The main aim of this dissertation is to study the structure and dynamics of molecular electronic devices in vacuum and in solvent environment, with special focus on the mechanical properties and cross-section geometries of the break-junction down to the atomic level. The problem statement relies on how to overcome the limitations of observations from experiments, to interpret and reduce the gap between experiential measurements and theoretical studies. In order to reach this goal, a molecular system involving gold nano-electrodes, organic dithiol molecules and a driving-spring model has been built based on the experimental set-up of the break junction (BJ) technique. This technique can be classified as the mechanical controllable break junction (MCBJ) and scanning tunneling / atomic force microscope break junction (STM/AFM-BJ). We then generated self-assembled monolayers and molecular junctions by combining grand-canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulation. These approaches allow us to calibrate the structure and dynamics of molecular junctions under multiple environmental factors simultaneously. In the final stage, conductance calculations are performed using the density functional theory (DFT) in combination with the Green's function techniques. The intermediate molecular junction structures could be used to perform electronic transport calculations to eventually close the force-structure-conductance loop.
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