I’m using the rdkit package to process some molecules.
I noticed that when creating a molecule from a SMILES string the library does some syntactic and some semantic checks. This question regards the semantic part (sanitization). (Just in case someone wants to take a look, the checks are described in detail here.
In the sanitization process the explicit and implicit valence of all atoms is computed and it fails when atoms have illegal valence. I don’t really understand what “illegal valence” mean in this context. I tried using some compounds with charged atoms to see if they have “illegal valence” but they didn’t. Examples:
O=[V]([O-])([O-])[O-] where the Oxygen in both cases is charged (once positively and once negatively).
What does “illegal valence” mean? Is it just using more electrons than the ones actually available in the atom? e.g. 2 bonds with a hydrogen.
Furthermore, if the previous is true, I suppose that even combinations that are potentially unstable (in practice) with a lot of charged atoms would still be considered “semantically valid”?