El mié, 22-02-2012 a las 11:16 -0500, Geoffrey Hutchison escribió:
> > Im asking because I am using CDK and OpenBabel, and I am suffering of
> > interoperability problems, because both tools have different ways of
> > defining aromaticity.
>
> There is no unified aromaticity model in chemistry. I'm not sure the
> aromaticity algorithm in Open Babel is publishable, and even if it were,
> there are numerous special cases. We have made sure in the 2.3.x release,
> that we can round-trip PubChem and ZINC, including appropriate SMILES
> strings. This requires a fairly liberal aromaticity model.
>
Hello. Aromaticity is in fact a very tricky issue. As I have pointed out
in previous messages, openbabel does not behave well when aromaticity
and metal atoms appear in the same compound. Metal complexes with
pyridine-like ligands are completely messed up by openbabel, breaking
aromaticity, with lots of spurious H-atoms appearing. Also ferrocene and
friends are regarded as non-aromatic, of course any organometallic
chemist will say that ferrocene is indeed an aromatic compound with
aromatic properties. See:
obabel -:"[Cu]([n]1ccccc1)([n]1ccccc1)(Cl)Cl" -osmi
[Cu](N1CCCCC1)(N1CCCCC1)(Cl)Cl
1 molecule converted
obabel
-:"[Fe]12345678([cH]9[cH]1[cH]2[cH]3[cH]49)[cH]1[cH]5[cH]6[cH]7[cH]81"
-osmi
[Fe]12345678(C9C1C2C3C49)C1C5C6C7C81
1 molecule converted
Best wishes,
Miguel Quirós
--
Miguel Quirós Olozábal
Departamento de Química Inorgánica. Facultad de Ciencias.
Universidad de Granada. 18071 Granada. SPAIN.
email: mquiros<at>ugr<dot>es
mquiros<arroba>ugr<punto>es
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