Passivated gold nanoparticles were synthesized through a microwave-assisted process in a two-phase system, in the presence of 1-dodecanethiol. An average particle size of 1.8 nm of the gold nanoparticles obtained and 0.35 S.D. was determined through HRTEM and STEM analysis. It was observed that these nanoparticles spontaneously self-assemble into self-supported superstructures of 1 μm in diameter avg and 400 nm thickness, yielding an off-white powder which can be handled as a simple powder. XRD analysis indicates that n-alkanethiol molecules used as a passivating compound, besides protecting against crystal growth, interact to form cubic ordered arrays between the nanoparticles. This interaction leads to the superstructure formation, with an average distance between nanoparticles in the array, of 3.56 nm. Theoretical calculations and molecular dynamics simulations were performed to analyze the resulting structure.