Understanding the transport characteristics of molecules bonded between metal electrodes is of fundamental importance for molecular scale electronics. It is well known that these transport characteristics are influenced by the intrinsic properties of the molecules, including their length, conformation, the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital and the alignment of this gap to the metal Fermi level. This talk will focus on the relation between intrinsic molecular properties, including molecular link chemistry and the conductance of single molecule junctions formed by breaking gold point-contacts in an environment of molecules. The relation between molecular conductance and molecule conformation for the simple case of a biphenyl, two benzene rings linked together by a single C-C bond will be presented. Specifically, I will show that for a series of biphenyl derivatives, the molecular junction conductance decreases with increasing twist angle, following a cosine squared dependence. I will also show that for substituted benzenes, the conductance varies inversely with the calculated ionization potential of the molecules, indicating that the tunneling transport in these molecules is analogous to hole tunneling through an insulating film. Finally, I will discuss some new results with pyridine linked molecules, and demonstrate mechanically activated switching in these single molecule junctions.