A Potential scenario for the implementation of molecular electronic systems is introduced by applying digital signal processing techniques to results from classical molecular dynamics simulations of a molecular system interconnected by nanosize gold clusters. Under this new scenario, signals can be introduced, processed, and read through interactions with the internal vibrational modes of the small molecular unit. We use modulation operations intrinsically inherent to any molecular system as a concept proof. As an example of this type of analysis, we focus on the individual oscillations between C-H and C-C bonds and cluster-cluster displacements.