I’ll be talking at the 6th Joint Sheffield Conference on Cheminformatics in July on Validation and Standardization of Molecular Structures in General and Sugars in Particular. This is a taster.
Sugars in Particular
One of the big problems with chemical structure algorithms is that they can’t, in general, cope with the ways that chemists are accustomed to drawing sugar molecules. They will lose the stereochemistry around the sugar ring, collapsing D-glucose, say, on to L-glucose, not to mention allose, altrose, gulose and all the others.
(ChemDraw, I should note, can interpret chair stereo properly, but it is very much an exception.)
The first step in determining correct stereochemistry for a chair atom is recognizing a chair hexagon. That is the subject of this post.