Dear All,
I need to convert iminol functional groups into amides.
Being new to reaction SMARTS I wrote the following code:
*********************
from rdkit import Chem
from rdkit.Chem import AllChem
#from rdkit.Chem.Draw import IPythonConsole
sm1 = 'CNC(C)=O'
m1 = Chem.MolFromSmiles(sm1)
#m1
## m1 is an amide
inchi = Chem.MolToInchi(m1)
m2 = Chem.MolFromInchi(inchi)
#m2
## m2 is an iminol, as expected from InChI
rxn = AllChem.ReactionFromSmarts('[C:1]([OH:2])=[N:3]>>[C:1](=[O:2])[NH:3]')
ps = rxn.RunReactants((m2,))
len(ps)
## 1
m3 = ps[0][0]
#m3
## m3 is wrong and cannot be sanitized
print(Chem.MolToSmiles(m3))
## CNC(C)=[OH]
rxn =
AllChem.ReactionFromSmarts('[H:4][0:1][C:2]=[N:3]>>[O:1]=[C:2][N:3][H:4]')
ps = rxn.RunReactants((m2,))
len(ps)
## 0
********************
The first reaction SMARTS I tried
('[C:1]([OH:2])=[N:3]>>[C:1](=[O:2])[NH:3]')
gives a result but with a trivalent neutral oxygen atom.
Reading more about SMIRKS theory, I tried:
'[H:4][0:1][C:2]=[N:3]>>[O:1]=[C:2][N:3][H:4]' without any success.
Could someone indicate me the correct iminol->amide reaction SMARTS?
Best regards,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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