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 <fran...@ebi.ac.uk> 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
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
