Physical Sciences and Mathematics Commons^™

Computational Study About Noncovalent Bonding Systems Involving Halogen, Chalcogen And Pnicogen Bonds, Jia Lu

All Graduate Theses and Dissertations, Fall 2023 to Present

First terms used in this thesis are introduced and defined as follows. In the periodic table, the elements in the 17^th column are named halogen including fluorine (F), chlorine (Cl), bromine (Br) and iodine (I). The elements in the 16^th column are named chalcogen including oxygen (O), sulfur (S), selenium (Se) and tellurium (Te). The elements in the 15^th column are named pnicogen including nitrogen (N), phosphorus (P), arsenic (As) and antimony (Sb).

After hydrogen bonds (B-H⋅⋅⋅B) are well studied and understood by scientists and researchers, halogen bonds (R-X⋅⋅⋅B) have drawn attention due to the similarities in …

Designing And Studying Redox-Active Molecules For Energy Storage And Desalination, Wenda Wu

All Graduate Theses and Dissertations, Fall 2023 to Present

Since the fast growth of the global population, energy scarcity has become a new threat to modern society. Those commonly seen resources like fossil, coal, and natural gas are nonrenewable energies, which cannot be replenished by human-scale time. In contrast, wind, solar, and hydropower are the three main renewable green energies under development with great efforts around the world. However, the intermittent character of these powers raises a new question: how to store them properly on large scales? By 2021, more than 90% of the electricity storage was taken by Lithium-ion batteries (LIBs). The usage of lithium brings concerns about …

The Concept Of Multicenter Bonds In Chemistry And Materials Science, Nikolay V. Tkachenko

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chemical bonds are components of a universal and compact language of chemistry that was empirically developed before the modern concepts of quantum physics. This language explains how molecules and solids keep together. In particular, Lewis’s shared electron-pair bonding model may be considered the most successful and generally accepted theory of chemical bonding due to its simplicity and predictive power. However, there is an entire world of chemical species where the classical Lewis bonding language fails to describe the bonding pattern adequately. Those cases include but are not limited to compounds with a significant electron delocalization (where electron density spread on …

Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Similarly to people, bacteria are under the treat of infection by viruses. To circumvent these threats, bacteria evolve complex immune systems. Our understanding of some of these immune systems has led to many advancements in the field of Biotechnology including tools that made expressing proteins for study in a lab easier, tools that revolutionized the feasibility of gene editing, and tools that could change the way we think about viral diagnostics and cancer therapeutics. A certain type of immune system that bacteria use to fight virus is called a CRISPR system. Presented here is work to understand the function of …

Investigations Of Prokaryotic Defense Systems, Hannah Domgaard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bacteria are constantly threatened with infection by mobile genetic elements (MGE) such as bacteriophage and plasmids. Bacteriophage and plasmids require the bacteria's cellular infrastructure to replicate their genomes. Rampant replication can lead to cell death which is one reason why bacteria have developed a diverse array of immune systems to prevent or limit infection. This thesis studies three types of bacterial immune systems, type IV-A CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeat –CRISPR associated), type V-A2 CRISPR-Cas systems, and Wadjet systems.

The type IV-A system lies adjacent to a dinG-like helicase gene. Research has shown that this system can target …

Development Of In Situ Second-Order Nonlinear Optical Scatterings For Molecular Behaviors At Aerosol Surfaces, Yuqin Qian

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Aerosol particles are one of the most important components of the atmosphere. During the growth of aerosol particles, they directly or indirectly affect air quality, human health, and environmental chemistry. Therefore, understanding the chemical and physical properties of such particles is an important scientific, engineering, and medical issue. The growth of aerosol particles in the atmosphere is closely related to the chemical structure at its surface, as well as the heterogeneous reactions which take place at and below the particle’s surface. However, there is a lack of suitable surface-specific analytical techniques which directly measure the chemical structure of aerosol particle …

Pesticide-Leaf Interactions And Their Implications For Pesticide Fate Modeling, Ashlie Kinross

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work described here provides measured data to improve the understanding of the interaction between a pesticide and leaf surface after application. Two methods were developed, one using a newly introduced instrument, for the extraction of pesticides from leaves. This is required to measure the concentration of pesticide in the leaves. Using one of the developed extraction methods, measurements were made to determine how a pesticide equilibrates between a leaf and the air above it. These measurements were incorporated into a pesticide fate model that predicts how a pesticide moves through the environment after application to an agricultural field. The …

Stability, Electronic Structure, And Nonlinear Optical Properties In Clusters And Materials: A Synergistic Experimental-Computational Analysis, Maksim Kulichenko

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The main objective of Chemistry as a science is an understanding of how and why certain atoms are bonded together and what effects these bonds cause. Modern computational chemistry offers a wide range of tools that greatly assist the exploration of vast chemical space replacing expensive trial-and-error experimental approaches. Computational chemistry may serve to characterize newly synthesized compounds and provide atomic scale insights inaccessible to experimentalists’ vision. Moreover, predictive power of computational chemistry may be used as a guidance for future experiments and for the rational design of new compounds with desired properties.

This dissertation demonstrates the capabilities of joint …

Designing And Decoding Chemical Bonds: A Computational Pipeline Backed Up By Magnetic Criteria And Experiment, Nikita Fedik

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

You may find plenty of definitions of chemistry but all of them, explicitly or not, are centered around chemical bonds. When we say “chemical properties”, “reactivity”, “stability”, “structure” etc., we have in mind chemical bonds and their reorganization which almost completely defines the behavior of the matter. Why some materials are ultrahard and can cut through steel while others are so soft that you can form them with your bare hands? You probably have already guessed that it occurs because their chemical bonding is very different. Although the elemental composition could be the same! In this Dissertation, we report results …

Foliar Photodegradation In Pesticide Environmental Modeling, Sean M. Lyons

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work described here was conducted to better understand how pesticides will behave following their application to crops or soil. This understanding will allow for better use of pesticides which will protect the environment and non-target organisms while remaining effective against pests. The Pesticide Dissipation form Agricultural Land (PeDAL) model was developed to simulate pesticide behavior following application and laboratory experiments focused on the photodegradation of select pesticides on alfalfa leaves were conducted to support this model.

Renewable Energy Conversion: Organic Redox Flow Batteries And Electrocatalytic Carbon Dioxide Reduction, Camden R. Debruler

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Steadily increasing global energy demands have pushed the industry to investigate renewable energy sources like solar and wind to help alleviate the strain on fossil fuel based non-renewable energy sources while also reducing carbon emissions. However, the energy producing power of these renewable technologies is limited by factors such as weather and the day-night cycle. Additional energy storage technologies are needed which are capable of storing excess energy during periods of high productivity, and delivering it when production rates fluctuate.

Batteries represent one possible energy storage device to meet this need. Specifically, redox flow batteries (RFBs) offer advantages in terms …

Developing Advanced Electrodes And Electrolytes For Energy Storage Beyond Li Ion Batteries, Kevin V. Nielson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Electric vehicles, smart phones, and portable computers are all powered by lithium-ion batteries. This is because Li-ion batteries can store more energy in less space than other battery technologies. Also, they are rechargeable and last for a long time. The most recent 2019 Nobel prize in chemistry was awarded to John Goodenough, M. Stanley Whittingham and Akira Yoshino “for the development of lithium-ion batteries”. Through their work, they have made possible cars that do not burn fossil fuels and phones that are wireless and portable. Not only can Li-ion power your phone, it is an incredibly efficient way to store …

Materials Design For High-Performance Organic Redox Flow Batteries And Electrocatalytic Carbon Dioxide And Nitrogen Reduction, Bo Hu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nowadays, the utilization of renewable energy resources such as solar and wind energy has been realized to be a sustainable and environmentally benign strategy to alleviate the world’s severe dependency on traditional fossil fuels, and thus enables the environmental recovery and sustainable development of the economy. The massive commercialization of solar and wind energy raises the demands for advanced energy storage technologies, among which the redox flow battery has been recognized as a promising solution due to it is low cost, safe, environmentally benign, and easy to be scaled up. All vanadium redox flow battery stands for the most important …

Cost-Effective Synthesis, Bioactivity And Cellular Uptake Study Of Aminoglycosides With Antimicrobial And Connexin Hemichannel Inhibitory Activity, Yagya P. Subedi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Amphiphilic kanamycin is one of the promising class of compounds for the treatment of fungal infections in plants and animal. Factor that lead to the restricting of compounds for commercialization includes, the higher cost of production and poor stability of the compound. However, the new lead, identified from the synthesis and biological testing, can be synthesized on a large scale with a cost comparable to commercial antifungals. The newly reported lead is stable at the acidic and basic conditions. Additionally, this compound has an excellent activity towards Candida auris, a multidrug-resistant superbug.

Heart disease is the leading cause of death …

Computational And Experimental Studies On Energy Storage Materials And Electrocatalysts, Jared B. Moss

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

With the growing global population comes the ever-increasing consumption of energy in powering cities, electric vehicles, and portable devices such as cell-phones. While the power grid is used to distribute energy to consumers, the energy sources needed to power the grid itself are unsustainable and inefficient. The primary energy sources powering the grid, being fossil fuels, natural gas, and nuclear, are unsustainable as the economically-accessible reserves are continually depleted in exchange for detrimental emissions and air-pollutants. Cleaner, renewable sources, such as solar, wind, and hydroelectric, are intermittent and unreliable during the peak hours of energy usage, that is dawn and …

Synthesis And Biological Studies Of Amphiphilic Compounds Derived From Saccharides And Aminoglycosides, Madher N. Alfindee

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Adjacent cells communicate through gap junctions (GJs). These GJs are formed by head to head docking of two hemichannels (HCs) from two adjacent cells. HCs are connexin hexamer proteins. Connexin mutation is the most frequent cause of childhood hearing loss. This hearing impairment affects 2 in every 2000 children. Inhibition of the HCs might be the key factor to treat such disorders. A library of amphiphilic kanamycins was synthesized to be tested as HC inhibitors. These compounds showed excellent inhibition activity in comparison with the parent compound (kanamycin A) with less toxicity.

A library of monosaccharide esters with varying carbon …

Electronic Transmutation: An Aid For The Rational Design Of New Chemical Materials Using The Knowledge Of Bonding And Structure Of Neighboring Elements, Katie A. Lundell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Everything in the universe is made up of elements from the periodic table. Each element has its own role that it plays in the formation of things it makes up. For instance, pencil lead is graphite. A series of honeycomb-like structures made up of carbon stacked on top of one another. Carbon’s neighbor to the left, boron doesn’t like to form such stacked honeycomb-like structures. But, what if there was a way to make boron act like carbon so it did like to form such structures? That question is the basis of the electronic transmutation concept presented in this dissertation. …

Carbon Monoxide On Demand: Light-Induced Co Release Of Flavonols, Stacey N. Anderson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Carbon monoxide (CO) is an extremely useful molecule with applications in industrial manufacturing, synthetic procedures as a C1 building block, and as a potential pharmaceutical to produce anti-inflammatory effects and vasodilation. However, the toxicity associated with CO has prevented its full utilization. In order to safely handle CO, compounds and molecules have been developed that act as storage materials for the gas. Ideal storage platforms only release CO upon stimulation via a trigger. Light activation is the most desirable trigger as it can be regulated in terms of the intensity and the wavelength of light used. The majority of light-induced …

Quantum Mechanical Studies Of N-H···N Hydrogen Bonding In Acetamide Derivatives And Amino Acids, Sandra J. Lundell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Proteins are made of vast chains of amino acids that twist and fold into intricate designs. These structures are held in place by networks of noncovalent interactions. One of these, the hydrogen bond, forms bridges between adjacent pieces of the protein chain and is one of the most important contributors to the shape and stability of proteins. Hydrogen bonds come in all shapes and sizes and a full understanding of these not only aids in our understanding of proteins in general but can bridge the gap to finding cures to many protein-related diseases, such as sickle-cell anemia. The primary aim …

Inorganic Electrocatalysts For Innovative Water Splitting And Organic Upgrading, Nan Jiang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The booming worldwide demand for energy and the increasing concerns about global warming due to fossil fuel consumption have urged the development of techniques for storing and converting renewable and clean energy resources. Electrocatlytic or photoelectrocatalytic water splitting to generate green energy carrier H₂ with sustainable energy input, like solar, has been regarded as an attractive strategy for carbon-neutral energy needs. However, the sluggish kinetics for both half reactions (HER and OER), high overpotentials and thermodynamic requirements, and H₂ and O₂ gas crossover have been regarded as the major challenges, which limit its widespread application.

On account …

Investigations Into Factors Affecting The Wpd-Loop In The Protein Tyrosine Phosphatases Yoph And Ptp1b, Gwendolyn Moise

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research in this dissertation documents connections between the primary amino acid sequence of proteins, the dynamics of proteins, and their catalytic function. This research project studied two proteins called protein-tyrosine phosphatases (PTPs): the human enzyme PTP1B, and the bacterial enzyme YopH. PTP1B is a human enzyme that down regulates the insulin receptor on the outer cellular membrane, and causes the insulin receptor to be less responsive to insulin. A deeper knowledge of how PTP1B is different from other human PTPs might be useful in designing drugs to increase insulin sensitivity in diabetics. Yersinia Pestis is the bacteria that caused …

Elucidating Molecular Interactions Of Shigella Type Three Secretion System Components Critical For Pathogenesis, R. Alan Burgess

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Shigella are pathogenic bacteria which commonly infect human hosts through the fecal-oral route. As the causative agent of shigellosis, a disease characterized by severe diarrhea, nausea, and vomiting, Shigella are responsible for an estimated 90 million infections and 100,000 deaths each year. With the emergence of antibiotic resistant strains of Shigella, the need for alternative treatments methods has become critical to fighting outbreaks of shigellosis and drug resistant strains. One such method is to target the infection system of the bacteria, called the type three secretion system (T3SS). The T3SS includes a complex needle and syringe-like apparatus that is …

Mechanistic Studies Of The Iron And Molybdenum Nitrogenases, Derek Harris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As a basic building block in many biological molecules the element nitrogen (N) is essential for life. Dinitrogen (N2) is abundant in Earth’s atmosphere, but this form is biologically unavailable. To be biologically available N2 must undergo an energy demanding reduction reaction to the fixed form, ammonia (NH3). The industrial Haber-Bosch process, which accounts for approximately 50% of the worlds fixed nitrogen, uses energy from fossil fuels to achieve high pressures and temperatures to facilitate the reaction. The energy used by Haber-Bosch accounts for approximately 2% of the world’s annual supply. The remainder of fixed nitrogen is produced biologically by …

First-Row Transition Metal Sulfides And Phosphides As Competent Electrocatalysts For Water Splitting, Nan Jiang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Solar energy is a carbon-neutral and renewable energy resource. Its nature of intermittence and unequal distribution requires efficient solar energy capture, conversion, and storage. Solar-driven water splitting to produce hydrogen and oxygen is widely considered as an appealing approach to meet this goal, in which hydrogen acts as a green energy carrier. Water splitting consists of two redox half reactions: hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Both reactions involve the transfer of multiple electrons and protons and possess high energy barriers to proceed at appreciable rates, hence catalysts are needed.

A large number of HER and OER …

Chemical Bonding In Novel 0-, 1-, 2-, And 3-Dimensional Chemical Species, Ivan A. Popov

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

While the trial and error approach is still being a dominant pathway for synthesis of various compounds in chemistry, computation-driven approaches have recently been shown to be a very efficient way towards the rational design of new materials with tailored properties. In principle, theoretical design of materials may not only significantly reduce the costs associated with the experiment, but may also result in the prediction of novel compounds possessing completely unexpected geometries. These compounds can serve as long-lived catalysts, powerful batteries, efficient solar cells, or reliable energy storage materials. Since geometric structure of any system is related to its electronic …

Conservative Tryptophan Mutations In Protein Tyrosine Phosphatase Ptp1b And Its Effect On Catalytic Rate And Chemical Reaction, Teisha Richan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B …

Role Of Atp Hydrolysis And Mechanism Of Substrate Reduction In Nitrogenase, Sudipta Shaw

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen is essential for life on earth as it is a major constituent of amino acids and nucleic acids. Nitrogen gas (N₂) is the most abundant form of nitrogen in the atmosphere but the strong N≡N bond makes it unavailable for most organisms. Certain prokaryotes known as diazotrophs possess the unique ability to convert N₂ to ammonia (NH₃) which can be utilized by other organisms as a source of nitrogen. The diazotrophs perform this difficult reaction with the help of a complex metalloenzyme, nitrogenase. This enzyme is a major contributor of the fixed source of …

Caffeine And Acetaminophen Concentration And Other Water Quality Parameters Along The Middle To Lower Bear River, Autumn Slade

Undergraduate Honors Capstone Projects

Various water quality parameters were measured at seven sites along the Middle to Lower Bear River and compared across the sites, to past data and to set standards in Utah and Idaho. Much of the data was comparable to past data with most state standards being met. However, nitrate was above indicator level for half of the sites, and turbidity is a problem at the last two sites. Also, chloride and unionized ammonia are at high levels by the last site. Overall, the river tended to decrease in water quality as it moved downstream, with dams like at Cutler Reservoir …

Computational Studies Of Microscopic Superfluidity In 4he Clusters, Angeline R. Wairegi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The onset of microscopic superfluidity has been reported in ultracold droplets of bosons (⁴He atoms or para-H₂ molecules) containing a variety of molecular dopants. The physics of these droplets involve both Bose-Einstein condensation (BEC) and superfluidity. The two phenomena, while closely related, are not exactly the same. Superfluidity is fundamentally a microscopic effect and thermodynamic limit is necessary; it is still remarkable, though, that the signature of superfluidity has been reported in doped droplets consisting of as few as 4 ⁴He atoms. The studies presented here adopt a molecular vantage point to investigate the quantum mechanics …

Synthesis, Structure-Activity Relationship Study, And Mode Of Action Study Of 1,4-Naphthoquinone Based Anticancer And Antimicrobial Agents, Jaya P. Shrestha

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The first three projects involve the synthesis and the mode of action study of 1,4-naphthoquinone based anticancer agents. These anticancer agents are highly potent against a wide range of cancer cell lines. These compounds showed ~8-fold selectivity towards the lung cancer cell line than the normal cell line. We also studied the mode of action and observed that generation of reactive oxygen species is the primary mode of action.

The final project involves the synthesis of multi-cationic antimicrobial agents. These compounds are active against both bacteria and fungi. These compounds are very easy to synthesize and can be scaled up …