Chemistry Commons^™

The Influence Of Instrumental Sources Of Variance On Mass Spectral Comparison Algorithms, Isabel Cristina Galvez Valencia

Graduate Theses, Dissertations, and Problem Reports (ETD)

Current search algorithms for the identification of substances based only on their electron ionization mass spectra provide the correct compound as their top result approximately 80% of the time. One contributing factor to the ~20% deviation in the first-hit recognition rate is that traditional algorithms work by comparing the unknown spectrum to an ‘ideal’ or consensus spectrum of each reference compound. The inclusion of replicate reference spectra in a database has been shown to improve the probability of ranking the correct identity in the number one position, but the variance in ion abundances caused by different conditions or different instruments …

Developing New Ionization Strategies For Characterizing Structural Flexibility, Heterogeneity, And Transformation Of Biopolymers, Daud Sharif

Graduate Theses, Dissertations, and Problem Reports (ETD)

Biopolymers, such as proteins and nucleic acids, serve important functions dictated by their structural folding. Information excavated from the intricate structural arrangements of biopolymers have been proved to be vital in diagnosing diseases, unveiling disease mechanisms, and developing new drugs. A continuous effort has been put to improve the characterization techniques of these biomolecules so that more precision can be achieved in terms of detailing their structure-function relationship. Mass spectrometry (MS) is one such technique that has become very relevant for structural biology with the emergence of soft ionization techniques such as electrospray ionization (ESI). A prerequisite to the application …

Development Of Novel Mass Spectrometry Method For The Analysis Of Complex Compounds, Jing Wang

Graduate Theses, Dissertations, and Problem Reports (ETD)

As mass spectrometry methods continue to advance, there is a growing need for innovative interfaces that can seamlessly integrate sample pretreatment, separation, and ionization, allowing for direct mass analysis while maintaining a simple and flexible system. The evolution of ambient ionization techniques has made it feasible to nebulize analyte compounds at ambient pressure. Moreover, single-cell proteomics using mass spectrometry is gaining increasing attention, necessitating the development of precise sample preparation techniques to enhance sensitivity. In this dissertation, I demonstrate the novel mass spectrometry system to couple the sample pretreatment with the direct mass spectrometry detection for the analysis of diverse …

Application Of Computational Biophysics Techniques To Characterize Cell Membrane-Associated Events, Kyle Billings

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule …

Investigating The Interactions Of The Iron-Sulfur Mitochondrial Protein, Mitoneet With Its Binding Partners, Ebenezer Osei Newton

Graduate Theses, Dissertations, and Problem Reports (ETD)

MitoNEET belongs to the CDGSH Iron-Sulfur Domain (CISD)-gene family of proteins and is a [2Fe-2S] cluster-containing protein found on the outer membrane of mitochondria. The specific functions of mitoNEET/CISD1 remain to be fully elucidated, but the protein is involved in regulating mitochondrial bioenergetics in several metabolic diseases. Unfortunately, drug discovery efforts targeting mitoNEET to improve metabolic disorders are hampered by the lack of ligand-binding assays for this mitochondrial protein. We have developed a protocol amenable for high-throughput screening (HTS) assay, by modifying an ATP fluorescence polarization method to facilitate drug discovery targeting mitoNEET. Based on our observation that adenosine triphosphate …

Drug Delivering Properties Of Novel Materials For Dentinal Desensitization, Abu Ahammadullah

Dissertations and Theses

This study focuses on the development of non-toxic dental materials that can adhere to dentin, occlude dentinal tubules, and release a drug with or without biological triggers. The properties of those materials are examined by SEM, UV-vis absorption spectroscopy, and a fluoride-selective electrode. The study also investigates the surface modification of calcium carbonate surface with casein, which stabilizes its micro-and nanoparticles in aqueous suspensions, making them suitable for use in dentifrices. The results indicate that the morphology and composition of the particles affect their ability to hold and release eugenol, with the casein-coated calcium carbonate microspheres being the most acid-sensitive …

Mechanical And Adhesive Properties Of Supramolecular, Mussel-Inspired Hydrogels, Daniel Darby

Theses and Dissertations--Chemical and Materials Engineering

The exceptional mechanical and adhesive properties of mussel byssal threads come from supramolecular interactions of ligands found in the proteins comprising them. Ligands can form hydrophobic interactions, π-π stacking interactions, and hydrogen bonds, but the strongest supramolecular interaction they demonstrate is metal-ligand coordination. Specifically, Histidine (His-) and nitrodopamine (nDOPA) ligands coordinate to metals in a bidentate fashion and take on tris-, bis-, and mono- modalities (3, 2, or 1 ligand per ion, respectively). The distribution of these modalities is controlled by equilibrium thermodynamics. These same ligands can be used as crosslinks in supramolecular hydrogel networks. Supramolecular hydrogel networks are dissipative, …

Molecular Understanding Of Zwitterions And Quantum Computing For Sustainability, Manh Tien Nguyen

Theses and Dissertations--Chemical and Materials Engineering

The sustainable development of society needs sustainable energy solutions and the mitigation of greenhouse gas emissions. One key subject in this area is the development of safe and efficient ion-based batteries. Moreover, CO₂ capture is a crucial pathway in mitigating emissions from the combustion of fossil fuels. Ongoing efforts are to improve both technologies' safety and efficiency. This thesis presents our efforts to conduct computational research on understanding advanced zwitterionic electrolytes and CO₂ capture. Chapters 2-4 illustrate the computational research to understand ionic solvation in zwitterionic electrolytes. Solid-state electrolytes are essential for safer batteries. While solid polymer electrolytes …

Analysis Of Fiber Uv Degradation Through An Environmental Chamber, Davis A. Eames

Undergraduate Research Posters

Environmentally degraded fibers could impact multiple aspects of a fiber comparison, considering that collected weathered fabrics/fibers may express an altered chemical structure and/or colorimetric property compared to their unexposed counterparts. Depending on the amount of degradation the evidence has suffered, it could be challenging for forensic scientists to make conclusions from their comparative analyses. Observations presented in this study were orchestrated to test the possible outcomes that sunlight has on fabric-based materials. Photodegradation of fabrics was investigated through the use of an environmental chamber for a duration of six weeks, which would be equivalent to three months of real-world UV …

Chemical Decomposition Of Flexible Polyurethane Foam To Generate A Media For Microbial Upcycling, Kaushik Baruah

Dissertations, Master's Theses and Master's Reports

Polyurethane waste is becoming a global concern as a large amount is being disposed of in landfills every year, and only a fraction is being recycled. Several polyurethane recycling techniques exist, of which ammonolysis and base-catalyzed hydrolysis is the least explored. Flexible polyurethane foam (FPUF) decomposition can generate amines that can act as a carbon source for the growth of microbial consortia. This study aims to generate a novel media capable of microbial upcycling via ammonolysis and base-catalyzed hydrolysis of flexible polyurethane foams (FPUFs) using ammonium hydroxide and subsequently determine the reaction conditions for maximum solubilization of polyurethane foam in …

Translating Chemistry, Structure, And Processing To The Solid-State Morphology And Function Of Organic Semiconductors Through Computational Modeling And Simulations, Chamikara D. Karunasena

Theses and Dissertations--Chemistry

The immense synthetic design space and material versatility have driven the exploration and development of organic semiconductors (OSC) over several decades. While many OSC designs focus on the chemistries of the molecular or polymer building blocks, a priori, multiscale control over the solid-state morphology is required for effective application of the active layer in a given technology. However, molecular assembly during solid-state formation is a complex function interconnecting the building block chemistry and the processing environment. Insufficient knowledge as to how these aspects engage, especially at the atomistic and molecular scales, has so far limited the ability to predict …

Developing And Deploying Data-Driven Tools For Accelerated Design Of Organic Semiconductors, Vinayak Bhat

Theses and Dissertations--Chemistry

Organic semiconductors have gained widespread attention due to their potential applications in flexible, low-cost, lightweight electronics, energy storage and generation technologies, and sensing applications. However, developing new organic semiconductors with improved performance remains a significant challenge due to the vast chemical space of possible molecular and materials structures. Furthermore, the high cost and time-consuming nature of experimental synthesis and characterization hinder the rapid discovery of new materials. To overcome these challenges, this dissertation presents a data-driven approach to organic semiconductor discovery. The primary focus of this work is the development of data-driven tools, namely machine learning models, to predict critical …

Surface Modification Of Carbon-Based Electrodes For Electrochemical Conversion Processes: Oxygen Reduction Reaction And Bicarbonate Conversion, Udari Shyamika Kodithuwakku Arachchige

Theses and Dissertations--Chemistry

Oxygen reduction reaction (ORR) and conversion of bicarbonate into value-added chemicals are two significant electrochemical processes for energy storage and conversion. ORR is an important electrochemical reaction in fuel cells and metal-air batteries that provide power conversion and storage capacity, respectively, for portable electronics, and electric vehicles. However, the performance of catalysts (e.g., platinum-based) is critically limited by slow kinetics, inefficient four-electron pathway, and surface deactivation. This limited performance of platinum-based catalysts, the scarcity of platinum, and vulnerable supply chains for critical minerals require the development of alternative electrocatalysts now more than ever. Carbon-based materials possess several key properties that …

Investigating Ru(Ii) Anticancer Agents With Non-Canonical Mechanisms Of Action, Richard Joseph Mitchell

Theses and Dissertations--Chemistry

Platinum(Pt)-based agents are used in approximately 50% of all cancers that are treated with chemotherapy. Unfortunately, the dose-limiting toxicity of these agents remains problematic for patients undergoing treatment. Additionally, Pt(II) therapeutics suffer from transporter-dependent uptake, limited chemical functionalization, and high susceptibility to inactivation by free thiols within the cytosol. Developing small molecules with non-canonical mechanisms of action is one strategy that can be employed to circumvent these limitations. Utilization of coordination complexes with ruthenium(Ru) metal centers is one attractive strategy. Ru(II) compounds are often octahedral, facilitating greater accessibility for chemical diversity; Ru(II) complexes use passive transport and transferrin-mediated transport for …

Water-Soluble Palladium, Copper, And Nickel Catalysts And Their Formation In Ligand-Free Suzuki-Miyaura Cross-Coupling Reactions, Priya Karna

Theses and Dissertations--Chemistry

Transition-metal catalyzed Suzuki-Miyaura (SM) cross coupling is a powerful synthetic method for constructing carbon-carbon and carbon-heteroatom bonds in designing organic compounds, agrochemicals, pharmaceuticals, and precursors for materials. However, the nature of catalysis and identity of the transition metal catalysts used in these reactions remain under debate or unknown. This dissertation reports the studies of three metals: Pd, Cu, and Ni. Pd-nanocluster catalysts and their formation in ligand-free SM reactions with Pd(II) nitrate as a precatalyst was investigated. The catalysts are water-soluble neutral Pd tetramer and trimer in their singlet electronic states as identified by UV-Vis absorption spectroscopy and are formed …

Development Of An Effective Au:Pd Bimetallic Heterogeneous Catalyst For Oxidative Lignin Depolymerization To Low Molecular Weight Aromatics, Gayan P. Karunasinghe

Theses and Dissertations--Chemistry

The principal concept behind biorefining involves the transformation of lignocellulosic biomass into valuable products and energy resources. Historically, biorefinery strategies for lignocellulosic biomass have primarily focused on improving the conversion of cellulose into ethanol, often neglecting the underutilized lignin component. Lignin consists of phenolic subunits, from which it follows that value-added products can be obtained from lignin depolymerization. Unfortunately, lignin utilization is particularly challenging due to its high structural irregularity and recalcitrance. The goal of this study was to develop an AuPd/Li-Al layered double hydroxide (LDH) bimetallic catalyst for efficient lignin depolymerization, resulting in the production of high-value aromatic compounds. …

Application Of Mass Spectrometry For The Characterization Of Synthetic Oligomers And Natural Lignin, Poorya Kamali

Theses and Dissertations--Chemistry

As part of the ongoing effort to substitute finite fuel and chemical resources with renewable ones, biomass is emerging as one of the most promising sources. Biomass consists of three main components of cellulose, hemicellulose, and lignin. Traditionally, cellulose has been used extensively in pulping industry, while lignin has been considered waste and is burned to generate heat. Lignin, a complex aromatic polymer component of biomass, has the potential to be used as a source of aromatic chemicals and pharmaceutical synthons. The recalcitrant nature of lignin, the lack of effective lignin breakdown methods and analytical techniques to analyze it are …

First Principles Calculations To Investigate Surface And Catalytic Properties Of Materials For Green Energy Generation, Keerthan Raghavendra Rao

Theses and Dissertations--Chemistry

Climate change due to greenhouse gas build up in the earth’s atmosphere is an existential threat to humanity. To mitigate climate change, a significant shift from fossil fuels is necessary. Over the years, several renewable energy sources like solar, wind, geothermal etc. have been explored with the aim providing carbon-free energy. In this work, we focus on using density functional theory (DFT) methods to investigate key functional properties of materials of interest for applications in solar cells and catalytic conversion for energy generation. We show geometric effects of carboxylic acid binding on a transition metal surface to impact the deoxygenation …

Synthetic Methodologies Using Nucleophile-Electrophile Chemistry, Jacob C. Hood

Graduate Research Theses & Dissertations

Synthetic organic chemistry is a vital part of the modern world – making up 15-20% of the U.S. economy. New synthetic reactions can lower manufacturing costs and create more environmentally friendly processes. Substitution, addition, and superelectrophilic chemistry are potent tools to afford potentially essential compounds. The work outlined in this dissertation recounts the expansion of synthetic methodologies employing substrates with a wide range of electrophilicities toward synthesizing heterocyclic molecules. These concepts are summarized in chapter 1. Chapter 2: N-Heterocyclic alcohols are excellent substrates for superacid-promoted Friedel-Crafts reactions. The N-heterocyclic alcohol ionizes to produce reactive, dicationic intermediates, providing good to excellent …

Insight Into The Nanostructure Of “Water-In-Salt” Solutions: A Saxs/Waxs Study On Imide-Based Lithium Salts Aqueous Solutions, Xinyi Liu

Graduate Research Theses & Dissertations

The fundamental understanding of the liquid electrolytes (LEs) solvation structure and electrode-electrolyte interface behavior is important to the entire electrochemical energy storage field. Understanding the solvation structures from a few angstroms to hundreds of nanometers will undoubtedly lay a good foundation for studying the macroscopic transport properties, such as viscosity and ionic conductivity, of the LEs."Water-in-salt" electrolytes that contain 21 m lithium bis(trifluoromethane sulfonyl)imide (LiTFSI) with excellent electrochemical and physical properties have been extensively investigated. However, the structural understanding of the LiTFSI in water is still lacking. Here, we perform synchrotron X-ray scattering to systemically study the structural variation of …

Chevrel Phase Materials For Electrocatalytic Chemical Conversion, Fan Xia

Graduate Research Theses & Dissertations

Electrocatalysis has played significant roles in energy conversion and environmental applications. This dissertation focusses on electrocatalytic performance of Chevrel phase material and building up relationship between structure with durability and activity.The dissertation mainly contains four parts. In chapter 2, the Ni2Mo6S8 catalyst exhibited in producing hydrogen peroxide with an outstanding selectivity of nearly 98%, derived from the combined ligand and ensemble effects of Ni, coupled with the strategic placement of Ni, Mo, and S in the active structure of the catalyst. Those synergistic effect results in a remarkable turnover frequency (TOF) of 30 s-1, leading to a hydrogen peroxide synthesis …

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Enhancing The Forensic Comparison Process Of Common Trace Materials Through The Development Of Practical And Systematic Methods, Meghan Nicole Prusinowski

Graduate Theses, Dissertations, and Problem Reports (ETD)

An ongoing advancement in forensic trace evidence has driven the development of new and objective methods for comparing various materials. While many standard guides have been published for use in trace laboratories, different areas require a more comprehensive understanding of error rates and an urgent need for harmonizing methods of examination and interpretation. Two critical areas are the forensic examination of physical fits and the comparison of spectral data, which depend highly on the examiner’s judgment.

The long-term goal of this study is to advance and modernize the comparative process of physical fit examinations and spectral interpretation. This goal is …

Computational Studies On Molecular Mechanisms For Dysregulation Of Monoamine Transporters By Hiv-1 Tat And Drug Discovery Of Novel Phosphodiesterase-2 Inhibitors, Charles A. Adeniran

Theses and Dissertations--Chemistry

Computational chemistry methods have been greatly used and has great potential in drug discovery and understanding the detailed molecular mechanism of biological processes. Scientific questions can initially be addressed using computational modeling and simulation studies. The common feature in this work is to understand intermolecular interactions related to protein targets in the brain, as it relates to HIV infection and Alzheimer’s Disease. HIV is among the world’s most deadly infectious diseases. Recent therapeutic advancements have begun to increase the life expectancy of people living with this virus. The mechanisms that lead to neurobiological complications known as HIV- associated neurocognitive disorders …

Exploring The Role Of Ring Annulation In Polycyclic Aromatic Hydrocarbons For Organic Electronic Applications, Tanner Smith

Theses and Dissertations--Chemistry

Organic materials offer promising potential for the next generation of electronic devices, as their tunability, processability, and low-temperature manufacturing make them a cheap and versatile alternative to traditional silicon-based electronics. The ability to systematically alter the electronic properties of organic materials is vital for their incorporation into device applications. Polycyclic aromatic hydrocarbons (PAHs) are of significant interest for organic electronic applications, as relevant properties are highly dependent on their size, structure, and functionalities, and thus can be tuned to fit a wide variety of applications. Due to the enormous number of structural isomers available in larger PAHs, the development of …

Bioanalytical Studies Of Disease Protein Profiles: Maldi-Tof Ms, Prajkta Satish Chivte

Graduate Research Theses & Dissertations

Coronavirus disease-2019 (COVID-19), which is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has ravaged the world for the past 3 years. Even today, there still exists a need for rapid, accurate, economical and non-invasive diagnostic testing platforms that yield high specificity and sensitivity towards the constantly mutating SARS-CoV-2. Research has consistently indicated saliva to be a more amenable specimen type for early detection of SARS-CoV-2, compared to the oral and nasopharyngeal swabs. Considering the limitations and high demand of the existing COVID-19 testing platforms, this dissertation work studies used MALDI-ToF MS (matrix-assisted laser desorption/ionization-time of …

Materials And Electrochemical Interfaces For High Energy Density Sodium Metal Batteries, Olusola John Dahunsi

Graduate Research Theses & Dissertations

Batteries with low-cost, high energy and safe features density are now widely demanded.This dissertation systematically and comprehensively studies the materials and electrochemical interfaces of sodium (Na) metallic anodes and metal-free anodes for high energy density sodium metal batteries (SMB) to meet energy storage demands. This dissertation is divided into two sections, with the first section focusing on the modifications made to pristine metallic sodium anodes using 1.6 at % tin (Sn) to create Na-Sn alloy anodes. The results confirm that the Na-Sn anode features interconnected Na15Sn4 backbones that support sodium structurally, enhance Na+/Na redox kinetics, and facilitate dendrite-free Na plating …

Structural Analysis Of Polar Aggregates And Inter-Ionic Distances In Room Temperature Ionic Liquids, Emily Elizabeth Dalbey

Graduate Research Theses & Dissertations

Ionic liquids have a wide variety of applications in chemistry due to their unique properties such as low flammability, low volatility, and high thermal and chemical stability. These properties make them great solvents, electrolytes for lithium-ion batteries, and more. Ionic liquids are salts whose components are mis-matched in size and shape leading to low melting points. To design an ionic liquid with a desired property it is key to first understand their structure. Lineshape analysis of the charge alternation peak from the experimentally measured or computationally calculated X-ray scattering data can give information about the size of the polar aggregates …

I. Design, Synthesis, And Evaluation Of The Human Phoshodiesterase-4 And Fungal Acetyl Coa Synthetase Enzyme Inhibitors Ii. Evaluation Of Biological Activity Of Kenyan Medicinal Plants, Chaitanya Kondam

Graduate Research Theses & Dissertations

Phosphodiesterase-4 (PDE4) enzyme mainly present in immune cells, epithelial cells, and brain cells that regulate inflammation and epithelial integrity in cells. Inhibition of PDE4 enzyme leads to regulation of various inflammatory mechanisms by elevation of cyclic adenosine monophosposphate (cAMP) levels in the cells. PDE4 enzyme is promising target for treatment of pulmonary, dermatological, and neurological inflammatory diseases. Several PDE4 inhibitor drugs Roflumilast, Apremilast, and Crisaborole were approved and marketed as Dalsirep, Otezla and Eucrisa for the treatment of inflammatory pulmonary diseases, psoriatic arthritis, and atopic dermatitis. However, these drugs have adverse effects such as nausea, emesis, and gastrointestinal effects. Benzothiazole …

The Application Of Photoelectron Spectroscopies In Analyzing The Impact Of Interfacial Energetics On Perovskite Solar Cells, Tuo Liu

Theses and Dissertations--Chemistry

In recent years, organic-inorganic metal halide perovskites (HP) have garnered tremendous attention in photovoltaic research. This attention is attributed to their low cost and excellent optoelectronic properties, including large absorption coefficients, tunable bandgaps, long charge-carrier diffusion lengths, and low densities of deep trap states. Inverted p-i-n architecture perovskite solar cells (PSCs) are of intense interest and are generally regarded as more amenable to low-temperature solution processing. Nevertheless, the development of inverted PSCs is lagging the conventional architecture devices. Imperfect energy level alignments and charge carrier recombination, especially at the interface between perovskite and electron transport layers (ETLs), are two main …