Interesting - I do hope your idea works out! This prompted me to see what happens with azulene, which is another case where the envelope is aromatic but neither of the individual rings are based on a simple neutral representation. This ends up being related to Peter's example; the input SMILES c1ccccc2c1ccc2 gets converted to c1cc2cccccc-2c1, where the fusion bond is perceived as 'pure single' rather than aromatic as it should be, so we do indeed end up with two non-aromatic rings embedded in an aromatic envelope.
Is there any way to define the aromaticity of an individual ring based on its mapping to an aromatic envelope? Are there any cases where that wouldn't be true? Chris On Tue, 23 Oct 2018 at 17:35, Greg Landrum <greg.land...@gmail.com> wrote: > > I'll try later (likely tomorrow) to explain what I meant a bit better. Or > maybe I'll just implement it (since it seems like it could be fairly easy). > > On Tue, Oct 23, 2018 at 6:13 PM Chris Earnshaw <cgearns...@gmail.com> > wrote: > >> >> Following this analysis means you don't need to consider the resonance >> form: >> A carbonyl or imine (open chain or in a partially saturated ring) group's >> carbon atom provides (effectively) 0 pi electrons >> 'Ordinary' aromatic carbons provide 1 pi-electron >> Pyridine-type nitrogens (2-connections) or pyridinium (3-connections) >> provide 1 pi-electron >> Pyrrole-type nitrogens (3-connections) provide 2 pi-electrons. >> >> So for example 3, that's >> [image: image.png] >> 10 pi-electrons in total, so the *system* is aromatic even though the >> electron counts look odd on a per-ring basis (not unlike azulene). >> > > On this specific instance: This is exactly what the RDKit currently does. > However, in this scheme the left ring, which has 7 pi electrons, is not > aromatic even though both the right ring and the envelope are. > > -greg > > >
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