Wrong bond informations for charged heterocycles

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Wrong bond informations for charged heterocycles

Bernd Doser
Dear all,

I use OpenBabel to determine chemical informations like bond orders and
formal charges. Therefore I convert a molecule in xyz-format, in which
only topology and atom positions are known, into cml-format. From
cml-format I can extract the needed informations: bond orders, formal
charges, aromaticity. This is working very well for neutral molecules,
but unfortunately not for charged heterocycles, e.g.

      Pyridinium   c1cc[nH+]cc1
      Protonated imidazole   c1c[nH+]c[nH]1
      Pyrylium   c1cc[o+]cc1
      Phenoxide anion   [O-]c1ccccc1

They all should be aromatic, but they aren't. I think the problem is
caused by the fact that aromaticity is determined before formal charges
are assigned, discussed by Geoff long time ago:


Unlike him I think this is still a problem. I can't switch to SDF or
SMILES, because they have already included bond informations, which I
even try to determine. Since I didn't have found a suitable solution
yet, I ask for your help. If there is no easy solution I hope a active
developer of OpenBabel can help, perhaps with the aid of a financial
recompense. It's very important for our company to fix this problem as
soon as possible.


Dr Bernd Doser
Scientific Software Developer

Avant-garde Materials Simulation
Merzhauser Strasse 177
79100 Freiburg im Breisgau, Germany

Phone: +49 761 479984-23
Homepage: http://www.avmatsim.de

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