Isomers are molecules made from the same number of each type of atom, but with some difference in the way the atoms are arranged, leading to differences in their properties. These differences may be quite marked – such as isomers that react in completely different ways – or very subtle, such as isomers that differ only in the way they interact with light.
…having the same molecular formula but different structural formulae.
In this type of isomerism, the sequence in which the atoms are bonded is different for each isomer. We can see this in the structural, or displayed, or skeletal formulae for the isomers, and the fact that the isomers will have fundamentally different names.
For example, straight-chain alkanes may have shorter branched-chain isomers with the same molecular formula e.g. hexane and 2-methylpentane. In each case the molecular formula is C6H14 but the structural formula for hexane is CH3(CH2)4CH3 while the structural formula for 2-methylpentane would be CH3CH(CH3)(CH2)2CH3.
We also see structural isomers with entirely different functional groups but the same molecular formula: Propanal, CH3CH2CHO and propanone, CH3COCH3 are structural isomers, as are propanoic acid CH3CH2COOH and methyl ethanoate CH3COOCH3.
Because of their different structures, structural isomers are likely to have different physical properties, and different chemical properties especially when their functional groups differ.
…having the same structural formula but a different 3D spatial arrangement of the atoms
Even if the atoms are bonded in the same sequence and have the same functional groups, there are still ways in which they can be different, and as a consequence have different properties. One way in which this can come about is when rotation of the bonds within a molecule is restricted or prevented. This is the case with the carbon to carbon double bond in alkenes, and leads to isomers labelled cis- and trans- or labelled as E- and Z-. Another way in which molecules can have a different spatial arrangement is when they are mirror images of each other that can’t be superimposed. We call this optical isomerism.
Cis- and trans- isomers
Here the restricted rotation around double bond results in two isomers. These two isomers may have different chemical properties.
e.g. The acid HOOCCH=CHCOOH can be extracted from unripe tomatoes and apples, and also from the wild flower Fumaria officinalis. When heated, the acid obtained from unripe tomatoes or apples reacts, eliminating water to form a cyclic acid anhydride. The acid from the wild flower, however, does not react.
The explanation for this, that the acid from the tomatoes or apples has the acid functional groups on the same side of the double bond where they can react, while the acid from the wild flower has the acid groups on opposite sides of the double bond where restricted rotation around the bond prevents them from reacting, gained van’t Hoff the first Nobel Prize in Chemistry for his contribution of the ideas of cis- and trans- isomers in stereochemistry.
The conditions for cis- and trans- stereoisomers are (i) each carbon of the C=C must have two different atoms or groups attached to it, and (ii) one of the atoms or groups on each carbon of the C=C must be the same. When these conditions are fulfilled we can have one isomer where the two common atoms or groups are both on the same side of the double bond (the cis- isomer) and because rotation around the double bond is restricted, this cannot convert to the configuration where the two common atoms or groups are on opposite sides of the double bond: the trans- isomer. Thus we have two different molecules with the same structural formula and a different spatial arrangement.
E- and Z- isomers
Many alkenes satisfy the first criterion for stereoisomerism: having a different atom or group on each carbon of the C=C, but do not satisfy the second one as they don’t have a common atom or group on each C atom of the C=C. The restricted rotation around the C=C still means that we will have two stereoisomers, but we need a naming convention to identify them that applies more generally.
We use Cahn-Ingold-Prelog rules (CIP rules) to designate one atom or group on each carbon of the C=C as the priority group, and then name them as a Z-isomer if the priority groups are on the same side, or an E- isomer if they are on opposite sides of the C=C. A simple way of remembering which isomer is which is E = EITHER SIDE, Z= ZAME SIDE.
Note that we can always identify a priority group, so this way of identifying isomers of alkenes works for all alkenes, including those for which cis- and trans- could also be used. As such, the simpler cis- and trans- notation is becoming less widely used.
Notice that although we have used the same molecule for both examples of cis-/trans- isomer and E-/Z- isomers, the cis-/trans- decision was based on where the common groups, in this case the -H atoms were located, whereas the E-/Z- decision was based on the priority groups which were in this example the methyl and ethyl groups. It is therefore important to realise that a cis- isomer is NOT always a Z- isomer, and a trans- isomer is NOT always an E- isomer. To appreciate why this is the case, we need to understand how to apply CIP rules to find the priority groups.
We take each carbon of the C=C in turn, and decide which of the the two groups or atoms bonded to it is the priority group. In this way we will have a priority group on each carbon of the C=C and we will be able to see whether they are on the same side, or opposite sides of the C=C.
Starting from the carbon atom in the double bond, we step outwards by one covalent bond and compare the two atoms we get to. If they are different, the heavier one makes the whole group that it is part of the priority group. If they are the same, we step outwards again until we find a point of difference, at which point the heavier atom makes the whole group that it is part of the priority group.
In molecule A, starting with the carbon atom on the left if we step outward we get to an H atom and a Br atom. The Br atom is heavier so Br is the priority group on that side. Now looking at the carbon atom on the right and stepping outward we get to an F atom and a Cl atom. The Cl is heavier so Cl is the priority group on this side. Br and Cl are on opposite sides of the C=C, so this is an E-isomer: E-2-bromo-1-chloro-1-fluoroethene.
In molecule B, starting with the carbon atom on the left of the C=C and stepping outwards we meet two more C atoms. Stepping outwards again we get to two H atoms and another C atom in each case, stepping outwards again we get to three H atoms in one case (the top group) and to two H atoms and a C atom (the bottom group). Here we have the first point of difference, and as the C atom is heavier than H the bottom group (the whole -CH2CH2CH3) becomes the priority group on this side. From the carbon atom on the right of the C=C we step outwards to two C atoms, so we step a second time. This step takes us to two H atoms and a C atom for the top group, and to an H, a C and a Cl atom for the bottom group. This is the first point of difference. Since the Cl is heavier than the H, the bottom group (the whole -CHClCH3) becomes the priority group on this side. The two priority groups are on the same side of the C=C and therefore this is the E-isomer: E-3,4-diethyl-2-methylhept-3-ene.
Note: it is the first point of difference that determines the priority group, not the overall mass of the group. Molecule E would still be an E- isomer even if the group on the top right were a very long alkyl chain with a total mass exceeding that of the -CHClCH3 group on the bottom right.
Another form of stereoisomerism occurs at carbon atoms that have four different atoms or groups attached to them. Because the shape around such carbon atoms is tetrahedral, there are two non-superimposable mirror image molecules having the same structure but a different 3D spatial arrangement. We might refer to these as optical isomers, or enantiomers. A carbon atom having four different atoms attached to it is referred to as a chiral carbon, and may be indicated with an asterisk *.
We draw the two optical isomers by drawing the mirror plane between them, then drawing the 3D tetrahedral arrangement for each molecule as mirror images. While there are labels (D- and L-, or laevo- and dextro-) we are not required to be able to label optical isomers, only identify when they exist.
It can be a challenge to find chiral carbon atoms in larger molecules that are displayed skeletally. It is important to remember that C-H bonds will not be shown in the skeletal formula, but they are there!