VMD-L Mailing List

From: Aleksei (erdelgado_at_udec.cl)
Date: Wed Apr 13 2022 - 22:28:14 CDT

I think pyridine may get you angles and bonds similar enough to do your
fitting and remove the offending interaction.

The carbons in benzene and pyridine already share atom type so it's not
a crazy idea either

El 13/4/22 a las 22:39, Daniel Fellner escribió:
> Unfortunately that isn't possible due to the geometry of the molecule and
> the angles in question, because while one side of the angle terminates at
> the carbonyl carbon, the other side is the first atom of the phenyl ring.
> Even the simplest replacement would retain the contaminating interactions,
> and would also change the electronics in the angle atoms significantly.
>
> Perhaps optimising these separately with Ener. Weight set to 0?
> Otherwise I
> think I'll try for the Hessian at a different geometry.
>
> *Daniel Fellner BSc(Hons)*
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326
>
>
> On Thu, 14 Apr 2022 at 14:02, Aleksei <erdelgado_at_udec.cl> wrote:
>
>> Optimize that angle in a different model molecule that has no phenyl
>> hydrogen nearby, then copy the parameter to your molecule of interest
>>
>> El 13/4/22 a las 13:33, Daniel Fellner escribió:
>>> It's me again,
>>>
>>> During some angle optimisation, I noticed two angles terminating in
>>> carbonyl carbon were converging to unbelievably low force constants.
>>> Testing these parameters in MM minimisation shows these angles deviate
>> from
>>> QM even more than the original parameters.
>>>
>>> I believe the issue is favourable 1,6 interactions between the carbonyl
>>> oxygen and a phenyl hydrogen nearby, contaminating the resulting PES.
>>> What's the best course of action? Exclude these angles from
>>> optimisation?
>>> Recalculate the Hessian at a geometry lacking these interactions?
>>> Iteratively fit these guided by IR? Or is there some way to decouple the
>>> interaction during optimisation/Hessian calculation?
>>>
>>> Kind regards,
>>>
>>> *Daniel Fellner BSc(Hons)*
>>> PhD Candidate
>>> School of Chemical Sciences
>>> University of Auckland
>>> Ph +64211605326
>>>
>>