Molecular monolayers at metal/semiconductor heterointerfaces affect electronic energy level alignment at the interface by modifying the interface's electrical dipole. On a free surface, the molecular dipole is usually manipulated by means of substitution at its external end. However, at an interface such outer substituents are in close proximity to the top contact, making the distinction between molecular and interfacial effects difficult. To examine how the interface dipole would be influenced by a single atom, internal to the molecule, we used a series of three molecules of identical binding and tail groups, differing only in the inner atom: aryl vinyl ether (PhO), aryl vinyl sulfide (PhS), and the corresponding molecule with a CH2 group - allyl benzene (PhC). Molecular monolayers based on all three molecules have been adsorbed on a flat, oxide-free Si surface. Extensive surface characterization, supported by density functional theory calculations, revealed high-quality, well-aligned monolayers exhibiting excellent chemical and electrical passivation of the silicon substrate, in all three cases. Current-voltage and capacitance-voltage analysis of Hg/PhX (X = C, O, S)/Si interfaces established that the type of internal atom has a significant effect on the Schottky barrier height at the interface, i.e., on the energy level alignment. Surprisingly, despite the formal chemical separation of the internal atom and the metallic electrode, Schottky barrier heights were not correlated to changes in the semiconductor's effective work function, deduced from Kelvin probe and ultraviolet photoemission spectroscopy on the monolayer-adsorbed Si surface. Rather, these changes correlated well with the ionization potential of the surface-adsorbed molecules. This is interpreted in terms of additional polarization at the molecule/metal interface, driven by potential equilibration considerations even in the absence of a formal chemical bond to the top Hg contact.