RDKIt two component reaction node

Hello,

I'm having some difficulties to run this 2 component reaction node for a simple reaction: amide formation from a list of carboxylic acids, amines and a reaction draw into marvin sketch.

May issue is that nothing is generated after node execution (empty data table).

Would appreciate some help here.

May be if someone has a flow chart that is working well I could manage to use it.

Thanks in advance. Regards,

JM

 

Hi,

Without seeing the example workflow it's hard to diagnose the problem, but the most likely causes of problems here are failing to include atom mapping information in reaction and providing the reactants in the wrong order (the first reactant should be provide in the top port).

I've attached an example worfklow that demonstrates a simple way of enumerating an amide bond formation.

-greg

 

Hi Greg,

thanks for your reply. By using the mapping function and modifying the reaction (Iremoval R group term )now it is working. Just wondering if there is a way to index properly product based on acid and amine names

For example: acid1 = AC-1, amine1 = AM-1, product = AC-1-AM-1

In the table, all products have the same product index term.

Thanks

JM

 

That turns out to not be as straightforward as it seems like it should be. We should consider adding an option to the reaction dialog to make this easier.

In the meantime, the attached workflow - which joins back to the source tables using canonical SMILES - should do what it sounds like you are looking for. I haven't really cleaned this one up yet; if it works for you I'll do a tidied up version.

Best,

-greg

Hi,

your workflow is working fine. Many thanks for your help

J-M

Hi Greg,

Just coming back regarding this amide reaction workflow. In my carboxylic acids list I have some compounds having ester function. It appears that the amide reaction reconize the esters as acids and so use them for the reaction, generating side products. I have tried to write implictly in the reaction the hydrogren on the hydroxy group but in this case the rdkit two component reaction is not working.

Do you if there is a way to limit this side reaction when usign marvin sketch node?

Many thanks for your help.

regards,

J-M