Hi, For aromaticity, I believe a ring has to have 4n+2 electrons along its periphery.
I would be curious to know what other SMILES generators make of this system. -P. On Wed, Jan 22, 2020 at 8:14 AM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Andrew, > > There's a bug here. > > Here's what I believe is happening: > The system as a whole has 10 pi electrons, so the RDKit perceives it as > aromatic. But then the logic that is used to flag the fusing bond in > azulene as single (instead of aromatic) prevents the bonds between the > central atom and the outer ones from being flagged as aromatic. This is > clearly wrong. Now we just need to figure out how to fix it. :-) > > As an aside: it's not particularly relevant to this discussion, but I > don't understand why the wikipedia page says that the compound is > anti-aromatic. I think the standard definition of anti-aromaticity (agrees > with the one linked to from the acepentalene page) requires the ring system > to have 4n electrons. That definitely doesn't apply here to either the > individual rings or the system as a whole. The system as a whole has 10 > electrons (4n+2), the individual rings each have 5 (neither aromatic nor > anti-aromatic), and the outer envelope has 9 (again, neither aromatic nor > anti-aromatic). > > Sorry for the super slow reply. > -greg > > > On Thu, Jan 9, 2020 at 9:56 PM Andrew Dalke <da...@dalkescientific.com> > wrote: > >> Hi all, >> >> Could someone explain the following, which uses the SMILES from >> https://en.wikipedia.org/wiki/Acepentalene : >> >> >>> from rdkit import Chem >> >>> Chem.CanonSmiles("C1=CC2=CC=C3C2=C1C=C3") >> 'c1cc2ccc3ccc1-c=3-2' >> >>> import rdkit >> >>> rdkit.__version__ >> '2019.09.1' >> >> I don't understand the aromatic "c" in the fused center of the 3 >> 5-membered rings. It's connected by non-aromatic bonds to the rest of the >> system. >> >> This broke some code of mine which expects that every aromatic atom must >> have at least two aromatic bonds. I thought that all aromatic atoms had to >> be in aromatic rings, and that all aromatic rings had to have aromatic bond. >> >> (I'm ignoring RDKit's support for aromatic triple bonds in this >> description.) >> >> I searched for "acepentalene" and "antiaromatic" in the issue tracker and >> the mailing list but found nothing relevant. >> >> Cheers, >> >> Andrew >> da...@dalkescientific.com >> >> >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- -P. Sent from a cell phone. Pls forgive brvty and m1$tea@ks.
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