By applying nonequilibrium Green's function formalism combined with the first-principles density functional theory, we investigate the electronic transport in two molecular junctions constituted by a substituted oligo (phenylene ehtynylene) sand-wiched between two Au electrodes. Our calculations show that the weak molecule-electrode coupling is responsible for the observation of the negative differential resistance (NDR) effect in experiments. When the coupling is weak, the projected density of states (PDOS) of the molecule and the electrodes undergoes a mismatch-match-mismatch procedure, which increases and then decreases the transmission peak intensities, leading to a NDR effect. We also find that the localization/delocalization of the molecular orbitals and the change of charge state of the molecule have no direct relation with the NDR effect, because they change little as the voltage increases.
