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 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
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