Electric conductance of a mechanically strained molecular junction from first principles: Crucial role of structural relaxation and conformation sampling

Density functional theory (DFT) based molecular dynamics simulations have been performed of a 1,4-benzenedithiol molecule attached to two gold electrodes. To model the mechanical manipulation in typical break junction and atomic force microscopy experiments, the distance between two electrodes was incrementally increased up to the rupture point. For each pulling distance, the electric conductance was calculated using the DFT nonequilibrium Green's-function approach for a statistically relevant sample of configurations extracted from the simulation. With increasing mechanical strain, the formation of monoatomic gold wires is observed. The conductance decreases by three orders of magnitude as the initial twofold coordination of the thiol sulfur to the gold is reduced to a single S-Au bond at each electrode and the order in the electrodes is destroyed. Independent of the pulling distance, the conductance was found to fluctuate by at least two orders of magnitude depending on the instantaneous junction geometry.