Junctions consisting of two electrodes and a single molecule acting as a wire can be investigated by scanning probe conductance measurements. The conductance for low temperature, short wire structures can be characterized by the elastic scattering of the electrons, as described by general Landauer formulas. Tuning the bridge energy levels either by field effect transistor (FET)-like behavior (charging) or by chemical bond formation can raise or lower the conductance by moving the poles of the molecular Green's function. For small molecular structures with particular HOMO/LUMO characteristics, functionalization might be a more effective means than Coulomb charging by external gates.