Hi Michal,
The problem here, I think, is that organometallic complexes like this one
involve bond types that are not well represented by SMILES, which really
assumes that a Lewis dot structure including shared electron pairs for all
bonds can be drawn. This is decidedly not the case here, where the molecule
can't even really properly be read in by the RDKit:
In [39]: m =
Chem.MolFromSmiles('[Eu]1234567OC(=CC(=[O]1)C)C.C(C=C(O2)C)(=[O]3)C.C(C=C(O4)C)(=[O]5)C.C1=[N]6C2=C(C=C1)C=CC1=C2[N]7=CC=C1')
[06:23:05] Explicit valence for atom # 5 O, 3, is greater than permitted
The UFF parameters that are available for Eu are for Eu6+3: an octahedrally
coordinated Eu+3. Your complex has 8 connections to the Eu, so it wouldn't
be covered by the UFF parameters anyway.
I just did a bit of playing around to see if I could construct a sample
molecule with a six-coordinate Eu+3 and make that work. I failed. This may
be an RDKit bug but I'm not quite sure. The corners of the code for dealing
with non-organic molecules are dark, dusty, and not particularly well
tested.
Best,
-greg
On Mon, Sep 14, 2015 at 2:26 PM, Michal Krompiec <[email protected]>
wrote:
> Hello,
> I was trying to generate 3D coordinates for an europium complex,
> [Eu(acac)3(phen)], with UFF, using RDKit nodes in KNIME (UFF is
> parametrized for lanthanides). Whereas the generation of coordinates seems
> to produce an almost sensible structure:
> [image: Inline images 3]
>
> subsequent geometry optimization does not: it moves the Eu atom way
> outside of the coordination sphere:
> [image: Inline images 4]
>
> Is it something with the bond types not specified correctly, or it is just
> not supposed to work with this type of molecules at all? The molecule is
> defined by the following SMILES (created with MarvinSketch):
>
> [Eu]1234567OC(=CC(=[O]1)C)C.C(C=C(O2)C)(=[O]3)C.C(C=C(O4)C)(=[O]5)C.C1=[N]6C2=C(C=C1)C=CC1=C2[N]7=CC=C1
> The same result is obtained with La instead of Eu.
> Best wishes,
> Michal
>
>
>
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