Physical Sciences and Mathematics Commons^™

Oxidative Carbon-Carbon Bond Cleavage Reactions Of Metal Flavonolato And Chlorodiketonate Complexes, Sushma L. Saraf

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research presented in this dissertation focuses on the oxidative cleavage of chemical bonds between two carbon atoms. This type of reactivity is of significant interest due to its potential application toward the development of ways to convert chemical feed stock into useful products such as pharmaceuticals, polymers and fuels in an environmentally benign and cost-efficient manner. Reactions that cleave specific carbon-carbon bonds, are catalyzed by earth-abundant metals, and involve O₂ as the terminal oxidant, are of particular interest.

Our strategy has been to study the oxidative carbon-carbon bond cleavage reactivity of metal complexes containing components similar to structures …

Fluorescent Probes To Investigate Homologous Recombination Dynamics, Eric Parker Davenport

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As the average cell’s DNA undergoes roughly 1 million molecular lesions per day, learning about one of the repair mechanisms which fixes damaged DNA is a worthwhile endeavor. Such work may provide insights into how to treat or prevent diseases such as cancers and associated genetic disorders. Homologous recombination (HR) is one pathway which is used by cells to repair a specific type of DNA damage, double-strand breaks. While HR is a complex process involving over 25 different proteins, exactly how HR works, including its regulation, is largely unknown. One protein in particular, Rad51, forms a filament on the damaged …

Computational Chemistry Of Non-Covalent Interaction And Its Application In Chemical Catalysis, Vincent De Paul Nzuwah Nziko

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Known to be weaker than conventional covalent bonds, non-covalent bonds, especially hydrogen bond, has shown to be of great importance in molecular structures such as DNA, RNA, proteins and other organic frameworks. In this dissertation, we looked at non-covalent interactions other than the hydrogen bond. Replacement of the bridging hydrogen atom in a typical hydrogen bond by other atoms such a halogen, chalcogen and tetrel lead to the formation of interactions which are comparable in strength to the hydrogen bond. Unlike the hydrogen bond which arises mainly from electrostatics, these unconventional interactions mostly result from induction. Besides studying the fundamentals …

Heterogeneous And Homogeneous Nickel-Based Electrocatalysts For Oxygen Evolution And Carbon Dioxide Reduction, Meili Sheng

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The growing global energy demand and the increasing concentration of CO₂ in the atmosphere have encouraged the development of renewable energy to replace carbon-based fossil fuels. Electrocatalytic water splitting to form H₂ and O₂ and reduction of CO₂ to CO are appealing processes and we can be directly utilize H₂ and CO as fuels or commodity chemicals in mature industrial processes, which will not alter the current carbon cycle. However, the O₂ evolution reaction of water splitting is a reaction of four-proton and four-electron transfer process, whose kinetics is very sluggish under normal conditions. …

Atp Usage In The Dark-Operative Protochlorophyllide Oxidoreductase, Mark S. Soffe

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chlorophylls are essential pigment molecules that function in photosynthesis, and serve to aid in utilizing energy from sunlight to power cellular processes in plants, and other organisms. To make chlorophyll, photosynthetic organisms devote an abundance of resources and energy to ensure their appropriate construction. This process of making chlorophylls is highlighted by the penultimate step in the pathway—the conversion of protochlorophyllide (Pchlide) to chlorophyllide a (Chlide).

This conversion can be mediated in two different ways, depending on the type of organism. The first method incorporates the use of a light-activated system called the light-dependent protochlorophyllide oxidoreductase (LPOR). This system, as …

Synthesis Of Fluorogenic Probes For Studying Biomass Degradation And Synthesis Of New Antifungal Aminoglycosides, Qian Zhang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For the first project, a library of fifteen commercially purchased and synthetic fluorogenic probes were employed for the investigation of biomass degradation using extract of white-rot fungi. These discoveries prove that it is possible to employ fungi for selective degradation or release of hemicelluloses from biomass. This work is supported by Sun Grant Western Regional Center/DOT "Bioprospecting for Enzymes to Break Lignin-Hemicellulose Bond" ($300,000,09/01/2011-08/31/2013)

The second project is focused on synthesizing new aminoglycoside analogs and exploring the potential to revive traditional antibacterial kanamycin as new type of antifungal agents. Although aminoglycosides antibiotics are mainly used as antibacterial agents, this project …

Relative Toxicity Of Select Dehydropyrrolizidine Alkaloids And Evaluation Of A Heterozygous P53 Knockout Mouse Model For Dehydropyrrolizidine Alkaloid Induced Carcinogenesis, Ammon W. Brown

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Dehydropyrrolizidine alkaloids (DHPAs) are toxins produced by approximately 3% of the world’s flowering plants that can be present naturally or as contaminants in animal feed and the human food supply. Many of these compounds have been determined to cause cancer in animals and probably also cause cancer in humans. Due to the difficulty in obtaining sufficient amounts of pure DHPAs most toxicity research has been done via injection of a small amount into the abdomen of a rodent, although natural exposure is exclusively oral. For the same reason, cancer research is limited to a handful of the hundreds of known …

Computational Prediction And Rational Design Of Novel Clusters, Nanoparticles, And Solid State Materials, Alexander S. Ivanov

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The prediction of structure at the atomic level is one of the most fundamental challenges in materials science. Indeed, the structure is arguably the most important piece of information about a material, as it determines pretty much all properties of a material. Knowing the structure, one can analyze a large number of properties of a material, even before it is synthesized – the crucial importance of structure prediction for computational molecular design. This dissertation describes the technique of reliable theoretical predictions and presents the results on the successfully predicted unusual clusters, nanoparticles and solid state materials. The major part of …

Structure And Multi-Center Bonding: From Atomic Clusters To Solid Phase Materials, Timur R. Galeev

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work presented in this dissertation has been focused on structure, stability, and chemical bonding of atomic clusters and solid-state compounds. The common thread was development of theoretical models and methods capable of interpreting bonding and hence, structures of these species. A major part of this work presents joint experimental and theoretical studies of a large series of doped boron clusters. The dissertation introduces a new theoretical tool for interpretation of bonding of solid phase materials in chemically intuitive terms of localized and multi-center bonds. Understanding how interactions between atoms in sub-nano clusters and solid-state compounds determine their structures, physical …

Detailed Analysis Of The Domains Of Mtr4 And How They Regulate Helicase Activity, Lacy Leigh Taylor

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The central dogma states that DNA is transcribed into RNA, which is then translated into protein. This concept conveys a minimal view of the role of RNA, portraying it simply as an intermediary between DNA and protein. However, it is now known that the role of RNA in the cell is critical in regulating protein expression both directly and indirectly. RNA in the cell typically goes through modifications to become active (on) and inactive (off) to eventually become targeted for degradation and start the cycle all over again. The protein complex that regulates the proper maturation and degradation of RNA …

Substrate Binding And Reduction Mechanism Of Molybdenum Nitrogenase, Zhiyong Yang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As a key constituent of proteins, nucleic acids, and other biomolecules, nitrogen is essential to all living organisms including human beings. Dinitrogen represents the largest pool of nitrogen, about 79% of the Earth’s atmosphere, yet it is unusable by most living organisms due to its inertness. There are two ways to fix this inert dinitrogen to usable ammonia. One is the industrial Haber-Bosch process, which needs to be conducted at high temperature and pressure. This process uses a lot of the non-renewable fossil fuel as the energy source. The other major pathway is the biological nitrogen fixation carried out by …

Oxidative Aliphatic Carbon-Carbon Bond Cleavage Reactions, Caleb J. Allpress

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work presented in this dissertation has focused on the activation and cleavage of chemical bonds between two carbon atoms. The selective oxidative activation of carbon-carbon bonds is important due to potential applications in the utilization of biomass for fuel production, applications in wastewater treatment and bioremediation, and in developing new reactions for organic synthesis of fine chemicals including pharmaceuticals. Ideally these reactions would be carried out with high atom economy at low temperatures and pressures, and using earth-abundant elements as reagents and catalysts. With these points in mind, nature provides an ideal model framework, carrying out its chemistry at …

Enhanced Structural Support Of Metal Sites As Nodes In Metal-Organic Frameworks Compared To Metal Complexes, Sanjit Das

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Crystalline porous materials have gained long-standing interest for their application in gas storage, separation and catalysis. These materials have been useful for domestic, scientific and industrial purposes for many decades. Zeolites are a well known example of such materials.

Metal-organic frameworks are a new class of crystalline porous materials. They have many advantages over the more widely known zeolites. Though metal-organic frameworks are relatively new, their basic structure, known as the secondary building unit, very closely resembles the structure of metal complexes. Such metal complexes have been characterized in chemistry for more than a century.

Chemical catalysis is a process …

Structural And Functional Characterization Of The Ldp3 (Vhz) Protein Tyrosine Phosphatase, Vyacheslav I. Kuznetsov

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein phosphorylation is as an important regulatory mechanism that controls a large number of physiologically important cellular processes. Proteins are phosphorylated on aliphatic (serine and threonine) as well aromatic (histidine and tyrosine) residues predominantly located on sterically accessible loops. Phosphorylation affects three- dimensional structures of proteins resulting in conformational changes which activate or deactivate enzymatic functions. Because of the ability of protein phosphorylation to modulate a multitude of diverse cellular processes, it became an appealing and promising target for drug therapy.

Attachment of phosphate is accomplished by kinases, whereas the removal of the phosphoryl group is performed by protein phosphatases. …

Synthesis And Biological Activity Of Aminoglycosides And 1,4-Naphthoquinone Derivatives, Marina Fosso Yatchang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research described in this dissertation is at the interface of organic chemistry and biology, and it aimed at designing and synthesizing biologically active molecules for the possible development of therapeutic agents.

Spinal muscular atrophy is an incurable disease that affects 1 in every 6000 babies, making it the leading genetic cause of infant mortality. While no treatment is available, efforts are being taken to solve this issue. Part of the work outlined in this dissertation was carried out in collaboration with researchers from the University of Missouri to investigate a potential therapeutic for this disease.

In addition, the continuous …

In Situ Measurements Of Electron-Beam-Induced Surface Voltage Of Highly Resistive Materials, Joshua Hodges

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Surface charging and subsequent electrostatic discharge due to interactions with the space environment is one of the primary concerns of spacecraft charging studies. Laboratory measurements of the evolution of surface voltages and dissipation currents under simulated space conditions are the primary method used to determine the response of key spacecraft materials to diverse incident fluxes. Increasing the database of information for the electronic properties of insulating materials can assist spacecraft designers in mitigating the harsh effects of the space environment.

The Utah State Materials Physics Group, with the funding of the NASA James Webb Space Telescope project and personnel support …

A Mechanistic Study Of Catalytic Promiscuity In Protein Phosphatase 1, Yuan Chu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

"Catalytic promiscuous" enzymes, which possess additional activities besides their "native" activity, albeit with a lower efficiency than the main reaction, have become a new frontier for biochemistry and have received considerable attention. Catalytic promiscuity has been suggested to contribute to enzyme evolution through the mechanism of gene duplication followed by specialization of one of the two copies for the new function. Mimicking this evolutionary shortcut could also provide a more efficient route to changing the function of proteins by directed evolution.

The promiscuous phosphatase PP1 is a member of the phosphoprotein phosphatase (PPP) gene family, which is critical for the …

The Mechanisms Of Hydride Exchange, Organic Combination And Displacement Reactions, Weifang Hao

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The primary aim of this dissertation was to seek the answer to the question: “Is the single transition-state model appropriate for the fundamental reactions in organic chemistry?” The goal was accomplished by performing enormous kinetic data collection and detailed mechanistic analysis on several typical fundamental organic chemical reactions. Three new methodologies for differentiating between a simple one-step and complex multi-step mechanism were developed and extensively confirmed during the application in the kinetic studies of all of the reaction discussed in this dissertation. The three methods consist of (1) half-life dependence of kapp, (2) sequential linear pseudo-first-order correlation, and (3) revised …

Production Of Biodiesel From Oleaginous Organisms Using Underutilized Wastewaters, Valerie Godfrey

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As part of the BioEnergy Team at Utah State Univeristy, my research objectives have been centered around the common theme of innovating new methods and
technology for producing biological compounds and, by means of chemical conversion and/or extraction, isolating new forms of biodiesel available for transportation fuel.
Within the broad scope of this project, I focused on the replacement of freshwater in cultivating such biological systems with wastewaters. If accomplished and correctly
applied, such research would reduce the environmental impact of biodiesel production by reducing the demand for freshwater. It also would reduce production costs by reducing the amount of …

Rationalizing Structure, Stability, And Chemical Bonding Of Pure And Doped Clusters Isolated And Solvated Multiply Charged Anions, And Solid State Materials, Alina P. Sergeeva

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chemistry is the study of materials and the changes that materials undergo. One can tune the properties of the known materials and design the novel materials with desired properties knowing what is responsible for the chemical reactivity, structure, and stability of those materials. The unified chemical bonding theory could address all these questions, but we do not have one available yet. The most accepted general theory of chemical bonding was proposed by Lewis in 1916, though Lewis’s theory fails to explain the bonding in materials with delocalized electron density such as sub-nano and nanoclusters, as well as aromatic organic and …

Structural And Functional Characterization Of The Essential Rna Helicase Mtr4, Ryan N. Jackson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

To insure the integrity of nuclear RNA, the eukaryotic cell employs surveillance systems that identify and degrade RNAs that are detrimental or unneeded. The failure of RNA surveillance systems can lead to neurodegenerative disease states and cancer. The essential RNA helicase Mtr4 is required for the degradation and processing of several nuclear RNAs. To further the understanding of RNA surveillance and processing in eukaryotes, Ryan Jackson of the Department of Chemistry and Biochemistry at Utah State University has determined the molecular structure of Mtr4 and has used this structure to interrogate Mtr4 function biochemically. The structure revealed that Mtr4 contains …

1. Improving The Yield Of Biodiesel From Microalgae And Other Lipids. 2. Studies Of The Wax Ester Biosynthetic Pathway And Potential Biotechnological Application, Bradley D. Wahlen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The production of biofuels and oleochemicals from renewable sources offers an opportunity to reduce our dependence on fossil fuels. The work contained in this dissertation has focused on developing and improving methods for the production of biodiesel from non-traditional feedstocks and understanding biosynthetic pathways that result in the production of oleochemicals and fuels.

Pure vegetable oil can account for 70-80% of the total cost of biodiesel production. Many low-cost oils contain high amounts of free fatty acids, which are unsuitable for base-catalyzed transesterification. Herein an approach is described that efficiently accomplishes the simultaneous esterification and transesterification of both free fatty …

The Kinetics And Mechanisms Of Some Fundamental Organic Reactions Of Nitro Compounds, Zhao Li

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In chemistry, kinetics is the study of the rates of chemical reactions. A reaction mechanism describes in detail exactly what takes place at each stage of an overall chemical reaction from reactants to products. The work outlined in this dissertation was carried out in order to find out the true mechanisms of some fundamental organic reactions of nitro compounds by means of a series of novel kinetic techniques and analysis methods.

The target reactions include (1) the proton transfer reactions of nitroalkanes and (2) the aromatic nucleophilic reactions of trinitroarenes, both of which are undeniably among the most elementary and …

Structural And Mechanistic Investigations Of Phosphothreonine Lyase Class Of Enzymes, Alok Gopalkrishna Shenoy

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Phosphorylation and dephosphorylation are a highly pervasive mechanism in biology that is used by the cell to modulate enzymes and proteins. The presence of a phosphate group can activate or deactivate an enzyme. The phosphate group is linked to a protein by a phosphoester bond that is known to be highly stable in cytoplasmic pH range. Thus the breaking and formation of these bonds need to be effected by enzymes.

Recent discovery of the activity carried out by certain virulence related proteins (OspF released by Shigella and SpvC released by Salmonella) have resulted in a necessity to create a new …

Ligand And Metal Effects On The Co-Release Reactivity Of Metal Acireductone And Flavonolate Complexes, Katarzyna Grubel

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research reported herein involves synthetic metal complexes of relevance to dioxygenase enzymes (Ni(II)-containing acireductone dioxygenase (Ni(II)-ARD) and quercentinase (2,4-flavonol dioxygenase) that promote oxidative carbon-carbon bond cleavage and CO release. The experiments focus on the elucidation of structure-reactivity relationships and evaluation of the conditions under which CO is generated.

It had been proposed that hydrogen bond donors in the secondary environment of the active site metal center in Ni(II)-ARD influence the coordination of the acireductone substrate on the nickel center. To evaluate this proposal, we investigated the Ni(II) coordination chemistry of an acireductone-type enolate anion using a supporting chelate ligand …

Kinetic, Mechanistic, And Structural Investigation Of Features Controlling Stereoselectivity Of (R)- And (S)-Hydroxypropyl Com Dehydrogenases From Xanthobacter Autrophicus Strain Py2, Dariusz Adam Sliwa

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Enantiopure alcohols are valuable intermediates in fine organic synthesis, in particular for preparation of biologically active compounds. The necessity of preparing single enantiomer drugs in an optically pure form has triggered much research, especially in the pharmaceutical industry. The biocatalytical production of chiral alcohols by alcohol dehydrogenase enzymes is characterized by the asymmetric reduction of the corresponding ketones, usually with high degree of stereoselectivity. The commercial value of the enzymes as stereoselective biocatalysts has been a significant driving force in understanding features that control their mechanism of catalysis and stereoselectivity. This work focuses on two enantiocomplementary dehydrogenase enzymes ((R …

Ab Initio Search For Novel Bxhy Building Blocks With Potential For Hydrogen Storage, Jared K. Olson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

On-board hydrogen storage presents a challenging barrier to the use of hydrogen as an energy source because the performance of current storage materials falls short of platform requirements. Because boron is one of the lightest chemical elements that can form strong covalent bonds with hydrogen, it provides an excellent opportunity to design new lightweight materials on the basis of novel boron hydride building blocks. Realizing this potential requires an understanding of the electronic structure, chemical bonding, and stability of neutral and anionic B_xH_y clusters with variable stoichiometry. While a large number of boron hydride compounds are known, …

Analysis Of Ammonia And Volatile Organic Amine Emissions In A Confined Poultry Facility, Hanh Hong Thi Dinh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The National Air Emission Monitoring Study (NAEMS) project was funded by the Agricultural Air Research Council (AARC) to evaluate agricultural emissions nationwide. Utah State University (USU) is conducting a parallel study on agricultural emissions at a Cache Valley poultry facility. As part of this parallel study, samples of animal feed, eggs and animal waste were collected weekly from three manure barns (designated: manure barn, barn 4 - manure belt and barn 5 - high rise) from May 2008 to November 2009.

These samples were analyzed to determine ammonia content, total Kjeldahl nitrogen content and ammonia emission. The yearly average calculated …

A Synthetic Biological Engineering Approach To Secretion- Based Recovery Of Polyhydroxyalkanoates And Other Cellular Products, Elisabeth Linton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, …

Pulsed-Laser Excited Photothermal Study Of Glasses And Nanoliter Cylindrical Sample Cell Based On Thermal Lens Spectroscopy, Prakash Raj Joshi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research in this dissertation presents Pulsed-Laser Excited photothermal studies of optical glasses and cylindrical sample cell.

First, a study of a photothermal lens experiment and the finite element analysis modeling for commercial colored glass filters is done. The ideal situation of a semiinfinite cylinder approximate model used to describe the photothermal lens experiment requires the boundary condition that there is no transfer of heat from the glass to surrounding when the glass is excited with a laser. The finite element analysis modeling for photothermal signal with coupling heat with surrounding shows the thermal heat transfer between the glass surface …