109.5°
107°
180°
H – C ≡ N