Two Component Reaction node + MarvinSketch only works for aryl-aryl coupling

[kermitthefrog01]

Hello,

I’ve set up a little workflow to generate new structures by connecting two aromatic rings.
I use Marvin Sketch (output to RxnCell) where I react

Aryl(1)-[Br] + Aryl(2)-[At] => Aryl(1)-Aryl(2)

and I feed the respective SMILES strings from two input tables. [Br] and [At] are used as placeholder atoms. Within MarvinSketch I map the “Aryl” entities, and the node works just fine.

Now, I want to couple non-aromatic systems, too, i.e. olefins, maybe also alkyl chains. So, my first try was to use ‘A’ (any atom except H) instead of “Aryl” but it generates an empty table even for the aforementioned aryl-aryl coupling. Same goes for the labels C, anygroup and anyatom.

I feel like I fundamentally misunderstood the usage of the node but couldn’t find anything in the forum that I could use to solve my problem.
I’d appreciate any pointers.

[kermitthefrog01]

I figured out that to make it work one needs to get the mapping for both the reactant and product (M1; M2) right within Marvin sketch - the order seems important. Also, it seems to matter which reactant is fed into which node input port. So, for now I’ll be checking four permutations if things don’t seem to work.
I solved one problem once (kind of) so I can’t say if this works reproducibly. I’ll update the thread when I gain new insights.