Structure and Dynamics of a Benzenedithiol Monolayer on a Au(111) Surface Yongsheng Leng,* ,†,‡ David J. Keffer, § and Peter T. Cummings †,‡ Department of Chemical Engineering, Vanderbilt UniVersity, NashVille, Tennessee 37235-1604, Chemical Sciences DiVision, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, and Department of Chemical Engineering, The UniVersity of Tennessee, KnoxVille, Tennessee 37996-2200 ReceiVed: February 17, 2003; In Final Form: June 23, 2003 We use the universal force field (UFF) developed by Rappe ´ et al. (Rappe ´, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. J. Am. Chem. Soc. 1992, 114, 10024) and the specific classical potentials developed from ab initio calculations for Au-benzenedithiol (BDT) molecule interaction to perform molecular dynamics (MD) simulations of a BDT monolayer on an extended Au(111) surface. The simulation system consists of 100 BDT molecules and three rigid Au layers in a simulation box that is rhombic in the plane of the Au surface. A multiple time scale algorithm, the double-reversible reference system propagator algorithm (double RESPA) based on the Nose ´ -Hoover dynamics scheme, and the Ewald summation with a boundary correction term for the treatment of long-range electrostatic interactions in a 2-D slab have been incorporated into the simulation technique. We investigate the local bonding properties of Au-BDT contacts and molecular orientation distributions of BDT molecules. These results show that whereas different basis sets from ab initio calculations may generate different local bonding geometric parameters (the bond length, etc.) the packing structures of BDT molecules maintain approximately the same well-ordered herringbone structure with small peak differences in the probability distributions of global geometric parameters. The methodology developed here opens an avenue for classical simulations of a metal-molecule-metal complex in molecular electronics devices. I. Introduction The possibility of building sophisticated electronic devices from individual molecules has recently been demonstrated with the use of advanced microfabrication and self-assembly techniques. 1-3 Current-voltage and conductance measurements of molecular junctions 4,5 spurred theoretical interest in the modeling of such molecular electronic devices, 6-11 which in turn provides interpretations and feedback to the experimental measurements and molecular electronics architectural design. It is now well established that the transport properties of metal- molecule-metal junctions strongly depend on the molecular conformations, 3,4,9 the temperature, 11 and the contact nature between organic molecules and electrodes (the chemical bonding property). 12,13 Therefore, a better understanding of the equilib- rium properties of molecular devices is critical to further calculations of transport characteristics. This task, in principle, requires an iterative procedure that combines quantum (elec- tronic structure) calculations and classical (molecular configu- ration) calculations. At the quantum level, significant progress has been made in the framework of density functional theory (DFT) to calculate metal -single-molecule-metal conductance. 6-9 However, in practice, the molecular configuration of organic molecules between electrodes and binding properties at the molecule-metal contacts are not known a priori, which may result in large uncertainties in the transport calculations. 7,14 Thus, molecular simulations of self-assembled monolayers (SAMs) are therefore necessary to provide such valuable information. Because the molecular configuration in the electronic device under zero bias is determined by the intra- and intermolecular interactions and by the binding properties at the organic molecule-metal interface, a good force field describing these interactions is crucial. In this paper, we present molecular dynamics (MD) simula- tions of benzenedithiol (BDT) molecules on Au(111) surfaces. This prototypical system of arylthiol molecules sandwiched between two gold electrodes demonstrates the ability to switch between conducting and nonconducting configurations depend- ing on an external applied voltage. 5 We concentrate here on the equilibrium structure and dynamical properties of BDT molecules adsorbed on one extended Au(111) surface at room temperature (298 K) (i.e., without the second electrode being introduced into the system and with one extra H atom attached to the top S atom in BDT). We will provide a full description of the force field and the development of the numerical algorithm in our MD simulations. All of the atomic species (C, H, S, and Au) in the simulations are treated explicitly. For the intra- and intermolecular interactions between BDT molecules and BDT-Au nonbonded interactions, we use the universal force field (UFF), 15 combined with electrostatic partial-charge interactions derived from Mulliken population analysis. For the BDT-Au bonded interactions, which play an important role in the nature of the binding between BDT molecules and the Au(111) surface, we use for the first time a group of specific bonding potentials developed from ab initio quantum mechanical calculations. 16-18 Although many ab initio calculations of methylthiolate (CH 3 S-) on Au(111) showed that the binding of sulfur headgroups was either on the hcp or the fcc hollow sites, 19-21 recent density functional theory (DFT) calculations 22,23 also showed that the back-bonded sulfur atom preferred bridge or bridgelike sites, depending on the chemistry of tail groups. * Corresponding author. E-mail: yongsheng.leng@vanderbilt.edu. † Vanderbilt University. ‡ Oak Ridge National Laboratory. § The University of Tennessee. 11940 J. Phys. Chem. B 2003, 107, 11940-11950 10.1021/jp034405s CCC: $25.00 © 2003 American Chemical Society Published on Web 10/04/2003