Hello,
I am trying to formulate a reaction that describes a disconnection of a
terminal methyl goup from a sulfide while leaving to ions - [S+] and [CH3-].
Herein is my code:
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Descriptors import *
mol = Chem.MolFromSmiles('CC(C)(C)SC')
rxn =
AllChem.ReactionFromSmarts('[CH0:1][S:2]-[CH3:3]>>[C:1][SH0+:2].[CH3-:3]')
ps = rxn.RunReactants((mol,))
print Chem.MolToSmiles(ps[0][0])
print Chem.MolToSmiles(ps[0][1])
Unfortunately, the output that I get is an [SH2+].[CH3-] ions.
How can I get rid of the redundant hydrogen atoms?
Thanks,
Nitzan
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