X-ray diffraction and computation yield the structure of alkanethiols on gold(111)

The structure of self- assembled monolayers ( SAMs) of long- chain alkyl sulfides on gold( 111) has been resolved by density functional theory- based molecular dynamics simulations and grazing incidence x- ray diffraction for hexanethiol and methylthiol. The analysis of molecular dynamics trajectories and the relative energies of possible SAM structures suggest a competition between SAM ordering, driven by the lateral van der Waals interaction between alkyl chains, and disordering of interfacial Au atoms, driven by the sulfur- gold interaction. We found that the sulfur atoms of the molecules bind at two distinct surface sites, and that the first gold surface layer contains gold atom vacancies ( which are partially redistributed over different sites) as well as gold adatoms that are laterally bound to two sulfur atoms.