We demonstrate that molecular gates using molecular electrostatic potentials (MEP) can be used on hydrogen-passivated silicon substrates without any disturbance of their behavior in vacuum; however, the use of graphite as a substrate strongly affects such behavior. As expected, the substrate may become one more design variable. The ability to have several substrate alternatives is very important for the practical implementation of this new scenario based on molecular potentials. In general, the effect of the substrate can be predetermined by calculating the MEP of the surface as this indicates how strongly its intrinsic potential is.