Molecular Dynamics Simulations of Au Penetration through Alkanethiol Monolayers on the Au(111) Surface

We present results on the energetics and dynamics of Au atoms interacting with alkanethiol monolayers using molecular dynamics in conjunction with quantum-mechanical calculations. Using a classical force field calibrated by first-principle calculations, we have found that under certain physical conditions, gold atoms can penetrate the molecular monolayer to join the underlying Au(111) surface. We have investigated the dependence of surface coverage and temperature, and have found that our results agree well with available experimental observations. The electronic structure of the system, the potential energy as a function of penetration depth, and the charge transfer at the interface between the molecules and the Au(111) surface are analyzed to determine the potential implications for experiments.