Dear Ari,
On Fri, Jul 31, 2009 at 9:18 PM, Aryeh
Gold-Parker<[email protected]> wrote:
>
> I am using the latest stable RDKIT Q2-2009, and getting:
>
>> In [30]: mol =
>> AllChem.MolFromSmiles('[Mg]c1ccc([se]1)-c1ccc(n1)-c1ccc([Mg])cc1')
>> [15:14:49] Can't kekulize mol
>
> I assume it is from the Mg radicals.
That's a reasonable theory, but it's not actually the problem:
[3] >>> m = Chem.MolFromSmiles('[Mg]c1ccc([se]1)-c1ccc(n1)-c1ccc([Mg])cc1')
[21:34:34] Can't kekulize mol
[4] >>> m = Chem.MolFromSmiles('c1ccc([se]1)-c1ccc(n1)-c1ccccc1')
[21:34:43] Can't kekulize mol
The problem is actually the five membered nitrogen-containing ring:
[14] >>> m = Chem.MolFromSmiles('c1cccn1')
[21:41:16] Can't kekulize mol
That nitrogen needs an H attached to it for the ring to be considered
to be aromatic:
[15] >>> m = Chem.MolFromSmiles('c1ccc[nH]1')
and then back to your original:
[16] >>> m = Chem.MolFromSmiles('[Mg]c1ccc([se]1)-c1ccc([nH]1)-c1ccc([Mg])cc1')
-greg
