Organic Chemistry for A-Level: Structure and Nomenclature

A. Hydrocarbon

1. Alkanes

Alkane is basically the single-bonded between carbon atoms, so alkane is called saturated hydrocarbon. It is called saturated hydrocarbon because there are no more atoms could be added to the bonding between carbon-carbon atoms. The general formula of alkanes is C_nH_(2n+2) and if it has branches, the properties would be different even they share the same molecular formula.

Could you give the reasons why this property could happen? (Hint: the definition of boiling point)


In alkane, because they are single bonded molecule, so the hybridisation of the carbon atoms is sp³ which forms the tetrahedral shape. For example, in ethane there are 2 carbon atoms are bonded together by single bond which is formed by an orbital of sp³ in each carbon atom. The overlap between those carbon atoms would form a single bond which is called sigma (σ) bond. The other orbitals of sp³ would bind the hydrogen atoms as shown in figure below. Therefore, in longer chain of alkanes it would form an unplanar structure.

2. Alkenes and alkynes

If alkane is the saturated hydrocarbon, so alkene and alkyne are the unsaturated hydrocarbons. The main characteristic that distinguishes between alkenes and alkynes is the bonding between carbon-carbon atoms.

In alkene, it has double bond in carbon-carbon atoms and the normal formula would be C_nH_2n. On the other hand, alkynes has triple bond in carbon-carbon atoms and the normal C_nH_(2n-2). Therefore, the properties of these three hydrocarbons would be different since the structures and the formulae are different.

If in alkane the atomic orbitals of s and p are hybridised to form sp² orbital, so in alkenes there are only one s orbital and two p orbitals are hybridised, and one p orbital is left unhybridised. Therefore the mixing between those orbitals is called sp² orbital which gives trigonal planar structure.

Firstly, a sigma bond is formed from two sp² orbitals. However, in alkenes there is a pair p orbitals unhybridised and they overlap to form a π bond. Since π bond is not formed in the same way as σ bond, so energetically π bond is weaker than σ bond. However, it gives an extra bond to an alkene to give stronger bond between carbon atoms compare to alkane. The effect of the existence of π bond is the restricted rotation on C=C and it gives alkene geometrical isomerism which is called cis-trans isomerism.


The triple bond in alkynes is formed by an s orbital and a p orbital hybridised and two p orbitals are unhybridised. The unhybridised p orbitals would form 2 π bonds and a σ bond is formed from 2 sp orbitals. From this hybridisation the structure of alkynes would be linear.

3. The carbon-carbon bond length

Due to hybridisation, the bond between hydrocarbons is different. The π bonding would shorten the bonding due to p-p overlap that requires shorter distance than sigma bond.

B. How to draw the organic molecules?

Basically the organic molecule would represent by 4 ways to draw it.
1. Displayed formula

All the bondings and all atoms in the molecules are drawn.

2. Skeletal formula

In this diagram, the molecule is represented by a line for each bond, so for alkenes there is a pair of line to represent the double bond and as well three line for alkynes. The bonding between carbon and hydrogen are not drawn, but carbon with the other atom is drawn. In some cases, C-H bond is drawn because it involves in the reaction or has important meaning.

3. Structural formula

No lines are drawn.

4. The 3D formula

The line represents the bonding is in the plane, the bold line are out of the plane and the dashed line are in the plane.

C. Nomenclature

Most of organic molecules can be named using IUPAC nomenclature and the nomenclature is followed.

1. Select the longest continuous carbon chain.
- This determines the base name.
2. Consider each branch and name similarly except change the name from –ane to –yl.
3. Number the C atoms so that substituents have the lowest possible number.
4. Name each substituent according to its identity and the number of the C atom to which it is attached.
- Use di, tri, tetra as appropriate.
5. Separate numbers from one another by commas.
6. List substituents alphabetically by name.

7. Adjust the main chain name based on the functional groups present
Functional group can be defined as an atom or group of atoms which gives rise to a homologous series.

This rules can be applied to all organic molecules but when the molecules get more complex, the systematic name could be a serious mess. For example this molecule below.

This relative small molecule which consists only 3 functional groups has IUPAC name methyl 8-methyl-3-[(phenylcarbonyl)oxy]-8-azabicyclo[3.2.1]octane-2-carboxylate and it starts a bit of mouthful. This molecule is commonly known as cocaine. If we increase the complexity of the molecule even more such as this molecule.

It has the IUPAC name S-[(2R,3S,4S,6S)-6-({[(2R,3S,4S,5R,6R)-5-{[(2S,4S,5S)-5-(Ethylamino)-4-methoxytetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-{[(2S,5Z,9S,13E)-9-hydroxy-12-[(methoxycarbonyl)amino]-13-[2-(methyltrisulfanyl) ethylidene]-11-oxobicyclo[7.3.1]trideca-1(12),5-diene-3,7-diyn-2-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl]amino}oxy)-4-hydroxy-2-methyltetrahydro-2H-pyran-3-yl] 4-{[(2S,3R,4R,5S,6S)-3,5-dihydroxy-4-me thoxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-3-iodo-5,6-dimethoxy-2-methylbenzenecarbothioate but it is commonly known as calicheamicin.

Even more interesting, a recent news that the attempt to synthesise the biggest non-peptide organic molecule is halted due to limited funding and the molecule is shown below.

This molecule hasn't had an IUPAC systematic name but it is known as maitotoxin (C₁₆₄H₂₅₆O₆₈S₂Na₂). This toxin is produced by Gambierdiscus toxinata and isolated for the first time from a fish in Tahiti.

Therefore, there is a certain limit that the IUPAC systematic name can be used.

D. Isomerism

1. Structural isomerism

The molecular formulae are the same, but they behave differently as a result of different structure. Example:
a. C₄H₁₀
It can be drawn as:

Both of them are C₄H₁₀, but they have different structure.
b. C₄H₁₀O
It can be drawn as:

Could you find another isomer which has alcohol functional group?

C₄H₁₀O can be drawn with another functional group as shown the picture below.

This isomer is called functional group isomer.

2. Stereoisomerism

This isomerism is related to spatial arrangement of an organic compound. Stereoisomerism only has 2 types which are cis-trans isomerism and optical isomerism.

a. Cis-trans isomerism

This isomerism mainly happens in alkenes due to restricted rotation around C=C bond.
i. These isomers have the same connectivity of atoms and differ only in the arrangement of atoms in space
ii. One molecule is designated cis (groups on same side) and the other is trans (groups on opposite side)

iii. Cis-trans isomerism is not possible if one carbon of the double bond has two identical groups

b. Optical isomerism

Optical isomerism mainly happens if there is at least a chiral centre. Chiral centre could be defined as a carbon atom that bonds 4 different functional groups. The characteristic of this chiral molecule is cannot be superimposed in similar way like our hands but they are the mirror image of each other.