Hi, Greg,
This is a bit of a meta-comment, so I hope it's appropriate here. I might
possibly make more comments on the github site.
After this discussion went dead (but before I retired from Schrödinger), I
looked into the origin of that bizarre multicyclic structure. It turned out
to have started life as a saturated cubane structure derived from a source
(PDB? I don't remember.) that doesn't include H's, and the double bonds
were added by some some translation procedure that sought to reconcile
valences. So it's not real.
Best,
-P.
On Wed, Mar 30, 2016 at 1:53 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> This is reviving a long-dead thread because I just marked the associated
> issue as "won't fix" and some of you might be interested in the reasons.
> Here's the bug: https://github.com/rdkit/rdkit/issues/523
> The comment explaining my thinking is here:
> https://github.com/rdkit/rdkit/issues/523#issuecomment-203247157
>
> If possible, please continue the discussion as part of the github issue.
> If you don't have a github account and aren't willing to get one, we can
> continue here.
>
> Because discussions about aromaticity have a tendency to get heated and
> off-topic very quickly, please do read the explanation of the RDKit's
> aromaticity model here: http://rdkit.org/docs/RDKit_Book.html#aromaticity
> before commenting. If you have an argument with the aromaticity model,
> please start a separate thread for it.
> Though a change to the model to treat anti-aromatic systems as aromatic
> would resolve it, this particular issue is *not* about how aromaticity is
> modeled.
>
> Best,
> -greg
>
>
>
> On Wed, Jun 17, 2015 at 8:22 AM, Peter Shenkin <shen...@gmail.com> wrote:
>
>> Hi, Greg,
>>
>> Within the SMILES framework, it seems to me that if you allow the atoms
>> to be aromatic, then these are two Kekule structures of the same aromatic
>> system, and however you do the canonicalization, they ought to canonicalize
>> to the same structure, which the two examples did not do. I don't think you
>> addressed this.
>>
>> I think now that there is no issue with having a double bond between two
>> aromatic atoms beyond our preconceptions. If that is a problem, you could
>> Kekulize it per your first picture, (though perhaps that is inconvenient in
>> the context of the implementation).
>>
>> I actually didn't realize why aromaticity (particularly the double bond)
>> made sense when I originally wrote, so the above is with the benefit of
>> hindsight, and your comments.
>>
>> I think the molecule is entertaining in several ways. In the cubane
>> geometry, the molecule cannot be conventionally aromatic. Might it actually
>> be antiaromatic? Could there be two forms?
>>
>> Dunno....
>> -P.
>>
>>
>> On Wed, Jun 17, 2015 at 1:25 AM, Greg Landrum <greg.land...@gmail.com>
>> wrote:
>>>
>>>
>>> The problematic part of your two molecules can be reduced to:
>>> [image: Inline image 3]
>>> and
>>> [image: Inline image 4]
>>> That second one shows the kekulized form that the RDKit ends up using.
>>>
>>> These produce the following canonical SMILES:
>>>
>>> In [31]: Chem.CanonSmiles('C1=CC2=CC=C12')
>>> Out[31]: 'c1cc2ccc1-2'
>>>
>>> In [32]: Chem.CanonSmiles('C1=CC2=C1C=C2')
>>> Out[32]: 'c1cc2ccc1=2'
>>>
>>>
>
>
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