Molecular dynamics calculations have been used to study the behaviour of dense monolayers of long-chain alkyl thiol molecules, HS(CH2)14X (X =—CH2—CH3, —C N, and —O—H) that form by self-assembly from solution onto a gold substrate. The simulation systems consisted of 90 flexible chains with sulphur headgroups and the appropriate terminal groups X. Periodic boundary conditions in the plane of the surface and a surface-corrugation potential encouraged the molecules to form a triangular lattice at a fixed surface density of 21.4 Å2 per chain. The interaction potentials were chosen to model monolayers of molecules on an Au(111) surface. Around room temperature, methyl-terminated chains are canted and rotating about their long axes, and there are a significant number of conformational defects at the chain ends. Monolayers formed from molecules with polar terminal groups adopt more rigid structures. For X =—OH, there is hydrogen bonding between the chain ends but the surface is disordered, with a significant fraction of ‘free’—OH groups. For X =—CN, the terminal groups are organized in a ferroelectric structure, which is incommensurate with the underlying triangular lattice of the sulphur headgroups. The simulated surface structures correlate well with deductions based on the wetting characteristics of these and related self-assembled monolayers.