[DFTB-Plus-User] Optimization of zwitterion in vacuum

[Alessandro Pirrotta]

Dear Reinaldo,

Thanks for the advice. Adding a first shell of solvation (water as a
solvent) seems to make things for the better in the vacuum calculation.
The C-C bond does not break any longer during the optimization.

Regards,
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

www.ki.ku.dk


On 14 August 2014 13:18, Reinaldo Pis Diez <reinaldo.pisdiez at gmail.com>
wrote:

> 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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