Dear Andrew,
the reason why Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1") returns
'CN[S@@](=O)c1ccccc1'
and Chem.CanonSmiles("CN1.[S@@]1(=O)C1=CC=CC=C1") returns
'CN[S@](=O)c1ccccc1'
is that there is a "ghost" atom involved in determining the sulfur
chirality, which is a lone pair, which is the sulfur lone pair, which
concurs in determining the atom parity. Even if this is not in the
Daylight specs, the lone-pair is usually treated as an implicit
nitrogen, and therefore considered as the first atom in the clockwise or
anticlockwise accounting:
http://sourceforge.net/p/cdk/mailman/message/34650435/
http://www.opensmiles.org/opensmiles.html#chirality
Therefore, the sulfoxide case is equivalent to the following:
Chem.CanonSmiles("CN[C@@H](O)C1=CC=CC=C1")
'CN[C@@H](O)c1ccccc1'
Chem.CanonSmiles("CN1.[C@@H]1(O)C1=CC=CC=C1")
'CN[C@H](O)c1ccccc1'
Best,
Paolo
On 02/08/16 15:30, Andrew Dalke wrote:
> Thanks Paolo and Hannes for pointing me to sulfoxide. I am enlightened!
>
> I assume this is something that every chemist knows, but it's not mentioned
> in the Daylight SMILES documentation (or the OpenSMILES documentation), so I
> had no clue. I wonder how many more cases there are like that.
>
> Any idea then on why the following two have inverted chiralities?
>
> >>> Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1")
> 'CN[S@@](=O)c1ccccc1'
>
> >>> Chem.CanonSmiles("C2.N23.[S@@]3(=O)C1=CC=CC=C1")
> 'CN[S@](=O)c1ccccc1'
>
>
>
>
> Andrew
> da...@dalkescientific.com
>
>
>
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