The conductance of molecular bridges tends to be overestimated by computational studies in comparison to measured values. While this well-established trend may be related to difficulties for achieving robust bridges, the employed computational scheme can also contribute to this tendency. In particular, caveats of the traditional functionals employed in first-principles-based calculations can lead to discrepancies reflected in exaggerated conductance. Here, we show that by employing a range-separated hybrid functional the calculated values are within the same order as the measured conductance for all four considered cases. On the other hand, with B3LYP, which is a widely used functional, the calculated values greatly overestimate the conductance (by about 1-2 orders of magnitude). The improved description of the conductance with a RSH functional builds on achieving a physically meaningful treatment of the quasi particles associated with the frontier orbitals.

Acetylthio-protected free base porphyrins are used to form scanning tunneling microscope-molecular break junctions. The porphyrin molecules are deprotected in situ, before the self-assembly. Two types of molecular junctions are formed in the junctions: Au-S-Por-SAc-Au and Au-S-Por-S-Au. Lower conductance values and higher conductance values are observed. Computational modeling attributes the lower conductance to the Au-S-Por-SAc-Au junctions and the higher conductance to the Au-S-Por-S-Au junctions. First-principles calculation suggests that the reduced conductance in the protected porphyrin originates from the presence of the acetyl end groups (-COCH), rather than from the elongation of the sulfur-gold (S-Au) bonds at the tip-molecule interface.

Thiol-based contacts are widely used in fabrication of molecular junctions but are associated with several drawbacks due to their chemical reactivity. In particular, their tendency to dimerize by forming sulfur–sulfur bonds is viewed as a barrier for large scale bridge fabrication. Instead, the use of functionalized sulfur end groups in the fabrication of the junctions is promoted. We analyze the effects of thiol functionalization by acetyl on the transport properties of porphyrin based bridges. In scanning tunneling microscopy (STM) experiments, where the conductance is measured as the tip is retracted, we observe molecular conductance steps due to junctions with acetyl protected thiols that are significantly lower than observed for junctions with deprotected thiols (by a factor of ≈5). Using a first-principles based computational approach, we explain the lower conductance of junctions with acetyl functionalized thiol and associate it to chemical changes of the sulfur, where essentially a tunneling barrier in the transport pathway is enforced. The acetyl protected thiol lowers the transmission mainly through its direct effect on the electronic structure. We show that the geometrical relaxation upon acetylation where the Au–S bond is elongated plays a smaller role in determining the conductance trends. Interestingly, we find that in a hypothetical deprotected case with an imposed longer Au–S bond distance to that of the protected thiol bond length the transmission is slightly increased.

Range-separated hybrid (RSH) functionals have been recently used to overcome the tendency of traditional density functional theory (DFT) calculations to overestimate the conductance of molecular junctions. Non-equilibrium conditions are addressed following non-equilibrium Green's function (NEGF) formulation with RSH functionals to study negative differential resistance (NDR) in molecular junctions of oligo phenylene ethylene derivatives linking gold electrodes. It is shown that the RSH-NEGF calculations indicate NDR onset bias that agrees well with measured trends, associate NDR to orbital localization at the drain contact, and analyze the role of junction asymmetry in NDR. The RSH-NEGF results are also compared with alternative DFT-NEGF combinations to highlight the importance of basing the computational study on a functional that achieves physically significant frontier orbitals. Finally, the effects of thermally accessible molecular fluctuations to enhance the NDR conductance drop are also discussed.