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Hi,
You might try the Reactor tool of ChemAxon (http://www.chemaxon.com/jchem/doc/user/Reactor.html#stereo).
You can specify inversion on the corresponding atom at the reaction center and
batch run it on your molecules. You can run it from the GUI, but it is even
simpler to use the command line:
react mymolecules.sdf -r inversion.rxn -o
results.sdf -f sdf
Best wishes,
Gyorgy
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