We could consider some quantum-mechanical calculations ... well, I always hated this discussion when I heard for my web service with millions of structures, I should consider quantum-mechanical calculations as part of the structure normalization/canonicalization ;-)
On Wed, Jun 17, 2015 at 8:22 AM, Peter Shenkin <shen...@gmail.com> wrote: > Hi, Greg, > > Within the SMILES framework, it seems to me that if you allow the atoms to > be aromatic, then these are two Kekule structures of the same aromatic > system, and however you do the canonicalization, they ought to canonicalize > to the same structure, which the two examples did not do. I don't think you > addressed this. > > I think now that there is no issue with having a double bond between two > aromatic atoms beyond our preconceptions. If that is a problem, you could > Kekulize it per your first picture, (though perhaps that is inconvenient in > the context of the implementation). > > I actually didn't realize why aromaticity (particularly the double bond) > made sense when I originally wrote, so the above is with the benefit of > hindsight, and your comments. > > I think the molecule is entertaining in several ways. In the cubane > geometry, the molecule cannot be conventionally aromatic. Might it actually > be antiaromatic? Could there be two forms? > > Dunno.... > -P. > > > On Wed, Jun 17, 2015 at 1:25 AM, Greg Landrum <greg.land...@gmail.com> > wrote: >> >> >> The problematic part of your two molecules can be reduced to: >> [image: Inline image 3] >> and >> [image: Inline image 4] >> That second one shows the kekulized form that the RDKit ends up using. >> >> These produce the following canonical SMILES: >> >> In [31]: Chem.CanonSmiles('C1=CC2=CC=C12') >> Out[31]: 'c1cc2ccc1-2' >> >> In [32]: Chem.CanonSmiles('C1=CC2=C1C=C2') >> Out[32]: 'c1cc2ccc1=2' >> >> > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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