Protonation-Induced Modulation of HOMO-Fermi Level Offset and Metal-Orbital Coupling in N-Containing Aromatic Self-Assembled Monolayer Tunnel Junctions

We investigate the effects of protonation on conductances G in molecular tunnel junctions based on self-assembled monolayers (SAMs). Here, we compare two different molecules where bipyridine dimethanethiols (BPMD2) have protonatable nitrogen atoms, and oligophenylene dimethanethiols (OPMD2) do not. By treating with HBF₄ acid, BPMD2 SAMs are partially protonated (∼66% monoprotonation), while OPMD2 remains unchanged, confirmed by X-ray photoelectron spectroscopy and reflection–absorption infrared spectroscopy. Conducting probe atomic force microscopy (CP-AFM) with Au or Pt coated tips is employed to form soft contacts with these SAMs on Au or Pt substrates. We observe that protonation of BPMD2 reduces G by approximately 1 order of magnitude, while OPMD2 showed essentially no change in G. To further understand the cause of the G decrease, we use an off-resonance single-level model (orSLM) analysis and extract the density of states parameters from the experimental current–voltage (I–V) characteristics. This analysis reveals that protonation shifts up the HOMO-Fermi level offset ε_h by ∼0.2 eV in BPMD2, as might be expected. However, protonation also induces a significant decrease in the metal-orbital coupling Γ, leading to an overall reduction in G. In contrast, OPMD2 junctions exhibit negligible changes in G, ε_h, and Γ upon treatment with HBF₄. Ultraviolet photoelectron spectroscopy (UPS) not only confirms the ε_h shift for BPMD2 but also reveals an increase in Au/SAM work function Φ by 0.4 eV after protonation. This is consistent with the formation of an interface dipole upon protonation of BPMD2. While further studies are needed for understanding the specific role of the counterions, the collective results show that protonation of SAMs with basic sites can tune both ε_h and Γ, and they demonstrate the applicability of the orSLM for quantitative analysis of chemically doped molecular tunnel junctions.