ReactionException: Double-bond stereo cannot be set.

I'm getting that error when applying ClC=C(Cl)Cl to the attached reaction. Should it be necessary to make that type of substrate more specific to trigger this type of reaction?

Please use this reaction instead of the other.

I have tried the following:

Code:

react -r bt0029_mapped.mrv "ClC=C(Cl)Cl" chemaxon.reaction.ReactionException: Double-bond stereo cannot be set. chemaxon.reaction.ReactionException: Double-bond stereo cannot be set.         at chemaxon.reaction.ReactionPerformer.setCisTrans(ReactionPerformer.java:1780)         at chemaxon.reaction.ReactionPerformer.reactHit(ReactionPerformer.java:747)         at chemaxon.reaction.ReactionPerformer.reactOne(ReactionPerformer.java:651)         at chemaxon.reaction.ReactionPerformer.reactBase(ReactionPerformer.java:625)         at chemaxon.reaction.ReactionPerformer.react(ReactionPerformer.java:585)        at chemaxon.reaction.Reactor.reactMain(Reactor.java:1249)         at chemaxon.reaction.Reactor.react(Reactor.java:1184)         at chemaxon.reaction.Reactor.processReaction(Reactor.java:1614)         at chemaxon.reaction.Reactor.run(Reactor.java:1777)         at chemaxon.reaction.Reactor.main(Reactor.java:2023)

This is a bug in the double bond stereo handling of Reactor. The message would be meaningful only if you got a product with a double bond for which the double bond stereo data could not be determined. But in case of the reactant: "ClC=C(Cl)Cl" and the possible product: "ClC(Cl)=C" the double bond stereo is not relevant since the ligands are symmetrical. I am planning to make Reactor recognize this situation and accept the symmetrical product (without setting any double bond stereo data) in this case.


The solution will be included in the next JChem release.





As a workaround you can first hydrogenize your reactants:

Code:

molconvert smiles:H -s "ClC=C(Cl)Cl" [H]C(Cl)=C(Cl)Cl

and then use Reactor with post-dehydrogenization:

Code:

react -r bt0029_mapped.mrv "[H]\C(Cl)=C(\Cl)Cl" -S "dehydrogenize" -y post ClC(Cl)=C Cl\C=C\Cl Cl\C=C/Cl

Thanks for the report and sorry for this inconvenience.