Trouble with R group reactions

We currently are using Jchem 3.2.6 and Marvin Sketch 4.1.8 and we are having trouble writing a reaction with an R group.


If we don't map the R group, the reaction will not get rid of the leaving group; it remains attached to the ring (see the attached triazine.mrv file). This happens on the command line. In Reactor GUI, no products are produced; we get an error message.

Code:

react -a changing -v -r ../molecules/triazine.mrv "CSc1ncncn1" CS[c]1(O)ncncn1

If we map the R group as an atom, we get an error message from the command line and from Reactor GUI (this is what we have done with the attached triazine2.mrv file).

Code:

react -a changing -v -r ../molecules/triazine2.mrv "CSc1ncncn1" Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 2147483647         at chemaxon.struc.CGraph.getNode(CGraph.java:226)         at chemaxon.struc.MoleculeGraph.getAtom(MoleculeGraph.java:1208)         at chemaxon.reaction.ReactionSearcher.getReactorData(ReactionSearcher.java:283)         at chemaxon.reaction.ReactionPerformer.reactHit(ReactionPerformer.java:854)         at chemaxon.reaction.ReactionPerformer.reactOne(ReactionPerformer.java:823)         at chemaxon.reaction.ReactionPerformer.reactBase(ReactionPerformer.java:793)         at chemaxon.reaction.ReactionPerformer.react(ReactionPerformer.java:749)         at chemaxon.reaction.Reactor.reactMain(Reactor.java:1582)         at chemaxon.reaction.Reactor.react(Reactor.java:1522)         at chemaxon.reaction.Reactor.processReaction(Reactor.java:1993)         at chemaxon.reaction.Reactor.run(Reactor.java:2172)         at chemaxon.reaction.Reactor.main(Reactor.java:2472)

We are not sure how to fix this problem. Any help you can give would be much appreciated! Thank you.

Hi,





Reactor does not support reaction schemes with orphan or widow R-groups (that have no counterpart on the other side of the reaction).





See also Reactor FAQ:


http://www.chemaxon.com/jchem/doc/user/ReactorFAQ.html#rgroups


http://www.chemaxon.com/jchem/doc/user/ReactorFAQ.html#ratoms





If the reaction scheme contains R-groups, then also "-a changing" option have to be used.





Best regards,


Zsolt

Even if we map the R1 group and put it on the product side of the reaction, we still receive an error message both in our system and on the command line. I have reattached the reaction, this time with the R1 group mapped on the product side. I still receive the error message below.

Code:

react -a changing -v -r ../molecules/triazine062607.mrv "CSc1ncncn1" Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 2147483647         at chemaxon.struc.CGraph.getNode(CGraph.java:226)         at chemaxon.struc.MoleculeGraph.getAtom(MoleculeGraph.java:1208)         at chemaxon.reaction.ReactionSearcher.getReactorData(ReactionSearcher.java:283)         at chemaxon.reaction.ReactionPerformer.reactHit(ReactionPerformer.java:854)         at chemaxon.reaction.ReactionPerformer.reactOne(ReactionPerformer.java:823)         at chemaxon.reaction.ReactionPerformer.reactBase(ReactionPerformer.java:793)         at chemaxon.reaction.ReactionPerformer.react(ReactionPerformer.java:749)         at chemaxon.reaction.Reactor.reactMain(Reactor.java:1582)         at chemaxon.reaction.Reactor.react(Reactor.java:1522)         at chemaxon.reaction.Reactor.processReaction(Reactor.java:1993)         at chemaxon.reaction.Reactor.run(Reactor.java:2172)         at chemaxon.reaction.Reactor.main(Reactor.java:2472)

Sorry, my answer was not completely exact. R-groups can not be used in place of "changing atoms" (see reaction mapping section of the Reactor users guide for explanation what a "changing atom" is).





R-groups can be used only in the "non changing" part of the molecules in the reaction scheme. I have attached an example reaction to demonstrate the usage of R-groups.

Code:

react -a changing -r triazine_example.mrv "CSc1ncncn1" CSc1ncnc(O)n1

Zsolt