Good passivation of Si, both electrically and chemically, is achieved by monolayers of 1,9-decadiene, directly bound to an oxide-free Si surface. The terminal C - C bond of the decadiene serves for further in situ reaction, without harming the surface passivation, to -OH- or -Br-terminated monolayers that have different dipole moments. Such a two-step procedure meets the conflicting requirements of binding mutually repelling dipolar groups to a surface, while chemically blocking all surface reactive sites. We demonstrate a change of 0.15 eV in the Si surface potential, which translates into a 0.4 eV variation in the Schottky barrier height of a Hg junction to those molecularly modified n-Si surfaces. Charge transport across such junctions is controlled both by tunneling across the molecular monolayer and by the Si space charge. For reliable insight into transport details, we resorted to detailed numerical simulations, which reveal that the Si space charge and the molecular tunneling barriers are coupled. As a result, attenuation due to the molecular tunneling is much weaker than in metal/molecule/metal molecular junctions. Simulation shows also that some interface states are present but that they have a negligible effect on Fermi level pinning. These states are efficiently decoupled from the metal (Hg) and interact mostly with the Si.