Dear All,
I wonder if anybody can help with the following? I am trying to
figure-out how to handle double-bond stereochemistry in reactions when
the stereochemistry is involved with the making / breaking bond.
Hopefully this example will explain better than that sentence(!):
rxn = AllChem.ReactionFromSmarts('[c:1][Cl,Br,I].[#6:2][B]>>[*:1][*:2]')
mol1 = Chem.MolFromSmiles('c1ccccc1Br')
mol2 = Chem.MolFromSmiles('C\C=C\B(O)O')
ps = rxn.RunReactants((mol1, mol2))
Chem.MolToSmiles(ps[0][0], True)
---> 'CC=Cc1ccccc1' (stereochemical information lost)
whereas using mol2 = Chem.MolFromSmiles('C\C=C\c1ccccc1B(O)O') gives
---> 'C/C=C/c1c(-c2ccccc2)cccc1' (stereochemical information retained)
Not quite the same, but I have read through some related SMIRKS info
here: http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html
<http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html> .
However, this explains how to handle stereo centres and stereo bonds in
reactions when they are explicitly defined on both sides of the
reaction. I guess what I am looking for is a shortcut for saying
'retain' or 'invert' stereochemistry at reacting centre (sp3) or bond
attached to reacting centre (sp2)...
Having got to the end of explaining that, I am thinking that the way I
should handle this is to check for 'problem' reactants and pass to a
more specific rSMARTS when required!
Kind regards
James
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