dehalogenation

Dear all,

I have a large database of molecules and I would like see how many scaffolds i get when i remove only halogen atoms. Could you advise me how can I do it simple and efficient. 

I read that Fragmenter may be one of the solution, but i do not know how to define the action rule.

 

I will be very appreciate for any help.

 

Bets regards

 

Rafal

Could you provide more information?

What is your expected output for 4‐bromo‐1,2‐dichlorobenzene?

Hi

 

Thank you Zsolt for your reply. For the example you provide, I have to get such transformation 4‐bromo‐1,2‐dichlorobenzene > benzene. Generally speaking, all halogen atoms should be removed from the molecule. Is it possible to define such general rule?

 

Kind regards

 

Rafal

Yes, it's possible with Reactor.

Example:

$ react -r "[#6]-[F,Cl,Br,I]>>[#6][H]" --ratio 0 "4‐bromo‐1,2‐dichlorobenzene"

C1=CC=CC=C1

If you need the transformation, not just the product:

$ react -r "[#6]-[F,Cl,Br,I]>>[#6][H]" --ratio 0 -t reaction "4‐bromo‐1,2‐dichlorobenzene"

ClC1=C(Cl)C=C(Br)C=C1>>C1=CC=CC=C1

-r "[#6]-[F,Cl,Br,I]>>[#6][H]" defines a simple dehalogenation reaction in SMARTS

--ratio 0 option makes it exhaustive (remove all halogens)

I think it's quite simple an efficient.

Thanks Zsolt, this is exactly what i wanted to do.

 

Regards

 

Rafal