Extensive molecular dynamics simulations of organic thiol monolayers self-assembled on gold were performed. Interaction parameters obtained from quantum mechanical calculations were used for the sulfur-metal bond, The first simulations concerned C-20 alkane monolayers for comparison with experiment Then dynamics simulations of a (4-mercaptophenyl)phthalimide (4-MPP) self-assembled monolayer on a Au(111) surface were performed. The structure and dynamics of the interphase were simulated at several surface densities and for two bonding geometries, one with the sulfur atom sp hybridized and one with sp(3) hybridization. The computed tilt angle for a high-density monolayer was 23 degrees for the sp-hybridized case, in good agreement with the experiments presented in the previous paper. The nature of the sulfur-metal bond strongly affected the observed tilt angle, and the angle increased with decreasing surface density. The distribution of rotation angles of the imide ring was broad. The molecules of the interphase exhibited substantial thermal fluctuations at room temperature but did not freely rotate.