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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