Conformational and conductance fluctuations in a single-molecule junction: Multiscale computational study

The key difficulty of interpreting single-molecule junction experiments arises from the uncertainties in the molecule-metal contact configurations. As an initial step toward theoretically resolving the problem, we apply a multiscale computational approach that automates force-field (FF) molecular-dynamics (MD) simulations and density-functional theory (DFT) and matrix Green's function calculations to study the correlation between the conformational and conductance fluctuations in an ideal hexanedithiolate (C6DT) single-molecule junction model. From the 300 K MD simulations of the junction model with the molecule-metal contacts modeled by the bonding of the sulfur linker atoms to the flat Au(111) surfaces, we observe noticeable movements of the S atoms that hop between hollow sites, and confirm that the potential surface derived from (Becke-3-Lee-Yang-Parr-DFT-derived) FF is fairly consistent with that obtained with (Perdew-Burke-Ernzerhof) DFT. The corresponding conductance histogram results in a single well-defined conductance peak irrespective of the C6DT mobility, so we conclude that while the multiple conductance peaks reported in several experiments cannot be explained with the considered ideal S-Au binding geometry, it can serve as a reference for more realistic molecule-metal contact models. Because the energetically preferable hollow sites correspond to the low-value side of the conductance distribution, we find that thermal fluctuations result in a slightly increased C6DT peak conductance value compared with that from the zero-temperature energy-minimized structure and that the conductance histogram can be better fit on a logarithmic scale.