Equilibrium structures and thermodynamic properties of dodecanethiol self-assembled monolayers on small (Au-140) and larger (Au-1289) gold nanocrystallites were investigated with the use of molecular dynamics simulations. Compact passivating monolayers are formed on the (111) and (100) facets of the nanocrystallites, with adsorption site geometries differing from those found on extended flat Au(111) and Au(100) surfaces, as well as with higher packing densities. At lower temperatures the passivating molecules organize into preferentially oriented molecular bundles with the molecules in the bundles aligned approximately parallel to each other. Thermal disordering starts at T greater than or equal to 200 K, initiating at the boundaries of the bundles and involving generation of intramolecular conformational (gauche) defects which occur first at bonds near the chains＇ outer terminus and propagate inward toward the underlying gold nanocrystalline surface as the temperature is increased. The disordering process culminates in melting of the molecular bundles, resulting in a uniform orientational distribution of the molecules around the gold nanocrystallites. From the inflection points in the calculated caloric curves, melting temperatures were determined as 280 and 294 K for the monolayers adsorbed on the smaller and larger gold nanocrystallites, respectively. These temperatures are significantly lower than the melting temperature estimated for a self-assembled monolayer of dodecanethiol adsorbed on an extended Au(111) surface. The theoretically predicted disordering mechanisms and melting scenario, resulting in a temperature-broadened transition, support recent experimental investigations.