The interaction of thiol molecules with the Au(111) surface was investigated with state-of-the-art first-principles methods. We report theoretical evidence for the existence of a physisorption precursor to chemisorption, in agreement with experiment. The origins of inconsistency in recent studies regarding the adsorption site, geometry, and energetics of CH3S on the Au(111) surface were also investigated. We show that the chemisorption site is between the hollow and bridge sites, with a large molecular tilting angle relative to the surface normal. The molecular structure of the overlayer is coverage dependent, with the molecular tilting angle increasing with decreasing coverage. Increasing chain length up to three carbon atoms affects both the chemisorption energetics and the tilt angle. The inconsistency of tilting angles, reported for the fcc site is found to be a consequence of multiple local minima. The ordered structure of thiol molecules at different coverages was also investigated, confirming the recent experimental findings that the c(4x2) structure model is preferred over (root3xroot3)R30degrees.