Reactor Behaviour

User e7455c8684

12-10-2007 20:22:27

For a reaction like fig1, a reagent like fig2, the product is invalid, but instead of returning null, the reactor just return fig3.





Is this correct?

ChemAxon e08c317633

13-10-2007 07:52:27

Yes, this is correct. Reactor will "replace" the carbon atoms that match carbon with map 3 in the reaction definition (see reaction1.png) with nitrogen atoms, regardless what else is connected to those carbon atoms.





If you want to "replace" only carbon atoms that have a connected hydrogen, then use the following reaction definition (see also reaction2.png):


Code:
[H:5][C:3]1=[C:2]C2=C([N:1]1)N=CC=C2>>[N:1]1[N:4]=[C:2]C2=C1N=CC=C2






Regards,


Zsolt

User e7455c8684

15-10-2007 00:43:05

but the reactor did an extra step by deleting the benzene ring that should connect with the nitrogen. The program in a sense is too "smart".





I think the correct way of doing this: first replace the carbon atom with nitrogen, then check the validity of the product, since the nitrogent got valence of 4, the product is invalide, so the reactor should return null.
Zsolt wrote:
Yes, this is correct. Reactor will "replace" the carbon atoms that match carbon with map 3 in the reaction definition (see reaction1.png) with nitrogen atoms, regardless what else is connected to those carbon atoms.





ChemAxon d76e6e95eb

15-10-2007 09:24:58

If we would like to be precise, Reactor never "replaces an atom" with another. Atoms/ligands connect or disconnect, reactions are always bond modifications.





The indol system is identified in your starting compound first. Then the bonds of the carbon is broken up. Finally, a new nitrogen atom is created and it is connected to the opened ring atoms.





Please let me illustrate the problem with another reaction, maybe you will understand the behaviour. Please see the generic reaction below. It is an acylation reaction, which can be used with various acid chlorides and amines. Please note, that the chloride atom is not swapped with a nitrogen atom! The chloride is eliminate and a nitrogen atom (with its ligands) is connected.

ChemAxon e08c317633

15-10-2007 10:58:18

My explanation was misleading, sorry. I just wanted to show a quick solution for the problem. I used quote marks to indicate that "replace" is just a simplification of what happens.





I have attached an image to show what your reaction definition really means. Note the "make or break" signs on the relevant bonds. R, R1, R2, ... groups are not specified in your reaction definition, so they can be anything.





Regards,


Zsolt