| 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 |
