Chemistry Commons^™

On The Origins Of Life — Modelling The Initial Stages Of Complex Coacervate Droplet Formation, Yixuan Wu

Western Libraries Undergraduate Research Awards (WLURAs)

Coacervate droplets are considered a plausible model for protocells due to their spontaneous formation and ability to compartmentalize macromolecules such as nucleic acid and peptides. Although experimental studies have observed and synthesized coacervates under different laboratory conditions, little is known about their structure. Here we present atomistic molecular dynamic simulations of the interactions between water and oppositely charged proteins that cluster together in a salt-dependent process. Observing such liquid-liquid phase separation on an atomic level would serve as a model for the initial stages of complex coacervate formation. Molecular Dynamics was used to compute diagnostics of the structure at different …

Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers

Legacy Theses & Dissertations (2009 - 2024)

Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …

Mechanism Of Action Of Dihydropteridine Reductase, Gabriela Arias De La Rosa

Dissertations, Theses, and Capstone Projects

Human dihydropteridine reductase is an enzyme that transfers a hydride from NADH to reduce quinonoid 7,8-dihydropterin (qBH₂) to 5,6,7,8-tetrahydropterin (BH₄), which is a cofactor important in the production of neurotransmitters.DHPR deficiency causes a drastic form of the neurological genetic disease phenylketonuria (PKU) that does not benefit from a phenylalanine-free diet.From site-directed mutagenesis studies, mostly on Rat DHPR, we know that certain residues are important for cofactor binding, substrate binding, and hydride transfer; however, there are still some questions about how DHPR works, particularly, because there is not a crystal structure of the tertiary complex: What is …

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 …

Concerted Hydrogen-Bond Breaking By Quantum Tunneling In The Water Hexamer Prism, Jeremy O. Richardson, Cristobal Perez, Simon Lobsiger, Adam A. Reid, Berhane Temelso, George C. Shields, Zbigniew Kisiel, David J. Wales, Brooks H. Pate, Stuart C. Althorpe

Faculty Journal Articles

The nature of the intermolecular forces between water molecules is the same in small hydrogen-bonded clusters as in the bulk. The rotational spectra of the clusters therefore give insight into the intermolecular forces present in liquid water and ice. The water hexamer is the smallest water cluster to support low-energy structures with branched three-dimensional

hydrogen-bond networks, rather than cyclic two-dimensional topologies. Here we report measurements of splitting patterns in rotational transitions of the water hexamer prism, and we used quantum simulations to show that they result from geared and antigeared rotations of a pair of water molecules. Unlike previously reported …

Importance And Reliability Of Small Basis Set Ccsd(T) Corrections To Mp2 Binding And Relative Energies Of Water Clusters, Berhane Temelso, Carla Renner, George Shields

Berhane Temelso

MP2 describes hydrogen-bonded systems well, yet a higher-order electron correlation correction in the form of a CCSD(T) calculation is usually necessary to achieve benchmark quality energies. We evaluated the importance and reliability of small basis set CCSD(T) corrections to MP2(δCCSD(T)) both on the binding (ΔE) and relative (ΔΔE) MP2 energies for a large number of systems including four water dimer stationary points and 57 other clusters up to undecamers, (H2O)11. By comparing the MP2 energies with CCSD(T) and the explicitly correlated MP2-F12 energies with variants of CCSD(T)-F12 using different basis sets, we were able to establish that the correction to …

Computational Study Of The Hydration Of Sulfuric Acid Dimers: Implications For Acid Dissociation And Aerosol Formation, Berhane Temelso, Thuong Ngoc Phan, George C. Shields

Berhane Temelso

We have investigated the thermodynamics of sulfuric acid dimer hydration using ab initio quantum mechanical methods. For (H2SO4)2(H2O)n where n = 0−6, we employed high-level ab initio calculations to locate the most stable minima for each cluster size. The results presented herein yield a detailed understanding of the first deprotonation of sulfuric acid as a function of temperature for a system consisting of two sulfuric acid molecules and up to six waters. At 0 K, a cluster of two sulfuric acid molecules and one water remains undissociated. Addition of a second water begins the deprotonation of the first sulfuric acid …

Computational Study Of The Hydration Of Sulfuric Acid Dimers: Implications For Acid Dissociation And Aerosol Formation, Berhane Temelso, Thuong Ngoc Phan, George C. Shields

Faculty Journal Articles

We have investigated the thermodynamics of sulfuric acid dimer hydration using ab initio quantum mechanical methods. For (H₂SO₄)₂(H₂O)_n where n = 0−6, we employed high-level ab initio calculations to locate the most stable minima for each cluster size. The results presented herein yield a detailed understanding of the first deprotonation of sulfuric acid as a function of temperature for a system consisting of two sulfuric acid molecules and up to six waters. At 0 K, a cluster of two sulfuric acid molecules and one water remains undissociated. Addition of a second …

Band Structures Of Layered Carbon/Boron Nitride Materials With Commensurate Lattices, Christopher C. Wells

Legacy Theses & Dissertations (2009 - 2024)

The electronic structures of systems consisting of hexagonal boron nitride layers and graphite sheets have been investigated in detail using density functional theory methods with two exchange correlation functions (local density approximation and generalized gradient approximation). The experimental data of graphene, graphite, monolayer hexagonal BN, and hexagonal BN were reproduced well with computational models. The commensurate models used in the investigation were generated by taking the averages of the lattice constants for graphite and h-BN.