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
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to