Energy bands of a thin film containing molecular clusters are tuned by controlling the size and the charge of the clusters during thin film deposition. Using atomic layer deposition, an ionic cluster film is formed in the gate region of a nanometer-scale transistor to adjust the threshold voltage, and a neutral cluster film is formed in the source and drain regions to adjust contact resistance. A work function semiconductor material such as a silver bromide or a lanthanum oxide is deposited so as to include clusters of different sizes such as dimers, trimers, and tetramers, formed from isolated monomers. A type of Atomic Layer Deposition system is used to deposit on semiconductor wafers molecular clusters to form thin film junctions having selected energy gaps. A beam of ions contains different ionic clusters which are then selected for deposition by passing the beam through a filter in which different apertures select clusters based on size and orientation.