Theses and Dissertations
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Item Embargo Chemically recyclable polymers via acceptorless dehydrogenative polymerization: synthesis and characterization of functional polyesters and polyamides(Colorado State University. Libraries, 2025) Harry, Katherine L., author; Miyake, Garret M., advisor; Chen, Eugene Y.-X., committee member; Kennan, Alan, committee member; Peers, Graham, committee memberThis dissertation presents advancements in the development of acceptorless dehydrogenative polymerization (ADP) and its application to the synthesis of polyesters, polyamides, and their copolymers. ADP is an emerging catalytic strategy that overcomes many limitations of traditional polymerization methods, offering key advantages such as improved atom economy, enhanced sustainability, and a broader monomer scope. These features position ADP as a powerful platform for the synthesis of functional, structurally diverse polymers. The motivation for this work stems from the escalating plastic waste crisis. While plastics have undeniably advanced modern society through their performance and versatility, the linear nature of their life cycle continues to drive global pollution. Polyolefins, in particular, combine excellent material properties with extreme resistance to degradation, allowing them to persist in the environment for decades. The central challenge is to create materials that not only rival polyolefins in performance but also offer improved pathways for depolymerization and recycling. In this context, both ruthenium- and manganese-catalyzed ADP are explored as strategies to synthesize a range of polymers with tunable properties and built-in degradability via ester linkages. These polymers can be selectively deconstructed, offering a pathway to closed-loop recycling. The dissertation highlights recent progress in ADP, its mechanistic underpinnings, and its potential to support a circular polymer economy.Item Embargo Chemical dynamics underpinning the compounded sequence and spatiotemporal topology controls in Lewis pair polymerization(Colorado State University. Libraries, 2025) Reilly, Liam T., author; Chen, Eugene Y.-X., advisor; Miyake, Garret M., committee member; Crans, Debbie C., committee member; Radford, Donald W., committee memberLewis Pair Polymerization (LPP) has emerged as a uniquely versatile platform for precision polymer synthesis. In particular, LPP's ability to regulate polymer comonomer sequence and topology sets it apart from alternative methodologies. This contribution unravels the chemical dynamics and mechanisms of control that underpin LPP's most unique capabilities. Specifically, this work elucidates the interplay of the kinetic and thermodynamic biases that arise within comonomer mixtures and demonstrates how this fundamental knowledge can be used to prepare advanced materials. Likewise, this work dissects the dynamic origin of LPP's spatiotemporal control and leverages these findings to develop a new route to access traditionally elusive polymers of advanced topology. Collectively, these efforts serve as an example of how fundamental research can lead to new frontiers in materials design and discovery.Item Embargo Electrochemical immunoassays for point-of-care detection of heart failure biomarkers in saliva: advancing accessible healthcare testing(Colorado State University. Libraries, 2025) Pittman, Trey W., author; Henry, Charles S., advisor; Levinger, Nancy E., committee member; Kennan, Alan, committee member; Kipper, Matt J., committee memberHeart failure (HF) remains a leading cause of morbidity and mortality worldwide, with early detection and ongoing management critical for improving patient outcomes. However, current medical testing methods are often invasive, expensive, and inaccessible to many populations, particularly those in rural or resource-limited settings. Electrochemical detection offers a promising pathway to address these limitations. Electrochemical assays on screen-printed carbon electrodes (SPCEs) are an attractive option due to their low cost, favorable electrochemical properties, and ability to be fabricated in unique geometries. When combined with microfluidics, these technologies open opportunities for automated platforms, multiplexed detection, and the use of non-invasive sample matrices like saliva. However, developing a sensor compatible with saliva, engineering a microfluidic platform capable of processing viscous samples, and integrating these components into a unified system all present significant challenges. This dissertation addresses these issues by developing a novel, non-invasive electrochemical immunoassay platform for the detection of HF biomarkers in saliva, towards rapid, affordable, and decentralized point-of-care testing (POCT), and exploring simpler detection modalities. By leveraging saliva as a sample and integrating advanced sensor technologies, this work aims to bridge the gap between clinical need and technological capability, ultimately supporting more equitable healthcare delivery. Chapter 2 introduces the development of an electrochemical immunosensor specifically designed for the detection of galectin-3 (Gal-3) in saliva. The sensor utilizes SPCEs and optimized surface chemistry to ensure stability and sensitivity suitable for clinical applications. The chapter details strategies to overcome challenges associated with the complex saliva matrix, including effective antibody immobilization and sample preparation protocols, resulting in reliable biomarker quantification. Chapter 3 expands the platform to enable multiplexed detection of both Gal-3 and S100A7, two biomarkers relevant to HF prognosis. A dual-electrode array is integrated into a capillary-driven microfluidic device, allowing simultaneous detection of multiple analytes from a single saliva sample. The device automates reagent delivery and streamlines the assay workflow, requiring minimal user intervention and delivering results rapidly and cost-effectively. In the microfluidic system, the assay quantifies salivary levels of Gal-3 and S100A7, demonstrating successful multiplex detection and differentiation between these biomarkers. Chapter 4 investigates surface modification and antibody immobilization strategies for label-free immunosensors using SPCEs. Commercial SPCEs are identified as superior to lab-fabricated counterparts due to their enhanced consistency and electrochemical performance. Air-plasma treatment is shown to enhance electrode properties, and a comparison of immobilization methods-including passive adsorption, Protein A binding, and EDC/NHS coupling-provides insight into optimal strategies for sensor performance. A proof-of-concept immunoassay for HF biomarker Gal-3 validates the platform's sensitivity and clinical relevance, advancing label-free SPCE-based biosensors for decentralized testing. This dissertation establishes a foundation for next-generation HF testing by demonstrating that non-invasive, saliva-based electrochemical immunoassays can deliver clinically relevant results at the point-of-care. The developed platform combines affordability, ease of use, and adaptability, making it suitable for widespread deployment in diverse healthcare environments. By reducing barriers to regular monitoring and early intervention, this work has the potential to transform HF management, reduce hospitalizations, and ultimately improve patient outcomes. Future directions include expanding the biomarker panel, further automating the testing process, and integrating digital health solutions to enhance remote patient monitoring and disease management.Item Embargo Leveraging machine learning methods for the accelerated design of sustainable materials(Colorado State University. Libraries, 2025) Stubbs, Christopher Diemer, author; Chen, Eugene Y.-X., advisor; Kim, Seonah, advisor; Bandar, Jeff, committee member; Shores, Matt, committee member; Wang, Qiang, committee memberMachine learning (ML) is a discipline which fundamentally seeks to learn patterns in existing data in order to answer questions about unseen data. The impact of ML is best exemplified by the 2024 Nobel Prizes in Physics and Chemistry, which were awarded for the development (Physics) and application (Chemistry) of ML models. However, in order to meet the growing needs of sustainable materials production, additional research on how ML models can be applied, explained, and improved is needed. In this work, we found that ML models are a powerful and explainable tool for predicting polymer (Chapter 1) and small molecule solubility (Chapter 2), in addition to copolymer properties (Chapter 3). Our studies of polymer solubility demonstrated that both homopolymer and copolymer solubility can be effectively modeled with simple tree-based methods such as Random Forest, that these models can be explained for individual and aggregate predictions using Shapley Additive Explanations (SHAP), and that ML can be used to remove polymer additives by identifying selective solvents. Motivated by the efficacy of our polymer solubility models, we next examined how graph neural networks (GNNs) can be applied towards predicting the multi-solvent solubility of small molecules. We found that we can significantly improve solubility prediction accuracy by critically evaluating how each solution is digitally represented, and that we can further improve performance by harmonizing computational and experimental data. Lastly, we studied the impact of choosing appropriate model algorithms and inputs for predicting the thermal (Tg, Tg) and mechanical (εb, Young's modulus) properties of block copolymers – finding that incorporating both materials and block information was crucial for accurate predictions, with materials information having the greatest contribution to model predictions. All of our databases, articles, and code are made freely accessible in hopes to advance the state of the field. In summary, this work highlights the efficacy of ML-based approaches towards accelerating the development of sustainable materials and processes.Item Embargo Site-selective C—H functionalization of pyridines via activated pyridinium intermediates(Colorado State University. Libraries, 2025) Hart, Marie A., author; McNally, Andrew, advisor; Bandar, Jeff, committee member; Szamel, Grzegorz, committee member; Hansen, Jeffrey, committee memberPyridines and related azines are ubiquitous in pharmaceuticals and agrochemicals development. Chemists rely on the development of new synthetic methods to modify these heterocycles. Described herein are the development of methods to functionalize azines and convert pyridines and diazines into new heterocycles. Chapter one introduces the importance of pyridines and related heterocycles in pharmaceuticals as well as methods to access and functionalize these molecules. Both classical and contemporary methods for the functionalization of pyridines are discussed to provide context for this work. Chapter two describes methods for regioselective functionalization of pyridines via Zincke imine intermediates. Electrophilic fluorination, aminomethylation, and amination products are accessed through this platform. Chapter three highlights the Zincke imine platform for the formation of 15N pyridine isotopologues. When combined with deuteration methods, [M+2] and [M+3] pyridines are synthesized with high isotope incorporation. Finally, chapter four presents a method for direct, regioselective C4-pyridine amination through N-Tf pyridinium salts. Nucleophilic addition of amines followed by rearomatization of the dihydropyridine intermediate allows for the synthesis of 4-aminopyridines.Item Embargo Functionalization of pyridines and pyrimidines via ring-opened intermediates(Colorado State University. Libraries, 2025) Uhlenbruck, Benjamin J. H., author; McNally, Andrew, advisor; Miyake, Garret, committee member; Chung, Jean, committee member; Kipper, Matt, committee memberPyridines and pyrimidines are prevalent in pharmaceuticals and agrochemicals, yet site-selective functionalization methods of these valuable structures are often limited. In this dissertation, we describe the development of pyridine and pyrimidine functionalization methods that will enable organic chemists to access functionalized heterocyclic materials more easily. Chapter One describes the importance of pyridines and pyrimidines in industry, along with current methods and limitations in functionalizing these azines. Chapter Two introduces a 3-selective chlorination of pyridines using ring-opened Zincke imine intermediates. The method differs from a method our group reported in 2022 by ring-opening pyridine with aniline instead of dibenzylamine. Ring-opening azines with aniline produces imines and N-Ph azine salts with interesting properties, and enables the transformations described in every chapter of this dissertation. Chapter Three describes a 3-selective fluorination of pyridines using Zincke imine intermediates. Chapter Four provides an overview of Structure-Activity-Relationship (SAR) studies, de novo heterocycle synthesis, and skeletal editing strategies, then describes a deconstruction-reconstruction approach for pyrimidine diversification. Chapter Five discusses stable isotopes in medicinal chemistry, then expands on the deconstruction-reconstruction strategy for stable isotope incorporation into pyrimidines.Item Open Access Unraveling biogeochemical cycling of carbon, sulfur and nitrogen with high resolution mass spectrometry: from California vineyards to thawing permafrost in Sweden(Colorado State University. Libraries, 2025) Logan, Merritt N., author; Borch, Thomas, advisor; Rappé, Anthony, committee member; Neilson, James, committee member; Conant, Richard, committee memberPermafrost—perennially frozen ground covering approximately one-fifth of the Northern Hemisphere's land—plays a crucial role in global biogeochemical cycles. These frozen soils are vast reservoirs, holding roughly twice the organic carbon found in the atmosphere and about half of the global subterranean organic nitrogen. However, rising temperatures, particularly in the Arctic where warming is two to four times faster than the global average, threaten permafrost stability. This thawing exposes previously sequestered organic matter to decomposition, potentially releasing billions of tons of carbon and nitrogen-containing greenhouse gases (GHGs). The unpredictable, long-term behavior of permafrost during and after thaw makes it extremely challenging to forecast its impact on global climate, leading to significant uncertainties and frequent omissions from Earth system models. While historical permafrost thaw occurred gradually, rising temperatures are now driving rapid thaw events, accelerating permafrost loss within just a few years. These rapidly thawing areas are identified as highly active GHG emitters, expected to contribute nearly half of permafrost-derived GHGs by 2300, despite impacting only about 1% of the permafrost area. Though carbonaceous GHGs often dominate research, emerging studies highlight that released nitrous oxide—formed through the mineralization of nitrogen reserves from deep, previously frozen soils—may also have a significant impact. The biogeochemical cycling of nitrogen in thawing permafrost is complex, influenced by organic matter composition, thaw rate, soil saturation, and microbial activity. Chapter 2 addresses these complexities by characterizing organic nitrogen across a permafrost thaw gradient at Stordalen Mire, Sweden. Employing Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) alongside Nuclear Magnetic Resonance (1H NMR) spectroscopy and metatranscriptomic analyses, we found elevated ammonium and dissolved organic nitrogen concentrations in the thaw front, with a reduced proportion of peptide-like or carbohydrate molecules. These findings are critical for understanding how the molecular composition of nitrogen changes during thaw, directly impacting its bioavailability and subsequent GHG emissions. The analytical techniques utilized for characterizing organic matter in environmental systems are further described in Chapter 3, which provides a critical review of FT-ICR MS applications. This methodological framework addresses analytical challenges and offers recommendations for sample collection, preparation, analysis, and data interpretation, serving as a vital resource for the field. This provides valuable guidelines for the continued and broader application of FT-ICR MS in a variety of environmental systems. Returning to permafrost, Chapter 4 investigates the interactions between iron minerals and organic carbon across the thaw transition. Reactive iron minerals in permafrost soils sequester organic carbon but can release it upon thaw through reductive dissolution. Using FT-ICR MS, we identified a significant pulse of dissolved organic carbon and Fe2+(aq) at the thaw front, with a higher proportion of aliphatic molecules observed in both dissolved and mineral–adsorbed fractions before thawing. These results suggest that reactive iron minerals at the thaw front play a crucial role as electron acceptors for anaerobic respiration, directly influencing the fate and mobility of released organic carbon and its potential for GHG production. Finally, Chapter 5 extends the application of FT−ICR MS to assess the environmental impact of agricultural sulfur use. In an independent study, we examined dissolved organic sulfur (DOS) in California vineyards and their downstream watersheds. Combining FT−ICR MS with sulfur isotope (δ34S) analysis, we detected vineyard-derived DOS in non-agricultural water systems. Our findings highlight that the mobilization of agriculturally derived organic sulfur can influence critical downstream biogeochemical processes, such as mercury methylation, underscoring the broader environmental consequences of land management practices. In summary, this dissertation demonstrates the power of FT-ICR MS, combined with a comprehensive suite of complementary analytical methodologies, to elucidate the complex molecular transformations of organic carbon, nitrogen, and sulfur in dynamic environmental systems. This molecular-level understanding is crucial for improving predictions of future climate impacts and informing environmental management strategies in a warming world.Item Embargo Tuning the topology and stereomicrostructure of sustainable poly(3-hydroxybutyrate) materials(Colorado State University. Libraries, 2025) Parker, Celine R., author; Chen, Eugene Y.-X., advisor; Bandar, Jeffrey S., committee member; Kennan, Alan J., committee member; Herrera-Alonso, Margarita, committee memberPoly(3-hydroxybutyrate) (P3HB), a member of the polyhydroxyalkanoate (PHA) family, is a biodegradable polyester with the potential to serve as a sustainable alternative to conventional, petrochemical-derived polymers. This dissertation explores chemocatalytic strategies to precisely tune the topology and stereomicrostructure of synthetic P3HB, enabling access to an increased range of thermal and mechanical properties. Chapter 1 provides and overview of recent advances in PHA chemosynthesis seeking to improve their performance, processability, and functionality, using strategies including stereocontrolled ring-opening polymerization (ROP) of 4- and 8-membered lactone monomers, fundamental redesign efforts to stabilize the PHA backbone against thermal and hydrolytic degradation, and the introduction of unusual substituents that increase the commercial utility of PHAs especially for biomedical applications. Providing one of the latest examples of innovation in this space, Chapter 2 showcases cyclic stereoregular P3HBs, selectively synthesized through a catalyst-enabled end-to-end cyclization strategy, which exhibit superior thermal and mechanical performance compared to their linear counterparts. Cyclization was made possible by increasing the ionic radius of the catalyst metal center (La > Y) and through utilizing the precatalyst's existing substituent, silylamide (-NHSiHMe2) as an initiator, providing a good leaving group able to readily undergo cyclization. Therefore this polymerization strategy is more simplified compared to linear ROP, as it does not require addition of a pro-tic alcohol for initiation. Chapter 3 provides another example of a simplified polymerization strategy that advances the scope of accessible materials. Using a single set of polymerization conditions (catalyst, solvent, initiator), a stereochemical spectrum of P3HBs ranging from tough thermoplastics to plastomers and adhesives can be accessed simply by modulating the diastereomeric monomer feed ratio (rac and meso-8DLMe). A selection of these materials were then incorporated into an all-P3HB tape, exemplifying their potential to re-place traditionally hard-to-recycle multi-material products. Using these simple chemosynthetic strategies, it is possible to tune the topology and stereomicrostructure of P3HB enabling access to a platform for sustainable materials innovation. To conclude this work, Chapter 4 provides an outlook on the future of development in this space according to the limitations that remain to be overcome, and the new opportunities made accessible by the discoveries described herein. Continued refinement of P3HB synthesis will enable their utility across a greater application space, advancing the market of sustainable plastics and benefitting society through the reduction of plastic waste accumulation.Item Embargo New approaches for the functionalization of pyridines and other azines using phosphonium salts(Colorado State University. Libraries, 2025) Brunner, Dane A., author; McNally, Andrew, advisor; Miyake, Garrett, committee member; Kennan, Alan, committee member; Hansen, Jeffrey, committee memberNitrogen-containing heterocycles (N-heterocycles) are critical motifs in pharmaceutical and agrochemical matter that have shaped modern society. Identifying new heterocyclic cores with the promise for further improving human life requires ready access to new molecular space. Disclosed herein are methods for the functionalization of N-heterocycles utilizing phosphonium ions through a variety of different processes, specifically C–C, C–O, C–N, and C–S bond formations directly from C–H precursors. These methods aim to address discrepancies in organic synthesis and expand upon known modes of chemical reactivity. Chapter one focuses on the unexpected discovery and optimization of a method for pyridine hydroxylation. This strategy operates via a mechanistically distinct mode of phosphorus ligand-coupling that incorporates the oxygen derived from a molecule of water. Chapter two extends this approach, enabling the primary amination of azines using ammonium salts. Chapter three demonstrates a selective alkylation of pyridines via the addition of carbon-centered radicals using phosphonium salts as a blocking group activator. This method overcomes the longstanding challenge of regioselectivity in heterocyclic radical alkylation chemistry, as well as enables the controlled difunctionalization of pyridine cores. Chapter four expands known phosphonium ion chemistry to enable mild nucleophilic aromatic substitution (SNAr) reactions of pyridines using neutral thiols. Furthermore, this method allows for facile C–H thiolation and peptide couplings in late-stage contexts.Item Embargo Stereomicrostructure engineering of biodegradable poly(3-hydroxybutyrate) towards mono-material products(Colorado State University. Libraries, 2025) Quinn, Ethan Carey, author; Chen, Eugene, advisor; McNally, Andy, committee member; Szamel, Grzegorz, committee member; Herrera-Alonso, Margarita, committee memberThis dissertation describes advancements in the synthesis, characterization, and applications of biodegradable poly(3-hydroxybutyrate) (P3HB). These advancements were facilitated through the modulation of P3HB's stereomicrostructure, the relation of stereocenters to one another in the polymer chain, and the installation of stereoerrors through engineering its stereomicrostructure. An extensive literature review is also included on (bio)degradable and chemically recyclable polyesters, methods used in the modulation of polyhydroxyalkanoates properties, and mono-material product design based on bio-based, biodegradable, and chemically recyclable plastics. Biologically, P3HB is synthesized as stereoperfect (sp) isotactic (it) P3HB, meaning all of the stereocenters are in the absolute (R) configuration, which leads to high strength and high melting transition temperature but brittleness and opacity which limits its commercial utility. P3HB can be chemocatalytically synthesized as it, syndiotactic (st), stereocenters alternate between (R) and (S); atactic, having no regularity in stereochemistry; as well as iso- (ir) or syndio-rich (sr) having character of it or st but also atactic regions. To create these stereodiverse P3HBs, two monomers are used: β-butyrolactone and the eight-membered dimethyl diolide (both rac and meso diastereomers and mixtures of them), and many organic and organometallic catalysts can be employed. In this dissertation, the chemocatalytic route is focused on for its fast kinetics, scalability, and its ability to access a wide-range of stereomicrostructures. The commercial implementation of P3HB has interested many as it can biodegrade in both managed (commercial composting) and unmanaged (fresh water and soil) environments, making it a viable option for reducing the massive amounts of plastics that are leaked into the environment. However, the lack of material performance and diversity in biologically produced P3HB has led to a limited range of applications. Herein, P3HB's stereomicrostructure was engineered to create biodegradable tough, optically clear thermoplastics for packaging applications in the form of sr- and ir-P3HB with installed stereoerrors, strong adhesives that outcompete commercial super glues in the form of sr-P3HB, and to in-between stereomicrostructures that act as thermoplastics, elastomers, and pressure sensitive adhesives. Further, these stereodiverse P3HBs were blended with sp-P3HB, and homologous P3HB blends were created with advanced synergistic material properties. Combining these advanced materials, mono-material products were created in the form of all-P3HB tapes. These mono-material products are biodegradable and greatly reduce the complexity of potential recycling routes that typically plagues multi-material products. Topological effects on P3HBs material properties were also explored by creating stereodiverse cyclic P3HB through judicious monomer and catalyst selection that showed varied material properties to their linear counterparts. Overall, this dissertation demonstrates that tuning P3HB's stereomicrostructure leads to useful biodegradable materials that can be employed in the fabrication of mono-material products.Item Open Access Nanoscale imaging of photonic and energy transfer processes in photocatalytic nanomaterials(Colorado State University. Libraries, 2025) Lustig, Danielle, author; Sambur, Justin, advisor; Krummel, Amber, committee member; Van Orden, Alan, committee member; Gelfand, Martin, committee memberWith the increasing demand for renewable energy, there is an urgent need to develop advanced materials that enhance solar energy conversion and photoelectrochemical reactions. This research addresses these challenges by investigating semiconductor nanomaterials, particularly hybrid molecule-nanocrystal composites, for next-generation photocatalysis and hydrogen production. This work focuses on two key strategies to improve light-harvesting efficiency: defect-mediated energy transfer and photon recycling. Chapters 1 through 5 explore defect-mediated energy transfer using zinc oxide nanocrystals coupled to molecular dye acceptors. Chapter 2 introduces defect-mediated energy transfer at the ensemble-level, while Chapter 3 introduces single-molecule microscopy as a tool to spatially resolve active donor–acceptor pairs and highlights the development of a single-molecule fluorescence microscopy imaging methodology to study defect-mediated energy transfer. Chapter 4 investigates single-molecule measurements of zinc oxide nanocrystal/dye conjugates, revealing how sample heterogeneity impacts energy transfer efficiency, and Chapter 5 discusses future directions to measure the defect donor transition dipole moment. Chapter 6 investigates photon recycling within nanostructured photoanode systems, where emitted photons are reabsorbed locally as a method to improve solar-to-hydrogen efficiency via a correlative widefield microspectroscopy approach. Lastly, Chapter 7 explores using single-molecule fluorescence microscopy to investigate the binding behavior of methyl viologen on the surface of single CdSe/CdS quantum dots via analysis of fluorescence blinking. Altogether, this dissertation advances the understanding of both photonic and energy transfer mechanisms in photocatalytic nanomaterials. By integrating spectroscopic and single-particle techniques, it lays the foundation for designing hybrid nanomaterials with optimized energy flow and charge dynamics. This research paves the way for designing next-generation materials and technologies to address the pressing need for sustainable energy solutions.Item Open Access Mechanically mediated trithiocarbonate addition to commodity polymers for a more circular economy(Colorado State University. Libraries, 2025) Estock, John, author; Hill, Megan, advisor; Chen, Eugene, committee member; Broeckling, Corey, committee memberMechanical recycling, while thought of as environmentally conscious, is not nearly as effective as it is lauded to be. Great levels of mechanical force cause chain-scission and lower product value while simultaneously only working once, maybe twice before the material is useless. Studies to harness the chain-scission with functional groups have proved possible but limited. This study shows the effect of adding bis(BTTC) and monomer to a mechanical recycling process to allow for post-recycling reactions with functionalized material. PMMA was shown to decrease in MW from 350 kDa down to ca. 15 kDa, then repolymerized back to 350 kDa. Other post-recycling reactions including block polymer synthesis and depolymerization are also possible and show promise. Expanding the scope outside of PMMA to other common plastics is studied as well, though it needs to be greatly expanded upon.Item Open Access Progress toward a cloneable bismuth nanoparticle(Colorado State University. Libraries, 2025) Solomon, Courtney, author; Ackerson, Chris, advisor; Snow, Chris, committee member; Tsunoda, Susan, committee memberElectron microscopy (EM) is a technique that obtains high resolution biological images. However, a major limitation is inadequate contrast between a protein of interest and the surrounding cellular background. To overcome this challenge, the Ackerson lab has developed a cloneable nanoparticles (cNPs) which is described as an inorganic particle enzymatic synthesized using a metal reducing enzymes. These electron dense nanoparticles serve as a contrast marker, enhancing the contrast between a protein of interest and the cellular background. The focus of my thesis is to create a small compact bismuth cNPs to improve contrast labelling in EM. The first chapter provides an overview of current biological imaging and introduces how cloneable nanoparticles have promising application as a contrast marker. It reviews the role of essential intracellular metals and details the development of a cloneable selenium nanoparticle made from a metal reducing enzyme, Glutathione Reductase-Like Metalloid Reductase (GRLMR), which reduces selenite to form zero valance selenium. This chapter concludes by outlining the advantages of using bismuth as a contrasting marker. The second chapter discusses the background of arsenate reductase (ArsC) which natively reduces arsenate to arsenite. Given the chemical and structural properties as arsenite and bismuth, I hypothesized that ArsC may be capable of reducing bismuth(III) glutathione. This hypothesis was tested through enzymatic activity assays and by observing particle formation using analytical techniques to determine whether ArsC can reduce Bi(GSH)3. The third chapter explores how a directed evolution approach is used to enhance ArsC's selectivity towards reducing Bi(GSH)3. I generated a random mutagenesis library of ArsC variants, with the next step focusing on screening or selecting for variants that exhibit improved activity towards Bi(GSH)3.Item Open Access Use of chemical ionization mass spectrometry for study of photochemical properties: ketone photolysis quantum yields(Colorado State University. Libraries, 2025) Berg, Tyson C., author; Farmer, Delphine K., advisor; Ravishankara, A. R., committee member; Sambur, Justin B., committee member; Jathar, Shantanu, committee memberMeasurements of organic radicals produced during organic trace gas photolysis are critical to our understanding of radical budgets throughout the troposphere. This dissertation demonstrates the utility of chemical ionization mass spectrometry for measurements of radical quantum yields in the photolysis of organic trace gases in the laboratory setting. Chapter 2 addresses the development of a coupled chemical ionization mass spectrometer with iodide reagent ions (I-CIMS) and wide band light source instrument design, which was used to measure the quantum yield for CH3C(O) from acetone photolysis, through measurement of CH3C(O)O2. Acetone is the most abundant oxygenated organic gas in the troposphere and its photolysis can account for up to 1/3 of radical production in the upper troposphere. The results from this chapter demonstrate that the I-CIMS can be used for acetone photolysis measurements under conditions of the troposphere. In Chapter 3, the I-CIMS measurements of the CH3C(O) quantum yield in acetone photolysis are expanded to temperatures (223 to 323 K) and pressures (150 to 850 mbar) reflecting the conditions of the troposphere. The measurements are used to parameterize the quantum yield of CH3C(O) for use in models of tropospheric radical production. The parameterization shows that acetone photolysis near the tropopause may be up to 1.4 times slower than previously expected. These are the only measurements of acetone photolysis under tropospheric conditions based on the detection of the dominant radical product, CH3C(O)O2. Chapter 4 explores a new, multiple-reagent ion system with Cl2- as the primary reagent ion (Cl2-CIMS). Cl2-CIMS provides higher sensitivity for small acyl peroxy radicals than achieved with I-CIMS. However, the higher background of Cl2-CIMS leads to higher limits of detection and the uncertainty on multiple reagent ion chemistries makes this system unsuitable for ambient measurements. Cl2-CIMS could be further improved through larger changes to the instrument design than those discussed here, and other novel reagent ion chemistries may be accessible using the multi-step ionization mechanism that produces Cl2-. Chemical ionization mass spectrometry is well-suited to fast, speciated measurements of radicals and is thus useful for measurements of complex photolysis mechanisms, like that of acetone in the troposphere. Further instrument development could improve CIMS sensitivities and limits of detection to organic radicals, expanding its utility to more photochemical systems and ambient measurements of radicals as well.Item Open Access Synthetic and spectroscopic investigations of electron spin relaxation(Colorado State University. Libraries, 2025) Moseley, Ian, author; Zadrozny, Joseph M., advisor; Finke, Rick, committee member; Prieto, Amy, committee member; Buchanan, Kristen, committee memberMolecular magnets (also referred to as single molecule magnets (SMMs)), are organometallic complexes which can retain their magnetization in the absence of an applied field. The loss of this magnetization due to environmental interactions is referred to as magnetic relaxation. Due to the small energy gap between electronic spin orientations, maintaining this magnetization typically requires the molecules be held at temperatures approaching absolute zero. This requirement is both costly and impractical for most of the envisioned applications, and as such considerable research efforts have been made to increase the operating temperatures of molecular magnets. This dissertation presents a series of investigations into the magnetic relaxation behavior of molecular magnets incorporating first-row transition metals coupled to adjacent spin centers through electron-electron interactions. Presented herein is a series of investigations which demonstrate a novel method for extending magnetic relaxation in spin-abundant environments, the synthesis and characterization of a low-coordinate iron species as a potential precursor to extended solids, the magnetic properties of a pair of iron-based coordination polymers, and an investigation into the design of electron paramagnetic resonance (EPR) imaging probes using spin forbidden transitions. This research serves as a starting point for future investigations into the control of magnetic relaxation phenomena through synthetic control of electron-electron interactions.Item Embargo Coherent vibrational dynamics in ethylene carbonate: insights from 2D infrared spectroscopy(Colorado State University. Libraries, 2025) Guerrieri, Luke Robert, author; Krummel, Amber T., advisor; Levinger, Nancy, committee member; Wilson, Jesse, committee member; Henry, Chuck, committee memberThe research presented in this dissertation explores the mechanisms of coherent vibrational relaxation in the cyclic carbonate ester, ethylene carbonate (EC). Coherent relaxation processes describe the redistribution of quantum superposition states, but relatively little is known about the molecular properties governing these processes for vibrational superpositions in chemical systems. EC, a highly coupled vibrational system with applications in organic battery electrolyte mixtures, serves as a model compound for studying coherent vibrational dynamics. The fundamental carbonyl stretch of EC couples to doubly excited states via Fermi resonance. An investigation of the carbonyl fundamental stretch using linear Fourier transform infrared spectroscopy (FTIR) and two-dimensional infrared spectroscopy (2DIR) reveals coherent relaxation mechanisms involving multiple vibrational degrees of freedom. Pump selective 2DIR experiments compare the relative intensities of coherent relaxation processes to different features in the 2DIR spectrum, finding a correlation between the spectral amplitude of coherent relaxation processes and Fermi resonance coupling strength. A follow up investigation uses 13C isotopic substitution to modify the Fermi resonance coupling strength in EC isotopologues. It is found that 13C substitution strengthens the Fermi resonance coupling in EC isotopologues; however, isotopic substitution is found to suppress the redistribution of quantum superpositions involving Fermi coupled vibrations. Analysis of vibrational lifetimes for the Fermi coupled states indicates that the relative strengths of coherent relaxation processes correlate with the strength of vibrational coupling to a manifold of experimental dark states. Those results suggest that coherent relaxation in EC is primarily driven by the delocalization of vibrational relaxation pathways, rather than the strength of direct coupling between Fermi coupled modes.Item Open Access Insight into alternative battery technologies using 3D configurations, protective coatings, and characterization of resistive properties(Colorado State University. Libraries, 2025) Windsor, Daniel S., author; Prieto, Amy L., advisor; Neilson, James R., committee member; Shores, Matthew P., committee member; Bandhauer, Todd M., committee memberThe omni presence of lithium-ion batteries (LIBs) have revolutionized the modern world due to this technology's implementation as an energy storage device in smart phones, wearable electronics, and electric vehicles. Lithium-ion batteries are well suited for these applications owing to the light weight of these systems and their ability to store a large amount of charge. For these reasons, LIBs are classified as energy dense systems, which describes the amount of energy a technology can store per unit mass. A battery metric where LIBs struggle in terms of performance is power density, or the amount of power a technology can produce per unit mass. These systems, also, require expensive feedstock materials that are geographically isolated which has profound impacts on economics and supply chain considerations for LIBs. Thus, if rechargeable batteries are to continue to advance, alternative battery configurations and chemistries must be studied. Chapter 1 describes the field of LIBs, in terms of the advantages and disadvantages of this technology. This discussion is followed by brief mentions of some of the champion materials found in the anodes, cathodes, and electrolytes currently implemented in LIBs. The discussion on the champion materials for LIBs also covers the drawbacks of each material, and ways in which future investigations can improve their performance. This is then followed by a section which highlights how alternative battery configurations and chemistries can address some of the inherent disadvantages of the LIBs system. This chapter concludes with a discussion on some important soft skills the author learned during the completion of this degree. Chapter 2 covers the development and advances made in the field of 3D batteries. This chapter begins with an introduction of the 3D battery field and includes a section which discusses the current advances made in the literature. This is then followed by a discussion on the computational advances made in the field of 3D batteries, where there is a critical need to develop digital twins of 3D batteries to better understand the chemo-mechanical dynamics of these complex systems. The following portion of this chapter covers the development of 3D batteries through the lens of critical performance metrics, being power density, energy density, and cyclability and scalability. For 3D batteries, this chapter identified that improvements in energy density is the area where further advances are most needed. Finally, this chapter discuss efforts being made in industry toward the commercialization of these 3D battery systems. Chapter 3 covers an investigation into the fundamental effect of a polymer protective coating, cyclized-polyacrylonitrile (cPAN), on the Na-ion (de)insertion chemistry of antimony-based anodes in sodium-ion batteries (NIBs). This investigation was able to determine that the cPAN coating had the most pronounced effect on the early cycle (cycles 1-10) Na-ion (de)insertion chemistry of the antimony-based anodes. The interfacial resistance was, also, diminished by the presence of the cPAN protective layer which implies that the cPAN helps to facilitate Na-ion transport at the electrode-electrolyte interface. Chapter 4 discusses a practical and beginners' approach to the learning electrochemical impedance spectroscopy (EIS) for rechargeable batteries. This chapter begins with a simple deconvolution of the EIS acronym, such that the reader has a deeper understanding of how each component of the acronym combines to create this technique. The chapter continues by discussing how to preform both qualitative and quantitative EIS analyses on rechargeable batteries, and finishes with a discussion on the EIS specifics of rechargeable battery systems. Chapter 5 covers the future areas in which the work presented in Chapter 3 can be extended. In particular this chapter discusses the critical need to quantify the SEI products of a cPAN coated antimony electrode, as early cycle numbers, and ways in which cPAN can be applied to high surface area substrates to ideally formulate a 3D sodium-ion battery.Item Embargo Core substitution of dihydrophenazine photoredox catalysts for organocatalyzed atom transfer radical polymerization(Colorado State University. Libraries, 2025) Puffer, Katherine, author; Miyake, Garret, advisor; Chen, Eugene, committee member; McNally, Andy, committee member; Peers, Graham, committee memberOrganocatalyzed atom transfer radical polymerization (O-ATRP) is a controlled radical polymerization method that uses organic photoredox catalysts (PCs) and visible light to produce polymers with well-defined structures. Organic PCs leverage an inherently sustainable resource, light, to drive chemical reactions under mild conditions and minimize dependency on rapidly depleting precious metals such as Ru and Ir, which are commonly used for catalysis. N,N-diaryl dihydrophenazine PCs in particular are notable for their success in mediating O-ATRP, producing polymers with low dispersities (Ð < 1.3). However, the non-unity initiator efficiency (I* < 100%) observed using dihydrophenazines in prior work shows their limited ability to achieve targeted molecular weights. This low I* has been attributed to a radical addition side reaction between the PC core and alkyl fragments generated during polymerization. In this work, core substitution (CS) is leveraged to modify PC structure as a route to block side reactivity and improve polymerization control. Exploration of alkyl CS revealed that the alkyl CS PC is the active catalyst during the majority of O-ATRP and can have improved catalytically relevant properties relative to the parent PC. Aryl and heteroatom CS PCs were also found to have improved PC properties, including longer excited state lifetimes and more highly reducing excited states. The new structure-property relationships revealed in this work were applied to improve polymerization outcomes and address current limitations of O-ATRP, such as expanding monomer scope and decreasing PC loadings. This work demonstrates the utility of CS as a versatile strategy to tune PC structure, properties, and performance while enhancing the ability of organic PCs to produce advanced polymeric materials.Item Open Access Applications of LC-QQQ for quantification of small molecules in biological media(Colorado State University. Libraries, 2025) Schwarz, Madeline Christine Roach, author; Reynolds, Melissa, advisor; Van Orden, Alan, committee member; Chung, Jean, committee member; VandeWoude, Sue, committee memberLiquid chromatography triple quadrupole mass spectrometry (LC-QQQ) is a popular instrumental technique with rising popularity in research and clinical laboratories. LC-QQQ allows for high analytical specificity due to specific biomarker detection, along with high analytical sensitivity due to the trace amounts of substances being accurately quantified. Due to these specific advantages, LC-QQQ is gaining popularity for clinical diagnoses to determine the extent of an infection or disease, leading to better informed treatment, or to determine the metabolic rate at which a drug moves through the body. Small molecules (<1000 Daltons) can be used as biomarkers for both clinical diagnosis and metabolomic studies and are detected at extremely low levels using LC-QQQ. This work endeavors to utilize LC-QQQ for two primary applications: first, for the detection of a biomarker for the purposes of diagnosing pulmonary fungal infections, second, for the detection of cannabinoids in plasma during their metabolism. Pulmonary fungal infections such as invasive pulmonary aspergillosis (IPA) have increased in incidence over the last decade due to the increased number of immunocompromised individuals. This increase is especially problematic when considering mortality rates associated with IPA are upwards of 70%. This mortality rate, in part, is due to the length of time it takes to diagnose a patient with IPA. When diagnosed early, mortality rates of IPA decrease by as much as 30%. Chapter 1 discusses current technologies employed in both medical and research laboratories to diagnose IIPA, including culture, imaging, polymerase chain reaction, peptide nucleic acid-fluorescence in situ hybridization, enzyme-linked immunosorbent assay, lateral flow assay, and liquid chromatography mass spectrometry. For each technique, Chapter 1 discusses both promising results and potential areas for improvement with each technique, paying special attention to liquid chromatography mass spectrometry as a potential diagnostic method. Due to the demonstrated need for diagnostic methods that decrease time-to-diagnosis for IPA, Chapter 2 discusses the development and implementation of a method for the quantification for low levels of glucosamine from Aspergillus species using LC-QQQ. The limit of detection in the final method used on samples of Aspergillus was calculated to be 0.020 ± 0.001, with a limit of quantification of 0.061 ± 0.004 ng/mL. The method described in Chapter 2 also has a high internal repeatability (R2 = 0.9996) and does not require a derivatization step for specificity. This allows for ease of translation to a clinical setting. The method was applied to several pathogenic species of Aspergillus, including Aspergillus fumigatus, which causes more than 90% of cases of IPA. Due to the reduced sample prep and run time, high analytical sensitivity, and high specificity the developed glucosamine detection method discussed in Chapter 2 was applied to samples of biological media relevant to clinical diagnosis of IPA in Chapter 3. Artificial sputum medium and artificial bronchioalveolar lavage fluid were used to determine the matrix effects of clinical samples on the developed method. The FDA's bioanalytical method development standards were applied, and it was determined that the artificial media cause extremely strong and inconsistent matrix effects. Separation methods were also tested to remove the glucosamine from the artificial media but were unsuccessful. These results show that the method requires further validation before it can be implemented on clinical samples. Chapter 4 delves into a method to detect CBD, Δ9-tetrahydrocannabinol, and their major metabolites using LC-QQQ. Cannabinoids and their metabolites are of major interest to the medical community due in part to their recent decriminalization. Chapter 4 details the LC-QQQ method developed, as well as the endeavors to account for matrix effects. Several protein precipitation methods were tested in an attempt to reduce sample preparation time and increase throughput. Unfortunately, the separation methods developed did not lead to quality control samples that met FDA standards, so more work is needed before the method can be applied to clinical samples. While the methods described are not fully realized for clinical sample testing, the research described provides valuable insights into a few areas. First, it is the first work to describe LC-QQQ detection of glucosamine derived from several fungal species. The work also provides insight for future method optimization work. Finally, this work demonstrates the effect that matrices can have on method development and some of the problem-solving steps that are required to bring a method from the research lab to a clinical setting.Item Open Access Extending the life of electrochemically deposited anodes in 3D sodium ion batteries with cPAN(Colorado State University. Libraries, 2025) Medina, Dylan, author; Prieto, Amy, advisor; Rappe, Anthony, committee member; Nazemi, Reza, committee memberHumanity constantly seeks to improve the simplicity of their lives, and as such develops technologies to assist with this endeavor. Almost all of these technologies rely on electricity. From large stationary objects to the small mobile devices we see everywhere, they must be charged. For some this means operation almost exclusively on a battery, for others they rely on constant power from the power grid, and most use a rechargeable battery charged from the power grid as a blend. But even power stations have limits for how much they can generate at a time and need to rely on power generated during low demand times to supplement higher demands, and such the power grid also relies on batteries. Chapter I discusses the basis of why energy storage is so important, the history of the modern lithium-ion battery, and where storage technology is heading to improve supplemental battery types. The basics of why sodium ion batteries are attractive as a supplement to lithium-ion batters is outlined. Finally, the geometries of 3D batteries are described, and a key feature leading to uneven distribution of material on 3D electrodes is highlighted. Chapter II focuses on developing a procedure to cyclize polyacrylonitrile (PAN) to act as a binder to keep material in electrical contact to the anode current collector after it fractures and separates. Simple equipment such as a dip coater and a tube furnace are used to evenly coat the substrate with the precursor, which is then annealed to form cPAN. Verification of the cyclization of PAN to form cPAN is done via Fourier Transform Infrared (FTIR) analysis, and sample thickness is measured using scanning electron microscopy (SEM). Once the procedure for the fabrication steps is verified, the actual anodes must be made. In chapter III, cyclic voltammetry is used to get the correct parameters for sample electrodeposition and the anodes are made. After samples were annealed with a layer of cPAN, SEM and energy-dispersive X-ray spectroscopy (EDS) are used to characterize the samples. There is a detailed discussion for the fabrication of a pouch half-cell, and some trends observed when they are evaluated as an electrode using battery cycler. Chapter IV attempts to get a realistic application by placing cPAN coated anodes in a full cell and placing them on a battery cycler. Every step along the way was characterized by measuring the internal resistance, which is noted as an indicator of how or why the cells may be acting abnormally. In conclusion, the overlap of each section is summarized and discussed. The hypothesis for why the cells do not cycle effectively is that the polymer is too thick. Future work will focus on repeating the coating of cPAN onto antimony anodes but with better control over thickness. Refinements to the process such as a thinner polymer layer, calendaring, and a better contact and compression system could provide insight and useful results in the future.