The properties of molecular devices can be engineered through modification of the conformation of the molecule and through chemical substitution. The following study presents the results of density functional theory studies of the properties of a metal-molecule assembly resulting from the interaction between an organic molecular linker, dimercaptoacetoamidobenzene and thirteen atom "magic number" gold nanoclusters. Bonding between two gold nanoclusters, changing the conformation of the linker molecule and the effect of chemical substitution in the linker are assessed through considering the geometry and electronic structure of the resulting assemblies. Changing the conformation in the molecule leads to significant changes in the electronic structure of the metal-linker metal complex. Chemical substitution in the molecular wire also has an effect on the electronic structure; however, energy level shifts are larger for conformational changes than for chemical substitution.