Probing and controlling the configurations and mechanical motions of the azobenzenes adsorbed on the metal substrates are preliminary for their applicability in various functional devices. In this work, we presented a detailed investigation of Raman properties of the dimercaptoazobenzene (DMAB) bound to gold nanoclusters using density functional calculations. It is demonstrated that the spectral features of the trans conformation of DMAB are quite different from the cis conformation, and the Raman intensities of the trans-DMAB are much larger. Magnitude of chemical enhancement for the adsorbed trans-DMAB is found to be close to or less than that for the adsorbed cis-DMAB for the molecule–cluster complexes. This change trend can be, to a large extent, governed by the energy difference between the highest occupied energy level of the molecule and the lowest unoccupied energy level of the gold. Moreover, it is further demonstrated that differences in Raman intensities of the two conformations can be amplified for the cluster–molecular–cluster junctions, and thus chemical enhancement is much larger for the trans conformation than the cis conformation, possibly facilitating the experimental identification of the trans/cis DMAB. Copyright © 2012 John Wiley & Sons, Ltd.