We observed that the negative differential resistance feature of four different arrangements of a thiol-ended trimer unit of cis-polyacetylene is greatly influenced by the orientation of the molecule with respect to the electrodes, and surprisingly, the feature has completely been lost in one of the arrangements. We provide convincing theoretical evidence for the nonexistence of the negative differential resistance feature by monitoring the shift in the transmission peak across the bias window combined with molecular projected self-consistent Hamiltonian states analyses. © 2008 American Chemical Society.