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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