Electronic Structure of Metal/Molecule//Metal Junctions:  A Density Functional Theory Study of the Influence of the Molecular Terminal Group

We report on density functional theory calculations of the electronic structure of Au(111)/molecule//Au(111) junctions in which thiol molecules are chemically bound at one end to a gold electrode (the “substrate”), while the other end has a separation of a few to several angstroms from a second gold electrode (the “tip”). Our goal is to investigate the role of different molecular terminal groups and of the tip−molecule distance either on the spatial dependence of the local density of states (LDOS) at the Fermi energy E f or on the energy dependence of the projected density of states onto different molecular subunits. We consider conjugated diphenylthiol (SPh2R) molecules with terminal groups R = H, SH, CH3, or CF3 as well as “mixed” conjugated−saturated phenylthiol-pentane (SPhC4CH3) and butanethiol-toluene (SC4PhCH3) molecules. For SPh2R molecules, the LDOS at E f exhibits an oscillatory exponential decay along the molecule, with an average decay constant that depends weakly on the R terminal group. For the mixed aromatic−aliphatic molecules instead, there are large differences in the LDOS at E f, with SC4PhCH3 showing a much larger LDOS in the proximity of the terminal CH3 group than SPhC4CH3.