Hi Sometime between 2014 and now there appears to have been a change in the way hypervalent halogen structures are handled. The old behaviour (involving some tweaking of atomic_data.cpp to allow the higher oxidation states) was to have a neutral halogen with double bonds to most of the oxygens, e.g. chlorate O=Cl(=O)[O-] perchlorate O=Cl(=O)(=O)[O-]
The current behaviour is to 'charge separate' the dative bonds, giving chlorate [O-][Cl2+]([O+])[O-] perchlorate [O-][Cl3+]([O-])([O+])[O-] Although this may be regarded as 'correct' (arguable!), it can cause problems of compatibility with other software and looks remarkably ugly. It's also inconsistent with the handling of hypervalent P and S compounds. Using the same convention, we should have - trimethylphosphine oxide C[P+]([O-])(C)C dimethylsulfoxide C[S+]([O-])C dimethylsulfone C[S2+]([O-])([O-])C - and I really don't want this to happen! Does anyone know a way to restore the old behaviour for chlorites, bromates, periodates etc.? Best regards, Chris Earnshaw ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
