OR reactions

Consider the reagents H₂ and Pd/C. They will convert alkenes and alkynes to alkanes, and imines and nitriles to amines. I can write a rule for that without any problem. But the reagents will also convert any C-Br bond in the molecule to C-H. How do I write a reaction rule that will process a starting material with EITHER a C=C OR a C-Br bond OR both? I looked at the sequential reactions, but it seems that if the product of the first step does not satisfy the condition of the second step, then the overall reaction fails completely.

Reactions should be separated mechanistically. The saturation of the olefine is different from the substitution of the halogen. Reactor converts starting compounds to products according to ONE given mechanism.





Our final reaction library will contain classification codes created by the required reaction conditions (pH, solvent, tempreture, pressure...). When we reach that phase, we will enhance the JChem toolkit to answer the following question:





"I have these reagents and these conditions. What will be the output?"





Then Reactor will try to process all reactions in the library having matching conditions. So it will tell you, that in the presence of Pd/C catalyst, under hydrogen pressure, the product will be saturated AND substitution can also take place.





I hope, that my explanation makes it understandable, that one reaction should contain one specific reaction mechanism only.

OK. I think what we can do is associate a set of reactions with a particular reagent, and we can run a starting material sequentially through each reaction in the set. If the starting material doesn't match the conditions of any particular reaction, the starting material will simply be returned, and we will move on to the next reaction. We only have to be careful about those cases in which a functional group that is a substrate for one reaction is created in another reaction. In that case, the order of reactions through which we run the starting material will play a role. But this should not be a serious problem for simple sophomore organic chemistry reactions.





Do you have a function for evaluating relative steric hindrance about diastereotopic faces of pi bonds? For example, if I epoxidize norbornene, can I predict that the major product will be exo, not endo?

The hindrance function (will soon be renamed to stericHindrance) of the Geometry plugin can be used to calculate the hindrance of an atom in the 3D space. This calculation can be time consuming, owing to the required geometry optimization.





You can also try to calculate the Dreiding energy of the product isomers (Geometry plugin).