Memorising molecular structures

By dkl9, written 2024-098, revised 2024-098 (0 revisions)


Organic molecules are like 汉字 (Chinese characters).

Organic molecules vary widely in complexity, from methane (CH4) to phthalic acid (C8H6O4, benzene-1,2-dicarboxylic acid) to N,N-dimethyltryptamine (C12H16N2) and beyond. 汉字 vary widely in complexity, from 人 ("person") to 百 ("hundred") to 游 ("to roam") and beyond. Organic molecules consist of functional groups, which are each defined in terms of a few atoms. 汉字 consist of radicals, which are each defined in terms of a few strokes. The parts of an organic molecule hint at its origin, uses, and properties. The parts of a 汉字 hint at its meaning and pronunciation.

You can learn 汉字 very effectively by breaking them down into a tree of components, inferring the full character with working memory. Sith organic molecules are like 汉字, you can work analogously to memorise molecular structures.

Reading Wikipedia in Lynx (a text-only web browser) only gives me the names of molecules, until I explicitly download images. Most molecules (except the most trivial) have systematic names which describe their structure in terms of smaller segments. This breakdown proceeds recursively, until it bottoms out in common functional groups (methyl, benzene, aldehyde, etc) or base molecules whose structure you can deduce from hints in text.

For example, let's memorise the structure of metformin. Metformin is N,N-dimethylbiguanide hydrochloride. The "N,N-dimethyl" and "hydrochloride" parts are simple: two terminal CH3's at the same nitrogen of biguanide, and HCl mixes with the main compound to form a salt. Biguanide is C2H7N5, which has a text-based description as HN(C(NH)NH2)2. Nitrogen usually takes three bonds; biguanide is centred around nitrogen, bonded to hydrogen and two copies of C(NH)NH2. Chemical intuition can lead us to conclude that those carbons each have two amine groups, one double-bonded. We can add a methyl group to nitrogen only when it has a hydrogen bonded to it to replace. The methyl groups of metformin are at the same site, and only two nitrogens of biguanide (one at each end, equivalent to each other) have the requisite two hydrogens.

So, a general algorithm to memorise molecular structures:

  1. Use a browser which shows only text, or blocks image-loading.
  2. Look up the molecule on Wikipedia or a chemical database.
  3. If the molecule is simple enough that you can confidently deduce the structure from the molecular formula, memorise that structure, and stop.
  4. Otherwise, look for systematic names.
  5. One of the systematic names should give references to other, smaller molecules.
  6. Mentally keep track of the tree-structured breakdown of the molecule, and recursively study those references, as starting from step 2.

Once you know all the functional groups and their arrangement, visualise (or draw out) the full molecule, and look up a diagram at the end to check your work. That should be easy, and will likely remain easy for a while afterward.