The electron transport characteristics of Oligoaniline molecular junctions terminated with thiol-ends are analyzed with the density functional theory and the Green's function approach. The molecular junction consists of an Oligoaniline molecule attached to metal electrodes at each end. By applying an electric field, the molecule conducts a current that depends on either the molecular conformation or the ionization state. Ab initio optimization methods are performed on various Oligoaniline systems to analyze how different conformational changes are associated with different conductivities. The density functional theory and Green's function are used to calculate the density of states, transmission probability functions, and current-voltage calculations for each Oligoaniline system to complement the results from the molecular analysis. An inelastic tunneling spectrum analysis is also performed through frequency calculations to examine the different characteristics of each conducting state. Molecular orbits of each conformation was used to investigate further the relation between structure and electrical properties of the molecular junction. The combined results from the different calculations provided insight into the possible mechanisms for electron transfer throughout the junction.

The continuing scaling down in size of microelectronics devices has motivated the development of molecular electronic devices, often called moletronics, which use molecules to function as electronic devices. One of the moletronics is the programmable molecular array. In this device, disordered arrays of metallic islands are interlinked by molecules. It is addressed by a small number of input/output leads located on the periphery of the device. In this dissertation, a thorough investigation of the programmable molecular array is performed. First, theoretical calculations for single molecules are carried out. The effect of bias voltage on the electron transmission through the molecule is reported. Next, electrical measurements are conducted on programmable molecular arrays. Negative differential resistance and memory phenomena are found. The electrical characteristics of the programmable molecular array populated with different molecules indicate that the metallic islands contribute to the above phenomena. The electrical conductance through the metallic islands is investigated, and conformational change of the metallic islands under bias is reported. Furthermore, a scenario is proposed to use molecular vibronics and electrostatic potential to transport and process signals inside the programmable molecular array. Simulated results are presented.