Archive for November, 2012

(This is not a post about carbohydrates, despite the title!)

Dodgy stereochemistry is a persistent problem.  Even if someone knows all of the stereocentres in a particular molecule, they might not necessarily draw them in a way that a machine, or even a person, can interpret.  There are rules about whether the pointy end or the blunt end of a bond indicates the stereocentre, and it’s surprising how often you see them done wrongly.

Today I’m going to talk about a particular IUPAC recommendation for drawing stereocentres that might at first glance seem surprising, the rule that you may only have one stereobond at a given stereocentre. If you have a wedged bond attached to an atom, you can’t have a hashed bond attached to the same atom. And vice versa.

Why is this?

You might think that as you’re supplying more information, you’re making the diagram easier to interpret. However, you’re running directly counter to the normal principles of communication.  You’re being more informative than required, and this sets off alarm bells in the reader.  What are you trying to say?  If you ask a passerby the time and they say “Well, it’s half past six Greenwich Mean Time” you’re entitled to wonder why they’re quoting the timezone. Maybe they’re trying to be funny.

Paul Grice thought about this whole problem in the 1970s and came up with a set of four principles, summarized in maxims, that listeners (or readers) assume that speakers are following.  These are they:

  • Be Truthful. Do not say what you believe to be false. Do not say that for which you lack adequate evidence.

Let us hope that this one is implicit in any chemical drawing!

  • Make your contribution as informative as is required.  Do not make your contribution more informative than required.

If you have two methyl groups coming off an atom, do not make one wedgy and one hashy. You are adding no new information!

Do not mark carbons with the letter C unless your target audience is schoolchildren.

  • Be relevant:

On the grand scale: do not illustrate an article with any old molecule—make sure the molecule mentioned is actually relevant.

On the scale of the drawing itself, however: If you have three bonds about an ordinary p-block atom, for example, make sure they’re at 120 degrees to each other.  If they aren’t, for example if two of them are at right angles, the reader will infer that something odd is going on.

  • Be clear:

Make sure all your double bonds actually look like double bonds rather than a single bond parallel to another single bond.  I suspect a lot of the success of ChemDraw is down to the fact that it produces attractive, clear chemical drawings.

Do people ever flout the maxims on purpose?

Oh yes.  People often flout the maxims when trying to be funny, or in a political interview.  Similarly there are all kinds of Gricean violations in the chemical drawings you see in patents: bonds which do not quite extend all the way to atoms, R groups labelled as Y (particularly dangerous as Y is yttrium!) or Q or W (also tungsten) or some other unusual letter and so forth.  Exactly why this happens so much more often in patents than in journal articles is left as an exercise for the reader.