Abstract
The bonding geometry at the metal−molecule interface plays an important role in determining the conductance behavior of metal−molecule−metal junctions. This bonding geometry has to be determined a priori in quantum mechanical current−voltage (I−V) calculations. To identify the detailed metal−molecule bonding configurations, we perform classical molecular simulations by combining grand canonical Monte Carlo (GCMC) sampling with molecular dynamics (MD) to explore the dynamic elongations of gold nanowires in the presence of benzenedithiol (BDT) molecules. A specific multitime-scale double reversible reference system propagator algorithm (double-RESPA) has been designed for the metal−organic complex in MD simulations to improve the simulation efficiency. We investigate the variations of bonding sites and bonding angles of BDT molecules on a stretched Au nanowire at a constant chemical potential. The density of BDT and the number of bonded and nonbonded BDT molecules in the simulation box is monitored during t...
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