The structure, dynamics, and thermodynamics of gold nanocrystallites passivated by alkylthiolate monolayers were investigated, using molecular dynamics simulations, in different environments-as isolated gas-phase clusters, when adsorbed on a graphite surface, and when assembled into three-dimensional superlattices. The packing arrangements and densities of the monolayers passivating the facets of the core gold nanocrystallites differ from those found on extended gold surfaces, exhibiting organization into molecular bundles of preferred orientations which upon heating undergo a reversible melting transition from the ordered bundled state to a uniform intermolecular orientational distribution. The equilibrium geometries of adsorbed nanocrystallites depend on the chain length of the passivating molecules which effectively lubricate the interface between the gold core and the graphite surface conferring high surface mobility to the crystallites, involving a collective slip-diffusion mechanism. The room-temperature equilibrium structure of the superlattice made of Au-140(C12H25S)(62) nanocrystallites is predicted to be tetragonally distorted fee with enhanced orientational bundling of the passivating molecules along the direction of the tetragonal distortion. The cohesion of the superlattice derives dominantly from the interactions between the interlocking molecular bundles. On the other hand, passivation by shorter chain molecules, Au-140(C4H9S)(62), results in a room-temperature body-centered cubic superlattice structure, transforming to a fee lattice at higher temperatures.