IB Chemistry on ICT, 3D software, Avogadro, Jmol, Swiss PDB, Pymol for Internal Assessment on angle strain of cyclic compound

1. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
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
✓ ✓

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 Chem EDDL
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 NIST data
✓Click here download Arguslab
Click here chem axon
Click here download Avagrado
Click here chem EdDL

3. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Click here J mol protein video
Chemical viewer 3D structure (Jmol)
Uses molecular modelling
1
J mol executable file
final product
J mol executable file
1
Designing cyclobutanemolecule
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 angle CCC
Measure bond length C – C
Click here J mol tutorial
2
2
3
File – Get MOL – type – cyclobutane
Right click – Computation – Optimize structure
Measure C – C – C bond angle
Press 3D Optimization before measurement
Get structure from
PDB and MOL
Right click to get console
Measure
distance/angle
Model kit to
design molecule

4. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
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 cyclobutane
Press copy to 3D or press 3D viewer
Measure C – C bond length/ C – C – C 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 C - C - C
Measure distance Measure distanceSelect atom
1
Draw cyclobutane
Press copy to 3D or press 3D viewer
Measure C – C 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

5. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
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 cyclobutane
Press copy to 3D or press 3D viewer
Measure C – C 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

6. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
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
1
2
Chemical viewer 3D structure (Avogadro)
Click here for pdb files
Click here download Avogadro
File – open cyclobutane. pdb file
Extension – Optimize geometry
Obtain file from any site as sdf/xml
Select measure
measure bond angle
Select E
Optimize geometry
View – Bond angle
View – Bond angle

7. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
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
Bond angle beta lactam ring
(cyclobutane ring)
Click here for pdb files
2
Wizard – measurement – measure bond angle
for beta lactam ring
4
Uses molecular modelling
2
3
Look for penicillin from PubChem
Down load 3D as sdf . file type
File – open from Pymol
Select measurement - angle

8. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Type -PDB ID – penicillin – save pdb file type
Click here Swiss PDB tutorial
1
2
Uses molecular modelling
1
2
Chemicalviewer 3D structure(Swiss PDB)
Click here for pdb files
File – open penicillin sdf file
Measure bond angle for beta lactam ring (cyclobutane)
Click here down Swiss PDB
Measure bond
length
Look for penicillin from PubChem
Down load 3D as sdf . file type
File – open from Swiss PDB
Measure bond
angle
Movement

9. Relationship between Angle Strain and Stability of Cyclic molecule
Possible ResearchQuestion
Data Collection from 3D modelling (beta lactam ring)
Bond angle Jmol Pymol Swiss Avogadro Average
∠N1C1C2 86.3 86.5 88.3 87.1 87.2
∠C1C2C3 86.7 87.6 88.6 88.2 87.8
∠C2C3N1 90.4 91.2 91.5 92.3 90.5
∠C3N1C1 92.2 93.2 92.3 93.2 92.7
Data Collection from Database (beta lactam ring)
Bond angle NCBI Emsembl UCSC Average
∠N1C1C2 87.2 86.6 87.5 86.9
∠C1C2C3 87.3 88.2 87.5 88.5
∠C2C3N1 91.3 90.1 90.1 90.4
∠C3N1C1 93.1 91.4 92.7 93.1
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD
Penicillin structure- beta lactamring
similar to (cyclobutane)
For steric reason, bond to nitrogen
not trigonal planar.
sp3
sp3
sp2
sp2
- How ring angle changes in penicillin structurecomparedto cyclobutane
- Is bond angle for beta lactamring the same as in cyclobutane,
- if not why/how much it differ
- Are all angle in beta lactamring the same for diff types of penicillin?
- Is bond angle for Csp3 and Csp2 in beta lactamof the same size?
- Is bond angle for Csp2 and Nsp2 in beta lactamring the same size?
- What is the relationship bet angle strain, bond angle and stability of
- beta lactamring in penicillin
- How much does 2 Csp3, 1 Csp2 and 1 Nsp2 deviate from ideal angle 109/ 120
C2
C1
C3
N1
Click here NCBI
Click here Ensembl
Click here UCSC
C1
N1
C3
C2
Click here Avagrado

10. Relationship between Angle Strain and Stability of Cyclic molecule
Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here ACD
Penicillin structure- beta lactamring
similar to (cyclobutane)
For steric reason, bond to nitrogen
not trigonal planar.
sp3
sp3
sp2
sp2
- How ring angle changes in penicillin structurecomparedto cyclobutane
- Is bond angle for beta lactamring the same as in cyclobutane,
- if not why/how much it differ
- Are all angle in beta lactamring the same for diff types of penicillin?
- Is bond angle for Csp3 and Csp2 in beta lactamof the same size?
- Is bond angle for Csp2 and Nsp2 in beta lactamring the same size?
- What is the relationship bet angle strain, bond angle and stability of
- beta lactamring in penicillin
- How much does 2 Csp3, 1 Csp2 and 1 Nsp2 deviate from ideal angle 109/ 120
Click here NCBI
Click here Ensembl
Click here UCSC
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?
Click here Avagrado

11. Click here ring strain (wiki)
Click here angle strain (master organic)
Angle strain – smaller angle (higher angle strain)
– more energeticbond
– more unstable/reactive
Angle strain destabilize molecule - higher reactivity
Angle strain leads to elevated heat of combustion.
Max bond strength result from effective overlap of atomic orbital.
Angle strain and torsional strain combine to create ring strain
Both affect stability of cyclic molecules
Angle strain- deviation from ideal angle
Ideal angle = 109o Angle = 60o
49o deviate from 109o
(angle/torsional strain)
Angle = 90o
49o deviate from 109o
(angle/torsional strain)
Angle = 108o
1o deviate from 109o
(angle/torsional strain)
Angle = 120o
11o deviate from 109o
(angle/torsional strain)
Molecule is NOT FLAT!!!!!
Possible Research Question – Bond angle and Stability of Cyclic molecule
Penicillin structure containingbeta lactamring (cyclobutane)

12. Click here ring strain (wiki)
Click here angle strain (master organic)
Angle strain – smaller angle (higher angle strain)
– more energeticbond
– more unstable/reactive
Angle strain destabilize molecule - higher reactivity
Angle strain leads to elevated heat of combustion.
Max bond strength result from effective overlap of atomic orbital.
Angle strain and torsional strain combine to create ring strain
Both affect stability of cyclic molecules
Angle strain- deviation from ideal angle
Ideal angle = 109o Angle = 60o
49o deviate from 109o
(angle/torsional strain)
Angle = 90o
49o deviate from 109o
(angle/torsional strain)
Angle = 108o
1o deviate from 109o
(angle/torsional strain)
Angle = 120o
11o deviate from 109o
(angle/torsional strain)
Molecule is NOT FLAT!!!!!
Possible ResearchQuestion – Bond angle and Stablility of Cyclic molecule
Cyclic molecule conformto form most stable structure(cyclohexane)
Cyclohexane is NOT FLAT!!!!!
Molecule adopt most stable form
Most stable
ideal bond angle
109o
More stable