Re: [Rdkit-discuss] Aromaticity question

[Greg L. <gre...@gm...>]

The current implementation requires "exocyclic" bonds to actually be
*non-ring* bonds in order to be recognized as such.
This is perhaps sub-optimal, but it's clearly defined and avoids arguments
about when exactly an "exocyclic" bond starts stealing electrons.

-greg

On Tue, Oct 23, 2018 at 12:46 PM Francis Atkinson <fr...@eb...> wrote:

> Ian,
>
>     I make it 6 electrons: two from the N, none from the C double bonded
> to the exocyclic N, and one each from four other carbons in the ring. It's
> isoelectronic with *e.g.* pyridone, which is aromatic in RDKit...
>
> In [1]: from rdkit import Chem
>
> In [2]: Chem.MolToSmiles(Chem.MolFromSmiles('O=c1[nH]cccc1'))
> Out[2]: 'O=c1cccc[nH]1'
>
>     The protonated/tautomerised version are indeed aromatic
> (interconverting bewteen these species was actually how I came across this
> issue), but I still reckon the unprotonated bicyclic should be aromatic
> too...
>
>         Francis
> On 23/10/2018 11:18, Ian Tickle wrote:
>
>
> Hi, it seems to me that neither is aromatic since the N-substituted hetero
> ring breaks the Huckel rule by having 7 e- (2 from the N and 1 each from
> the 5 Cs).  If you remove 1 e- from the N (so it's [n+]) and also make the
> external double bond into a single (picking up a proton on the other N) it
> becomes pyridinium which is certainly aromatic.
>
> [n+]12ccccc1NCCC2
>
> [n+]12ccccc1NC.CC2
>
> What does it make of those?
>
> Cheers
>
> -- Ian
>
>
> On Tue, 23 Oct 2018 at 10:37, Francis Atkinson <fr...@eb...> wrote:
>
>> Hello,
>>
>>      In the following pair of molecules, the bicyclic is non-aromatic,
>> whereas the 'ring-opened' analogue is aromatic...
>>
>> In [1]: from rdkit import Chem
>>
>> In [2]: Chem.MolToSmiles(Chem.MolFromSmiles('n12ccccc1=NCCC2'))
>> Out[2]: 'C1=CC2=NCCCN2C=C1'
>>
>> In [3]: Chem.MolToSmiles(Chem.MolFromSmiles('n12ccccc1=NC.CC2'))
>> Out[3]: 'CCn1ccccc1=NC'
>>
>> Notebook version:
>>
>> https://nbviewer.jupyter.org/gist/flatkinson/b88eb42510a79594a9e37042eeb7e224
>>
>> This seems counter-intuitive to me: I don't see why the pyridine in the
>> first molecule shouldn't be aromatic, just as it is in the second.
>>
>> Am I missing something here?
>>
>>      Thanks,
>>
>>          Francis
>>
>> --
>> Dr Francis L Atkinson
>>
>> Chemogenomics Group
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> United Kingdom
>>
>> (01223) 494473
>>
>>
>>
>> _______________________________________________
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>>
> --
> Dr Francis L Atkinson
>
> Chemogenomics Group
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
> (01223) 494473
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>