Chemistry Theses and Dissertations
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This collection contains some of the theses and dissertations produced by students in the University of Oregon Chemistry Graduate Program. Paper copies of these and other dissertations and theses are available through the UO Libraries.
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Item Embargo Charge Transport Phenomena in Fe-Based High Surface Area Materials(University of Oregon, 2024-08-07) McKenzie, Jacob; Brozek, CarlWhile conductive metal-organic frameworks (MOFs) and open-framework metal chalcogenides (OFMCs) have received considerable attention in recent years, there are still fundamental questions that remain unanswered. With literature abound describing ion and solvent-dependent conductivity in mesoporous media and nonporous conductive polymers we expect such phenomena to be heightened and unique at the interfacial extremes that microporous materials and 2D Van Der Waals (vdw) materials possess. We utilize the unique properties of Fe-based materials to design model systems in TMA2FeGe4S10 (TMA: tetramethyl ammonium) and Fe(SCN)2(pyz)2 to explore the impact of solvent and electrochemically inert ions on charge transfer and transport. Taken together, this dissertation describes for the first time, critical solvent and ion interactions at interfacial extremes, which must be considered in the design of advanced energy storage technologies where solvent and ion presence is ubiquitous. These advanced energy storage technologies will prove critical in supporting renewable energy generation, to reduce and eventually eliminate CO2 emission.Item Open Access Fundamentals of Electrochemical Interfaces: Insights into Electrodes, Electrolytes, and Ion Transfer Kinetics(University of Oregon, 2024-08-07) Zhao, Yang; Boettcher, ShannonElectrochemistry is a field that lies at the crossroads of electricity and chemistry, focusing on the transformation between electrical and chemical potentials, typically occurring at the electrochemical interfaces - the dynamic region between electrode (electron conductors) and electrolyte (ionic conductors) where electrons are transferred, and ions/molecules are converted. The performance of modern electrochemical technologies for energy conversion and storage, which presents promising approaches for reducing pollutants and facilitating environmentally sustainable chemical processing, relies on a deeper and more profound comprehension of the electrochemical interfaces, specifically at atomic/molecular-scale and in relation to the fundamental steps of the interfacial reactions. However, even in a simple or elementary electrochemical system, the fundamental investigation is challenging, as the processes and the mechanisms that underlie them are complex. The presence of multiple phases contributes to the complexity, which is further amplified when taking into account the interaction of numerous factors influenced by varying potential bias which results in a potential gradient across the interface and the accompanying electric fields. This dissertation provides a comprehensive exploration of electrochemical interfaces, by delving into three fundamental aspects: electrodes, electrolytes, and ion transfer kinetics, each contributing significantly to our comprehensive understanding of electrochemical systems. We illustrate the underlying operational mechanism and design principles for porous carbon electrodes in redox-enhanced electrochemical capacitors. Additionally, we quantitatively assess how thermodynamics, kinetics, and interface layers control the apparent hydrogen evolution reaction activities in water-in-salt electrolytes. Furthermore, for the first time, we experimentally measured and determined the ion-transfer kinetic parameters using a model system of Ag electrodissolution and electrodeposition. Together, this dissertation provides key insights into the fundamental mechanisms that drive electrochemical systems, potentially contribute to the future innovations in energy technologies. This dissertation includes previously published co-authored materials.Item Open Access Understanding Interfacial Chemistry in Metal Based Soft Materials(University of Oregon, 2024-08-07) LeRoy, Michael; Brozek, CarlSoft materials are a class of materials including colloids, polymers, DNA, and proteins. Due to their organization on the mesoscopic length scales they exhibit a wide variety of properties such as self-assembly and response to external stimuli. This has led soft materials to be employed in a wide array of applications ranging from catalysis, electrochemistry, and membrane technologies. Ionic liquids and metal-organic framework are two distinct classes of hybrid organic-inorganic soft materials, that are well studied and used as filler materials for polymer membrane separation technologies. However, a current challenge is understanding how the interfacial chemistry between these filler materials and polymer impacts membrane structures and properties. In this dissertation, molecular chemistry is used to explore how mesoscopic properties give rise to those found in the bulk of ionic liquids and nanoscale metal-organic frameworks respectively.Item Open Access Structural and Electronic Coupling in Nanoscale Materials(University of Oregon, 2024-08-07) McDowell, Benjamin; Nazin, GeorgeAs modern electronic devices continue to shrink in size, the limitations of Si as a transistor material become increasingly imminent. To overcome these limitations, it is necessary to explore alternative materials that can be used in electronic devices that surpass the miniaturization limit of Si-based devices. In this effort, it is important to develop an understanding of how materials behave when they are reduced in size and scale down to ultra-thin structures. Here, we explore how ultra-thin dielectric materials behave differently than their bulk counterparts, experiencing chemical interactions at interfaces that can result in unexpected structures and electronic properties. By using a combination of scanning tunneling microsocopy/spectroscopy and density functional theory, we study several manifestations of distinct structural and electronic properties arising in ultra-thin materials. We extend this physical picture to understand how the properties of these films affect adsorbed nanostructures, analogous to interactions occurring in a transistor setting.Item Open Access USING CIRCULAR DICHROISM AND FLUORESCENCE SPECTROSCOPY TO STUDY THE IMPACT OF 2-AMINOPURINE ON RNA FOLDING(University of Oregon, 2024-08-07) Hoeher, Janson; Widom, JuliaRNA is an important biological molecule, with its function helping out with different processes in cells. How RNA functions is related to its structure, with different structured RNA behaving in different ways. Studying RNA structure is thus important to understand its function. One example of this are riboswitches, which help regulate gene expression. By binding a ligand, the riboswitch refolds, causing a change in gene expression. One method of studying RNA structure is by utilizing fluorescent base analogues of the native bases. To study the riboswitch, the fluorescent base analogue 2-aminopurine (2-AP) was substituted into six different locations in the L3 region of the preQ1 riboswitch. Using circular dichroism (CD) and fluorescence spectroscopy, along with fluorescence lifetimes, it was discovered that all modified locations were detrimental to the riboswitch’s ability to bind the ligand. In addition, fluorescence-detected circular dichroism (FDCD) was used to study short RNA molecules containing 2-AP, of up to three nucleotides in length. By comparing FDCD to CD, it was determined that in dinucleotides, the fluorescence came almost entirely from unstacked populations. Comparatively, while most of the fluorescence from the trinucleotide came from unstacked populations, some came from stacked populations. Through FDCD and CD, the amount of each construct in stacked and unstacked populations can be determined. This dissertation includes previously published co-authored material.Item Open Access QUANTITATIVE DETERMINATION OF GAS-PHASE THERMODYNAMIC BARRIERS OF PROTEINS FOR NATIVE ION MOBILITY-MASS SPECTROMETRY: APPLICATIONS AND IMPLEMENTATION OF AN IMPROVED IMPULSIVE COLLISION THEORY(University of Oregon, 2024-08-07) Shepherd, Samantha; Prell, JamesIon mobility-mass spectrometry is a powerful tool for identifying and elucidating biomolecular structures and behaviors. This technique is able to retain even weak and non-covalent interactions permitting the study of native or native-like gas-phase biomolecular complexes including folded proteins, protein-protein complexes, and protein-ligand complexes. Historically, energetic and thermodynamic information has been limited to techniques on specialized instrumentation and/or computationally expensive strategies. This changed with the development of “proto-IonSPA” to allow rapid determination of thermochemical barriers for protein dissociation and unfolding on modern, commercially available instrumentation. In this work, reproducibility, repeatability, and applications of the use of thermochemical measurements on modern, commercially available instruments are assessed, inspired by a need to compare gas-phase dissociation and unfolding of proteins more broadly. This groundwork enables the development of an Improved Impulsive Collision Theory (IICT) in a Monte-Carlo python script, which in turn improves qualitative and quantitative understanding of activation in Collision Induced Unfolding and Dissociation. This program further enables the determination of gas-phase thermochemical barriers for the dissociation of proteins in modern commercially available mass spectrometers. Reasonable agreement is shown with literature standards and between different mass spectrometer designs and experimental parameters. This agreement is particularly noteworthy due to the drastic difference in timescales being compared (seconds in the literature to as low as microseconds in this work) This dissertation includes previously published co-authored material.Item Open Access INVESTIGATION OF PNICTOGEN-ASSISTED SELF-ASSEMBLY AND SELF- SORTING DESIGN PRINCIPLES TOWARDS PREORGANIZED MACROCYCLES(University of Oregon, 2024-08-07) Mayhugh, Jacob; Johnson, DarrenShape-persistent molecules have abundant chemical potential as organic functional materials. Access to these molecular cages and macrocycles, however, is nontrivial and often require long or low-yielding synthetic pathways that bottleneck their potential applications. To ameliorate this, dynamic covalent chemistry has shown to be promising in the formation of shape-persistent molecules as it marries the error-correction of self-assembly with thermodynamic control while giving the robustness of a covalent bond. The DWJ lab focuses on utilizing dynamic covalent reactions towards the facile preorganization of macrocyclic ensembles through the pnictogen-assisted self-assembly of oligothiols. This dissertation expands upon disulfide self-assembly design principles for a holistic understanding of the method’s boundaries.Chapter I introduces supramolecular concepts that are the cornerstone of this project. Specifically, self-assembly and dynamic covalent chemistry is introduced, with background information on the project’s beginnings provided as well. In Chapter II, the synthetic scope of disulfide self-assembly is explored. Following, Chapter III utilizes our newfound understanding to explore efficient pathways into material formation. iv Specifically, Perylene Diimide-containing macrocycles are generated in an efficient and high throughput dynamic pathway with implication on tailored organic materials. Chapter IV investigates the self-assembly of multicomponent oligothiol systems (self-sorting) towards the predictive assembly of three-dimensional architectures. Chapter V concludes the dissertation and provides potential future directions for this project. This dissertation includes co-authored and previously published results.Item Open Access THE DEVELOPMENT AND APPLICATION OF TRANSITION METAL–HYRDIDES IN CATALYSIS FOR ALKENE HYDROSILYLATION AND ISOMERIATION REACTIONS(University of Oregon, 2024-08-07) Chang, Alison; Cook, AmandaMetal-mediated alkene transformations is a rapidly developing field to obtain various organic precursors for pharmaceutical compounds, industrial chemicals, and consumer products. The pursuit of developing Earth-abundant catalysts is of great interest due to catalyst affordability in comparison to precious metal catalysts. Specifically, Ni catalysts serve as viable alternatives to previous metal catalysts due to the versatile reactivity of Ni. In addition to catalyst development, the catalyst mechanism is also just as important to inform future catalyst design. This often results in guided catalyst optimization and byproduct inhibition. The focal point of this thesis surrounds the development and investigation of Ni-catalyzed alkene hydrosilylation and alkene isomerization. Particularly, the formation of Ni–H intermediates to mediate these organic transformations. Reaction and catalyst optimization, substrate scope, and mechanism determination are reported for both alkene hydrosilylation and isomerization systems. Chapter I highlights the utility of Ni–H in these organic reactions, motivating our work described in Chapters II-VI. Chapter II reports on the reaction development and substrate scope of the homogeneous hydrosilylation (NHC)Ni (NHC = N-heterocyclic carbene) catalyst. Chapter III outlines the mechanistic investigation of the (NHC)Ni-catalyzed alkene hydrosilylation system described in Chapters II. Chapter IV is a continuation of the catalytic system developed in Chapter II and III and delves more deeply to explore the electronic structure of (NHC)Ni(alkene) catalysts. Modification of the NHC ligand gives rise to trends in catalytic ability. To obtain a deeper understanding of this system, ligand steric and electronic variation are tested to observe its influence on catalyst behavior. Chapter V illustrates the incorporation of the in situ hydrosilylation system developed in Chapter II into the remote hydrosilylation of a long chain alkene. This work also includes preliminary data on an in situ generated Ni-catalyzed alkene isomerization system in combination with a hydrosilylation system to install a silicon group distal to the initial reaction site. Chapter VI outlines the development, characterization, and investigation of a heterogeneous Ni alkene isomerization system. This chapter includes catalyst substrate scope, preliminary mechanistic data, and comparison to other Ni-catalyzed alkene isomerization systems. This dissertation includes previously published and unpublished coauthored material.Item Open Access CONFORMATIONAL DYNAMICS OF DNA AND PROTEIN-DNA COMPLEXES AT SINGLE-STRANDED-DOUBLE-STRANDED DNA JUNCTIONS(University of Oregon, 2024-03-25) Maurer, Jack; Marcus, AndrewMost biological systems, particularly protein-DNA complexes, leverage a dynamic evolution of their structure to perform a myriad of functions within the context of the cell. Decades of detailed biophysical research have established that the intricacies of such systems stem heavily from their dynamic evolution, abandoning the previous notion of a purely static ‘structure-function’ relationship. This dissertation introduces a new polarization-sensitive methodology for studying the dynamic evolution of local conformation in single-molecules of dsDNA containing an i(Cy3)2 dimer. The methodology developed during this dissertation is applied to DNA under a variety of experimental conditions as well as protein-DNA complexes. A massively parallel computational pipeline was developed in the course of this work to aid the optimization of kinetic network models, which forms the basis for all current analyses of single-molecule data in the Marcus and von Hippel lab. The primary discovery of this work is the persistence of four relevant conformational macrostates in DNA only systems and five relevant conformational macrostates in the protein-DNA systems examined. The thermodynamic and mechanical stability of these systems is analyzed in detail and structural mechanisms are proposed to merge the observed dynamics with hypothesized local conformations during the dynamic evolution of these ubiquitous biological systems.Item Open Access The Design, Synthesis, and Properties of Strained Alkyne Cycloparaphenylenes.(University of Oregon, 2024-03-25) Fehr, Julia; Jasti, RameshStrained molecules possess the potential energy required to do work in the form of further chemical transformations. Strained alkynes in particular are an attractive handle for such applications as they can undergo the metal-free strain-promoted azide-alkyne cycloaddition (SPAAC). Beyond heightening reactivity, imparting strain also affects other properties, as has been shown in the study of strained conjugated molecules. In this context, strain modulates the electronics of the molecules and typically heightens their conductivity and solubility. These ideas are described in detail in Chapter 1. This work includes published and unpublished coauthored material that highlights both of these applications by focusing on the design and study of strained alkyne-containing carbon nanohoops (also known as [n+1] cycloparaphenylenes or [n+1]CPPs). Carbon nanohoops are highly strained conjugated macrocycles composed primarily of para-substituted phenylene units. Incorporation of an alkyne into the backbone of these molecules provides a handle for controlled strain-promoted reactivity. Modulating the topology and electronics of [n+1]CPPs to in turn alter reactivity towards the SPAAC reaction is the focus of Chapter 2 of this work. Chapter 3 focuses on exploring other types of strain-promoted reactivity, in particular alkyne cyclotrimerization resulting in the formation of pinwheel-shaped large molecules. Finally, early efforts to modulate the emission color of a [n+1]CPP, to synthesize a thermally-activated delayed fluorescence nanohoop, and to synthesize a di-alkyne carbon nanohoop are described in Chapter 4.Item Open Access The Active Template Approach to Mechanically Interlocked Nanocarbons(University of Oregon, 2024-03-25) May, James; Jasti, RameshGraphitic carbon nanomaterials hold tremendous promise for a variety of applications. The realization of this potential, however, has been hampered by the lack of synthetic methods by which we can prepare such materials in a selective manner. On the other hand, through organic synthesis we can construct small molecule analogues of these materials, a.k.a. molecular nanocarbons, in which the structure and composition can be precisely controlled. In doing so, we uncover the fundamental properties associated with these materials at the molecular size regime and begin to fill the gap between molecular and material properties. Furthermore, with organic synthesis we can begin to create nanocarbon structures with exotic topologies that do naturally occur in extended materials. In doing so, the structural landscape available to explore is limited only by the creativity of the pursuer and the synthetic methods available to them. With this in mind, the incorporation of molecular nanocarbons into mechanically interlocked architectures represents an exciting yet underexplored venture in the context of carbon nanoscience. In this dissertation I describe the development of active-metal template methods to incorporate [n]cycloparaphenylenes ([n]CPPs) into mechanically interlocked molecules (MIMs).Item Open Access Enhancing the Antiaromaticity of s-Indacenes Through Heterocycle Fusion(University of Oregon, 2024-03-25) Warren, Gabrielle; Hendon, ChristopherAntiaromaticity, while associated with instability, imparts beneficial properties such as decreased HOMO-LUMO energy gaps. Compounds containing antiaromatic subunits are not only of fundamental interest, but of interest as components in organic electronics. Since antiaromatic compounds are generally unstable, various strategies for isolating these compounds, such as annulation of aromatic subunits, have been developed. While this strategy stabilizes the antiaromatic subunit, it generally decreases the degree of antiaromaticity. Thus, methods to stabilize yet maintain or increase the degree of antiaromaticity are desirable. Recently, we found that fusion of aromatic heterocycles to s-indacene, a known antiaromatic molecule, yields isolable compounds with increased antiaromaticity in the s-indacene core. In this dissertation I will discuss the background of s-indacene and an overview of tuning the antiaromaticity of s-indacene, how fusion of naphthothiophene units increases the antiaromaticity of s-indacene and the development a computational understanding for the effect of heterocycle fusion on s-indacene.Chapter I is an overview of the literature about s-indacene followed by a discussion of the methods used to tune the antiaromaticity of s-indacene by the Haley group. Chapter II describes the synthesis of four naphthothiophene-fused s-indacenes, one of which increased the antiaromaticity of the s-indacene core above unsubstituted s-indacene. Chapter III extends the work of Chapter II further developing the synthesis of naphthothiophene-fused s-indacenes, varying the aryl substituents, and providing a detailed comparison of the properties of all isomers. Finally, Chapter IV explores fourteen different benzoheterocycle-fused s-indacenes through a variety of computational techniques to understand the effect of the heteroatom on the antiaromaticity of the s-indacene core. This dissertation includes previously published and unpublished co-authored material.Item Open Access Functionalized Carbon Nanohoops: Nitrogen-Doped Partial Belts, Macrocyclic Ligands, and The Inherent Strain That Affects Their Chemical Properties(University of Oregon, 2024-03-25) Price, Tavis; Jasti, RameshCycloparaphenylenes and related nanohoops offer a new topology to organic chemists to expand the catalogue of electro-responsive materials. Developments in their synthesis have made many functional groups and arenes accessible for insertion into the bent nanohoop backbone. It is necessary to continue expanding our synthetic toolbox for developing more nanohoops with emergent properties for use in future devices and fundamental exploration of the electronic processes in organic materials. As more diverse nanohoops are developed, it important to characterize their optical and electrochemical properties to advance the field in reliable structure-property relationships. Computational analysis of these exact structures offers a glimpse into these emergent properties to narrow down the list of possible structures. Corroboration with experimental measurements can ameliorate flaws in computational predictions by explaining the delocalized character of π-electrons in the cyclic π-system. Fundamentally, we can also gain insight into how inherent strain affects the optoelectronic properties of any arene substituted into the nanohoop backbone.The following manuscript explains how research on carbon nanobelts has developed over the past 70 years and the nitrogen-doped structures that have come after to tease out more unique properties. The development of synthetic methods leading to pyridinium, quaternary nitrogen, partial belt structures is discussed in the chapter following the history of nanobelts. Chapter 3 presents a new nanohoop ligand using a terpyridine fragment and addresses the optoelectronic differences between the nanohoop-iridium complex and the small molecule analogue. The remaining chapters focus on the computational results of the reactivity of inherently strained molecules, their host-guest properties, and their optoelectronic properties to provide a deeper understanding and relate the structure with the intrinsic properties of strained nanohoop derivatives. These final chapters include previously published co-authored material.Item Open Access Chemistry and Physics of Water Dissociation in Bipolar Membranes(University of Oregon, 2024-03-25) Chen, Lihaokun; Boettcher, ShannonWater dissociation (WD, H2O → H+ + OH−) is the core process in bipolar membranes (BPMs) that limits energy efficiency. Both electric-field and catalytic effects have been invoked to describe WD, but the interplay of the two and the underlying design principles for WD catalysts remain unclear. Furthermore, how WD is driven by voltage and catalyzed is not understood. In Chapter II, by using precise layers of metal-oxide nanoparticles, membrane-electrolyzer platforms, materials characterization, and impedance analysis, we illustrate the role of electronic conductivity in modulating the performance of WD catalysts in the BPM junction through screening and focusing the interfacial electric field and thus electrochemical potential gradients. In contrast, the ionic conductivity of the same layer is not a significant factor in limiting performance. BPM water electrolyzers, optimized via these findings, use ~30-nm-diameter anatase TiO2 as an earth-abundant WD catalyst, and generate O2 and H2 at 500 mA cm−2 with a record-low total cell voltage below 2 V. These advanced BPMs might accelerate deployment of new electrodialysis, carbon-capture, and carbon-utilization technology. In Chapter III, we report BPM electrolyzers with two reference electrodes to measure temperature-dependent WD current and overpotential (ηwd) without soluble electrolyte. Using TiO2-P25-nanoparticle catalyst and Arrhenius-type analysis, Ea,wd was 25–30 kJ/mol, independent of ηwd, with a pre-exponential factor proportional to ηwd that decreases ~10-fold in D2O. We propose a new WD mechanism where metal-oxide nanoparticles, polarized by the BPM-junction voltage, serve as proton i) acceptors (from water) on the negative-charged side of the particle to generate free OH−, ii) donors on the positive-charged side to generate H3O+, and iii) surface conductors that connect spatially separate donor/acceptor sites. Increasing electric-field with ηwd orients water for proton-transfer, increasing the pre-exponential factor, but is insufficient to lower Ea.This dissertation includes previously published and unpublished co-authored materials.Item Open Access Investigation of Ternary Layered Thin Film Materials(University of Oregon, 2024-01-09) Lemon, Mellie; Johnson, DavidThis dissertation focuses on the use of the modulated elemental reactants synthesis method to target previously unknown, metastable compounds. The nucleation and growth of the compounds discovered were monitored via x-ray characterization techniques, leading to insights on the reaction pathways and parameters for trapping kinetic products. The insights about the growth technique contribute to the goal of materials discovery by design. The exploration of the physics behind Laue oscillations and the incorporation of Laue oscillation fitting into GSAS-II is an advance in x-ray characterization techniques, and enabled a deeper, fundamental understanding of the growth of layered compounds.This thesis begins with background and motivation for thin film synthesis before delving into an in-depth description of the modulated elemental reactants synthesis method. An exploration of the reaction pathways of MER precursors as they crystallize into metastable products is described, with three novel materials presented as experimental examples. For Fe0.8V0.2Se2, nucleation of VSe2 grains during the deposition kinetically favor the growth of highly Fe-substituted VSe2. For (PbSe)1+δ(FeSe2)2, interlayer interactions with PbSe stabilize the formation of a novel, hexagonal FeSe2 phase. For (Pb3Mn2Se5)0.6(VSe2), finite size effects and interlayer stabilization promote the formation of a novel, quintuple layer Pb3Mn2Se5 unit cell. In each example, nucleation during the deposition controls the formation of the targeted metastable phases. The second section describes how to extract the maximum amount of structural information from Laue oscillations in thin film samples. Laue oscillations are theoretically explored to understand how to distribution of domains sizes impact their intensities. Laue oscillation fitting is incorporated into the crystallography data analysis software GSAS-II. Laue oscillations are key in the development of an approach to determine the distribution and extent of substitution and/or intercalation of dopant atoms, which is demonstrated for FexV1-ySe2 samples. The remainder of this thesis focuses on the experimental synthesis and characterization of novel Fe-containing phases from MER precursors. This includes the synthesis of a Pb1-xFexSe phase, a range of FexV1-ySe2 compounds with more Fe incorporation than had previously been achieved, and a family of (PbSe)1+δ(FeSe2)n heterostructures.Item Open Access Advancing Anion-Exchange-Membrane Water Electrolyzer Devices: Catalyst Layer Interactions, Degradation Pathways, and Operational Development(University of Oregon, 2024-01-09) Lindquist, Grace; Boettcher, ShannonWater electrolyzers (WEs) are a key technology for a sustainable economy. When powered by renewable electricity, WEs produce green hydrogen, which can be used for energy, fertilizer, and industrial applications and thus displace fossil fuels. Pure-water anion-exchange-membrane (AEM) WEs offer the advantages of commercialized WE systems (high current density, low cross over, output gas compression, etc.) while enabling the use of less-expensive components and catalysts. However, current systems lack competitive performance and durability needed for commercialization, largely limited by the poor stability of anion-exchange polymers used in the membrane and catalyst layers. Further, while non-platinum-group-metal oxygen-evolution catalysts show excellent performance and durability in alkaline electrolyte, this has not transferred directly to pure-water AEMWEs. The following dissertation is a comprehensive analysis of the fundamental processes that dictate pure-water AEMWE performance and stability. Chapter I introduces AEMWEs in the context of industry-scale devices. Chapter II reports AEMWE cell performance comprising entirely of commercially available materials, detailing the key preparation, and operation techniques. In Chapter III, the structural stability and ionomer interactions of non-platinum-group-metal (non-PGM) anode catalysts are characterized. The results show catalyst electrical conductivity is key to obtaining high-performing systems and that many non-PGM catalysts restructure during operation, resulting in lower lifetimes. Chapter IV investigates ionomer degradation during device operation, revealing anode ionomer oxidation is the dominant degradation mechanism for all AEM-based electrolyzers tested. Improved device stability using oxidation-resistant catalyst layer binders is shown and new design strategies for advanced ionomer and catalyst layer development are provided. Chapter V provides a summary of the findings in Chapters III and IV and describes the future outlook for advanced catalyst layer development. Lastly, Chapter VI introduces advanced applications for AEMWE systems, detailing technical barriers and possible research approaches to developing AEM electrolyzers for impure-water splitting. These results significantly improve upon past understanding of pure water AEMWE devices by revealing the fundamental catalyst layer processes resulting in AEMWE device failure under relevant conditions, demonstrating a viable non-PGM catalyst for AEMWE operation, and illustrating underlying design rules for engineering anode catalyst/ionomer layers with higher performance and durability. This dissertation contains previously published and un-published co-authored materials.Item Open Access Nanoparticles of Metal-Organic Frameworks: A General Synthetic Method and Size-Dependent Properties(University of Oregon, 2023-07-06) Marshall, Checkers; Brozek, CarlMetal-organic framework nanoparticles exhibit both high internal surface area and good colloidal stability in a variety of solvents including biological media. These materials are sought after for a range of applications, mainly in drug delivery, catalysis, and separation membranes. Considerable effort has been put into controlling the size and shape of MOF crystals to develop materials that, due to small particle size and good colloidal stability, may be solution-processable. In this thesis, a simple model to help predict size trends in MOF nanoparticle syntheses is developed, then the model is applied both to well-known and novel MOF nanoparticle systems. In Chapter 2, I first present a simple equilibrium model to further our understanding of how to control MOF nanoparticle size. MOF nanoparticles can be synthesized via several top-down and bottom-up approaches. One of the most prevalent bottom-up methods is to use “modulators,” molecules added to the growth media to change the reaction conditions and therefore the crystals’ growth. This chapter encompasses a literature-based perspective on how the presence and identity of a modulator will impact the final size of a MOF nanoparticle and introduces the “Seesaw model" to explain these effects. In Chapter 3, I then apply this model to the well-known nanoMOF systems Zn(mIm)2 (ZIF-8) and Cu3BTC2 (HKUST-1). We show that, by using a mixture of a conjugate acid/base pair, that both modulator equivalents and proton activity play a role in determining final particle size. In Chapter 4, I first develop the synthesis for a novel nanoMOF system, a family of metal-triazolate MOFs, then explore the MOF Fe(1,2,3-triazolate)2 in more depth for its size-dependent optical and electronic properties. Finally, in Chapter 5, the effects of ion identity, solvent identity, particle size, and film thickness on the redox activity of Fe(TA)2 thin films is studied in depth. This dissertation contains both published and unpublished co-authored material.Item Open Access Modulating the Electronic Structure of Metal–Organic Frameworks through Nuclear Rearrangement(University of Oregon, 2023-07-06) Fabrizio, Kevin; Brozek, CarlThe emergence of metal-organic frameworks (MOFs) as a class of versatile and renewable materials has instigated a paradigm shift in the field of chemistry. Their exceptional properties, such as high surface area, tunable porosity, and chemical and thermal stability, have garnered intense research interest for a wide range of applications, including gas storage, separation, sensing, and catalysis. Among the expansive library of MOFs, photoredox-active MOFs have gained particular attention due to their ability to reversibly store charges and photocatalytically degrade contaminants – a task necessary in the fight against climate change. However, poor orbital overlap and charge delocalization in most MOFs limit their efficiency in visible-light catalysis. In this dissertation, we explore the idea of improving MOF photocatalyst performance through reversible external stimuli. Each chapter delves into a distinct external stimulus and its effect on the electronic structure of MOFs. We investigate how cations, crystal size, and temperature affect nuclear rearrangements in MOFs, leading to a deepened understanding of how to improve photocatalytic performance. Taken together, this dissertation provides an analysis of the effect of nuclear rearrangement on defining the electronic structure in MOFs, and it lays a foundation for the development of new, highly efficient MOF photocatalysts.Item Embargo Local Structure and Conformational Disorder at Single-Strand--Double-Strand DNA Junctions(University of Oregon, 2023-03-24) Heussman, Dylan; Cina, JeffreyDNA functions as a stable repository for heritable information across generations. However, the structure of DNA within the cell must be dynamic, allowing for thermally induced fluctuations to facilitate the recognition and assembly of functional protein-DNA complexes. For example, the local conformations of the sugar-phosphate backbones near the replication fork junction are likely recognized by protein components during DNA replication. The presence of local backbone disorder (i.e., the absence of an ordered conformation) within duplex and ss-ds DNA junctions indicates a distribution of local backbone conformations that could, for example, facilitate kinetic competition between distinct protein regulatory factors. By fitting a theoretical model to experimental absorbance and circular dichroism (CD) spectra, the ensemble average conformations (relative orientation and distances) of Cy3 dimer probes within the DNA constructs was determined as a function of insertion site position and temperature. The results of our analyses were subsequently compared using increasingly complex models of exciton coupling between individual Cy3 labeling sites. To investigate local conformational disorder of the sugar-phosphate backbones as a function of temperature and proximity to protein binding sites, two-dimensional fluorescence spectroscopy (2DFS) was used, which allowed for direct characterization of the local conformational disorder at the Cy3 labeling sites. The presence of local disorder at and near ss-ds DNA junctions suggests that these sites undergo rapid interconversion between different conformations, which were studied under varying DNA composition and buffer conditions, and with a novel technique, single molecule polarization sweep microscopy. The effect of assembling T4 bacteriophage helicase loading (gp59) and single strand binding protein (gp32) on the DNA ds-ss junction was examined and some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites. This dissertation includes previously published and unpublished co-authored material.Item Open Access Defining the Molecular Mechanisms that Regulate SHIP1 Activity and Membrane Localization in Immune Cells(University of Oregon, 2023-03-24) Waddell, Grace; Hansen, ScottSpatial heterogeneity in many membrane proximal signaling reactions emerges from biochemical reactions involving phosphatidylinositol phosphate (PIP) lipids, kinases, phosphatases, and Rho-family GTPases. Interconnected positive and negative feedback loops control the communication between these distinct families of signaling molecules to regulate cell polarization, cortical oscillations, and transient spikes in biochemical activities. Together, these networks of biochemical reactions provide the molecular basis for signal adaptation modules that control cell polarity and migration. Of particular importance to these cellular processes is the hematopoietic-cell-specific lipid phosphatase, SHIP1, which regulates the dephosphorylation of PI(3,4,5)P3 lipids to generate PI(3,4)P2. We find that in non-migratory PLB-985 cells, SHIP1 colocalizes to cortical oscillations with Cdc42 GTPase and FBP17. In the presence of chemoattractant, SHIP1 polarizes to leading-edge membranes of migrating cells. Molecular dissection of SHIP1 domain organization and activities identified a minimal C-terminal motif that is necessary and sufficient for targeting to SHIP1 to cortical oscillations. Using supported lipid bilayers to biochemically characterize SHIP1 revealed that the full-length protein is autoinhibited. SHIP1 autoinhibition is predominantly regulated by its N-terminal SH2 domain and can be relived with the addition of immune receptor derived phosphotyrosine peptides. Finally, single molecule dwell time measurements in vitro and in vivo revealed that interactions between SHIP1 and various lipid species are surprisingly weak and likely serve a secondary role following membrane recruitment mediated by SHIP1-protein interactions. This dissertation includes unpublished co-authored material.