Hi Lukas, Sorry for the slow reply on this one. The algorithm the RDKit uses to assign the number of radical electrons to an atom is really only useful for main-group elements. As you can see, it generates results that don't make much sense for transition metals.
I guess a more sensible approach here would be to just use the minimum number of unpaired valence electrons. Since Mn+2 has 5 valence electrons this would result in a radical count of 1. Here's the github issue for this: https://github.com/rdkit/rdkit/issues/3330 On Mon, Jul 27, 2020 at 10:16 PM Lukas Pravda <lpra...@ebi.ac.uk> wrote: > Dear rdkit community, > > > > I’m not quite sure if this is more of an rdkit or a chemistry related > question. I’d like to understand why a manganese ion has 3 radical > electrons when interpreted by rdkit. I have not seen radicals in any other > metal ion so far. > > > > The code to get the depiction looks like this: > > from rdkit import Chem > > from rdkit.Chem import Draw > > > > width = 500 > > > > m = Chem.MolFromInchi('InChI=1S/Mn/q+2') > > drawer = Draw.rdMolDraw2D.MolDraw2DSVG(width, width) > > > > Draw.rdMolDraw2D.PrepareMolForDrawing(m, wedgeBonds=True, kekulize=True, > addChiralHs=True) > > > > drawer.DrawMolecule(m) > > drawer.FinishDrawing() > > > > with open('2d_mol.svg', 'w') as f: > > svg = drawer.GetDrawingText() > > f.write(svg) > > > > print('done') > > > > and the depiction you get looks like the one on the page: > https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/MN Thank > you in advance for clarification. > > > > > > rdkit through python 2020.03.4 on mac 10.15.6 > > > > Best, > > Lukas > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
