We have shown an accurate theoretical description for electronic transport properties of molecular junctions. By applying the elastic scattering Green's function theory approach in combination with the frontier molecular orbital theory for describing the surface-molecule coupling and the hybrid density-functional theory for geometrical and electronic structures calculations, reliable predictions are obtained about the chemical and physical modifications on the current-voltage characteristics of molecular junctions, due to molecular geometrical relaxation, the choice of terminal atoms, the effect of donor/acceptor substitutions, as well as their thermal rotations.