Yes, I've seen the same phenomenon in multiple SMILES generators.
Even Daylight's (when they had it up on a public web site).
>From a chemical perspective, it isn't sensible that the pyridone-like ring
in molecule 1 should not be seen as aromatic in the canonical
SMILES, especially since the
Hi Paolo,
Hmmm, I think this is displaying a bug (or at the very least unexpected
behaviour) in the aromaticity code. The issue isn’t the aromaticity of the
imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’ second
molecule is identical to the first except that one bond in
(Now with link - you can tell it's Friday night)
Hi Mark, Alexis,
Yes, I was too fast in composing my previous reply and I did not pay enough
attention to the molecules.
After reading Alexis' reply, I looked more carefully at his original
question and at that point I remembered having seen a
Hi Mark, Alexis,
I was too fast in composing my previous reply and I did not pay enough
attention to the molecules.
After reading Alexis' reply, I went back to his original question and at
that point I remembered having seen a similar behaviour before from RDKit
on condensed ring systems
Hi Paolo,
Many thanks for your response. I suspected that the dihydro-imidazol ring
was involved in this behaviour.
Still can't get my head around this aromaticity behaviour, but I trust you!
It seems that the fused dihydro-imidazol is somehow "stealing" the
aromaticity of the pyridine ring...
Hi Alexis,
The second molecule (smiles2) is indeed aromatic, but the first (smiles1)
is not, as the imidazole ring condensed to the pyridine is partially
saturated.
The smiles1a analogue where I have added a double bond is aromatic, and
upon canonicalization it yields an aromatic SMILES as
Hi everyone,
Why is it that when I canonicalize the following smiles_1 I get its
unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
get its expected aromatic form?
>From rdkit import Chem
smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
smiles
==> 'C1=CC2=NCCN2C=C1'
smiles2
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