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\documentclass[aps,jcp,preprint,showpacs,superscriptaddress,groupedaddress]{revtex4} % for double-spaced preprint |
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\documentclass[aps,preprint,showpacs,superscriptaddress,groupedaddress]{revtex4-1} |
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\usepackage{graphicx} % needed for figures |
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\usepackage{dcolumn} % needed for some tables |
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\usepackage{bm} % for math |
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\usepackage{amssymb} % for math |
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%\usepackage{booktabs} |
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\usepackage{booktabs} |
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\usepackage[english]{babel} |
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\usepackage{multirow} |
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\usepackage{tablefootnote} |
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\usepackage{times} |
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\usepackage[version=3]{mhchem} |
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\usepackage{lineno} |
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\email{gezelter@nd.edu} |
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\affiliation{Department of Chemistry and Biochemistry, University of |
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Notre Dame, Notre Dame, IN 46556} |
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\date{\today} |
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\begin{abstract} |
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This document supplies force field parameters for the united-atom |
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sites, bond, bend, and torsion parameters, as well as the cross |
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interactions between the united-atom sites and the gold atoms. These |
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parameters were used in the simulations presented in the main text. |
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\end{abstract} |
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\maketitle |
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Gold -- gold interactions were described by the quantum Sutton-Chen |
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(QSC) model.\cite{Qi:1999ph} The hexane solvent is described by the |
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TraPPE united atom model,\cite{TraPPE-UA.alkanes} where sites are |
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Lennard-Jones potentials were used for non-bonded interactions. |
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\begin{table}[h] |
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\bibpunct{}{}{,}{n}{}{,} |
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\centering |
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\caption{Properties of the United atom sites. \label{tab:atypes}} |
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\begin{tabular}{ c|cccc } |
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\colrule |
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\ce{CH3} & 15.04 & 0.1947 & 3.75 & \\ |
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\ce{CH2} & 14.03 & 0.09141 & 3.95 & \\ |
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\ce{CH} & 13.02 & 0.01987 & 4.68 & \\ |
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\ce{CHene} & 13.02 & 0.09340 & 3.73 & \\ |
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CH & 13.02 & 0.01987 & 4.68 & \\ |
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CHene & 13.02 & 0.09340 & 3.73 & \\ |
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\ce{CH2ene} & 14.03 & 0.16891 & 3.675 & \\ |
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S & 32.0655 & 0.2504 & 4.45 & Refs. \protect\cite{landman:1998} ($\sigma$) and \protect\cite{vlugt:cpc2007154} ($\epsilon$) \\ |
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\ce{CHar} & 13.02 & 0.1004 & 3.695 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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CHar & 13.02 & 0.1004 & 3.695 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH2ar} & 14.03 & 0.1004 & 3.695 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\botrule |
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\end{tabular} |
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\bibpunct{[}{]}{,}{n}{,}{,} |
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\end{table} |
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The TraPPE-UA force field includes parameters for thiol |
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field.\cite{Jorgensen:1996sf} |
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|
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\begin{table}[h] |
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\bibpunct{}{}{,}{n}{}{,} |
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\centering |
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\caption{Bond parameters. \label{tab:bond}} |
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\begin{tabular}{ cc|lll } |
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\colrule |
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\ce{CH3} & \ce{CH3} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkanes} and \protect\cite{Jorgensen:1996sf}\\ |
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\ce{CH3} & \ce{CH2} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkanes} and \protect\cite{Jorgensen:1996sf} \\ |
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\ce{CH3} & \ce{CH} & 1.540 & 536 & \\ |
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\ce{CH3} & CH & 1.540 & 536 & \\ |
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\ce{CH2} & \ce{CH2} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkanes} and \protect\cite{Jorgensen:1996sf} \\ |
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\ce{CH2} & \ce{CH} & 1.540 & 536 & \\ |
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\ce{CH} & \ce{CH} & 1.540 & 536 & \\ |
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\ce{CHene} & \ce{CHene} & 1.330 & 1098 & \\ |
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\ce{CH2ene} & \ce{CHene} & 1.330 & 1098 & \\ |
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\ce{CH3} & \ce{CHene} & 1.540 & 634 & \\ |
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\ce{CH2} & \ce{CHene} & 1.540 & 634 & \\ |
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\ce{CH2} & CH & 1.540 & 536 & \\ |
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CH & CH & 1.540 & 536 & \\ |
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CHene & CHene & 1.330 & 1098 & \\ |
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\ce{CH2ene} & CHene & 1.330 & 1098 & \\ |
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\ce{CH3} & CHene & 1.540 & 634 & \\ |
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\ce{CH2} & CHene & 1.540 & 634 & \\ |
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S & \ce{CH2} & 1.820 & 444 & \\ |
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\ce{CHar} & \ce{CHar} & 1.40 & 938 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf} \\ |
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\ce{CHar} & \ce{CH2} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf}\\ |
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\ce{CHar} & \ce{CH3} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf}\\ |
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\ce{CH2ar} & \ce{CHar} & 1.40 & 938 & |
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Refs. and |
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\protect\cite{Jorgensen:1996sf} \\ |
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S & \ce{CHar} & 1.80384 & 527.951 & fit \\ |
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CHar & CHar & 1.40 & 938 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf} \\ |
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CHar & \ce{CH2} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf}\\ |
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CHar & \ce{CH3} & 1.540 & 536 & Refs. \protect\cite{TraPPE-UA.alkylbenzenes} and \protect\cite{Jorgensen:1996sf}\\ |
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\ce{CH2ar} & CHar & 1.40 & 938 & Refs. and \protect\cite{Jorgensen:1996sf} \\ |
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S & CHar & 1.80384 & 527.951 & This Work \\ |
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\botrule |
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\end{tabular} |
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\bibpunct{[}{]}{,}{n}{,}{,} |
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\end{table} |
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|
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To describe the interactions between metal (Au) and non-metal atoms, |
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\begin{table}[h] |
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\bibpunct{}{}{,}{n}{,}{,} |
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\centering |
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\caption{Bend angle parameters. The central atom in the bend is atom $j$.\label{tab:bend}} |
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\begin{tabular}{ ccc|lll } |
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\ce{CH3} & \ce{CH2} & \ce{CH3} & 114.0 & 124.20& Ref. \protect\cite{TraPPE-UA.thiols}\\ |
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\ce{CH3} & \ce{CH2} & \ce{CH2} & 114.0 & 124.20& Ref. \protect\cite{TraPPE-UA.thiols}\\ |
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\ce{CH2} & \ce{CH2} & \ce{CH2} & 114.0 & 124.20& Ref. \protect\cite{TraPPE-UA.thiols}\\ |
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\ce{CH3} & \ce{CH2} & \ce{CH} & 114.0 & 124.20& Ref. \protect\cite{TraPPE-UA.thiols}\\ |
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\ce{CHene} & \ce{CHene} & \ce{CH3} & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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\ce{CHene} & \ce{CHene} & \ce{CHene} & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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\ce{CH2ene} & \ce{CHene} & \ce{CH3} & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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\ce{CHene} & \ce{CHene} & \ce{CH2} & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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\ce{CH2} & \ce{CH2} & \ce{CHene} & 114.0 & 124.20& Ref. \protect\cite{TraPPE-UA.thiols}\\ |
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\ce{CHar} & \ce{CHar} & \ce{CHar} & 120.0 & 126.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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\ce{CHar} & \ce{CHar} & \ce{CH2} & 120.0 & 140.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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\ce{CHar} & \ce{CHar} & \ce{CH3} & 120.0 & 140.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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\ce{CHar} & \ce{CHar} & \ce{CH2ar} & 120.0 & 126.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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S & \ce{CH2} & \ce{CHene} & 109.97 & 127.37 & fit \\ |
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S & \ce{CH2} & \ce{CHar} & 109.97 & 127.37 & fit \\ |
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S & \ce{CHar} & \ce{CHar} & 123.911 & 138.093 & fit \\ |
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\ce{CH3} & \ce{CH2} & CH & 114.0 & 124.20& Ref. \protect\cite{TraPPE-UA.thiols}\\ |
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CHene & CHene & \ce{CH3} & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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CHene & CHene & CHene & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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\ce{CH2ene} & CHene & \ce{CH3} & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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CHene & CHene & \ce{CH2} & 119.7 & 139.94& Ref. \protect\cite{Maerzke:2009qy}\\ |
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\ce{CH2} & \ce{CH2} & CHene & 114.0 & 124.20& Ref. \protect\cite{TraPPE-UA.thiols}\\ |
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CHar & CHar & CHar & 120.0 & 126.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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CHar & CHar & \ce{CH2} & 120.0 & 140.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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CHar & CHar & \ce{CH3} & 120.0 & 140.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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CHar & CHar & \ce{CH2ar} & 120.0 & 126.0 & Refs. \protect\cite{Maerzke:2009qy} and \\ |
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S & \ce{CH2} & CHene & 109.97 & 127.37 & This work \\ |
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S & \ce{CH2} & CHar & 109.97 & 127.37 & This work \\ |
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S & CHar & CHar & 123.911 & 138.093 & This work \\ |
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\botrule |
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\end{tabular} |
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\bibpunct{[}{]}{,}{n}{,}{,} |
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\end{table} |
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|
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\begin{table}[h] |
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\bibpunct{}{}{,}{n}{,}{,} |
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\centering |
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\caption{Torsion parameters. The central atoms for each torsion are atoms $j$ and $k$, |
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and wildcard atom types are denoted by ``X''. All $c_n$ parameters |
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\colrule |
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\ce{CH3} & \ce{CH2} & \ce{CH2} & \ce{CH3} & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH3} & \ce{CH2} & \ce{CH2} & \ce{CH2} & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH3} & \ce{CH2} & \ce{CH2} & \ce{CH} & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH3} & \ce{CH2} & \ce{CH2} & CH & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH2} & \ce{CH2} & \ce{CH2} & \ce{CH2} & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH2} & \ce{CH2} & \ce{CH2} & S & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH3} & \ce{CH2} & \ce{CH2} & S & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ \colrule |
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X & \ce{CHene} & \ce{CHene} & X & \multicolumn{4}{c}{\multirow{2}{*}{$V = \frac{0.008112}{2} (\phi - 180.0)^2$}} & \multirow{2}{*}{Ref. \protect\cite{TraPPE-UA.alkylbenzenes}} \\ |
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X & \ce{CHar} & \ce{CHar} & X & & & & & \\ \colrule |
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\ce{CH2} & \ce{CH2} & \ce{CHene} & \ce{CHene} & 1.368 & 0.1716 & -0.2181 & -0.56081 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH2} & \ce{CH2} & \ce{CH2} & \ce{CHene} & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CHene} & \ce{CHene} & \ce{CH2} & S & 3.20753 & 0.207417& -0.912929& -0.958538 & fit \\ |
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\ce{CHar} & \ce{CHar} & \ce{CH2} & S & 3.20753 & 0.207417& -0.912929& -0.958538 & fit \\ |
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X & CHene & CHene & X & \multicolumn{4}{c}{\multirow{2}{*}{$V = \frac{0.008112}{2} (\phi - 180.0)^2$}} & \multirow{2}{*}{Ref. \protect\cite{TraPPE-UA.alkylbenzenes}} \\ |
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X & CHar & CHar & X & & & & & \\ \colrule |
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\ce{CH2} & \ce{CH2} & CHene & CHene & 1.368 & 0.1716 & -0.2181 & -0.56081 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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\ce{CH2} & \ce{CH2} & \ce{CH2} & CHene & 0.0 & 0.7055 & -0.13551 & 1.5725 & Ref. \protect\cite{TraPPE-UA.alkylbenzenes}\\ |
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CHene & CHene & \ce{CH2} & S & 3.20753 & 0.207417& -0.912929& -0.958538 & This work \\ |
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CHar & CHar & \ce{CH2} & S & 3.20753 & 0.207417& -0.912929& -0.958538 & This work \\ |
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\botrule |
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\end{tabular} |
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\bibpunct{[}{]}{,}{n}{,}{,} |
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\end{table} |
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\begin{table}[h] |
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\bibpunct{}{}{,}{n}{,}{,} |
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\centering |
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\caption{Non-bonded cross interaction parameters between gold atoms and the united atom sites\label{tab:nb}} |
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\begin{tabular}{ cc|ccc } |
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\colrule |
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Au &\ce{CH3} &3.54 &0.2146& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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Au &\ce{CH2} &3.54 &0.1749& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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Au &\ce{CHene} &3.4625 &0.1680& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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Au &\ce{CHar} &3.4625 &0.1680& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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Au &CHene &3.4625 &0.1680& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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Au &CHar &3.4625 &0.1680& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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Au &\ce{CH2ar} &3.4625 &0.1680& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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Au &S &2.40 &8.465& Ref. \protect\cite{vlugt:cpc2007154}\\ |
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\botrule |
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\end {tabular} |
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\bibpunct{[}{]}{,}{n}{,}{,} |
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\end{table} |
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\newpage |
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\bibliographystyle{aip} |
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\bibliography{NPthiols} |
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\end{document} |
