Organic electronic materials, possessing conjugated π-systems, are extensively used as the active layers in organic electronic devices, where they are responsible for charge transport. In this dissertation, we employ a combination of quantum-mechanical and molecular- mechanics methods to provide insight into how molecular structure, orientation, packing, and local molecular environment influence the energetic landscape experienced by an excess charge in these organic electronic materials. We begin with an overview of charge transport in organic electronic materials with a focus on electronic polarization while discussing recent models, followed by a review of the computational methods employed throughout our investigations. We provide a bottom-up approach to the problem of describing electronic polarization by first laying the framework of our model and comparing calculated properties of bulk materials to available experimental data and previously proposed models. We then explore the effects of changing the electronic structure of our systems though perfluorination, and investigate the effects of modifying the crystalline packing through the addition of bulky functional groups while investigating how the non-bonded interactions between molecular neighbors change in different packing motifs. As interfaces are common in organic electronics and important processes such as charge transport and charge separation occur at these interfaces, we model organic-vacuum and organic-organic interfaces to determine the effect changing the environment from bulk to interface has on the electronic polarization. We first investigate the effects of removing polarizable medium adjacent to the charge carrier and then, by modeling a realistic organic- organic interface in a model solar cell, probe the environment of each molecular site at the interface to gain a more complete understanding of the complex energetic landscape. Finally, we conclude with a study of the non-bonded interactions in linear oligoacene dimers, model π-conjugated materials, to assess the impact of dimer configuration and acene length on the intermolecular interaction energy, and highlight the importance of dispersion and charge penetration to these systems.

A G-quadruplex (GQ) is a type of noncanonical nucleic acid structure that can form in regions of nucleic acids rich in guanine nucleotides. The guanine bases form a square planar conformation via Hoogsteen hydrogen bonding. These stacked tetrads have inward-facing carbonyl oxygens, facilitating the coordination of ions. Improper GQ conformations can lead to improper regulation of gene expression, potentially resulting in genetic diseases or cancer. Here, we performed molecular dynamics simulations using the Drude polarizable force field (FF) to gain insight into factors contributing to the stability of two GQs. One is the bcl-2 promoter region GQ, which is implicated in several types of cancer including B-cell lymphoma, and the second is the sc1 RNA GQ, which binds to the Fragile-X Mental Retardation Protein (FMRP) and is implicated in the development of Fragile X Syndrome (FXS). Aberrant bcl-2 GQ conformations result in increased production of the BCL2 protein, which is an apoptosis inhibitor. As such, we aim to characterize the factors stabilizing the GQ for future small-molecule development to prevent apoptosis inhibition and therefore cancer. The FMRP protein functions as a regulator of sc1 conformation to control the translation of proteins required for frontal lobe development. FXS arises from a nonsense mutation that causes the deletion of the C-terminal region of FMRP, rendering it non-function. Therefore, we aim to simulate sc1 when FMRP is bound as well as unbound to provide insight into the types of interactions that must be maintained and therefore mimicked by a small molecule drug. / Master of Science in Life Sciences / DNA is commonly represented as a double helix and RNA is thought of as a simple single stranded, disordered molecule, but DNA and RNA can both adopt more complicated structures. An example of this is the G-quadruplex (GQ), a structure that can form in regions of DNA and RNA that are rich in guanine. These guanine bases form a stable core structure that can act as an "on-off" switch for different processes in the cell. Alterations to GQ structure can lead to dysfunction and different types of disease. Here, we perform atomistic computer simulations to further understand factors that contribute to GQ stability, focusing on two different GQs, one of plays a role in several types of cancer, and the other whose regulation is in Fragile X Syndrome (FXS). Furthermore, we study the Fragile X Mental Retardation Protein, which is what brain cells normally use to regulate expression of proteins needed for frontal lobe development by modulating specific GQ structure. The information from these simulations can be used to potentially develop drugs for these conditions.