Dear users,
I have been struggling for days trying to model a specific reaction but
cannot succeed in matching the corresponding SMARTS notation, I am
reproducing my code below,
My molecule is:
/reactant = 'c1ccc(N)c(N)c1'/
I am trying to prepare a second ring by reacting the two primary amines.
The final molecule should be:
/product = 'c1cccc2nn[nH]c12'/
//
In this way, I am setting the SMARTS reaction pattern as:
/reaction_smarts =
'[cX3]1[cX3][cX3][cX3]($[NX3H2:1])[cX3]($[NX3H2:2])[cX3]1>>[cX3]1[cX3][cX3][cX3][cX3]2$[nX3:1]=[nX3]-[nX3H:2]$[cX3]12'/
And after running the reaction,
/rxn = AllChem.ReactionFromSmarts(reaction_smarts)/
/product = rxn.RunReactants((reactant,))/
I am not getting no product at all,
Any hint on what may be my problem would be greatly appreciated,
Thank you very much in advance for the help,
regards
Alfredo
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