Hi Greg,
Thanks for your reply, I'm aware that complexes of this kind are completely
outside of this code's scope. I was just hoping it might still work here.
Indeed, RDKit does not parse this molecule in SMILES format, but I was able
to smuggle it through as MOL (in KNIME). But anyway, as only 6-valent Eu is
defined in UFF, this is not the way forward for my purpose.
Best wishes,
Michal
On 15 September 2015 at 10:54, Greg Landrum <greg.land...@gmail.com> wrote:
> 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 <
> michal.kromp...@gmail.com> 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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