Physical Sciences and Mathematics Commons^™

Predicting The Hydration Free Energy Of Small Alkanes And Alcohols From Custom, Electronic Structure-Based Force Fields, T. Ryan Rogers

Graduate Theses and Dissertations

Mathematical theories reveal the fundamental physics involved in experimentalphenomena. Computer models of such theories are routinely used to corroborate or explain experiments and predict properties of chemical systems. Therefore, an important effort in computational chemistry is the development of more accurate and efficient chemical models. Current-generation models are only beginning to approach experimental-quality predictions of hydration free energies (HFEs).Using computations of quantum mechanical (QM) forces and classical simulations based on these forces, I investigate models to predict several properties of solutes and solutions. This dissertation is a collection of projects exemplifying methods used to gain insight into chemical systems.

Simulations …

Protein Nano-Object Integrator (Pronoi) For Generating Atomic Style Objects For Molecular Modeling, Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li, Emil Alexov

Publications

Background

With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system.

Results

Here we report the Protein Nano-Object Integrator (ProNOI) which allows for …

Low Energy (E,2e) Studies From Ch₄: Results From Symmetric Coplanar Experiments And Molecular Three-Body Distorted Wave Theory, Kate L. Nixon, Andrew James Murray, Hari Chaluvadi, Chuangang Ning, Don H. Madison

Physics Faculty Research & Creative Works

Low energy experimental and theoretical triply differential cross sections are presented for electron impact ionization of methane (CH₄) for both the highest occupied molecular orbital (HOMO) and next highest occupied molecular orbital (NHOMO). The HOMO is a predominantly p-type orbital which is labeled 1t₂ and the NHOMO is predominantly s-type labeled 2a ₁. Coplanar symmetric (symmetric both in final state electron energies and observation angles) are presented for final state electron energies ranging from 2.5 to 20 eV. The theoretical M3DW (molecular three-body distorted wave) results are in surprisingly good agreement with experiment for the HOMO …