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 <fran...@ebi.ac.uk
<mailto: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
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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
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