To study the electronic transport of molecular wire circuits, we present a time-independent scattering formalism which includes an ab initio description of the molecular electronic structure. This allows us to obtain the molecule-metal coupling description at the same level of theory. The conductance of junction alpha, alpha(') xylyl dithiol and benzene-1,4-dithiol between gold electrodes is obtained and compared with available experimental data. The conductance depends dramatically on the relative position of the Fermi energy of the metal with respect to the molecular levels. We obtain an estimate for the injecting energy of the electron onto the molecule by varying the distance between the molecule and the attached gold clusters. Contrary to the standard assumption, we find that the injecting energy lies close to the molecular highest occupied molecular orbital, rather than in the middle of the gap; it is just the work function of the bulk metal. Finally, the adequacy of the widely used extended Huckel method for conductance calculations is discussed.