Computational Chemistry Commons^™

Consequences Of Oxidative Dna Damage: Base-Pair Dissociation, Singlet Oxygenation And Dna-Protein Crosslinking, May Myat Moe

Dissertations, Theses, and Capstone Projects

8-Oxo-2′-deoxyguanosine (OG) is a common DNA lesion resulting from oxidatively generated damage and pairs with complementary cytidine (C) in Watson Crick base-pairing within duplex DNA. The WC-OG·C lesion, if not recognized or repaired, not only leads to G⋅C→T⋅A transversion mutations (through Hoogsteen (HG) base pairing of OG⋅A), but also renders the base pair being more vlunerable to ionizing radiation and singlet oxygen (1O2) damage. Leveraging on our previous accomplishments on the study of gas-phase reactions of 1O2 with 2′-deoxyguanosine radical cations, my research thesis expanded to the investigation of reaction dynamics of 9-methyl-8-oxoguanine (9MOG) radical cations. The experiments of following …

Investigating Dna Damage Caused By Reactive Oxygen And Nitrogen Species Via Guided-Ion-Beam Scattering And Computational Techniques, Jonathan Benny

Dissertations, Theses, and Capstone Projects

Among DNA nucleobases, guanine (G) is the primary target for one-electron ionization and oxidation, generating G●+ through various processes, including photooxidation, electrocatalytic oxidation, DNA-binding transition metals, ionizing radiation, and photolysis. This is due to the low adiabatic ionization potential and oxidation potential of guanine. Electron holes from other nucleobases can move to guanine, proving that G●+ production traps oxidative DNA damage. G●+ formation can exacerbate DNA damages and cause secondary reactions from reactive oxygen species (ROS) and reactive nitrogen species (RNS) during pathological processes. The following three projects were conducted using a customized electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer, …

Studies On The Synthesis, Function, And Properties Of Troponoids, John-Charles A. Baucom

Dissertations, Theses, and Capstone Projects

Troponoids are a unique class of non-benzenoid aromatic compounds with a wide range of demonstrated applications in pharmaceuticals and molecular sensing. The cycloheptatrienone scaffold possesses a noteworthy degree of tunability as a function of ring oxygenation. This manuscript describes our efforts toward a better understanding of the physical consequences of the scaffold to better utilize the motif. Chapter the first discusses our efforts at elucidating the mechanism of troponoid inhibition of the Hepatitis B virus reverse transcriptase RNAse H enzymatic domain. Using homology modeling in conjunction with traditional in vitro assays we were able to establish the likely mechanism of …

Solvation Thermodynamic Mapping Approaches For Computer-Aided Drug Discovery, Vjay Molino

Dissertations, Theses, and Capstone Projects

The drug discovery process is inherently long and costly, prompting the development and integration of computational tools to mitigate these challenges. One of area explored in computer-aided drug discovery is to understand the role of solvation in protein-drug binding and to develop computational tools and methods that can be integrated in the drug discovery process. Grid Inhomogeneous Solvation Theory (GIST) is a tool that provides a framework for mapping solvation thermodynamiproperties of water molecules on the protein surface.This thesis explores the use of GIST in generating pharmacophore models and elucidates the role of solvation in protein structural fluctuations.

One of …

Novel Alchemical Methodologies For Modeling Molecular Binding, Solmaz Azimi

Dissertations, Theses, and Capstone Projects

Molecular recognition is fundamental to all biological and biochemical processes. Understanding the interactions between molecules is the foundation for drug discovery and development, for understanding biological processes, and for the design of biosensors and nanomaterials. There is tremendous interest in the development of computer models to predict molecular association equilibria. In structure-based drug discovery enterprises, predicting the strength and selectivity of a small molecule to a biological target can advance target identification, aid ligand design, and accelerate high-throughput screening of drug compounds. This work focuses on free energy models, a class of computational methodologies grounded on the fundamental physical and …

The Role Of Confined Hydration And Water Reorganization In Molecular Binding, Joe Z. Wu

Dissertations, Theses, and Capstone Projects

An important factor in guiding the development of drug discovery efforts is the comprehensive assessment of a ligand or drug’s ability to bind its receptor. The metric used to measure this interaction strength is by calculating the binding free energy (BFE). To achieve this accurately, we combine two concepts: (1) Grid Inhomogeneous Solvation Theory (GIST) returns the local water thermodynamic and structural contributions to free energy; and the (2) Alchemical Transfer Method (ATM) obtains the absolute (ABFE) and relative binding free energy (RBFE) estimates between ligand pairs. In this work, we employ Alchemical Water-Transfer to tether bridging water(s) during the …

In Memoriam - Nora Sabelli: Master Orchestrator Of Grant Programs And Mentor For Advancing The Interdisciplinary Learning Sciences Field, Eric Hamilton, Jeremy Roschelle, Roy Pea, Barbara Means, Louis Gomez, Kim Gomez, Nancy Butler Songer

Education Division Scholarship

On Friday, September 6, 2024, the learning sciences field lost a giant in Dr. Nora Sabelli, 87 years old, a personal mentor to many researchers and an inspiration to so many learning scientists and STEM leaders. Nora’s first professional career was as a computational chemist, and later she became a passionate leader in research for improving STEM education. Nora’s time as a senior program officer at the National Science Foundation’s (NSF) Education and Human Resources (EHR) directorate was legendary; she was a force of nature who reshaped funding priorities for stronger science and a stronger connection of science to education …

Synthesis And Characterization Of Bimetallic Plasmonic Nanoparticles Using Linear And Nonlinear Spectroscopy, Daniel Babayode

LSU Doctoral Dissertations

Recent exploration in the field of nanomaterials has led to the investigation of noble metal nanoparticles for various nanomedical applications. The spectroscopy of these nanoparticles is studied using both linear and nonlinear optical processes such as second harmonic generation (SHG), two-photon fluorescence (TPF), and extinction spectroscopy. Details pertaining to the growth dynamics of silver-gold core-shell (Ag@Au CS) nanoparticles (NPs) and gold-silver-gold core-shell-shell (Au@Ag@Au CSS) nanoparticles (NPs) are currently being investigated in order to obtain better control and optimization of the nanoparticle size and surface morphology. Transmission electron microscopy (TEM) images show that the nanoparticles have tunable core and shell sizes …

Functionalized 2d Hexaazatriphenylene As Hydrogen Storage Platform: A Dft-Guided Design Approach, Islam Gomaa

Nanotechnology Research Centre

No abstract provided.

First-Principles Modeling Of Nitazoxanide Analogues As Prospective Pfor-Targeted Antibacterials, Islam Gomaa

Nanotechnology Research Centre

Pyruvate:ferredoxin oxidoreductase (PFOR) is a key Achilles’ heel in anaerobic pathogens. We integrate electronic-structure calculations (DFT), cheminformatic QSAR metrics, and residue-resolved docking to distill a concise “recognition code” and translate it into practical design rules. Using nitazoxanide (Nita; ΔG(bind) ≈ −10.0 kcal·mol−1) as a well-established reference, productive binding requires a conserved triad: a hydrogen-bond donor addressing Thr-997 and Cys-840, a π–π stack with Phe-869, and a recurrent π–σ contact to Thr-997 that orients the scaffold. Deacetylation to tizoxanide unmasks the phenolic donor and raises local electrophilicity, yet it also slightly loosens pocket packing (−9.6 kcal·mol−1). Strategic halogenation introduces a σ-hole …

Structure–Property Relationships Mediated By Lone Pairs And Vacancies In Oxychalcogenides: A Combined Experimental And Theoretical Study, Hoa Hn Nguyen

Chemistry & Biochemistry Dissertations - Archive

Structure–property relationships in some oxychalcogenide materials are strongly governed by the interplay between stereochemically active lone pairs and anion vacancy formation. Through a combination of density functional theory (DFT), synchrotron and neutron total scattering and optical characterization, this work elucidates how local symmetry breaking, chemical substitution, and vacancy dynamics influence electronic and optical behavior across several lone pair-containing systems. In crystalline TeO₂, all three polymorphs exhibit wide band gaps with Te⁴⁺ 5s² lone pairs contributing significantly near the valence band edge. Oxygen vacancy formation is thermodynamically favorable and induces asymmetric charge redistribution and enhanced polarizability, supporting …

Demystifying Misconceptions In Introductory Undergraduate Chemistry Education With 3d Printed Molecular Orbitals, Hiwot Endeshaw, Daniel J. O'Leary

Pomona Senior Theses

Spatial abilities are invaluable skills for the science, technology, engineering, and mathematics (STEM) subjects. However, women, people from low socioeconomic backgrounds, and ethnic minorities are more likely to have less developed spatial abilities, which is one of the many contributing factors for the lack of diversity in STEM subjects like chemistry. Teaching spatial skills to undergraduate chemistry students may address this issue and help increase the diversity of students who go on to continue their education in the subject. 3D printing technology in higher education has exploded in recent years, presenting a unique opportunity to teach “hard to grasp” concepts …

Phytochemistry Of Dalea Candida Var. Oligophylla, Ryan E. Galperin

All Master's Theses

The focus of this project was the plant Dalea candida and its phytochemistry. The plant compounds were isolated and purified by an array of chromatographic techniques. The structures of the pure compounds were determined by one-dimensional and two-dimensional ¹H and ¹³C NMR spectroscopy, supported by infrared and ultraviolet spectroscopy, experimental and calculated circular dichroism spectroscopy, and mass spectrometry. Plant parts were worked on separately since they typically differ in content. Purified compounds will be tested for biological activities. Based on our results, eight new or known compound were isolated, specifically four new compounds and four known compounds. Compound …

Investigation Of The Binding Mechanism Between The Supplemental And Tail Regions Of Mirna And Mrna Within Argonaute 2, Christina Ms Karadiakos

Electronic Theses & Dissertations (2024 - present)

MicroRNAs (miRNA) are a class of small non-coding RNAs that play a key role in gene silencing. miRNAs form an RNA-induced silencing complex (RISC) with the argonaute 2 (AGO2) protein in order to control gene expression through silencing messenger RNAs (mRNA). The ability for a miRNA-mRNA complex to fit into AGO2 and form the RISC is based on the location and characteristics of a central bulge, but the mechanism and interactions that lead to a functional RISC remain unknown. Using available experimental data, we modeled the miR-34 and NOTCH1 duplex inside of AGO2 with only the seed region base paired. …

Towards Developing Glut2 Specific Probes For Biochemical And Biomedical Applications, Abdelrahman Ismail

Dissertations, Master's Theses and Master's Reports

Facilitated Glucose transporters (GLUTs) are membrane proteins responsible for the uptake of simple sugars and other structurally similar metabolites in all mammalian cells. One of the hallmarks of cancer is dysfunctional sugar metabolism, known as the Warburg effect, and one of the manifestations of that effect is abnormal GLUT expression. There are 14 known GLUT proteins with different expression patterns in different tissues, and tumors tend to express certain GLUTs that are not present in surrounding healthy tissue. Therefore, selective targeting of GLUTs presents a potentially powerful tool for diagnostics and treatment of cancer and other diseases. This has been …

Beyond The Phonon Gas Model (Pgm): Unraveling The Unique Mechanistic Processes Dictating Thermal Transport In Highly Anharmonic And Disordered Materials, Sandip Thakur

Open Access Dissertations

Thermal transport in nonmetallic solids has traditionally been described by the phonon gas model (PGM), in which heat is carried by weakly interacting phonon quasiparticles in an ordered crystalline lattice. However, this model breaks down in materials characterized by strong anharmonicity, dynamic disorder, or structural complexity, features prevalent in many next-generation materials used in energy conversion, optoelectronics, and thermal management. This dissertation investigates thermal transport in such complex materials, including metal halide perovskites (MHPs), covalent organic frameworks (COFs), metal organic frameworks (MOFs), and 2D-3D heterostructures, through large-scale molecular dynamics (MD) simulations and frequency-resolved spectral analyses.

In MHPs, the work reveals …

Individual And Collective Properties Of Tunable Photochemical Belousov-Zhabotinsky Micro-Reactors, Kudakwashe Benedict Shumba

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell-like model chemical systems are powerful tools that can be used to explore the role of intercellular coupling on population level behaviors in communities of biological cells. Firstly, we present a new method for fabricating such micro-reactors using the photosensitive Belousov–Zhabotinsky (BZ) reaction system employed in silica microparticles. These BZ micro-reactors have a tunable response to photochemical coupling, varying from a fully excitatory response to a fully inhibitory response. Their response can be tuned through variations in either the reactive mixture or, on an individual micro-reactor level, by changes in the synthesis temperature used during the fabrication of the silica …

Rational Design Of Small Molecules Targeting Mitochondrial Redox Proteins, Matheus Barbosa Belchior

Graduate Theses, Dissertations, and Problem Reports (ETD)

Reactive oxygen species play a crucial role in many cellular processes. Despite being a natural byproduct of cellular metabolism, overexpression of these species causes damage to the cell, leading to cell dysfunction. Central to the regulation of these highly reactive molecule is the mitochondria. Impairment in its function has been associated with oxidative stress within the cell. Herein, a ligand-based and structure-based approach to design new small molecules to inhibit mitochondrial redox proteins associated with oxidative stress and reactive oxygen species. In the first project two molecules were synthesized and characterized as potential monoamine oxidase B inhibitors. Results showed two …

Multiscale Computational Chemistry Studies Of The Catalytic Mechanisms Of Non-Heme Fe(Ii)/2-Oxoglutarate-Dependent Oxygenases, Simahudeen Bathir Jaber Sathik Rifayee

Dissertations, Master's Theses and Master's Reports

Enzymes catalyze complex biological transformations. Non-heme Fe(II)/2-oxoglutarate (2OG)–dependent enzymes are highly versatile catalysts capable of selective C–H oxidation, enabling transformations such as hydroxylation, halogenation, desaturation, demethylation, ring rearrangements, epoxidation, and electrophilic aromatic substitution. These enzymes are involved in various biological processes, including fatty acid metabolism, hypoxic signaling, collagen maturation, and transcriptional regulation. Computational Modeling provides detailed knowledge of the enzymes including atomistic details of the important catalytic species, conformational and electronic effects, which are crucial to enzyme engineering and drug design efforts. This dissertation implements advanced multi-scale molecular modelling techniques including Molecular dynamics and Quantum Mechanic / Molecular Mechanics calculations …

Towards Automating The Study And Discovery Of Electroactive Π-Conjugated Molecules, Rebekah Ann Duke-Crockett

Theses and Dissertations--Chemistry

Chemistry is entering a new paradigm of automation and data-driven discovery. Automated discovery is grounded in well-curated “big data.” As generative and predictive models fueled by simulation data see growing success, emerging robotic automation enables the generation of unprecedented volumes of experimental data. Automation-powered, data-driven approaches hold tremendous potential for groundbreaking insights and innovations, particularly in the study and discovery of electroactive π-conjugated molecules. Realizing this potential, however, requires democratizing chemical data and the automation needed to generate and use it. There is a need to expand access to the tools for findable, accessible, interoperable, and reusable (FAIR) data management …

Machine Learning Models For Molecular-Based Functional Organic Materials, Moses Ogbaje

Theses and Dissertations--Chemistry

Organic semiconductors (OSC) are of interest for a wide range of flexible optoelectronics applications, including transistors, solar cells, and sensors, to name a few. Despite their promise, the design and optimization of OSC pose significant challenges due to the complexity of the structures of the molecular building blocks, varied packing configurations of these building blocks in the solid state, which impacts the optical and electronic response, and sensitivity of the solid-state packing to material processing conditions. Accurately predicting the solid-state properties of OSC traditionally requires high-level quantum mechanical methods. These methods, however, can be computationally demanding, particularly for large molecules …

Investigation Of Protein-Ligand Binding Interactions Through The Computational Methods Of Molecular Dynamics And Graph Neural Networks, Alexander Benjamin Wroe

Graduate Theses, Dissertations, and Problem Reports (ETD)

Studies in protein ligand binding are a significant focus in the field of medicinal chemistry

and biochemistry, facilitating a greater understanding of the structure-function relationship

of the protein and controlling function via drug development. In this research, we identify

new binding sites for lipids on the microbial membrane protein, proteorhodopsin, and apply

machine learning approaches to accelerate the generation of binding affinity-like data for the

use in the identification of potential small molecule drugs. The platelet activating factor

receptor. Cardiolipin, a lipid in membranes, and proteorhodopsin, a microbial proton pump,

are both commonly found in microbial membranes, but little is …

Unraveling The Reactivity Of Nitrate Ester Explosives: Insights From Femtosecond Time-Resolved Mass Spectrometry And Computational Chemistry, Erica Britt

Theses and Dissertations

This dissertation uncovers the ultrafast molecular mechanisms underlying the decomposition of nitrate ester explosives—nitroglycerin (NG), ethylene glycol dinitrate (EGDN), and amyl nitrate—through the integration of femtosecond time-resolved mass spectrometry and advanced computational chemistry. Although these compounds play fundamental roles in both military and civilian contexts, the precise molecular dynamics governing their pronounced reactivity and impact sensitivity have remained inadequately characterized. Our research establishes that low O–NO2 bond dissociation energies are the primary driver of ultrafast fragmentation and high reactivity in all three esters. The distinctive molecular architectures of these esters dictate their explosive properties: NG’s tri-nitrate configuration leads to exceptional …

Contributions To Journal Of Electrochemistry, The Flagship Journal Of Chinese Chemical Society Electrochemical Committee, Will Be Listed As A New Recommendation Policy For China Youth Awards Of Electrochemist, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Intrinsic Gas-Phase Behavior Of Uranium Species: A Comprehensive Reactivity Study Of [O=U≡Ch]+ And [Uh]+, Justin Terhorst

Electronic Theses and Dissertations

The intrinsic chemistry of actinide elements, particularly uranium, remains a key challenge in understanding f-block reactivity due to the complexity introduced by solvent interactions, counter-ions, and complex equilibria in the condensed phase. In this dissertation, a systematic gas-phase study utilizing preparative tandem ion-trap mass spectrometry (PTMSⁿ) is presented, focusing on the reactivity of uranium-centered species, specifically [OUCH]⁺, an oxy uranium methylidyne species, and [UH]⁺ ions. By stripping away solvent effects and isolating the ions, PTMSⁿ provides a powerful platform to probe the fundamental chemical behavior of uranium species in their intrinsic state.

The …

Rna Structural-Dynamical Hierarchy: Sars-Cov, Sars-Cov-2, And Delta/Omicron Variant S2m Monomers, Kissing Complexes, And Extended Duplexes, Adam Kensinger

Electronic Theses and Dissertations

The power and promise of ribonucleic acid (RNA) molecules are only beginning to be realized in living organisms and pharmaceutical intervention. Specifically, defining the chemical physics of RNA’s heterogenous structural ensemble and dynamics, which has experienced expansive growth over the last few years, is central to a complete understanding, yet continues to be a significant challenge. A 41-nucleotide hairpin called the stem-loop II motif (s2m), present in the viral genomes of severe acute respiratory syndrome (SARS), SARS-coronavirus-2 (SARS-CoV-2), and the Delta and Omicron variants responsible for the COVID-19 pandemic, is a potential antiviral target due to its high sequence conservation …

Assembly Of Ppsu-Oligomers, Mariam Nesterov

Student Theses and Dissertations

The development of nanostructures for delivering multiple proteins to targeted antibodies has become a promising avenue in biotechnology, driven by advancements in synthetic polymers like poly(propylene sulfone), PPSU. However, the PPSU polymer faces a major limitation - its high insolubility. To address this challenge, this study investigates whether PPSU oligomers can enhance both the solubility and stability of lysozyme, a model protein that is cost-effective and widely accessible. Using dimer, trimer, tetramer, and hexamer configurations, we analyzed the interactions between PPSU oligomer and lysozyme under varying conditions. Our results show that the dimer and trimer are water soluble (no aggregate …

Computational Logp Calculations And Determination Of Lipophilicity Values Of Fluorinated Morphine Derivatives, Mirabella Romano, Allison Vu, Emily Chen

Student Scholar Symposium Abstracts and Posters

The addictive effect of opioids impacted 60 million people globally in 2023. This opioid crisis necessitates the development of opioid derivatives that maintain analgesic efficacy while minimizing addictive effects from opioid use. The present work focuses on morphine, a commonly prescribed opioid with high affinity to the mu-opioid receptor (MOR). Morphine binds non-selectively within both healthy and inflamed tissue. By modifying morphine’s structure through fluorination to counteract its non-selective binding, the drug’s pharmacological ability to provide effective pain relief comes with a lower risk of addiction. Specifically, the addition of fluorine to differing beta positions of the main binding site …

Theoretical Investigation Of Hydrogen Abstraction From Fluorinated Propanones And Fluorinated Propanals, Laurel Washburn

Honors Theses

Per- and polyfluoroalkyl substances (PFAS) are a class of thousands of industrially used compounds often called “forever” chemicals because of their slow degradation process that leads to accumulation in soil, dust, drinking water, and the body. PFAS are used for their grease and water resistance properties but some of these compounds are toxic at extremely low levels. To better understand the effects of these types of compounds, the main pathways of their degradation need to be further investigated. This study analyzes computationally the hydrogen abstraction reactions by both hydroxyl radical and triplet oxygen atom for all possible fluorinated propanones and …

Nuclear Fuel Cycle Chemistry: A Density Functional Study, Eduardo Montoya

UNLV Theses, Dissertations, Professional Papers, and Capstones

The nuclear fuel cycle aptly describes the life cycle of nuclear fuel sources such as uranium. From its early forms in naturally bearing ores, to its high-temperature sintering into a fuel pellet, the chemistry uranium experiences throughout the fuel cycle is diverse, driving many experimental efforts towards understanding its chemistry to both improve nuclear technologies and advance the safety and handling of nuclear materials. Computing techniques and methodologies can be used to supplement experimental research and are readily available to researchers interested in utilizing computing-based data to support experimental findings. Density functional theory (DFT) is commonly practiced, reliably predicting the …