We present a study of the charge transmission behavior of a series of dithiol polyenes in the context of molecular junctions. Using the Landauer theory and zero voltage approximation the Green's functions of the inserted molecules are calculated from a fully ab initio wave function based procedure. Various possibilities in approximating the correlation space are explored and quantitatively evaluated. Our results show that the transmission behavior of a molecular junction is not a monotonic function of the length of the employed molecule. Moreover we introduce the analytic solution of a suitable model system to countercheck the ab initio results and find a remarkable degree of correspondence.