This is a really interesting part of the HL organic course. Structural isomers are substances with the same molecular formula but a different structural formula. I think we can get our heads around that pretty easily, for example, take botanic acid and ethyl ethanoate – both molecules have the molecular formula C4H8O2 but look and behave (and smell) very differently.

However stereoisomers are conceptually much more difficult to understand – this time they have the same molecular formula but the same structural formula as well – the thing that makes them different is how the atoms are arranged in 3D or in space. This is a little bit harder to imagine isn’t it?

One analogy that is used to help understand this is your hands – you have a left and right hand. They both have four fingers and one thumb. They look the same BUT they are opposites or mirror images of each other.

This is analogy is just a model though – and it does break down!

Conformational isomers are (according to the guide):

“Isomers, which interconvert by rotation about a σ (or single) bond”.

 A really straight forwards example of this would be ethane. The two CH3 groups can line up or be opposite each other. The isomers look different but are in fact the same thing [some purists would argue these are not isomers at all …..]


Image taken from: Wikipedia

Configuational isomers can be split up into cis / trans and E / Z isomers and optical isomers.

For the sake of simplicity I will cover optical isomers later.

All cis/ trans isomers will be E/ Z isomers but not all E / Z isomers are cis / trans isomers.

Both types of isomers will have a carbon – carbon double bond.


Well, here is the detail…..

If we have a molecule such as but-2-ene there are two arrangements of the methyl groups – either on the same side as the double bond or opposite sides. Since the double bond contains the π bond the groups are unable to rotate freely. They are locked in place.

This means that the two methyl groups can be on the same side or opposite sides of the double bond…. Which means the molecule can have two possible shapes …. and densities …. and London (dispersion) forces.

If the groups are on the same side it is ‘cis’ and on different sides ‘trans’


The following is trans-bute-2-ene:


And cis-but-2-ene:


Images sourced from: Wikipedia

Cis and trans is applied when the two substituents (non Hydrogen’s) are identical.

If the substituents are different, the CIP (Cahn Ingold Prelog) rules are used:

This could apply to a molecule such as bromo-chloro-fluoro-iodo-ethene (!)

As all the substituents are different a different way of prioritizing substituents must be used.

Firstly, identify the two groups attached to the first carbon – in this example we may consider F and Cl on the first carbon. The group with the highest Ar is given the highest priority. So in this case it would be Cl.

The same is carried out for the other carbon – in this example the highest priority would go to I (not Br).

If both high priority substituent groups are on the same side, the molecule is given the Z configuration (ie, Z- bromo-chloro-fluoro-iodo-ethene) and if the groups are on opposite sides, the E configuration is used (ie, bromo-chloro-fluoro-iodo-ethene)


Image sourced from: Wikipedia

The terminology comes from the German words for opposite (Entgegen or E) and together (German word = Zusammen = Z)

There are some unusual cases where a molecule could be E and cis?! Try drawing out chlorobut-2ene and you will see why!