The thermodynamics of self-assembled monolayer formation: a computational and experimental study of thiols on a flat gold surface

A methodology based on molecular dynamics simulations is presented to determine the chemical potential of thiol self-assembled monolayers on a gold surface. The thiol de-solvation and then the monolayer formation are described by thermodynamic integration with a gradual decoupling of one molecule from the environment, with the necessary corrections to account for standard state changes. The procedure is applied both to physisorbed undissociated thiol molecules and to chemisorbed dissociated thiyl radicals, considering in the latter case the possible chemical potential of the produced hydrogen. We considered monolayers formed by either 7-mercapto-4-methylcoumarin (MMC) or 3-mercapto-propanoic acid (MPA) on a flat gold surface: the free energy profiles with respect to the monolayer density are consistent with a transition from a very stable lying-down phase at low densities to a standing-up phase at higher densities, as expected. The maximum densities of thermodynamically stable monolayers are compared to experimental measures performed with reference-free grazing-incidence X-ray fluorescence (RF-GIXRF) on the same systems, finding a better agreement in the case of chemisorbed thiyl radicals.