Hi Oops - typo! The chlorate and perchlorate oxygens should all be [O-]. I was copying by hand from a different computer...
Regards, Chris On 21 November 2017 at 09:19, Paolo Tosco <paolo.to...@unito.it> wrote: > Hi Chris, > > if the behaviour with chlorate and perchlorate is the one you report > > chlorate [O-][Cl2+]([O+])[O-] > perchlorate [O-][Cl3+]([O-])([O+])[O-] > > it looks wrong to me as there is an overall formal charge of +1. All O's > should bear a -1 charge. > > Cheers, > p. > > > > On 11/21/17 09:12, Chris Earnshaw wrote: >> >> 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 > > ------------------------------------------------------------------------------ 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
