RDkit Two component node problem


I want to do a virtual Suzuki coupling with the RDkit Two component node.
As far as I understood the description, the Amine/acidchlorid example and the RDKit book, the reaction is created by the SMARTS defining the leaving groups with defined coupling atoms for the two reactants and SMARTS on how the reactant coupling atoms are to be  connected.
I want to use an aromatic halide "Cl[#6:1]" and boronic acids "B(O)(O)([#6:2]".
Both SMARTS work fine in the RDKit Substructure node.

The reaction was constructed as [B(O)(O)([#6:1]).Cl[#6:2]]>>[#6:1]-[#6:2]
and the error I get from this is:

RDKit Two Component Reaction     Configure failed (ChemicalReactionParserException): null

What am I doing wrong ?

Many thanks for your help

Hi Gilbert,

I believe the error is due to superfluous square brackets on the LHS.  The rSMARTS should read:


(actually I normally do away with the explicit mapped atoms and bond on the RHS, so would have B(O)(O)([#6:1]).Cl[#6:2]>>[*:1][*:2])

This should work - but remember the top input must be your boronics, and the bottom input your chlorides - or you will get zero rows output!

Kind regards


Great, James, thanks a lot !

I was confused by the square brackets in the amine/acid chlorides example...

Thanks again for your help !

Kind regards