We study the effects of molecular structure on the electronic transport and mechanical stability of single-molecule junctions formed with Au point contacts. Two types of linear conjugated molecular wires are compared: those functionalized with methylsulfide or amine aurophilic groups at (1) both or (2) only one of its phenyl termini. Using scanning tunneling and atomic force microscope break-junction techniques, the conductance of mono- and difunctionalized molecular wires and its dependence on junction elongation and rupture forces were studied. Charge transport through monofunctionalized wires is observed when the molecular bridge is coupled through a S-Au donor-acceptor bond on one end and a relatively weak Au-pi interaction on the other end. For monofunctionalized molecular wires, junctions can be mechanically stabilized by installing a second aurophilic group at the meta position that, however, does not in itself contribute conduction pathway. These results reveal the important interplay between electronic coupling through metal-pi interactions and quantum mechanical effects introduced by chemical substitution on the conjugated system. This study affords a strategy to deterministically tune the electrical and mechanical properties through molecular wires.