Multiple additions to one amine

Hello,

Sorry if this is the wrong forum for this, but I'm banging my head against the wall trying to program Reactor. I haven't found an example that fits this type of reaction.

The reaction: terminal epoxide + polyamine (containing secondary, primary, and tertiary amines)

I'd like the epoxide to react multiple times (2x on the primary amines, 1x on the secondary, and 0 on any tertiary amines)

Any help with this would be GREATLY appreciated. Thanks!

 

Chris

 

Hi Chris,

With Reactor version 5.2.x or below it cannot be done in one step. In one step reactor can connect only one epoxide with one amine (note: it connects them in all suitable positions), so you have to re-run reactor multiple times, and each time replace the amine reactant file with the product file generated in the previous step. Let me know if you need help with this.

 

The good news is that from 5.3 version (coming this month) it can be done in one step, because there will be a runtime parameter to set the ratio of the reactants for Reactor.

Example (version 5.3):

$ react -r epoxide+amine.mrv -t reaction --ratio 4:1 epoxide.smiles amines.smiles
CCC1CO1.CN>>CCC(O)CN(C)CC(O)CC
CCC1CO1.CNC>>CCC(O)CN(C)C
CCC1CO1.NCCN>>CCC(O)CN(CCN(CC(O)CC)CC(O)CC)CC(O)CC

"--ratio 4:1" option means that there is 4x surplus of the first reactant.

In amines.smiles file there is a primary, a secondary, a tertiary amine, and a polyamine. As you see the epoxide reacts 2 times with primary amine, once with the secondary amine, 4 times with polyamine, and does not react with the tertiary amine. It's important to specify the hydrogen atom, and map it as orphan atom in the reaction (see the attached epoxide+amine.mrv reaction file).

Zsolt

Thank you very much; that's very helpful. I'm looking forward to trying out 5.3

Regards,

Chris