At present, organic molecules are among the best candidate "building blocks" for the construction of self-assembling nanoscale devices based on metal substrates. Control of the formation of specific patterns In the submonolayer regime is usually achieved by appropriate choice and/or functionalization of the adsorbates. The effect of this intervention, though, is limited by the typically short-range character of the bonding. We present here a theoretical study on the system rubrene/gold to show that substrate-induced molecular charging can Instead determine the assembly on larger scales. OFT calculations and electrostatic considerations are used to discuss the charge transfer at the metal/organic Interface. This allows rationalization of previous puzzling experimental results and, in particular, of the unusual molecular gap broadening upon adsorption observed in STS spectra. The self-assembly process is further studied by means of classical molecular dynamics simulations. The charged adsorbates are modeled as mutually repulsive standing dipoles, with van der Waals interactions Intervening at short distances. The striking resemblance between the experimental STM images and the results of our MD simulations shows that this simple model is able to capture the key effects driving the assembly in this system. The competition between long-range repulsive Interactions and short-range attractive forces leads to characteristic and easily recognizable 1D patterns. We suggest that experimental evidence of the presence of similar patterns in other meta/organic systems can provide crucial information on the electronic level alignment at the interface, that is, on the occurrence of charge-transfer processes between metal and organic adsorbates.