We report molecular dynamics computer simulations of gold passivated nanoparticles and gold nanoparticle arrays. We investigate Au₁₄₀ butane and dodecanethiol passivated clusters. In particular we analyse the effect that the metal core structure has on the interparticle forces and the self assembly of small nanoparticle arrays. We find that the core geometry has very little influence on the intermolecular forces, except for interparticle distances close to contact. Also the core geometry has little influence in determining the structure of the molecular arrays. The structure of the arrays is very rich, from open structures, similar to the ones appearing in limited diffusion process, to compact structures, whose symmetry depends on the chain length of the surfactants. We discuss our results with reference to recent experiments on nanoparticle arrays.