Dear rdkitters,
I am trying to use rdkit descriptors to investigate protonation of
molecules in the gas phase
while testing my procedure on Ritalin, I try to calculate the protonation
energy on different functional groups in the molecule
although my understanding tells me protonation should occur on the
secondary amine, energy calculations point at the keto group as the
favorable site.
Bellow is my code
Is it wrong to use this approach? Is it a problem of using the wrong
parameters?
Any help would be greatly appreciated
Yours
Nitzan
test_ion1 = Chem.MolFromSmiles('COC(=O)C(c1ccccc1)C1CCCC[NH2+]1')
test_ion1 = Chem.Add Hs(test_ion1)
AllChem.Embed Molecule( test_ion1,randomSeed=2)
AllChem.MMFFOptimizeMolecule(test_ion1,maxlters-1000,mmffVariant="MMFF94")
Prop1 = AllChem.MMFFGetMoleculeProperties(test_ion1,mmffVariant="MMFF94")
ff1 = AllChem.MMFFGetMoleculeForceField (test_ion1,Prop1)
print ff1.CalcEnergy()
test_ion2 = Chem.MolFromSmiles('COC(=[OH+])C(c1ccccc1)C1CCCCN1')
test_ion2 = Chem.Add Hs(test_ion2)
AllChem.Embed Molecule(test_ion2,randomSeed=2)
AllChem.MMFFOptimizeMolecule( test_ion2,maxlters-1000,mmffVariant="MMFF94")
Prop2 = AllChem.MMFFGetMoleculeProperties(test_ion2,mmffVariant="MMFF94")
ff2 = AllChem.MMFFGetMoleculeForceField (test_ion2,Prop2)
print ff2.CalcEnergy()
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