| 59 |
|
modified the parameters for the CTS atom to maintain charge neutrality |
| 60 |
|
in the molecule. |
| 61 |
|
|
| 62 |
< |
Bonds are typically rigid in TraPPE-UA, and for flexible bonds, we |
| 63 |
< |
utilized bond stretching spring constants from |
| 62 |
> |
Bonds are typically rigid in TraPPE-UA, so although we used |
| 63 |
> |
equilibrium bond distances from TraPPE-UA, for flexible bonds, we |
| 64 |
> |
adapted bond stretching spring constants from the OPLS-AA force |
| 65 |
> |
field.\cite{Jorgensen:1996sf} |
| 66 |
|
|
| 67 |
|
\begin{table}[h] |
| 68 |
|
\centering |
| 71 |
|
\toprule |
| 72 |
|
$i$&$j$ & $r_0$ (\AA) & $k (\mathrm{~kcal/mole/\AA}^2)$ & source\\ |
| 73 |
|
\colrule |
| 74 |
< |
\ce{CH3} & \ce{CH3} & 1.540 & 536 & \\ |
| 75 |
< |
\ce{CH3} & \ce{CH2} & 1.540 & 536 & \\ |
| 74 |
> |
\ce{CH3} & \ce{CH3} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkanes} and \protect\cite{Jorgensen:1996sf}\\ |
| 75 |
> |
\ce{CH3} & \ce{CH2} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkanes} and \protect\cite{Jorgensen:1996sf} \\ |
| 76 |
|
\ce{CH3} & \ce{CH} & 1.540 & 536 & \\ |
| 77 |
< |
\ce{CH2} & \ce{CH2} & 1.540 & 536 & \\ |
| 77 |
> |
\ce{CH2} & \ce{CH2} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkanes} and \protect\cite{Jorgensen:1996sf} \\ |
| 78 |
|
\ce{CH2} & \ce{CH} & 1.540 & 536 & \\ |
| 79 |
|
\ce{CH} & \ce{CH} & 1.540 & 536 & \\ |
| 80 |
|
\ce{CHene} & \ce{CHene} & 1.330 & 1098 & \\ |
| 82 |
|
\ce{CH3} & \ce{CHene} & 1.540 & 634 & \\ |
| 83 |
|
\ce{CH2} & \ce{CHene} & 1.540 & 634 & \\ |
| 84 |
|
S & \ce{CH2} & 1.820 & 444 & \\ |
| 85 |
< |
\ce{CHar} & \ce{CHar} & 1.40 & 938 & \\ |
| 86 |
< |
\ce{CHar} & \ce{CH2} & 1.540 & 536 & \\ |
| 87 |
< |
\ce{CHar} & \ce{CH3} & 1.540 & 536 & \\ |
| 85 |
> |
\ce{CHar} & \ce{CHar} & 1.40 & 938 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf} \\ |
| 86 |
> |
\ce{CHar} & \ce{CH2} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf}\\ |
| 87 |
> |
\ce{CHar} & \ce{CH3} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf}\\ |
| 88 |
|
\ce{CH2ar} & \ce{CHar} & 1.40 & 938 & |
| 89 |
< |
\protect\cite{William-L.-Jorgensen:1996uq} \\ |
| 89 |
> |
Refs. and |
| 90 |
> |
\protect\cite{Jorgensen:1996sf} \\ |
| 91 |
|
S & \ce{CHar} & 1.80384 & 527.951 & fit \\ |
| 92 |
|
\botrule |
| 93 |
|
\end{tabular} |
| 94 |
|
\end{table} |
| 95 |
|
|
| 93 |
– |
|
| 96 |
|
To describe the interactions between metal (Au) and non-metal atoms, |
| 97 |
|
potential energy terms were adapted from an adsorption study of alkyl |
| 98 |
|
thiols on gold surfaces by Vlugt, \textit{et |
| 176 |
|
\centering |
| 177 |
|
\caption{Torsion parameters. The central atoms for each torsion are atoms $j$ and $k$, |
| 178 |
|
and wildcard atom types are denoted by ``X''. All $c_n$ parameters |
| 179 |
< |
have units of kcal/mol. The torsions around doubly-bonded carbons |
| 179 |
> |
have units of kcal/mol. The torsions around carbon-carbon double bonds |
| 180 |
|
are harmonic and assume a trans (180$\degree$) geometry. The force |
| 181 |
|
constant for this torsion is given in $\mathrm{kcal~mol~}^{-1}\mathrm{degrees}^{-2}$. \label{tab:torsion}} |
| 182 |
|
\begin{tabular}{ cccc|lllll } |
