| 241 |
|
investigated, one which has little vibrational overlap with the |
| 242 |
|
alkanethiol and plane-like shape (toluene), and one which has similar |
| 243 |
|
vibrational frequencies and chain-like shape ({\it n}-hexane). The |
| 244 |
< |
initial configurations generated by Packmol are further equilibrated |
| 245 |
< |
with the $x$ and $y$ dimensions fixed, only allowing length scale |
| 246 |
< |
change in $z$ dimension. This is to ensure that the equilibration of |
| 247 |
< |
liquid phase does not affect the metal crystal structure in $x$ and |
| 248 |
< |
$y$ dimensions. Further equilibration are run under NVT and then NVE ensembles. |
| 244 |
> |
spacing filled by solvent molecules, i.e. the gap between periodically |
| 245 |
> |
repeated Au-butanethiol surfaces should be carefully chosen so that it |
| 246 |
> |
would not be too short to affect the liquid phase structure, nor too |
| 247 |
> |
long, leading to over cooling (freezing) or heating (boiling) when a |
| 248 |
> |
thermal flux is applied. In our simulations, this spacing is usually |
| 249 |
> |
$35 \sim 60$\AA. |
| 250 |
> |
|
| 251 |
> |
The initial configurations generated by Packmol are further |
| 252 |
> |
equilibrated with the $x$ and $y$ dimensions fixed, only allowing |
| 253 |
> |
length scale change in $z$ dimension. This is to ensure that the |
| 254 |
> |
equilibration of liquid phase does not affect the metal crystal |
| 255 |
> |
structure in $x$ and $y$ dimensions. Further equilibration are run |
| 256 |
> |
under NVT and then NVE ensembles. |
| 257 |
|
|
| 258 |
|
After the systems reach equilibrium, NIVS is implemented to impose a |
| 259 |
|
periodic unphysical thermal flux between the metal and the liquid |
| 260 |
< |
phase. Most of our simulations have this flux from the metal to the |
| 260 |
> |
phase. Most of our simulations are under an average temperature of |
| 261 |
> |
$\sim$200K. Therefore, this flux usually comes from the metal to the |
| 262 |
|
liquid so that the liquid has a higher temperature and would not |
| 263 |
|
freeze due to excessively low temperature. This induced temperature |
| 264 |
|
gradient is stablized and the simulation cell is devided evenly into |
| 276 |
|
\label{derivativeG2} |
| 277 |
|
\end{equation} |
| 278 |
|
|
| 270 |
– |
|
| 279 |
|
\subsection{Force Field Parameters} |
| 280 |
+ |
Our simulations include various components. Therefore, force field |
| 281 |
+ |
parameter descriptions are needed for interactions both between the |
| 282 |
+ |
same type of particles and between particles of different species. |
| 283 |
|
|
| 284 |
|
The Au-Au interactions in metal lattice slab is described by the |
| 285 |
|
quantum Sutton-Chen (QSC) formulation.\cite{PhysRevB.59.3527} The QSC |
| 287 |
|
reparametrized for accurate surface energies compared to the |
| 288 |
|
Sutton-Chen potentials\cite{Chen90}. |
| 289 |
|
|
| 290 |
< |
Straight chain {\it n}-hexane and aromatic toluene are respectively |
| 291 |
< |
used as solvents. For hexane, both United-Atom\cite{TraPPE-UA.alkanes} |
| 292 |
< |
and All-Atom\cite{OPLSAA} force fields are used for comparison; for |
| 293 |
< |
toluene, United-Atom\cite{TraPPE-UA.alkylbenzenes} force fields are |
| 294 |
< |
used with rigid body constraints applied. (maybe needs more details |
| 295 |
< |
about rigid body) |
| 290 |
> |
For both solvent molecules, straight chain {\it n}-hexane and aromatic |
| 291 |
> |
toluene, United-Atom (UA) and All-Atom (AA) models are used |
| 292 |
> |
respectively. The TraPPE-UA |
| 293 |
> |
parameters\cite{TraPPE-UA.alkanes,TraPPE-UA.alkylbenzenes} are used |
| 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] |
| 302 |
|
|
| 303 |
+ |
Besides the TraPPE-UA models, AA models are included in our studies as |
| 304 |
+ |
well. For hexane, the OPLS all-atom\cite{OPLSAA} force field is |
| 305 |
+ |
used. [MORE DETAILS] |
| 306 |
+ |
For toluene, |
| 307 |
+ |
|
| 308 |
|
Buatnethiol molecules are used as capping agent for some of our |
| 309 |
|
simulations. United-Atom\cite{TraPPE-UA.thiols} and All-Atom models |
| 310 |
|
are respectively used corresponding to the force field type of |
