Here, we use and develop first-principles methods based on density functional theory (DFT) and beyond to understand and predict charge transport phenomena in the novel class of nanostructured devices: molecular junctions. Molecular junctions, individual molecules contacted to two metallic leads, which can be systematically altered by modifying the chemistry of each component, serve as test beds for the study of transport at the nanoscale. To date, various experimental methods have been designed to reliably assemble and measure transport properties of molecular junctions. Furthermore, theoretical methods built on DFT designed to yield quantitative agreement with these experiments for certain classes of molecular junctions have been developed. In order to gain insight into a broader range of molecular junctions and environmental effects associated with the surrounding solution, this dissertation will employ, explore and extend first-principles DFT calculations coupled with approximate self-energy corrections known to yield quantitative agreement with experiments for certain classes of molecular junctions.;To start we examine molecular junctions in which the molecule is strongly hybridized with the leads: a challenging limit for the existing methodology. Using a physically motivated tight-binding model, we find that the experimental trends observed for such molecules can be explained by the presence of a so-called "gateway" state associated with the chemical bond that bridges the molecule and the lead. We discuss the ingredients of a self-energy corrected DFT based approach to quantitatively predict conductance in the presence of these hybridization effects.;We also develop and apply an approach to account for the surrounding environment on the conductance, which has been predominantly ignored in past transport calculations due to computational complexity. Many experiments are performed in a solution of non-conducting molecules; far from benign, this solution is known to impact the measured conductance by as much as a factor of two. Here, we show that the dominant effect of the solution stems from nearby molecules binding to the lead surface surrounding the junction and altering the local electrostatics. This effect operates in much the same way adsorbates alter the work function of a surface. We develop a framework which implicitly includes the surrounding molecules through an electrostatic-based lattice model with parameters from DFT calculations, reducing the computational complexity of this problem while retaining predictive power. Our approach for computing environmental effects on charge transport in such junctions will pave the way for a better understanding of the physics of nanoscale devices, which are known to be highly sensitive to their surroundings.
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