We present a detailed theoretical characterization of the energetic alignment between the HOMO level of a series of thiolated oligophenylenes of increasing chain size, and the Fermi level of gold electrodes, using density functional theory (DFT) calculations for molecular self-assembled monolayers (SAMs) chemisorbed on an Au (111) surface, and the nonequilibrium Green's function (NEGF) formalism coupled to DFT for single molecule junctions. The additional role of the dynamic electronic polarization effects neglected in standard DFT calculations is also discussed. Interestingly, whereas the HOMO energy varies significantly among the unsubstituted oligomers in the gas phase, their alignment with respect to the Fermi level of the electrode is almost insensitive to chain size upon chemisorption, thus pointing to a strong pinning effect. The energy at which the HOMO is pinned strongly depends on the degree of interfacial hybridization, and hence on the contact geometry, as well as on the degree of surface coverage although a different mechanism enters into play.anchoring unit. Over the years, a large body of knowledge has been accumulated on the morphologies of such SAMs and on structure-property relationships for the work function shifts [3,4] ; in molecular electronics, many theoretical and experimental studies have focused on the changes in the transmission spectra and I/V characteristics when elongating the size of conjugated oligomers. [5][6][7] In contrast, less attention has been paid to structure-property relationships driving the alignment of the frontier electronic levels with respect to the Fermi level of the metallic electrodes; this energy offset can be deduced by ultraviolet photoelectron spectroscopy (UPS) measurements, [8,9] estimated from I/V characteristics of molecular junctions by using simple analytical models, [8,[10][11][12] or measured photocurrent spectra. [13] The alignment of the HOMO is clearly a key quantity in SAMs, providing electronic levels that favor charge injection in organic layers or in molecular junctions.Theory can prove useful in this context to shed light on this issue, even though it remains extremely challenging to predict the Fermi level alignment quantitatively via first-principles calculations, typically based on density functional theory (DFT). [14][15][16][17][18] This is due to the fact that the ionization potential/electron affinity (IP/EA) of SAM-forming molecules attached to metallic electrodes is governed by several effects not present for the isolated molecules: (i) the electronic polarization of the metal (i.e., image effects) and of the neighboring molecules in presence of a net charge, that both lower the IP and increase the EA of the molecules (i.e., stabilize the formation of a positive charge or negative charge on the molecules); these effects are neglected when performing standard DFT calculations on neutral systems; (ii) the hybridization of the orbitals of the anchoring group with the orbitals of the metallic atoms and the resulting charge reorganization ...