294 |
|
for our UA solvent molecules. In these models, pseudo-atoms are |
295 |
|
located at the carbon centers for alkyl groups. By eliminating |
296 |
|
explicit hydrogen atoms, these models are simple and computationally |
297 |
< |
efficient, while maintains good accuracy. [LOW BOILING POINT IS A |
298 |
< |
KNOWN PROBLEM FOR TRAPPE-UA ALKANES, NEED MORE DISCUSSION] |
299 |
< |
for |
300 |
< |
toluene, force fields are |
301 |
< |
used with rigid body constraints applied.[MORE DETAILS NEEDED] |
297 |
> |
efficient, while maintains good accuracy. However, the TraPPE-UA for |
298 |
> |
alkanes is known to predict a lower boiling point than experimental |
299 |
> |
values. Considering that after an unphysical thermal flux is applied |
300 |
> |
to a system, the temperature of ``hot'' area in the liquid phase would be |
301 |
> |
significantly higher than the average, to prevent over heating and |
302 |
> |
boiling of the liquid phase, the average temperature in our |
303 |
> |
simulations should be much lower than the liquid boiling point. [NEED MORE DISCUSSION] |
304 |
> |
For UA-toluene model, rigid body constraints are applied, so that the |
305 |
> |
benzene ring and the methyl-C(aromatic) bond are kept rigid. This |
306 |
> |
would save computational time.[MORE DETAILS NEEDED] |
307 |
|
|
308 |
< |
Besides the TraPPE-UA models, AA models are included in our studies as |
309 |
< |
well. For hexane, the OPLS all-atom\cite{OPLSAA} force field is |
310 |
< |
used. [MORE DETAILS] |
311 |
< |
For toluene, |
308 |
> |
Besides the TraPPE-UA models, AA models for both organic solvents are |
309 |
> |
included in our studies as well. For hexane, the OPLS |
310 |
> |
all-atom\cite{OPLSAA} force field is used. [MORE DETAILS] |
311 |
> |
For toluene, the United Force Field developed by Rapp\'{e} {\it et |
312 |
> |
al.}\cite{doi:10.1021/ja00051a040} is adopted.[MORE DETAILS] |
313 |
|
|
314 |
< |
Buatnethiol molecules are used as capping agent for some of our |
315 |
< |
simulations. United-Atom\cite{TraPPE-UA.thiols} and All-Atom models |
316 |
< |
are respectively used corresponding to the force field type of |
317 |
< |
solvent. |
314 |
> |
The capping agent in our simulations, the butanethiol molecules can |
315 |
> |
either use UA or AA model. The TraPPE-UA force fields includes |
316 |
> |
parameters for thiol molecules\cite{TraPPE-UA.thiols} and are used in |
317 |
> |
our simulations corresponding to our TraPPE-UA models for solvent. |
318 |
> |
and All-Atom models [NEED CITATIONS] |
319 |
> |
However, the model choice (UA or AA) of capping agent can be different |
320 |
> |
from the solvent. Regardless of model choice, the force field |
321 |
> |
parameters for interactions between capping agent and solvent can be |
322 |
> |
derived using Lorentz-Berthelot Mixing Rule. |
323 |
|
|
324 |
|
To describe the interactions between metal Au and non-metal capping |
325 |
|
agent and solvent, we refer to Vlugt\cite{vlugt:cpc2007154} and derive |
326 |
< |
other interactions which are not parametrized in their work. (can add |
326 |
> |
other interactions which are not yet finely parametrized. [can add |
327 |
|
hautman and klein's paper here and more discussion; need to put |
328 |
< |
aromatic-metal interaction approximation here) |
328 |
> |
aromatic-metal interaction approximation here]\cite{doi:10.1021/jp034405s} |
329 |
|
|
330 |
|
[TABULATED FORCE FIELD PARAMETERS NEEDED] |
331 |
|
|
332 |
+ |
|
333 |
+ |
[SURFACE RECONSTRUCTION PREVENTS SIMULATION TEMP TO GO HIGHER] |
334 |
+ |
|
335 |
+ |
|
336 |
|
\section{Results} |
337 |
+ |
[REARRANGEMENT NEEDED] |
338 |
|
\subsection{Toluene Solvent} |
339 |
|
|
340 |
|
The results (Table \ref{AuThiolToluene}) show a |