[DFTB-Plus-User] Optimization of zwitterion in vacuum
Reinaldo Pis Diez
reinaldo.pisdiez at gmail.com
Thu Aug 14 13:18:49 CEST 2014
Dear Alessandro,
Zwittrerions are almost impossible to stabilize in vacuum, you need
solvent effects to do it.
I don't know if, in your case, the presence of other molecules
and/or the metal electrodes could play a sort of stabilizing role,
but if you get strange results, then, the problem should be
associated to the medium in which you are making your calculations.
Regards,
Reinaldo
On 08/14/2014 04:15 AM, Alessandro Pirrotta wrote:
> Dear all,
>
> I am using DFTB+NEGF. The system I am studying is formed by a
> molecular junction with gold electrodes where the device region is
> formed by three molecule, one of these is a zwitterion aminoacid.
> The SC NEGF calculation does not converge, ergo I cannot trust the
> transmission I get.
>
> I tried to optimize the aminoacid in vacuum and the C-C bond
> between the carboxyl group and the alpha carbon has a length of
> 2.3 Å in the optimized structure (way too long).
>
> Does anyone know how to get around this problem? I am only
> interested in getting the transport calculation to work properly.
>
> Thanks,
> Alessandro
>
> *Alessandro Pirrotta*
> PhD student
>
> *Faculty of Science**
> *Department of Chemistry &
> Nano-Science Center
> University of Copenhagen
> Universitetsparken 5, C321
> 2100 Copenhagen Ø
> Denmark
>
> DIR +45 21 18 11 90
> MOB +45 52 81 23 41
>
> alessandro.pirrotta at chem.ku.dk <mailto:alessandro.pirrotta at chem.ku.dk>
>
> www.ki.ku.dk <http://www.ki.ku.dk/>
>
>
>
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