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)
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. H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H OH
Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
Does bond angle change for 1, 2 and 3o hydrocarbonof diff functional gp
RSC DatabookletCRC database Chem spider.
Effect of functional gp, OH/COO/NH2/CO/CNhas on mp/bp/polarity/solubility.
How m/p, b/p, polarity/EN/solubility change moving down homologous series
Does atomic size halogen affect bond angle for CH3F, CH3CI, CH3Br, CH3I
Will diff position OH gp affect b/p of alcohol
CH3CH2CH2CH2CH2OH/CH3CH2CH2CH(OH)CH3/CH3CH2CH(OH)CH2CH3
How substitution of diff halogen gp affect the b/p, polarity and dipole moment.
Does bond angle change for 1, 2 or 3o alcohol/halogenoalkane
1o - CH3CH2CI 2o- (CH3)2CHCI 3o - (CH3)3CCI
1o - CH3CH2OH 2o- (CH3)2CHOH 3o - (CH3)3COH
Click here NIST data
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H CI
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H CI H
1o 2o 3o
Data Collection from 3D modelling (Alcohol/Halogenoalkane)
Bond angle Jmol Pymol Rasmol ACD Lab Average
1o ∠HCCI 109.013 109.011 109.021 109.021 109.012
2o ∠HCCI 109.011 109.032 109.022 109.031 109.021
3o ∠HCCI 109.021 109.011 109.021 109.021 109.013
Data Collection from Database (Alcohol/Halogenoalkane)
H CH3 H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H CI H
Bond angle CRC RSC NIST Chemfind Average
1o ∠HCCI 109.011 109.012 109.023 109.012 109.011
2o ∠HCCI 109.011 109.012 109.012 109.031 109.013
3o ∠HCCI 109.011 109.012 109.011 109.024 109.011
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H OH H
H CH3 H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H OH H
Bond angle Jmol Pymol Rasmol ACD Lab Average
1o ∠HCOH 109.013 109.011 109.021 109.021 109.012
2o ∠HCOH 109.011 109.032 109.022 109.031 109.021
3o ∠HCOH 109.021 109.011 109.021 109.021 109.013
Bond angle CRC RSC NIST Chemfind Average
1o ∠HCOH 109.011 109.012 109.023 109.012 109.011
2o ∠HCOH 109.011 109.012 109.012 109.031 109.013
3o ∠HCOH 109.011 109.012 109.011 109.024 109.011

9. H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H OH
Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here RasmolClick here ACD
Dose bond angle change for 1, 2 and 3o hydrocarbonof diff functional gp
RSC DatabookletCRC database Chem spider.
Effect of functional gp, OH/COO/NH2/CO/CNhas on mp/bp/polarity/solubility.
How m/p, b/p, polarity/EN/solubility change moving down homologous series
Does atomic size halogen affect bond angle for CH3F, CH3CI, CH3Br, CH3I
Will diff position OH gp affect b/p of alcohol
CH3CH2CH2CH2CH2OH/CH3CH2CH2CH(OH)CH3/CH3CH2CH(OH)CH2CH3
How substitution of diff halogen gp affect the b/p, polarity and dipole moment.
Does bond angle change for 1, 2 or 3o alcohol/halogenoalkane
1o - CH3CH2CI 2o- (CH3)2CHCI 3o - (CH3)3CCI
1o - CH3CH2OH 2o- (CH3)2CHOH 3o - (CH3)3COH
Click here NIST data
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H CI
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H CI H
1o 2o 3o
H CH3 H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H CI H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H OH H
H CH3 H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H OH H
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 and3D model predictionbefore making conclusion
Computationprogrammeis always based on approximationand we cannot conclusive prove anything
Reflect of validity and reliability of data
Is model a true representation of reality?

10. • memberdifferby CH2 gp
• same functionalgroup
• similar chemicalproperties
• chemicalformulaCnH2n+2
• end with ane
Class Functionalgp Suffix Example Formula
Alkane C - C - ane ethane CnH2n+2
Homologous Series
Class Functional Suffix Example Formula
Alkene Alkenyl - ene ethene CnH2n
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H H
• memberdiffer by CH2 gp
• same functionalgroup
• similar chemicalproperties
• chemicalformula CnH2n
• end with ene
H
‫׀‬
H - C – H
‫׀‬
H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H H H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
Number
carbon
Word IUPAC name Structure formula Molecular
formula
1 Meth Methane CH4 CH4
2 Eth Ethane CH3CH3 C2H6
3 Prop Propane CH3CH2CH3 C3H8
4 But Butane CH3(CH2)2CH3 C4H10
5 Pent Pentane CH3(CH2)3CH3 C5H12
6 Hex Hexane CH3(CH2)4CH3 C6H14
7 Hept Heptane CH3(CH2)5CH3 C7H16
8 Oct Octane CH3(CH2)6CH3 C8H18
9 Non Nonane CH3(CH2)7CH3 C9H20
10 Dec Decane CH3(CH2)8CH3 C10H22
methane ethane propane butane
Saturated hydrocarbon (C – C single bond)
Number
carbon
IUPAC name Structure formula Molecular
formula
2 Ethene CH2CH2 C2H4
3 Propene CH2=CHCH3 C3H6
4 Butene CH2=CHCH2CH3 C4H8
5 Pentene CH2=CH(CH2)2CH3 C5H10
6 Hexene CH2=CH(CH2)3CH3 C6H12
7 Heptene CH2=CH(CH2)4CH3 C7H14
8 Octene CH2=CH(CH2)5CH3 C8H16
9 Nonene CH2=CH(CH2)6CH3 C9H18
10 Decene CH2=CH(CH2)7CH3 C10H20
H H
‫׀‬ ‫׀‬
C = C
‫׀‬ ‫׀‬
H H
H H H
‫׀‬ ‫׀‬ ‫׀‬
C = C – C - H
‫׀‬ ‫׀‬
H H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
C = C – C – C - H
‫׀‬ ‫׀‬ ‫׀‬
H H H
Unsaturated hydrocarbon (C = C double bond)
H H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
C = C – C – C – C - H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
ethene propene butene pentene

11. Class Functional group/name Examples
alkene C = C Alkenyl ethene
alkyne C ≡ C Alkynyl ethyne
alcohol OH Hydroxyl ethanol
ether C – O - C Ether methoxymethane
ketone O
‖
C – C - C
Carbonyl propanone
aldehyde CHO Aldehyde ethanal
Carboxylic acid COOH Carboxyl ethanoic acid
ester O
‖
C – O -R
Ester ethyl ethanoate
amide O
‖
C – NH2
Amide propanamide
amine NH2 Amine ethanamine
nitrile C ≡ N Nitrile propanenitrile
Class Functional gp Suffix Example Formula
Alkane C - C - ane ethane CnH2n+2
Homologous Series
carbon IUPAC name Structure formula Molecular
formula
Boiling
point
1 Methane CH4 CH4 Gas
2 Ethane CH3CH3 C2H6 Gas
3 Propane CH3CH2CH3 C3H8 Gas
4 Butane CH3(CH2)2CH3 C4H10 Gas
5 Pentane CH3(CH2)3CH3 C5H12 Liquid
6 Hexane CH3(CH2)4CH3 C6H14 Liquid
Physical properties
• Increase RMM / molecular size
•RMM increase ↑ - Van Der Waals forces stronger ↑
↓
Melting /boiling point increases ↑
(Increasing polarisability ↑)
London dispersion forces/temporary dipole ↑
1 2 3 4 5 6 7 8 9 10
number carbons – RMM ↑
150
100
50
0
-50
-100
-150
-200
m/p+ b/p
increase ↑
boiling point
room temp
gas
liquid
Homologous Series
number
Carbons / RMM ↑1 2 3 4 5 6 7 8 9 10
boiling point
boiling point increase with increase carbon atoms
alcohol
alkane
alkene
alkyne
London dispersion force
(temporary dipole)
H2 bonding
carboxylic acid > alkane/alkene/alkyne
alcohol
carboxylic acid

12. • member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n+2
• end with ane
Class Functionalgp Suffix Example Formula
Alkane C - C - ane ethane CnH2n+2
Homologous Series
Class Functional Suffix Example Formula
Alkene C = C - ene ethene CnH2n
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H H
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n
• end with ene
H
‫׀‬
H - C – H
‫׀‬
H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬
H H H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – C – H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
Number
carbon
Word IUPAC name Structure formula Molecular
formula
1 Meth Methane CH4 CH4
2 Eth Ethane CH3CH3 C2H6
3 Prop Propane CH3CH2CH3 C3H8
4 But Butane CH3(CH2)2CH3 C4H10
5 Pent Pentane CH3(CH2)3CH3 C5H12
methane ethane propane butane
Saturated hydrocarbon
Number
carbon
IUPAC name Structure formula Molecular
formula
2 Ethene CH2=CH2 C2H4
3 Propene CH2=CHCH3 C3H6
4 Butene CH2=CHCH2CH3 C4H8
5 Pentene CH2=CH(CH2)2CH3 C5H10
6 Hexene CH2=CH(CH2)3CH3 C6H12
H H
‫׀‬ ‫׀‬
C = C
‫׀‬ ‫׀‬
H H
H H H
‫׀‬ ‫׀‬ ‫׀‬
C = C – C - H
‫׀‬ ‫׀‬
H H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
C = C – C – C - H
‫׀‬ ‫׀‬ ‫׀‬
H H H
Unsaturated hydrocarbon
H H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
C = C – C – C – C - H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
ethene propene butene pentene
Structural formula – arrangement atoms in molecule (2/3D) Structural formula – arrangement atoms in molecule (2/3D)
Display full SF Condensed SF Ball /stick model Spacefilling
ethane
CH3CH3
H H
‫׀‬ ‫׀‬
H - C – C – H
‫׀‬ ‫׀‬
H H
propene
Display full SF Condensed SF Ball /stick model Spacefilling
H H H
‫׀‬ ‫׀‬ ‫׀‬
C = C – C - H
‫׀‬ ‫׀‬
H H
CH2=CHCH3

13. • member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n-2
• end with yne
Class Functional gp Suffix Example Formula
Alkyne C ≡ C - yne ethyne CnH2n-2
Homologous Series
Class Functional Suffix Example Formula
Alcohol Hydroxyl - ol methanol CnH2n+1OH
H - C ≡ C – H
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n+1OH
• end with ol
H
‫׀‬
H - C ≡ C – C – H
‫׀‬
H
Number
carbon
IUPAC name Structure formula Molecular formula
2 Ethyne CH≡CH C2H2
3 Propyne H-C≡C-CH3 C3H4
4 Butyne H-C≡C-CH2CH3 C4H6
5 Pentyne H-C≡C-(CH2)2CH3 C5H8
6 Hexyne H-C≡C-(CH2)3CH3 C6H10
ethyne propyne butyne
Number
carbon
IUPAC name Structure formula Molecular
formula
1 Methanol CH3OH CH3OH
2 Ethanol CH3CH2OH C2H5OH
3 Propanol CH3CH2CH2OH C3H7OH
4 Butanol CH3(CH2)2CH2OH C4H9OH
5 Pentanol CH3(CH2)3CH2OH C5H11OH
methanol ethanol propanol butanol
H H
‫׀‬ ‫׀‬
H - C ≡ C – C – C- H
‫׀‬ ‫׀‬
H H
H
‫׀‬
H - C – OH
‫׀‬
H
H H
‫׀‬ ‫׀‬
H - C – C – OH
‫׀‬ ‫׀‬
H H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – OH
‫׀‬ ‫׀‬ ‫׀‬
H H H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – C – OH
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
Functional gp Hydrocarbon skeleton Hydrocarbon skeleton Functional gp
Structural formula – arrangement atoms in molecule (2/3D)
Ball /stick model SpacefillingCondensed SFDisplay full SF
H
‫׀‬
H - C ≡ C – C – H
‫׀‬
H
CH≡C-CH3
propyne
Structural formula – arrangement atoms in molecule (2/3D)
Display full SF Condensed SF Ball /stick model Spacefilling
H H
‫׀‬ ‫׀‬
H - C – C – OH
‫׀‬ ‫׀‬
H H
CH3CH2OH
ethanol

14. • member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2nO
• end with one
Class Functionalgp Suffix Example Formula
Ketone Carbonyl (C=O) - one propanone CnH2nO
Homologous Series
Class Fumctional Suffix Example Formula
Aldehyde Aldehyde - al methanal CnH2nO
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2nO
• end with al
Number
carbon
IUPAC name Structure formula Molecular
formula
3 Propanone CH3COCH3 C3H6O
4 Butanone CH3COCH2CH3 C4H8O
5 Pentanone CH3CH2COCH2CH3 C5H10O
6 Hexanone CH3CH2COCH2CH2CH3 C6H12O
7 Heptanone CH3CH2COCH2CH2CH2CH3 C7H14O
propanone butanone pentanone
Number
carbon
IUPAC name Structure formula Molecular
formula
1 Methanal HCHO CH2O
2 Ethanal CH3CHO C2H4O
3 Propanal CH3CH2CHO C3H6O
4 Butanal CH3(CH2)2CHO C4H8O
5 Pentanal CH3(CH2)3CHO C5H10O
methanal ethanal propanal butanal
H - C = O
‫׀‬
H
H
‫׀‬
H - C – C = O
‫׀‬ ‫׀‬
H H
H H
‫׀‬ ‫׀‬
H - C – C – C = O
‫׀‬ ‫׀‬ ‫׀‬
H H H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – C = O
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
H O H
‫׀‬ ‖ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬
H H
H O H H
‫׀‬ ‖ ‫׀‬ ‫׀‬
H - C – C – C – C - H
‫׀‬ ‫׀‬ ‫׀‬
H H H
H O H H H
‫׀‬ ‖ ‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – C – C - H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
Functional gp Hydrocarbon skeleton Hydrocarbon skeleton Functional gp
Structural formula – arrangement atoms in molecule (2/3D) Structural formula – arrangement atoms in molecule (2/3D)
Display full SF Condensed SF Ball /stick model Spacefilling Display full SF Condensed SF Ball /stick model Spacefilling
H O H
‫׀‬ ‖ ‫׀‬
H - C – C – C – H
‫׀‬ ‫׀‬
H H
CH3COCH3
propanone ethanal
H
‫׀‬
H - C – C = O
‫׀‬ ‫׀‬
H H
CH3CHO

15. • member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n+1COOH
• end with oic acid
Class Functional Suffix Example Formula
Carboxylic acid Carboxyl - oic acid ethanoic acid CnH2n+1COOH
Homologous Series
Class Functional Suffix Formula
Ester Ester - oate R –COO-R
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2nO2
• end with oate
methanoic acid ethanoic acid propanoic acid
Number
carbon
IUPAC name Structure formula Molecular
formula
1 Methyl methanoate HCOOCH3 R–COO-R
2 Methyl ethanoate CH3COOCH3 R–COO-R
3 Methyl propanoate CH3CH2COOCH3 R–COO-R
4 Methyl butanoate CH3CH2CH2COOCH3
R–COO-R
methyl methanoate methyl ethanoate methyl propanoate
Number
carbon
IUPAC name Structure formula Molecular formula
1 Methanoic acid HCOOH HCOOH
2 Ethanoic acid CH3COOH CH3COOH
3 Propanoic acid CH3CH2COOH C2H5COOH
4 Butanoic acid CH3(CH2)2COOH C3H7COOH
5 Pentanoic acid CH3(CH2)3COOH C4H9COOH
O
‖
H - C - O H
H O
‫׀‬ ‖
H - C - C - OH
‫׀‬
H
H H O
‫׀‬ ‫׀‬ ‖
H - C – C – C - OH
‫׀‬ ‫׀‬
H H
O H
‖ ‫׀‬
H - C – O – C - H
‫׀‬
H
H O H
‫׀‬ ‖ ‫׀‬
H - C - C – O - C - H
‫׀‬ ‫׀‬
H H
H H O H
‫׀‬ ‫׀‬ ‖ ‫׀‬
H - C – C – C – O - C - H
‫׀‬ ‫׀‬ ‫׀‬
H H H
Structural formula – arrangement atoms in molecule (2/3D)
Hydrocarbon skeleton Functional gp
Display full SF Condensed SF Ball /stick model Spacefilling
O
‖
H - C - O H
methanoic acid
HCOOH
Hydrocarbon skeleton Functional gp
Structural formula – arrangement atoms in molecule (2/3D)
Display full SF Condensed SF Ball /stick model Spacefilling
O H
‖ ‫׀‬
H - C – O – C - H
‫׀‬
H
HCOOCH3
Methyl methanoate

16. • member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n+1NH2
• end with amine
Class Functional Suffix Example Formula
Amine NH2 - amine ethanamine CnH2n+1NH2
Homologous Series
Class Functional Suffix Example Formula
Amide Amide - amide ethanamide CnH2n+1CONH2
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – N - H
‫׀‬ ‫׀‬
H H
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n+1CONH2
• end with amide
H H
‫׀‬ ‫׀‬
H - C – N - H
‫׀‬
H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – N - H
‫׀‬ ‫׀‬ ‫׀‬
H H H
Number
carbon
IUPAC name Structure formula Molecular formula
1 Methanamine CH3NH2 CH3NH2
2 Ethanamine CH3CH2NH2 C2H5NH2
3 Propanamine CH3CH2CH2NH2 C3H7NH2
4 Butanamine CH3(CH2)2CH2NH2 C4H9NH2
5 Pentanamine CH3(CH2)3CH3NH2 C5H11NH2
methanamine ethanamine propanamine
Number
carbon
IUPAC name Structure formula Molecular formula
1 Methanamide HCONH2 HCONH2
2 Ethanamide CH3CONH2 CH3CONH2
3 Propanamide CH3CH2CONH2 C3H7CONH2
4 Butanamide CH3(CH2)2CONH2 C4H9CONH2
5 Pentanamide CH3(CH2)3CONH2 C5H11CONH2
O H
‖ ‫׀‬
H - C – N - H
H O H
‫׀‬ ‖ ‫׀‬
H - C – C – N - H
‫׀‬
H
H H O H
‫׀‬ ‫׀‬ ‖ ‫׀‬
H - C – C – C – N - H
‫׀‬ ‫׀‬
H H
methanamide ethanamide propanamide
Structural formula – arrangement atoms in molecule (2/3D)
Hydrocarbon skeleton Functional gp
Display full SF Condensed SF Ball /stick model Spacefilling
methanamine
H H
‫׀‬ ‫׀‬
H - C – N - H
‫׀‬
H
CH3NH2
Hydrocarbon skeleton Functional gp
Structural formula – arrangement atoms in molecule (2/3D)
Display full SF Condensed SF Ball /stick model Spacefilling
methanamide
O H
‖ ‫׀‬
H - C – N - H HCONH2

17. • member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n+1CN
• end with nitrile
Class Functional Suffix Example Formula
Nitrile C ≡ N - nitrile ethanenitrile CnH2n+1CN
Homologous Series
Class Functional Suffix Example
Ether Ether -oxyalkane methoxymethane
H
‫׀‬
H - C – C ≡ N
‫׀‬
H
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula R – O - R
• end with oxyalkane
H - C ≡ N
H H
‫׀‬ ‫׀‬
H - C – C – C ≡ N
‫׀‬ ‫׀‬
H H
Number
carbon
IUPAC name Structure formula Molecular formula
1 Methanenitrile HCN HCN
2 Ethanenitrile CH3CN CH3CN
3 Propanenitrile CH3CH2CN C2H5CN
4 Butanenitrile CH3(CH2)2CN C3H7CN
5 Pentanenitrile CH3(CH2)3CN C4H9CN
methanenitrile ethanenitrile propanenitrile butanenitrile
Number
carbon
IUPAC name Structure formula Molecular
formula
1 Methoxymethane CH3 - O – CH3 R –O -R
2 Methoxyethane CH3CH2 - O – CH3 R –O -R
3 Methoxypropane CH3CH2CH2 - O –CH3 R –O -R
4 Methoxybutane CH3(CH2 )3 - O –CH3 R –O -R
5 Methoxypentane CH3(CH2 )4 - O –CH3 R –O -R
methoxymethane methoxyethane methoxypropane
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – C ≡ N
‫׀‬ ‫׀‬ ‫׀‬
H H H
H H
‫׀‬ ‫׀‬
H - C – O – C - H
‫׀‬ ‫׀‬
H H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C - C – O - C - H
‫׀‬ ‫׀‬ ‫׀‬
H H H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – O - C - H
‫׀‬ ‫׀‬ ‫׀‬
H H H
Structural formula – arrangement atoms in molecule (2/3D)
Hydrocarbon skeleton Functional gp
Display full SF Condensed SF Ball /stick model Spacefilling
ethanenitrile
H
‫׀‬
H - C – C ≡ N
‫׀‬
H
CH3CN
Structural formula – arrangement atoms in molecule (2/3D)
Display full SF Condensed SF Ball /stick model Spacefilling
methoxymethane
H H
‫׀‬ ‫׀‬
H - C – O – C - H
‫׀‬ ‫׀‬
H H
CH3–O– CH3
Hydrocarbon skeleton Functional gp

18. H H
‫׀‬ ‫׀‬
H - C – C – CI
‫׀‬ ‫׀‬
H H
Class Functional Prefix Example
Halogenoalkane F, CI, Br, I - chloro chloroethane
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n-1 X
Homologous Series
Class Functional Suffix Example Formula
Alcohol Hydroxyl - ol methanol CnH2n+1OH
• member differ by CH2 gp
• same functional group
• similar chemical properties
• chemical formula CnH2n+1OH
• end with ol
chloromethane chloroethane chloropropane
Number
carbon
IUPAC name Structure formula Molecular
formula
1 Methanol CH3OH CH3OH
2 Ethanol CH3CH2OH C2H5OH
3 Propanol CH3CH2CH2OH C3H7OH
4 Butanol CH3(CH2)2CH2OH C4H9OH
5 Pentanol CH3(CH2)3CH2OH C5H11OH
methanol ethanol propanol butanol
H
‫׀‬
H - C – OH
‫׀‬
H
H H
‫׀‬ ‫׀‬
H - C – C – OH
‫׀‬ ‫׀‬
H H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – OH
‫׀‬ ‫׀‬ ‫׀‬
H H H
H H H H
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – C – OH
‫׀‬ ‫׀‬ ‫׀‬ ‫׀‬
H H H H
Hydrocarbon skeleton Functional gp
Structural formula – arrangement atoms in molecule (2/3D)
Ball /stick model SpacefillingCondensed SFDisplay full SF
CH3CI
chloromethane
Structural formula – arrangement atoms in molecule (2/3D)
Display full SF Condensed SF Ball /stick model Spacefilling
H H
‫׀‬ ‫׀‬
H - C – C – OH
‫׀‬ ‫׀‬
H H
CH3CH2OH
ethanol
H
‫׀‬
H - C – CI
‫׀‬
H
H H H
‫׀‬ ‫׀‬ ‫׀‬
H - C – C – C – CI
‫׀‬ ‫׀‬ ‫׀‬
H H H
Hydrocarbon skeleton Functional gp
Number
carbon
IUPAC name Structure formula Molecular
formula
1 chloromethane CH3CI CH3CI
2 chloroethane CH3CH2CI C2H5CI
3 chloropropane CH3CH2CH2CI C3H7CI
4 chlorobutane CH3(CH2)2CH2CI C4H9CI
5 chloropentane CH3(CH2)3CH2CI C5H11CI
H
‫׀‬
H - C – CI
‫׀‬
H