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

1. http://lawrencekok.blogspot.com
Prepared by
Lawrence Kok
Tutorial on 3D modelling software using Jmol, Pymol, ACD
Lab and Rasmol for Internal Assessment.

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
Organic software for 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.
✓ ✓

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
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 distance using 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

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
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

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 software for 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

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 software for 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

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
Organic software for 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 Optimization before measurement
Compare it to J mol
Compare it to CRC Data booklet
Compare it 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 optimization before measurement
Compare it to J mol
Compare it to CRC Data booklet
Compare it to Chem EDDL
Compute the average bond length /angle
Finish product in 3D viewer

8. 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 structure from
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 optimization before measurement
Compare it to J mol
Compare it to CRC Data booklet
Compare it 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
Calculate all properties
2
3
Generate 3D view
Press 3D Optimization bef measure bond length
1
Organic software for 3D model (ACD Lab)

9. Possible Research Question
Find a substitute which has a much stable bond but meet CFC/refrigerant criteria
How halogen, F, CI, Br and I affect bond length/strength/bp/polarity of CFC
How presence of hydrocarbon chain affect bond strength/length/bp of CFC
How presence of diff halogen affect bond length/strength/bp of CFC
How presence of C sp2/ C sp3 affect bond length/strength/b/p of CFC
CFC/refrigerant – Bond bet (Carbon – Halogen) is strong
Low reactivity/High ∆H vap – Absorb heat/High polarity
High b/p (range -51 to -128C). Must be able to be liquified.
CI
‫׀‬
F – C – CI
‫׀‬
H
CI
‫׀‬
F – C – CI
‫׀‬
CI
CI
‫׀‬
F – C – CI
‫׀‬
F
C – F
CI
‫׀‬
I – C – CI
‫׀‬
H
CI
‫׀‬
I – C – CI
‫׀‬
Br
C – C – F C – C – C – F
C = C
CI
CI
C = C
F
F
C = C
FF
FH
Bond length Jmol Pymol Rasmol ACD Lab Average
C – F 137 138 138 137 137
C – CI 176 177 176 175 176
C – Br 195 195 194 195 195
C – I 215 214 215 215 215
Data Collection from 3D modelling
Bond angle Jmol Pymol Rasmol ACD Lab Average
∠HCF 109.013 109.011 109.021 109.021 109.012
∠HCCI 109.011 109.032 109.022 109.031 109.021
∠HCBr 109.021 109.011 109.021 109.021 109.013
∠HCI 109.011 109.021 109.011 109.011 109.11
Data Collection from Database
Bond angle CRC RSC Chemspi Chemfind Average
∠HCF 109.011 109.012 109.023 109.012 109.011
∠HCCI 109.012 109.012 109.012 109.031 109.013
∠HCBr 109.011 109.012 109.011 109.024 109.013
∠HCI 109.011 109.022 109.012 109.011 109.11
Bond length CRC RSC Chemspi Chemfind Average
C – F 136 137 137 137 137
C – CI 177 177 176 176 176
C – Br 194 194 195 195 195
C – I 214 215 215 215 215
vs
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD

10. Possible Research Question
Find a substitute which has a much stable bond but meet CFC/refrigerant criteria
How halogen, F, CI, Br and I affect bond length/strength/bp/polarity of CFC
How presence of hydrocarbon chain affect bond strength/length/bp of CFC
How presence of diff halogen affect bond length/strength/bp of CFC
How presence of C sp2/ C sp3 affect bond length/strength/b/p of CFC
CFC/refrigerant – Bond bet (Carbon – Halogen) is strong
Low reactivity/High ∆H vap – Absorb heat/High polarity
High b/p (range -51 to -128C). Must be able to be liquified.
CI
‫׀‬
F – C – CI
‫׀‬
H
CI
‫׀‬
F – C – CI
‫׀‬
CI
CI
‫׀‬
F – C – CI
‫׀‬
F
C – F
CI
‫׀‬
I – C – CI
‫׀‬
H
CI
‫׀‬
I – C – CI
‫׀‬
Br
C – C – F C – C – C – F
C = C
CI
CI
C = C
F
F
C = C
FF
FH
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
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?

11. Delocalization of electrons
Resonance structures ozone
resonance structure 1 resonance structure 2
resonance hybrid
• All bond O-O are identical in length and strength
• Hybrid of 2 resonance structure
• NO O-O (single) or O=O (double) bonds found
• Only O ----- O bond
• Intermediate in character bet single and double bond
• Bond Order = 2
11
Ozone
3O
Click here on video ozone
Resonance
• Describing delocalization of electrons within a molecule/polyatomic ion
where bonding cannot be express by ONE single Lewis structure
•Delocalization of π bond – π electrons spread over more than 2 nuclei
•π electrons are shared
•π electrons spread – more stable
• Pale blue gas, polar, dimagnetic
• Oxidizing agent
• Potent respiratory hazard and pollutant at ground level
• Beneficial prevent UV B/C from reaching Earth surface
• Highest ozone level in stratosphere (10 km and 50 km)
UV radiation
Ozone at stratosphere
strongest radiation
3O

12. FORMAL CHARGE (FC)
Formal Charge
•Tool/Model for comparing which Lewis structures is more acceptable
•Treat covalent bond with equal electron distribution no electronegativity differences bet atom
•Electronegative atom has negative while least electronegative atom has positive formal charge
Formula formal charge
V - valence electrons of atom
L – lone pair electron
B – bonding electron molecule
✓
Formal charge sulfur dioxide
formal charge for O
V- Valence electron O = 6
L- Lone pair electron O = 4
B- Bonding electron O = 4
L +
FC = 6 – (4 +2) = 0
formal charge for O
V- Valence electron O = 6
L- Lone pair electron O = 6
B- Bonding electron O = 2
FC = 6 – (6+1) = -1
formal charge for O
V- Valence electron O = 6
L - Lone pair electron O = 2
B - Bonding electron O = 6
FC = 6 – (2+3) = +1
All resonance structure contribute to electronic structure.
Real structure is combination of them.
Lowest formal charge (stable), contribute more than less stable structure.
Sum of formal charges must be zero for neutral or equal to charge on ion. ✓0
+1
-1
✓
L + L + L +

13. Ozone Good and Bad
Good Side Bad Side
Ozone in Strastophere
• blocks UV B + C
Ozone in Troposphere act as
• Greenhouse gas
Ozone in ground level act as
•Pollutant
•Photochemical
Click here on ozone depletion
substances ODS (phaseout)
Why ozone able to absorb UV B and UV C?
Breakdown of ozone – High UV radiation
– Skin cancer
- DNA mutation
Ozone depletion
UV Exposure
Ozone Hole

14. Ozone absorb UV radiation
Ozone absorb UV B/C
Ozone formation
O=O
Double
bond
O=O=O
Inter
mediate
Bond length/pm 121 127
Bond enthalpy/kJ
mol-1
498 363
Bond order 2 1.5
Dissociation by UV <242nm <330nm
Ozone weaker bond
•Absorb UV A/B
(wavelength 330nm)
Bonding
O2 and O3
Oxygen stronger bond
•Absorb UV C
(wavelength 230nm)
* Free radical -reactive species with unpair electron
How ozone layer protect life on earth?
Ozone Cycle
How Ozone
protect?
O2 split by
high UV to O· (radical)
O· radical combine to form ozone
1
2
3 Ozone absorb UV B/C
4 Ozone reform again
Ozone cycle
Ozone created/destroyed by Chapman cycle
Oxygen reform again
Weaker bond in ozone broken UV
O• + O2 → O3
O3 + hv → O2 + O•
O3 + O• → 2O2
O2 + hv → 2O•
O• + O2 → O3
O3 formation
O3 destruction
+
+

15. Ozone absorb UV radiation
Ozone absorb UV B/C
Ozone formation
O=O O=O=O
Bond length/pm 121 127
Bond enthalpy/kJ mol-1
498 363
Bond order 2 1.5
Dissociation by UV <242nm <330nm
Ozone weaker bond
•Absorb UV A/B
(wavelength 330nm)
Bonding
O2 and O3
Oxygen stronger bond
•Absorb UV C
(wavelength 230nm)
How ozone layer protect life on earth?
Ozone Cycle
How Ozone
protect?
O2 split by
high UV to O· (radical)
O· radical combine to form ozone
1
2
3 Ozone absorb UV B/C
4 Ozone reform again
Ozone created/destroyed by Chapman cycle
Oxygen reform again
Weaker bond in ozone broken UV
O• + O2 → O3
O3 + hv → O2 + O•
O3 + O• → 2O2
O2 + hv → 2O•
O• + O2 → O3
BE O3 = 363 kJmol-1
Wavelength need to break O3 bond
Energy 1 mole, 6.02 x 1023
= 363 kJ
Energy 1 photon = E = hf
In nature: Ozone formation = Ozone destruction (without CFC free radical)
Velocity of light (c) = frequency(f) x wavelength(λ) - c = f λ
• All electromagnetic waves travel at speed of light (3.00 x 108
ms-1
)
• Radiation with high frequency – short wavelength↑ ↓
• Electromagnetic radiation/photon carry a quantum of energy given by
E = hf λ
hc
E = h = plank constant = 6.626 x 10-34
Js
f = frequency
λ = wavelength
BE O2 = 498 kJmol-1
Wavelength need to break O3 bond
Energy 1 mole, 6.02 x 1023
= 498 kJ
Energy 1 photon = E = hf
JE 19
23
1003.6
1002.6
363000 −
×=
×
=
nm
E
hc
330
1003.6
1031063.6
19
834
=
×
×××
== −
−
λ
λ
λ
hc
E =
JE 19
23
1027.8
1002.6
498000 −
×=
×
=
nm
E
hc
241
1027.8
1031063.6
19
834
=
×
×××
== −
−
λ
λ
λ
hc
E =
easier to break ! harder to break !

16. Ozone absorb UV B/C
CFC breaks down
How CFC breaks down ?
High UV B/C
How CI·
radical destroy
ozone?
✓
Catalytic destruction of ozone
Ozone Depleting Substances (ODS)
How CFC destroys ozone ?
CI free radicals form
CI· react O3 form CIO· radical
CIO· react O· form CI· radical
Net - ozone break down.
Carbon
Fluorine
Chlorine
•CI + O3 → •CIO + O2
•CIO + O• → •CI + O2
O3 + O• → 2O2
+
F
‫׀‬
H – C – F
‫׀‬
CI
F
‫׀‬
F – C – CI
‫׀‬
CI
CI
‫׀‬
F – C – CI
‫׀‬
CI

17. Ozone absorb UV B/C
NOx breaks down
How CFC breaks down ?
High UV B/C
How NO· radical
destroy ozone?
✓
Catalytic destruction of ozone
Ozone Depleting Substances (ODS)
NO· free radicals form
NO· react O3 form NO2· radical
NO2· react O· form NO· radical
Net - ozone break down.
Oxides of Nitrogen
Nitrogen Dioxide
(NO2)
Nitrogen monoxide
(nitric oxide NO)
Nitrous oxide
N2O
Break down to form NO· free radical (unpair electron)
Sources of NOx
NO• + O3 → NO2• + O2
NO2• + O• → NO• + O2
O3 + O• → 2O2

18. Catalytic destruction of ozone
Ozone Depleting Substances (ODS)
Source of ODS
• Halogenated substance
• Man-made halocarbon refrigerant, solvent, propellant
• Foam-blowing agent (CFCs, HCFCs, freons, halons).
Montreal Protocol ban CFC, halon, and ODS like
carbon tetrachloride and trichloroethane.
CFC
•Contain chlorine, fluorine atoms
•Extremely stable with strong bonds, long half life
•Stability allow CFC to stratosphere
•High UV radiation react with CFC
•High UV break CFC (photochemical decomposition)
•Free Cl radical form - destroying ozone.
Trichloroflouromethane
CFC-11
Dichlorodifluoromethane
CFC-12
Chlorodifluoromethane
HCFC-22
Why
halogenated
CFC used?
Less harmful
Very harmful
Why fluorinated is safer?
CI
‫׀‬
F – C – CI
‫׀‬
CI
CI
‫׀‬
F – C – CI
‫׀‬
F
H
‫׀‬
F – C – CI
‫׀‬
F
Bond length Bond strength
C – F 138 484
C – CI 176 338
C – Br 195 276
C – I 215 238

19. Acknowledgements
Thanks to source of pictures and video used in this presentation
Thanks to Creative Commons for excellent contribution on licenses
http://spaceplace.nasa.gov/greenhouse/en/
http://www.ozonedepletion.info/education/part3/ozonesources.html
http://creativecommons.org/licenses/
http://www.ciesin.org/docs/011-462/011-462.html
http://www.epmagazine.org/storage/165/benzene-evidence.aspx
Prepared by Lawrence Kok
Check out more video tutorials from my site and hope you enjoy this tutorial
http://lawrencekok.blogspot.com