Chemistry Theses and Dissertations

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https://hdl.handle.net/1794/2046

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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Open Access
Unique Mechanisms of Colloidal Stability Probed by Surface-Specific Vibrational Spectroscopy
(University of Oregon, 2024-12-19) Mapile, Ashley; Scatena, Lawrence
The stability of nanoparticles suspended in a solution, known as colloids, is crucial for their application in drug delivery systems, the solution processibility required for drop-casting films, and the long-term storage or transport of sensitive chemical materials. While current mechanisms for colloidal stability include implicit models of solvation – namely Derjaguin-Landau-Verwey-Overbeek (DLVO) and Flory-Huggins theories – these classical approaches neglect the role of specific solvent-surface interactions. Analyzing these surface-specific interactions in colloidal stability becomes increasingly relevant for nanosized particles, which have a highly accessible surface area compared to their bulk counterparts.This dissertation seeks to understand unconventional mechanisms of colloidal stability that are not explained by traditional theories alone, with oil-in-water emulsions and nanoparticles of metal-organic frameworks (nanoMOFs) as model materials. Leveraging the surface-specific spectroscopic technique, vibrational sum frequency scattering spectroscopy (VSFSS), this work provides a molecular-level understanding of the specific surface interactions that contribute to colloidal stability. In particular, emulsions can be stabilized by a steric layer of polymer alone, with colloidal behavior tunable by pH, electrolyte concentration, molecular weight, and temperature. These sterically-stabilized emulsions find applications in drug delivery systems that must withstand extreme physiological conditions. For bare nanoMOFs, an ordered solvation shell and solvent-metal surface binding contribute to unforeseen long-term stability in common solvents. Additionally, nanoMOFs coated with a polymeric binding agent – similar to those used in the paint industry – yield ultra-strong mixed-matrix membranes for gas separation technologies. Ultimately, this work bridges molecular interfacial chemistry with material properties, emphasizing the importance of understanding mechanisms of colloidal stability. This dissertation includes previously published co-authored material.
Open Access
Fourier Transform Based Analysis of Mass Spectra: Disentangling Mass Heterogeneity and Polydispersity
(University of Oregon, 2024-12-19) Swansiger, Andrew; Prell, James
Understanding the interactions of small molecules with biomolecules and their complexes is fundamental to the clinical interpretation of biological functions and pharmaceutical development. Conversely, these delicate interactions present a multiplexed problem requiring highly specific and sensitive analytical techniques to capture their subtle variances. Advances in soft ionization mass spectrometry (MS) methods such as electrospray ionization (ESI) and desorption electrospray ionization (DESI) have brought together solution phase separation techniques and sensitive gas phase analysis, reducing both sample concentration and purification requirements and enabling fast multiplexed analysis of data-rich biological samples. As the limitations on analyte size and complexity continue to be pushed back by instrumental and experimental innovations, MS deconvolution tools need to continually advance to keep pace with the increased mass heterogeneity and polydispersity of what we can successfully spray. Among current MS deconvolution algorithms, Fourier transform and Gábor transform (FT/GT) provide a consistent and invertible transform for quick recognition of several classes of periodic signal from polydisperse samples, requiring very few a priori assumptions about the sample while extracting the charge and mass information required by other algorithms for accurate modeling of congested mass spectra. The Prell group’s iFAMS software represents the state-of-the-art in Fourier deconvolution of mass spectra, enabling flexible selection of analyte signals from a spectrogram of m/z and frequency to filter out interferent ions. However, assignment of aperiodic mass shifts in data-rich spectra still proves challenging, as they do not produce unique frequency signals, requiring an understanding of previously unutilized aspects of FT/GT deconvolution for mass spectrometry. Additionally, although iFAMS results are highly reproducible, applications of iFAMS data analysis have remained mostly exploratory, as GT lacks a sufficiently high-throughput implementation for analysis of large data sets. In the first half of this dissertation, a new tool for mass spectrometry Fourier analysis is developed, utilizing the phase angle information from FT/GT for the characterization of small mass variants embedded in polydisperse mediums such as polymers and lipid membranes. The new method of FT/GT macromolecular mass defect (MMD) analysis achieved similar mass accuracy to mass-domain deconvolution methods and is robust to high instrument noise and low mass contaminants, enabling cross-validation of mass-domain deconvolution models. In a workflow complemented with liquid chromatography mass spectrometry, FT/GT MMD analysis enables characterization of polymer reaction intermediates. The second half of the dissertation extends the reproducibility of FT/GT analysis to protein quantitation of MS imaging data from biological tissue, developing a new workflow for batch deconvolution to process tens of thousands of spectra in a few hours. The distinct protein ion patterns generated by GT simplify characterization of brain tissue eluents, while expanding the range of isolatable proteoform signal available for imaging. This dissertation includes previously published and unpublished co-authored material.
Open Access
Substitution and Analysis of Additional Heteroatoms in 1,2λ5-Azaphosphinines
(University of Oregon, 2024-12-19) McNeill, John; Haley, Michael
Azaphosphinines are, simply put, six-membered heterocycles containing one nitrogen and one phosphorus atom. While garnering more attention in the last couple decades, they are still decidedly understudied. This lack of research is primarily due to the difficult and often intense reaction conditions required to synthesize them. This is especially true for the azaphosphinine moiety’s early iterations. In the Haley and Johnson groups we have found a facile synthetic pathway that allows us to circumvent these issues. In this dissertation I will discuss not only a history of the azaphosphinine functional group but also the results of my independent research. The main body of my Ph.D. work is concerned with the substitution of additional heteroatoms into our thoroughly studied azaphosphinines. These substitutions result in dramatic changes to both the supramolecular and photophysical properties of the heterocycles. While most of the work I will discuss is related to different orientations of pyrido-fused azaphosphinines, I also include a study on the thionation of the ubiquitous phosphoryl group. Chapter I is a holistic review of azaphosphinines. I begin by discussing the nomenclature and unusual electronic properties of these heterocycles before detailing a chronological progression of the literature concerning the three isomers and both valencies of the azaphosphinine functional group. In Chapter II I describe the synthesis and unexpected tautomerization effects observed in pyrido[2,3-e]-1,2λ5- azaphosphinines. Chapter III continues to explore the electronic effects of a pyrido fusion, but in this case, we are now considering the internal charge transfer present in pyrido[3,4-e]-1,2λ5-azaphosphinines. And lastly Chapter IV examines the thionating effect of Lawesson’s Reagent on our heterocycles and the dramatic impacts this transformation has on their photophysical properties. This dissertation includes previously published co-authored material.
Open Access
Towards an Understanding of S100A9 Activation of TLR4: Incorporating a Biochemical and Evolutionary Perspective.
(University of Oregon, 2024-12-19) Chisholm, Lauren; Harms, Michael
The central puzzle of my dissertation work is understanding how two molecules with very different physiochemical properties activate the same receptor, Toll-like receptor 4 (TLR4). TLR4 is an innate immune receptor that responds to both the bacterial glycosylated phospholipid LPS and small soluble host proteins. Despite decades of work, we have little mechanistic understanding of how soluble proteins activate this receptor. S100A9 is one such soluble protein, or Damage Associated Molecular Pattern (DAMP), that activates inflammatory pathways via Toll-like receptor 4 (TLR4). This activity plays important homeostatic roles in tissue repair, but can also contribute to inflammatory diseases. The mechanism of activation is unknown. Learning more about the mechanism of S100A9-induced inflammation can improve our understanding of many disease pathologies, as well as providing a promising new therapeutic target. In this dissertation I describe my work addressing this gap in the literature, using biochemical, biophysical, computational, and evolutionary methods. This dissertation includes previously published and unpublished co- authored material.
Open Access
Advancing the Chemical Understanding of Hydrogen Sulfide and Related Reactive Sulfur Species with Small Molecule Tools for Delivery and Sensing
(University of Oregon, 2024-12-19) Fosnacht, Kaylin; Pluth, Michael
Reactive sulfur species (RSS), such as thiols, polysulfides, hydrogen sulfide (H2S), and persulfides (RSSH), play essential roles in biological chemistry, including roles in redox homeostasis and small molecule signaling pathways. Previously known as a toxic gas, H2S was established as a gasotransmitter in the late 1990’s and is defined as a membrane permeable small molecule that is endogenously produced and involved in specific cell signaling pathways. For this reason, the association of H2S imbalances with various diseases, such as Parkinson’s disease, diabetes, and asthma, has been studied and changes in endogenous H2S are indicated as a potential disease biomarker. More recently, the importance of persulfides and other RSS in addition to H2S has become a major research focus due to their overlap in activity with H2S and newly discovered importance in biological processes. In particular, recent work has further clarified that many cellular signaling processes initially attributed to H2S are likely due to persulfides. Overall, understanding the RSS pool both fundamentally and also in biological systems is crucial. Carefully developed tools to both detect and deliver RSS are needed to further understand the rich chemistry of RSS within the body.Within this dissertation three main aims are addressed: (1) improved H2S sensing tools for longer duration studies, (2) donor molecules that release RSS, and (3) increasing fundamental understanding of persulfide reactivity. Chapter I is a comprehensive review of fluorescent probes of H2S and other RSS and includes discussion of the important advantages and limitations of each probe type. Chapter II features a cell-trappable H2S probe that provides a large, selective fluorescence turn-on to H2S and was used to sense H2S in live cells. Chapter III details a palette of thiol-activated H2S donors that also produce a fluorescent response in the blue to NIR emission wavelength range. Notably, the NIR donor was applied to live rats to image the fluorescence turn-on when subcutaneously delivered. Chapter IV describes the development of a small library of esterase-activated persulfide donors and kinetic analysis of persulfide release, donor side reactivity, and observed persulfide persistence. Chapter V is a combined computational and experimental analysis of persulfide reactivity with thiols where increasing steric bulk or electron withdrawal near the persulfide can shunt persulfide reactivity through the transpersulfidation pathway. Experimentally, we used a persulfide donor and persulfide trapping agent to monitor and measure transpersulfidation from a bulky penicillamine-based persulfide to a cysteine-based thiol, which is the first direct observation of transpersulfidation between low molecular weight species. This dissertation includes previously published co-authored material.
Embargo
Charge Transport Phenomena in Fe-Based High Surface Area Materials
(University of Oregon, 2024-08-07) McKenzie, Jacob; Brozek, Carl
While 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.
Open Access
Fundamentals of Electrochemical Interfaces: Insights into Electrodes, Electrolytes, and Ion Transfer Kinetics
(University of Oregon, 2024-08-07) Zhao, Yang; Boettcher, Shannon
Electrochemistry 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.
Open Access
Understanding Interfacial Chemistry in Metal Based Soft Materials
(University of Oregon, 2024-08-07) LeRoy, Michael; Brozek, Carl
Soft 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.
Open Access
Structural and Electronic Coupling in Nanoscale Materials
(University of Oregon, 2024-08-07) McDowell, Benjamin; Nazin, George
As 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.
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, Julia
RNA 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.
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, James
Ion 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.
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, Darren
Shape-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.
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, Amanda
Metal-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.
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, Andrew
Most 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.
Open Access
The Design, Synthesis, and Properties of Strained Alkyne Cycloparaphenylenes.
(University of Oregon, 2024-03-25) Fehr, Julia; Jasti, Ramesh
Strained 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.
Open Access
The Active Template Approach to Mechanically Interlocked Nanocarbons
(University of Oregon, 2024-03-25) May, James; Jasti, Ramesh
Graphitic 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).
Open Access
Enhancing the Antiaromaticity of s-Indacenes Through Heterocycle Fusion
(University of Oregon, 2024-03-25) Warren, Gabrielle; Hendon, Christopher
Antiaromaticity, 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.
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, Ramesh
Cycloparaphenylenes 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.
Open Access
Chemistry and Physics of Water Dissociation in Bipolar Membranes
(University of Oregon, 2024-03-25) Chen, Lihaokun; Boettcher, Shannon
Water 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.
Open Access
Investigation of Ternary Layered Thin Film Materials
(University of Oregon, 2024-01-09) Lemon, Mellie; Johnson, David
This 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.