Sorry about this, but I think that 'perhaps sub-optimal' should be replaced
by 'definitely wrong'. The 'quasi-aromatic' system in these two structures
is identical and should behave as such, but in practice one of them matches
a pyridine SMARTS pattern and the other doesn't. That shouldn't be affected
by whether the saturated substituents form a ring or not. I do appreciate
that it gets messy to deal with as fused rings may be fully conjugated, but
the current behaviour seems to be disturbingly inconsistent. It would be
suboptimal to say that no exocyclic bond is allowed to steal electrons, but
that may be better than what's happening here.
Apologies for the dissent!
Chris Earnshaw
On Tue, 23 Oct 2018 at 11:57, Greg Landrum <greg.land...@gmail.com> wrote:
> 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 <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> 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
>>>
>> --
>> 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
>>
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