Molecular junctions are essentially modified electrodes familiar to electrochemists where the electrolyte is replaced by a conducting "contact." It is generally hypothesized that changing molecular structure will alter system energy levels leading to a change in the transport barrier. Here, we show the conductance of seven different aromatic molecules covalently bonded to carbon implies a modest range (<0.5 eV) in the observed transport barrier despite widely different free molecule HOMO energies (>2 eV range). These results are explained by considering the effect of bonding the molecule to the substrate. Upon bonding, electronic inductive effects modulate the energy levels of the system resulting in compression of the tunneling barrier. Modification of the molecule with donating or withdrawing groups modulate the molecular orbital energies and the contact energy level resulting in a leveling effect that compresses the tunneling barrier into a range much smaller than expected. Whereas the value of the tunneling barrier can be varied by using a different class of molecules (alkanes), using only aromatic structures results in a similar equilibrium value for the tunnel barrier for different structures resulting from partial charge transfer between the molecular layer and the substrate. Thus, the system does not obey the Schottky-Mott limit, and the interaction between the molecular layer and the substrate acts to influence the energy level alignment. These results indicate that the entire system must be considered to determine the impact of a variety of electronic factors that act to determine the tunnel barrier.energy alignment | molecular electronics | electronic coupling | charge transport | Fermi-level pinning T he conductance of electrical charge through and across molecular entities is the basis of molecular and organic electronics (1, 2). Understanding, controlling, and designing electronic circuits using organic molecules as components is a major goal of molecular electronics (3); however, it has been a challenge to identify all of the factors that govern the conductance of a molecular junction. Rather than being a simple property of the molecule itself, many circumstances contribute to the measured electronic properties of the junction. Some of the important features include the nature of the molecule-contact bonding (4), the properties of the contact materials (5, 6), the orientation of the molecules relative to the contacts (7), and the structure of the molecule (5,8,9). Although there is no general consensus on exactly how each of these features affects the conductance of the junction, it is generally agreed that the alignment of the molecular and contact energy levels is an important factor (10-13). The offset between the substrate Fermi energy (E f ) and the molecular orbital closest in energy to E f is often used to estimate charge transport barriers in the context of tunneling or charge injection models; however, it is increasingly clear that the situation is complex and that there is no simple meth...