Can’t see the isomer for the (decision) trees

Secondary school pupils in Year 10, and sometimes even Year 9, learn about the existence of different compounds sharing the same molecular formula. Generally speaking, that is not the most difficult topic — I can say so from personal experience as a chemistry teacher. Yet things still go wrong from time to time.

Almost every year, chemistry examinations at HAVO level contain questions such as: draw at least three structures of C₅H₁₂. Alongside the structure of pentane, the incorrect structure of ‘1-methylbutane’ occasionally crops up — which is not an isomer but is, in fact, a bent pentane molecule.

At VWO level, the subject matter goes deeper. Pupils learn about stereoisomerism and cis-trans isomerism. The latter, in particular, they find tricky. Identifying a chiral centre in a structural formula usually goes well enough. But does cis-trans isomerism occur in, say, 1,2-difluorocyclopent-1-ene? The answer is no: C1, C2, and the fluorine atoms all lie together in a flat plane.

A helping hand

Scientists at Gazi University in Ankara are attempting to make life a little easier for chemistry students. They have captured all forms of isomerism within a single large decision tree. This diagram can be used to determine, for a given molecular formula, whether isomerism occurs and, if so, which kind. They tested this tool by having just over thirty students complete a test first without and then with the decision tree. Did their ability to recognise isomers improve?

The results are, in truth, hardly surprising. It is plainly visible that students using a decision tree are better at judging whether a molecule has isomers at all. With the diagram to hand, students also more frequently identified the correct variant.

Nevertheless, the researchers believe a critical caveat is warranted regarding their findings. The decision tree does not function solely as a tool for recognising isomerism — it also serves as a cheat sheet for all the names. Some students in the first round of testing may well have spotted that a molecule exhibited isomerism, but been unable to arrive at the correct name for the type of isomer without the decision tree. It is not inconceivable, for instance, that a student without the decision tree correctly identifies the right form but has forgotten that it is called an E-isomer, and so answers the question incorrectly.

Confusing

The diagram struck me as far too extensive for Dutch secondary school pupils. But the decision tree will not work well for chemistry students either, thinks Stefan van der Vorm. He is a researcher at Leiden University and teaches organic chemistry.

According to Van der Vorm, students need only be able to identify a few variants of isomerism in the structure of a molecule, beyond the structural isomers they will recognise in any case. Which precise form it happens to be is generally less relevant. Only a handful of isomers need to be committed to memory, he explains, because those are the ones that play a determining role in the reactions molecules can undergo.

‘I only consider stereoisomerism important,’ says Van der Vorm. More specifically, students should be able to determine, for mirror-image molecules, whether a molecule has R– or S-isomerism. They should also know the difference between enantiomers and diastereomers.

These types are relevant because, when synthesising molecules that have stereoisomers, the different variants often arise simultaneously. As a chemist working in an organic laboratory, you need to be able to recognise that and separate them from one another, Van der Vorm explains. Isomers have very specific applications, particularly in biology — one variant may fit into an enzyme pocket, for example, whilst the other does not.

Pruning

Just as he would for school pupils, Van der Vorm would prune the decision tree considerably for chemistry students. As far as he is concerned, the Turkish educational researchers should never have included the entire section on ring conformers — think of the chair and boat conformations of cyclohexane. After all, these involve the same molecule continuously converting from one form into another.

The same applies to rotational isomers. Consider butane, for instance, which can be drawn with all the carbons in a straight line (anti-conformation) or bent into a U-shape (gauche-conformation). They are identical through nothing more than rotation around a single C–C bond. ‘This is simply confusing,’ says Van der Vorm.

Setting aside the substantive criticism, Van der Vorm is concerned that a decision tree will encourage the look-it-up behaviour he regularly observes in first-year students. Some information simply has to be known off by heart — you cannot be constantly reaching for a diagram, he explains. And whether something is an E– or a Z-isomer need not feature in a decision tree, Van der Vorm believes; that can be captured in a few simple rules around systematic labelling, which students ought to learn by heart.

Below you will find the decision tree in question, available to download as a PDF.