UC San Diego

Fully understanding the behavior of functional nanomaterials requires insight into atomic motion, electron delocalization, bond formation, and interparticle interactions. The resolution required to study these phenomena, particularly under experimentally relevant conditions, often exceeds the capabilities of modern nano characterization equipment. Molecular simulation offers a computational microscope with which to investigate these systems at the necessary scale. Yet for many nanomaterial systems of practical interest, the simulation infrastructure needed to gain that insight simply does not exist. This dissertation constructs missing infrastructure across three nanomaterial systems of increasing complexity, enabling mechanistic questions about these systems to be answered with molecular-scale precision for the first time.Chapter two considers the smallest system: a single conjugated polymer chain. A method to quantify the effects of intermonomer improper torsion on electron delocalization in conjugated polymers is introduced. Calculations across P3HT, PTB7, and PNDI-T reveal that improper torsion generally disrupts conjugation, though PNDI-T maintains delocalization at significant bending angles due to its extended π-system, suggesting a mechanism by which certain donor-acceptor polymers retain charge transport under strain.Chapter three scales to molecular behavior influencing a mesoscale network. Photo crosslinking in quantum dot films is modeled using molecular dynamics combined with a Monte Carlo percolation model, achieving quantitative agreement with experimental film retention data. The model reveals the mechanism by which films using ligand-type crosslinkers reach the needed film retention threshold at roughly one-quarter the UV dose of those with additive-type crosslinkers.Chapter four examines the most complex system: citrate-capped gold nanoparticles functionalized with peptides. A complete simulation framework is developed to measure aggregation free energies across a twelve-peptide series, reproducing the class distinctions observed experimentally and identifying counterion release followed by peptide bridging as the molecular mechanism of assembly.Together, these projects extend the reach of molecular simulation as a tool for nanoscale characterization, and lay the groundwork for future exploration and development.