Molecular Simulation Studies on the Elongation of Gold Nanowires in Benzenedithiol

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 the entire elongation process. Simulation results show that BDT molecules can form a denser monolayer on Au nanowires than at the Au (111) surface, owing to the many atomic steps on curved surfaces. Moreover, the chemical bonding of BDT on the Au nanowire significantly effect the elongation behavior of Au nanowires compared with those in vacuum. Our present results will be valuable to the understanding of the broken junction mechanism in molecular electronics conductance measurements.

Stretching of BDT-gold molecular junctions: thiol or thiolate termination?

“…More recently, French et al 15,16 have applied a sophisticated method that combines Monte Carlo simulations and classical molecular dynamics to simulate the junction stretching process, allowing the sampling of hundreds of contact geometries between the molecule and the electrodes. In addition, it is generally assumed in the literature [11][12][13][14][15][16][30][31][32][33][34][35][36] that when the molecule attaches to the gold electrodes, the hydrogen atoms linked to the thiol groups are dissociated to form a thiolate-Au bond. However, recent DFT calculations on the details of the adsorption of the benzene-1,4-dithiol on gold have been reported.…”

Large-Scale Atomistic Simulations of Environmental Effects on the Formation and Properties of Molecular Junctions

“…Methods based on classical force fields have also been used to simulate molecular junctions 27-30 and related systems. [35][36][37] Classical force field (CFF) methods (i.e., molecular dynamics -MD -and…”

An improved smoothed molecular dynamics method with high‐order shape function

“…The decomposition between high frequency and low frequency modes is therefore one of the promising solutions. This decomposition idea directly leads to typical methods such as the constraint method, 1 subspace method, 2,3 and the RESPA method 4,5 . Reducing the tremendous degrees of freedom (DOFs) is the most effective way to increase spatial scale.…”