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 >
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