Dear all,
for sure, having a double bond surrounded by four single bonds makes
the assignment of the E/Z configuration simpler.
My might want also to consider nitrones
https://en.wikipedia.org/wiki/Nitrone
that are sometimes written (CAS does it!) with
a nitrogen atom surrounded by a C=C and a C=O double bond.
Best regards,
Jean-Marc
Le 14/03/2016 13:51, Greg Landrum a écrit :
Dear all,
After reading through this, thinking about it, and searching some
more, I decided to adopt an alternate solution.
Instead of removing the stereochemistry of the P=C double bond in in
molecules like:
C/C=P(=O)/OC1=CC=CC=C1
I added that substructure to the list of things that sanitization
"corrects". It now yields the zwitterionic [P+]-[O-] form. Here's an
example:
In [*4*]: m = Chem.MolFromSmiles('C/C=P(=O)/OC1=CC=CC=C1')
In [*5*]: print(Chem.MolToSmiles(m,True))
C/C=[P+](\[O-])Oc1ccccc1
Best,
-greg
On Thu, Mar 10, 2016 at 8:11 PM, Greg Landrum <[email protected]
<mailto:[email protected]>> wrote:
Dear all,
Here's a question for the chemists in the group: do we need to be
concerned about representing the stereochemistry of the P=C bond
in substructures like O=P(/O)=C/C under normal circumstances?
Here's a pubchem compound example that has the double bond crossed
(possibly leading one to believe that it could have stereochemistry):
https://pubchem.ncbi.nlm.nih.gov/compound/56981965
Here's the corresponding substance record (which is how PubChem
received the structure):
https://pubchem.ncbi.nlm.nih.gov/substance/135741697
Another example, this time without the crossed bond in the
compound record:
https://pubchem.ncbi.nlm.nih.gov/compound/87396055
Best,
-greg
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CNRS UMR 7312
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