Current-voltage characteristics of trimer unit of cis-polyacetylene and fused thiophene trimer have been analyzed by employing nonequilibrium Green's functions technique. In the present investigation, both the molecular systems have thiol end group and they form a self-assembled monolayer on Au (1 1 1) surface. The current-voltage characteristics of fused thiophene trimer and trimer unit of cis-polyacetylene illustrates that negative differential resistance feature gets sufficiently improved due to the addition of heteroatom sulphur to the cis conformation. The negative differential resistance feature is observed over the bias range of ±1.6 V to ±2.45 V for fused thiophene trimer and ±2.1 to ±2.45 V for trimer unit of cis-polyacetylene. Manifestation of negative differential resistance feature has been explained by monitoring the shift in transmission resonance peak across the bias window with varying bias voltages. Modification of negative differential resistance feature due to addition of heteroatom (sulphur) to the cis configuration has been explained at the molecular level through an analysis of molecular projected self-consistent Hamiltonian states. © 2008 Elsevier B.V. All rights reserved.