Since the entire system is antiaromatic, why are any carbons at all shown
as aromatic in the SMILES?

-P.

On Thu, Jan 9, 2020 at 3:56 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
>
>
>
>
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