[Rdkit-discuss] Stereochemistry inversion upon replacement

[Fiorella Ruggiu]

Hi everyone,

I tried to virtually deprotect molecules using
the AllChem.ReplaceSubstructs() function. Stereochemistry of adjacent atoms
gets inverted in ChiralTag but not in _CIPCode. This gives me the wrong
output SMILES:

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Draw import IPythonConsole

mol=Chem.MolFromSmiles('CC[C@@H](NC(=O)OCC1c2ccccc2-c2ccccc12)C1=CC=CC=C1')
mol
[image: image.png]

for atom in rms[0].GetAtoms():
    if atom.HasProp('_CIPCode'):
        print(atom.GetProp('_CIPCode'))
        print(atom.GetChiralTag())

R
CHI_TETRAHEDRAL_CCW


fmoc = Chem.MolFromSmarts('NC(=O)OCC1c2ccccc2-c2ccccc12')
fmoc_repl = Chem.MolFromSmiles('N')
rms = AllChem.ReplaceSubstructs(mol,fmoc,fmoc_repl,replaceAll=True)
rms[0]

[image: image.png]
Chem.MolToSmiles(rms[0])

'CC[C@H](N)c1ccccc1'


for atom in rms[0].GetAtoms():
    if atom.HasProp('_CIPCode'):
        print(atom.GetProp('_CIPCode'))
        print(atom.GetChiralTag())

R
CHI_TETRAHEDRAL_CW


How come the ChiralTag changes upon the replacement? Sorry if this is
documented somewhere but I didn't quite find it. It works in this case
to do atom.SetChiralTag() to change the stereochemistry in the smiles.

Thanks a lot,
Fio


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