Hi Jean-Marc,
Try the reaction smarts '[C:1]([OH:2])=[N:3]>>[C:1](=[OH0:2])[NH:3]'. The
only difference is the addition of "H0" to product atom :2. The problem is
that the hydrogen count from the reactant atom gets copied over unless
specified otherwise.
Hope this helps,
Ivan
On Wed, Feb 6, 2019 at 9:37 AM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
> 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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