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 oil 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 (SPhC4CH(3)) and bUtanethiol-toluene (SC4PhCH3) molecules. For SPh2R molecules, the LDOS at E-f exhibits an oscillatory exponential decay along the molecule, with an average C, 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 SC4PhCH(3) showing a much larger LDOS in the proximity of the terminal CH3 group than ShC4CH(3).