Molecular dynamics Simulations of alkanethiol monolayers with azobenzene molecules on the au(111) surface

Azobenzene derivatives have potential applications as optomechanical devices and molecular switches. The fabrication of such devices requires attachment of selected molecules to macroscopic surfaces or leads. In this work, we consider heterogeneous systems consisting of a host alkanethiol (dodecanethiol) monolayer with thiol-terminated azobenzene molecules on the Au(111) surface. Studies of the structure and dynamics of the system using classical molecular dynamics simulations reveal a phase transition that is characterized by changes in the tilt angle, heat capacity, and diffusion constant of the host molecules. The results for the pure monolayer are compared to the corresponding heterogeneous systems containing the cis and trans isomers of azobenzene. The temperature dependence of the structure and dynamics of the monolayers is analyzed in detail. Finally, we discuss the implications of our results for the interpretation of recent experiments.