Ian,
I think the idea is that the (out-of-plane) p orbital on the
carbonyl C is both part of the ring pi-system and the carbonyl
pi-system. However, both pi-electrons in the carbonyl 'belong to' the
oxygen because it's more electronegative, and they thus aren't counted
in the 4N+2.
I am sure that explanation would pain a theoretical chemist, but,
as Greg has pointed out, this is as much an informatics issue as a
chemistry issue.
The RDKit aromaticity perception is quite an inclusive one: others
(/e.g./ Biovia's) are less so and wouldn't count pyridone as aromatic.
Francis
On 23/10/2018 12:48, Ian Tickle wrote:
Francis
Sorry yes you're right, the C with the exocyclic d.b. doesn't
contribute its p electron to the pi system, but then doesn't that
break the aromaticity since a continuous ring of contributing p
orbitals is surely a requirementI would say that 2-pyridone should not
be classed as aromatic for the same reason but its tautomer
2-hydroxypyridine Oc1ccccn1 clearly is. In 2-pyridone the ring C-C
bond lengths alternate between conjugated single (1.45) and double
(1.34) whereas in 2-hydoxypyridine they are all around the aromatic
C-C length (1.39).
I guess it all depends on how you define 'aromatic' but as I
understand it there are 4 necessary conditions:
1. Must be cyclic.
2. Every atom in the ring must be conjugated (i.e. contributes a p
orbital to the pi system).
3. Must have 4n+2 pi electrons.
4. Ring must be planar (i.e. any stereochemical distortion breaks the
aromaticity even if the other 3 conditions are fulfilled).
You could add that bond lengths between like atom types should be
about equal, but that follows from the other conditions.
Cheers
-- Ian
On Tue, 23 Oct 2018 at 11:45, Francis Atkinson <fran...@ebi.ac.uk
<mailto:fran...@ebi.ac.uk>> 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 <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
--
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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