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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A Bioorthogonal Approach to Studying Platinum Drug Targets Using Modified Platinum (II) Complexes With Alkyne- and Azide-Containing Handles
(University of Oregon, 2015-08-18) White, Jonathan; DeRose, Victoria
The compound cisplatin and related FDA-approved Pt(II) therapeutics have been used ubiquitously to treat a variety of cancers since the late 1970’s. Despite the success of Pt therapeutics, their use is limited by undesirable side-effects such as hearing loss, peripheral neuropathy, and severe kidney damage, in addition to intrinsic and acquired resistances. Despite the need to further study and understand this important class of compounds, we lack a comprehensive understanding of global Pt drug targets which would lend vital insight into the molecular mechanisms of action of Pt. This dissertation describes a novel technology using modified Pt(II) drug analogues which contain bioorthogonally reactive handles to study Pt drug targets using post-binding covalent modifications. Chapter I describes the history of Pt anticancer therapeutics and early efforts made to elucidate their mechanism of activity. New methods to track and analyze Pt in biological systems are needed to further study Pt therapeutics, for which we have chosen to modify Pt compounds to contain small, minimally invasive bioorthogonally reactive handles. These handles allow for subsequent fluorescent detection or isolation via the azide-alkyne cycloaddition reaction, or prototypical “click” reaction. Chapter II describes the synthesis of the first difunctional click-modified Pt(II) complex capable of post-binding covalent click modification. Both rRNA and tRNA were identified as targets of Pt in vivo. Chapter III describes the use of another azide-appended Pt chelate complex in post-binding target studies. Click labeling of Pt-bound model protein was demonstrated, along with the further characterization of Pt-rRNA targets, which are shown to be relatively long-lived in Saccharomyces cerevisiae. Chapter IV describes the first alkyne-appended Pt(II) complex capable of post-binding click modification, which undergoes a re-arrangement to form the stable N-sulfonyl amide upon fluorescent “turn-on” ligation with dansyl azide. Chapter V reports the azide analogue of the aforementioned Pt-alkyne complex and demonstrates fluorescent localization studies in triple-negative human breast cancer cell lines, observing significant nucleolar and nuclear Pt localization. Finally, Chapter VI summarizes miscellaneous work in developing additional syntheses to generate small, azide-appended ethylenediamine and peptide-coupled alkyne derivatives of cisplatin. This dissertation includes previously published and unpublished co-authored material.
Open Access
A Liquid-Helium-Free High-Stability Cryogenic Scanning Tunneling Microscope for Atomic-Scale Spectroscopy
(University of Oregon, 2015-08-18) Hackley, Jason; MarcusNazin, AndrewGeorge
This dissertation provides a brief introduction into scanning tunneling microscopy, and then Chapter III reports on the design and operation of a cryogenic ultra-high vacuum scanning tunneling microscope (STM) coupled to a closed-cycle cryostat (CCC). The STM is thermally linked to the CCC through helium exchange gas confined inside a volume enclosed by highly flexible rubber bellows. The STM is thus mechanically decoupled from the CCC, which results in a significant reduction of the mechanical noise transferred from the CCC to the STM. Noise analysis of the tunneling current shows current fluctuations up to 4% of the total current, which translates into tip-sample distance variations of up to 1.5 picometers. This noise level is sufficiently low for atomic-resolution imaging of a wide variety of surfaces. To demonstrate this, atomic-resolution images of Au(111) and NaCl(100)/Au(111) surfaces, as well as of carbon nanotubes deposited on Au(111), were obtained. Other performance characteristics such as thermal drift analysis and a cool-down analysis are reported. Scanning tunneling spectroscopy (STS) measurements based on the lock-in technique were also carried out and showed no detectable presence of noise from the CCC. These results demonstrate that the constructed CCC-coupled STM is a highly stable instrument capable of highly detailed spectroscopic investigations of materials and surfaces at the atomic-scale. A study of electron transport in single-walled carbon nanotubes (SWCNTs) was also conducted. In Chapter IV, STS is used to study the quantum-confined electronic states in SWCNTs deposited on the Au(111) surface. The STS spectra show the vibrational overtones which suggest rippling distortion and dimerization of carbon atoms on the SWCNT surface. This study experimentally connects the properties of well-defined localized electronic states to the properties of their associated vibronic states. In Chapter V, a study of PbS nanocrystals was conducted to study the effect of localized sub-bandgap states associated with surface imperfections. A correlation between their properties and the atomic-scale structure of chemical imperfections responsible for their appearance was established to understand the nature of such surface states. This dissertation includes both previously published/unpublished and co-authored material.
Open Access
A Molecular Approach to Nanoparticles: Using the Molecular-Interface to Influence Growth, Enhance Electrochemical Behavior and Drive Biocompatibility
(University of Oregon, 2020-02-27) Kellon, Jaclyn; Hutchison, James
Nanoparticles have garnered much interest over the past 30 years due to their unique size-dependent properties. The majority of research initially focused on developing synthetic methods to produce uniform materials with a wide range of core compositions, sizes and morphologies. The second generation of nanoparticle research has focused on modifying and improving upon existing synthetic methods to access more complex nanoparticle compositions and morphologies. In addition, chemists have begun exploring methods of introducing functionality into the ligand shell and modifying the surface chemistry of nanoparticle cores to access or enhance desired properties. This dissertation focuses on this newer class of nanoparticles, specifically looking at the influence of the ligand shell as a molecular-interface between the nanoparticle core and its surroundings. Three distinct areas of research are explored throughout this dissertation: 1) using the ligand shell to enhance electrochemical behavior, 2) understanding how coordinating molecules influence nanoparticle growth and 3) investigating the influence of a molecular coating on nanoparticle toxicity. The first two studies presented here explore how the molecular-interface can be employed to attach nanoparticles to conductive substrates. Methods of fabricating nanoparticle-functionalized electrodes with a defined molecular interface are introduced in the first study while the second study demonstrates the enhanced electrochemical behavior achievable in these systems. The role of coordinating molecules and air in the formation of cobalt oxide nanoparticles are explored in the third study. Lastly, the fourth is a systematic study to determine which structural features of metal oxide nanoparticles drive nanoparticle toxicity. The structure-property relationships described in this dissertation can be used for the smart design of safer new materials.
Open Access
A New Mechanism for Genomic Nucleosome Positioning by Native ISWI and Engineered CHD Chromatin Remodeling Proteins is Driven by Sequence-Specific DNA Binding.
(University of Oregon, 2021-09-13) Donovan, Drake; Selker, Eric
Encoded within DNA are all the instructions that a cell needs to survive, and these instructions must be regulated such that cells take the appropriate actions in response to environmental and developmental cues. One way that the DNA is regulated is that a portion of it is wrapped around proteins to form structures known as nucleosomes, which makes the wrapped DNA inaccessible to the machinery that reads the genetic code. Thus, the location of these nucleosome structures on the DNA plays a large role in which genes are active at what times. The location of nucleosomes on the DNA is partially regulated by a family of enzymes called chromatin remodeling proteins. While the function of chromatin remodeling proteins to position nucleosomes is well understood, the mechanisms by which they do so have not been thoroughly tested and are thought to be non-specific. It is unknown, for example, how chromatin remodeling proteins know when and where to position a nucleosome on a given DNA sequence. Reconciling how these supposedly non-specific molecular machines result in highly specific chromatin structures is the focus of this dissertation. The first part of this work challenges the idea that a chromatin remodeling protein in yeast, Isw2, acts as a non-specific nucleosome spacer. Instead, the use of biochemical and genomic techniques shows us that Isw2 is directly targeted to particular nucleosomes in a sequence-specific manner through interactions with other proteins. Further, it suggests that this mechanism may potentially exist in humans. In the second part of this work, we use the idea of sequence-specific targeting seen in Isw2 to engineer another chromatin remodeling protein, Chd1. This allows us to directly target particular nucleosomes in a synthetic manner both in test tubes and in living cells. Excitingly, we show that the use of these engineered proteins allows us to control DNA access and downstream biological outputs in yeast. Overall, this dissertation contributes a completely new understanding of how chromatin remodeling proteins can be directed to act on specific target nucleosomes both natively in eukaryotes and synthetically by researchers. This dissertation includes previously published co-authored material.
Open Access
A Study of the Behavior and Localization of PT(II) Azide and Alkyne-Modified Derivatives in Cells Using Bioorthogonal Chemistry and Fluorescence Microscopy
(University of Oregon, 2016-11-21) Moghaddam, Alan; DeRose, Victoria
Despite their ubiquitous use, Pt(II) anti-cancer drugs still suffer from many issues such as off-drug target effects, renal and nephrotoxicity as well as acquired and intrinsic drug resistance. To obtain a better understanding of how to mitigate these deleterious effects can be mitigated we first must know all the targets of these drugs. Highlighted in this dissertation is previous work performed by groups exploring the localization of Pt in cells using fluorescence microscopy. While Pt drugs such as cisplatin contain no native fluorescence, a great deal of work has been done to covalently modify complexes with fluorescent tags. From studies using this technique, it been reported that Pt can target a number of compartments within the cell ranging from the nucleus to the cytoplasm. With each different derivative being observed in varied cell lines it becomes difficult to deconvolute a universal pattern to where Pt localizes, furthermore, the connected fluorophore could also bias Pt localization. To add general functionality and eliminate the bias of a pre-tethered fluorophore our lab has developed a number of different azide and alkyne-modified complexes that append a “reactive handle” to Pt compounds. This modification allows for use of the bioorthogonal azide-alkyne click reaction we are able to observe Pt localization after treatment. The focus of this work includes method development to conjugate a fluorophore to our Pt complexes in vitro and in cell cultures. We examined a number of different cell lines and observed frequent localization in the nucleolus of the cell. Also in this work is the development of methods to append multiple fluorophores to each Pt site to increase our ability to visualize these complexes in cells. Finally, we have also constructed a new Pt-azide that exhibits slower exchange kinetics due to a chelating exchangeable group. The use of this new complex will enable studies to determine whether changing the leaving group results in differential localization of Pt drugs in cells.
Open Access
Activity of Atypical Protein Kinase C: From Regulation to Substrate Localization
(University of Oregon, 2014-06-17) Graybill, Chiharu; Stevens, Tom
The phosphorylation activity of protein kinases is involved in virtually all biological processes of living organisms. As uncontrolled kinase cascades cause devastating defects such as cancer, cells employ complex regulatory networks to precisely control their activity. Atypical Protein Kinase C (aPKC) is a well-conserved protein kinase that plays a central role in the establishment of the Par complex-mediated cell polarity. The goal of my research is to understand how aPKC activity is regulated and how aPKC phosphorylates its substrates. The first part of my study focused on the mechanism by which intra- and intermolecular interactions regulate aPKC activity. aPKC contains a pseudosubstrate domain that acts as an internal inhibitor. Despite the presence of the cis-acting inhibitor, another Par complex member, Par-6, is thought to repress aPKC activity. To examine the precise mechanism by which the pseudosubstrate domain and Par-6 regulate aPKC activity, I reconstituted the system in vitro and performed a detailed kinetic analysis. We confirmed that the pseudosubstrate domain is responsible for the autoinhibition. Surprisingly, rather than acting as an inhibitor, Par-6 activates aPKC by displacing the pseudosubstrate from the kinase domain. Par-6 activation of aPKC is consistent with our observation that the Par-6/aPKC complex, but not aPKC alone, releases its substrate from the cell membrane in Drosophila S2 cells. The data support a model in which aPKC activity is coupled to localization via Par-6. In the second part, I investigated how the phosphorylation activity of aPKC is coupled to cortical displacement of fate determinants, which often contain multiple phospho-accepting residues. Using Lgl as a model substrate in S2 localization assays, I examined the role of multiple phosphorylations and found that multi-site phosphorylation is required for cortical release. Also, I examined how aPKC phosphorylates Lgl in an in vitro kinase assay and found that aPKC cooperatively phosphorylates Lgl in an ordered manner. These results provide new insights into how multiple phosphorylation and phosphorylation rates could regulate localization behaviors of fate determinants at the cortex. This dissertation contains previously published coauthored materials as well as unpublished materials.
Open Access
Adaptive Evolution in Primate Immune Receptors
(University of Oregon, 2021-09-13) Paterson, Nicole; Barber, Matthew
Pathogens and parasites have evolved effective strategies to gain access to host resources. The immune system fends off these attacks, often through detection of pathogen associated molecules and clearance of infection. This results in interactions between host and pathogen that often take place at molecular interfaces of immune receptors that act as a first line of defense to infection. Such receptors must identify pathogen-specific molecules and mount an appropriate response. Due to the frequency of such high stakes interactions between immune receptors and pathogen-derived molecules, the immune system is under constant evolutionary pressure to innovate new modes of defense and detection, while the pathogen is under pressure to evade these efforts and mount offensive attacks. This dynamic, called evolutionary conflict, is the underlying evolutionary principle inspiring this work. Because proteins evolve functions through DNA modifications, we study the effects of nucleotide variation across related species and test how variation affects the dynamics of protein interactions. We show that phylogenetic relationship is not a good indicator of functional similarity in the systems we tested. In the first study in Chapter II, we found that presence of certain amino acids in ligand-binding hotspots are more likely to have an effect on whether a Staphylococcus aureus inhibitor binds to immune receptor than overall sequence homology. In the second study that comprises Chapter III, we found a similar lack of correlation between predicted functional outcomes and familial relationship. Similar to the study in Chapter II, we found that certain sites could have an outsized effect on function that could be translated across multiple species. Interestingly, site-level similarities at “hotspot” regions were a better indicator of function than phylogenetic relationships.
Open Access
Advanced Characterization of Aqueous Inorganic Nanoscale Clusters
(University of Oregon, 2015-08-18) Jackson Jr, Milton; Page, Catherine
Inorganic nanoscale clusters have garnered significant interest for many practical applications within the fields of materials chemistry, inorganic chemistry, geochemistry, and environmental chemistry. However, the fundamental inner workings of how these materials interact in the solid state and solution continues to be a very elusive problem for scientists. My dissertation focuses on taking non-traditional approaches and characterization techniques to further understand the dynamic interactions of some of the aforementioned clusters. Chapter I is a comprehensive survey and perspective on selected characterization techniques used to study Group 13 aqueous nanoscale clusters and other polyoxometalates in solution. Chapter II focuses on utilizing Raman spectroscopy, infrared spectroscopy, and quantum mechanical computations to unambiguously identify Group 13 tridecameric species in the solid state and aqueous solution. Chapter III discusses the first instance of transmetalation of aqueous aluminum clusters via salt addition of In(NO3)3 in aqueous or methanol. Chapters IV and V explore the effects that aprotic and protic solvents can have on the solution speciation of the flat aluminum tridecamer. Chapter VI discusses the utility of using electrochemically synthesized gallium tridecamer and its functional use as a thin film semiconductor. Chapter VII describes a unique graduate level chemistry course designed to allow students to conduct and generate publication-worthy research within the timeframe of the course. Chapter VIII ventures out beyond the group 13 cluster and introduces techniques used to study the formation and stability of aqueous hafnium clusters. Chapter IX details the synthesis and characterization of rhombic structured copper clusters in the solid state. Finally, chapter X highlights my unfinished projects that can propel future research within the lab. This dissertation includes previously published and unpublished co-authored material.
Open Access
Advances in Supramolecular Catalysis: Studies of Bifurcated Hamilton Receptors
(University of Oregon, 2016-02-23) McGrath, Jacqueline; Doxsee, Kenneth
Bidentate ligands are a commonly used class of ligands in catalysis that generate highly-active and selective catalysts. Such bidentate ligands, however, often suffer from synthetic challenges, which can be alleviated by the use of simpler monodentate ligands that assemble through non-covalent interactions to mimic the structure of bidentate ligands at the metal center. To produce a strongly assembled catalyst complex, the Hamilton receptor motif was utilized. Hamilton receptors form six hydrogen bonds with complementary guests and have binding affinities for barbiturates of up to 104 M-1 in CDCl3. Complete bifurcation of the Hamilton scaffold produces a modular ligand structure that allows for modification of either end of the supramolecular ligand structure. Similarly, the barbiturate guest can be synthetically altered creating both chiral guests and guests with differing amounts of steric bulk. Both experimental titration data and density functional theory calculations show that steric bulk discourages binding of the guest while a pre-organized host encourages guest inclusion. Electronic effects on the bifurcated Hamilton system were studied by varying the electron donating or withdrawing ability of the benzamide moiety on the host molecule. Electron withdrawing moieties produce more acidic amide hydrogens on the host which are able to participate in stronger hydrogen bonds with the guest resulting in a stronger host-guest complex. The effects of substitutions on the barbiturate guest were examined as well, and increased steric bulk on the guest resulted in decreased affinities with the host. The bifurcated Hamilton receptor ligands were examined in the palladium-catalyzed Heck reaction of iodobenzene with butyl acrylate. Pd2(OAc)4 was used as a control and all reaction yields with the diphenylphosphine ligand-stabilized Pd were greater than or equal to those obtained with Pd2(OAc)4 alone. The reaction rates did not correlate with the determined binding constants, suggesting that phosphine substitution on the guest plays a larger role than affinity of the complex for the guest. Reaction temperatures were varied, and at lower temperatures the yields increased implying that the strength of the hydrogen bonds between the metal complex and the guest does play a secondary role in the catalysis. This dissertation includes previously published co-authored material.
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, Shannon
Water 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.
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.
Open Access
Amorphous Metal Oxide Thin Films from Aqueous Precursors: New Routes to High-κ Dielectrics, Impact of Annealing Atmosphere Humidity, and Elucidation of Non-uniform Composition Profiles
(University of Oregon, 2018-04-10) Woods, Keenan; Boettcher, Shannon
Metal oxide thin films serve as critical components in many modern technologies, including microelectronic devices. Industrial state-of-the-art production utilizes vapor-phase techniques to make high-quality (dense, smooth, uniform) thin film materials. However, vapor-phase techniques require large energy inputs and expensive equipment and precursors. Solution-phase routes to metal oxides have attracted great interest as cost-effective alternatives to vapor-phase methods and also offer the potential of large-area coverage, facile control of metal composition, and low-temperature processing. Solution deposition has previously been dominated by sol-gel routes, which utilize organic ligands, additives, and/or solvents. However, sol-gel films are often porous and contain residual carbon impurities, which can negatively impact device properties. All-inorganic aqueous routes produce dense, ultrasmooth films without carbon impurities, but the mechanisms involved in converting aqueous precursors to metal oxides are virtually unexplored. Understanding these mechanisms and the parameters that influence them is critical for widespread use of aqueous approaches to prepare microelectronic components. Additionally, understanding (and controlling) density and composition inhomogeneities is important for optimizing electronic properties. An overview of deposition approaches and the challenges facing aqueous routes are presented in Chapter I. A summary of thin film characterization techniques central to this work is given in Chapter II. This dissertation contributes to the field of solution-phase deposition by focusing on three areas. First, an all-inorganic aqueous route to high-κ metal oxide dielectrics is developed for two ternary systems. Chapters III and IV detail the film formation chemistry and film properties of lanthanum zirconium oxide (LZO) and zirconium aluminum oxide (ZAO), respectively. The functionality of these dielectrics as device components is also demonstrated. Second, the impact of steam annealing on the evolution of aqueous-derived films is reported. Chapter V demonstrates that steam annealing lowers processing temperatures by effectively reducing residual counterion content, improving film stability with respect to water absorption, and enhancing dielectric properties of LZO films. Third, density and composition inhomogeneities in aqueous-derived films are investigated. Chapters VI and VII examine density inhomogeneities in single- and multi-metal component thin films, respectively, and show that these density inhomogeneities are related to inhomogeneous metal component distributions. This dissertation includes previously published coauthored material.
Open Access
Anion Sensing in Polar Media by Fluorecent Small Molecule Receptors via Halogen Bonding
(University of Oregon, 2022-10-26) Bates, Hannah; Johnson, Darren
Anions are a ubiquitous class of molecule which play critical roles in many of the environments with which humans concern themselves. From our physiology to nuclear waste to our water supply, anions have been the focus of much of the host- guest chemistry to have emerged within the last five decades. Host-guest chemists have used supramolecular tools, including halogen and hydrogen bonding, along with many others, to reversibly binding these and many other analytes. The purposes of binding are as wide ranging as real-time molecular recognition, catalysis, mechanically interlocked molecules, purification, and many others. Due to the many factors that can contribute to the efficacy of host-guest systems, including solvent effects, pocket size, molecular geometry, pH and others, most systems must be fined tuned for their particular application. One frequently encountered challenge is the competitive nature of any polar solvents, especially water, in solution state binding. Halogen bonding has recently come onto the scene as a potential answer to this problem, often demonstrating higher binding affinities than comparable hydrogen bonding molecules in polar environments. Despite its promise, much remains to be learned about how to best deploy halogen bonding motifs. This lacuna motivates the work covered in this thesis, which explores the design principles behind incorporating halogen bond donors effectively in a variety of arylethynyl; systems which were inspired by similar hydrogen bonding scaffolds published by the Johnson and Haley groups. After examining the successes and pitfalls of these halogen bond receptors in Chapter 3, Chapters 4 and 5 go on to report on the use of halogen bond and hydrogen bond systems in tandem, which are shown to bind the chloride anion notably well in appreciably polar organic solvents. These studies, suggest that the accepted definition of a halogen bond, as presented by IUPAC and discussed in Chapter 1, biases chemists to place undue importance on ensuring that the location of a polarizing group is as close as possible to the halogen-bond donor. Finally, future studies that can help flush out the ideas established in this thesis are reviewed in Chapter 6.
Open Access
Anions and electron-deficient aromatic rings
(University of Oregon, 2008-06) Berryman, Orion Boyd, 1981-
More than two-thirds of all enzyme substrates and cofactors are anionic, emphasizing the essential role that anions play in biological processes. Moreover, anions can have detrimental effects on the environment by causing ground water contamination when anions such as perchlorate, phosphate and nitrate develop in intolerable levels. Owing to the prevalent nature of anions, traditional strategies employed to target anions--including hydrogen bonding, metal ion coordination and electrostatic interactions--have been extensively studied. An alternative approach to anion binding would complement the powerful array of existing techniques. Recently, in the supramolecular chemistry community, new insight has been cast on how anions attractively interact with electron-deficient arenes, suggesting that aromatic rings are a viable anion binding strategy to balance existing methods. Chapter I provides a historical perspective of anions interacting with electron- deficient arenes. This outlook has its origins in the late 1800s with the discovery of colored charge-transfer complexes between donor and acceptor molecules and continues with the progression of the field leading up to the recent supramolecular fascination. Chapter II represents our initial efforts at measuring anion/arene interactions in solution. In particular, sulfonamide based hydrogen bonding receptors were developed with pendant aromatic rings to test the strength of anion/arene interactions in solution. Complementary computational chemistry and crystallography were utilized to supplement the solution studies. Chapter III describes our quantum calculations and crystallographic efforts at using only electron-deficient arenes to bind halides. A Cambridge Structure Database survey supports our emphasis of understanding multiple anion/arene interactions. Chapter IV illustrates how tripodal anion receptors can be developed to bind anions using only electron-deficient aromatic rings. Furthermore, subtle changes in anion binding geometries are observed with isomeric receptors and corroborated with Density Functional Theory calculations. Chapter V is dedicated to the preparation of electron-deficient anion receptors that are conformationally stabilized by hydrogen bonds. Chapter VI is committed to using our knowledge of anion binding to study a series of ethynyl-pyridine sulfonamides capable of hydrogen bonding to small molecules and anions. In conclusion, Chapter VII is a summary and future prospective for the field of anion/arene interactions. This dissertation includes previously published and co-authored material.
Open Access
Auto-Regulation of the MBNL1 Pre-mRNA
(University of Oregon, 2011-06) Gates, Devika P., 1984-
Muscleblind-like 1 (MBNL1) is a splicing factor whose improper cellular localization is a central component of myotonic dystrophy (DM). In DM, the lack of properly localized MBNL1 leads to mis-splicing of many pre-mRNAs. The mechanism by which MBNL1 regulates it pre-mRNA targets is not well understood. In order to determine the mechanism by which MBNL1 regulates alternative splicing, a consensus RNA binding motif for Mbl (the Drosophila ortholog of MBNL1) and MBNL1 were determined using SELEX (Systematic Evolution of Ligands by Exponential Enrichment). These consensus motifs allowed for the identification of high affinity endogenous sites within pre-mRNAs that are regulated by MBNL1. In vitro binding studies showed that MBNL1 bound to RNAs that contained the consensus motif surrounded by pyrimidines. Some of these sites were identified upstream of exon 5 within the MBNL1 pre-mRNA, and we have shown that MBNL1 auto-regulates the exclusion of exon 5 in HeLa cells. The region of the MBNL1 gene that includes exon 5 and flanking intronic sequence is highly conserved in vertebrate genomes. The 3' end of intron 4 is non-canonical in that it contains an AAG 3' splice site and a predicted branchpoint that is 141 nucleotides from the 3' splice site. Using a mini-gene that includes exon 4, intron 4, exon 5, intron 5 and exon 6 of MBNL1, we show that MBNL1 regulates inclusion of exon 5. Mapping of the intron 4 branchpoint confirms that branching occurs primarily at the predicted distant branchpoint. Structure probing and footprinting reveal that the highly conserved region between the branchpoint and the 3' splice site is primarily unstructured, and MBNL1 binds within this region of the pre-mRNA, which we have termed the MBNL1 response element. Deletion of the response element eliminates MBNL1 splicing regulation and leads to complete inclusion of exon 5, which is consistent with the suppressive effect of MBNL1 on splicing. This dissertation includes previously published co-authored material as well as my recent co-authored material that has been submitted for publication.
Open Access
Autoinhibition and ultrasensitivity in the Galphai-Pins-Mud spindle orientation pathway
(University of Oregon, 2010-09) Smith, Nicholas Robert, 1981-
Protein-protein interaction networks translate environmental inputs into specific physiological outputs. The signaling proteins in these networks require regulatory mechanisms to ensure proper molecular function. Two common regulatory features of signaling proteins are autoinhibition and ultrasensitivity. Autoinhibition locks the protein in an inactive state through cis interactions with a regulatory module until it is activated by a specific input signal. Ultrasensitivity, defined as steep activation after a threshold, allows cells to convert graded inputs into more switch-like outputs and can lead to complex decision making behaviors such as bistability. Although these mechanisms are common features of signaling proteins, their molecular origins are poorly understood. I used the Drosophila Pins protein, a regulator of spindle positioning in neuroblast cells, as a model to study the molecular origin and function of autoinhibition and ultrasensitivity. Pins and its binding partners. Gαi and Mud, form a signaling pathway required for coordinating spindle positioning with cellular polarity in Drosophila neuroblasts. I found Pins switches from an autoinhibited to an activate state by modular allostery. Gαi binding to the third of three GoLoco (GL) domains allows Pins to interact with the microtubule binding protein Mud. The GL3 region is required for autoinhibitoon, as amino acids upstream and within GL3 constitute this regulatory behavior. This autoinhibitory module is conserved in LGN, the mammalian Pins orthologue. I also demonstrated that Gαi activation of Pins is ultrasensitive. A Pins protein containing inactivating point mutations to GLs l and 2 exhibits non-ultrasensitive (graded) activation. Ultrasensitivity is required for Pins function in vivo as the graded Pins mutant fails to robustly orient the mitotic spindle. I considered two models for the source of ultrasensitivity in this pathway: cooperative or "decoy" Gai binding. I found ultrasensitivity arises from a decoy mechanism in which GLs 1 and 2 compete with the activating GL3 for the input, Gai. These findings suggest that molecular ultrasensitivity can be generated without cooperativity. This decoy mechanism is relatively simple, suggesting ultrasensitive responses can be evolved by the inclusion of domain repeats, a common feature observed in signaling proteins. This dissertation includes previously published and unpublished co-authored material.
Open Access
Barbiturates and Modified Hamilton Receptors for Supramolecular Catalysis, Sensing, and Materials Applications
(University of Oregon, 2019-01-11) Seidenkranz, Daniel; Haley, Michael
Supramolecular chemistry (chemistry beyond the molecule) is the study and synthesis of complex molecular architectures from simple subunits using non-covalent interactions. The types of non-covalent interactions that are used for the self-assembly of these complex molecular architectures include electrostatic interactions (e.g. ionic, halogen, and hydrogen bonding), π-effects, van der Waals interactions, metal coordination, and hydrophobic effects. While these interactions are often used in concert, some of the most successful and ubiquitous approaches for the design and construction of new host–guest architectures are the incorporation of hydrogen bonding motifs. A popular class of molecules capable of making strong, highly directional hydrogen bonds is barbiturates. Barbiturates have a well-known reputation as potent hypnotics, anticonvulsants, and anxiolytics but recent years have seen a renewed interest in these molecules due to their unique, symmetric acceptor-donor-acceptor hydrogen bonding motif. In addition, receptors with complementary hydrogen bonding motifs capable of binding barbiturates have also been reported, namely those based on the work of Hamilton et al. Collectively, barbiturates and their receptors have seen widespread use in a variety of applications including sensing, optoelectronics, catalysis, and the design of soft materials. The work presented in this dissertation describes the development of novel Hamilton receptors for supramolecular catalysis and barbiturate sensing, as well as the design of new synthetic barbiturates. Together this body of research aims to extend the utility of these types of host–guest systems as well as continue to develop and refine the supramolecular design principles that govern the binding interactions between barbiturates and a variety of Hamilton-type receptors. This dissertation includes both previously published/unpublished and co-authored material.
Open Access
Binding of Hydrogen Sulfide to biologically relevant scaffolds: Metal systems and non-covalent binding
(University of Oregon, 2017-05-01) Hartle, Matthew; Pluth, Michael
Hydrogen Sulfide (H2S) is an important biologically produced gasotransmitter along with carbon monoxide (CO) and nitric oxide (NO). Unlike CO and NO, the bioinorganic chemistry of H2S reactivity with biologically relevant metal centers remains underinvestigated. To address this gap, several model bio(in)organic complexes were used to understand the ligation and reaction chemistry of H2S, including phthalocyanine, protoporphyrin IX, tetraphenyl porphyrin, and a pyridine diimine zinc complex. In addition to being a reactive gasotransmitter, the hydrosulfide anion (HS–) has been found to be an important biological anion. Studies with readily available cobalt and zinc phthalocyanines in organic solution illustrated the importance of protonation state in the ligation and redox chemistry of H2S and highlighted the need for an organic-soluble source of HS–. To address this need, we developed a simple method to prepare tetrabutylammonium hydrosulfide (NBu4SH). Using NBu4SH, we expanded the knowledge of H2S reaction chemistry to encompass a significantly larger set of biologically relevant metals beyond iron using the protoporphyrin IX scaffold, revealing three principle reaction pathways: binding, no response, or reduction and binding. Iron in biology is of particular importance given its role in oxygen transport in hemoglobin. The swamp-dwelling bivalve L. Pectinata hemoglobin 1 (Hb1) transports H2S, via ligation to heme, to symbiotic bacteria. The stabilization of H2S in Hb1 is believed to be from one of the following: a protected pocket, hydrogen bonding with a proximal glutamate residue, or a complex combination of these or other factors. By using Collman's "Picket-Fence" porphyrin to isolate the protected pocket model, we determined that a protected pocket alone as insufficient to account for H2S stabilization on Hb1. This realization led to an examination of hydrogen bonding in the secondary coordination sphere of a zinc complex. Finally, we explored the role of HS– as a biologically relevant anion using a bis(ethynylaniline) supramolecular receptor. We determined that rather than covalently modifying the receptor molecule, HS– was bound in the pocket, similar to bacterial anion transport channel. This dissertation includes previously published co-authored material.
Open Access
Boron in Disguise: Towards BN Biomimics
(University of Oregon, 2011-09) Abbey, Eric Ryan, 1980-
Chemists have long recognized the potential of the BN bond to mimic CC double bonds in aromatic systems. Phenyl and indole are two of the most important arenes in natural systems, as well as medicine, applied chemistry, and materials science. Despite the potential of BN arenes as phenyl and indole mimics in biomolecules, few isoelectronic and isostructural BN biomolecules have been synthesized. Substitution of BN for C=C imparts tunability to aromatic systems, giving new and potentially valuable properties to the resulting molecules. Our group has sought to expand the utility of BN arenes by developing the synthetic arsenal available to chemists seeking to incorporate the BN bond into biological and other organic molecules of importance. The scope of this dissertation is twofold: (1) development of the first "fused" BN indole, including a survey of its reactivity towards electrophiles, synthesis of the parent N -H compound with complete characterization, and a comparison to natural indole and (2) expansion of the synthetic methodologies for constructing 1,2-dihydro-1,2-azaborine derivatives, including complete structural characterization of a family of "pre-aromatic" and aromatic compounds and a protection-free synthesis of azaborines. The contributions outlined in this dissertation expand both the fundamental understanding of BN isosterism in aromatic molecules and the synthetic toolbox for chemists seeking to incorporate BN arenes into biological and other organic motifs. This dissertation includes previously published and unpublished coauthored material.
Open Access
Cellular RNA Targeting by Platinum (II) Anticancer Therapeutics
(University of Oregon, 2014-06-17) Osborn, Maire; Hawley, Diane
Cis-diamminedichloroplatinum (II), or cisplatin, is a widely prescribed anticancer compound, currently one of only three platinum (II) complexes FDA approved for cancer treatment. Despite its widespread use, we lack a comprehensive picture of global drug targets, which would lend valuable insights into the molecular mechanisms of action and resistance in different tissues. Drug binding to genomic DNA is an accepted cause of downstream apoptotic signaling, but less than 10% of Pt (in the case of cisplatin) accumulates within genomic DNA. Non-genomic contributions to cisplatin's therapeutic action are also under active investigation. In particular, cisplatin treatment can disrupt RNA-based processes such as splicing and translation. Pt(II) targeting of non-DNA species such as RNA may contribute to or sensitize a cell to the downstream effects of this drug, including the induction of apoptosis. Chapter I summarizes the activity profile of Pt(II) therapeutics, describing cellular uptake, cellular localization, incidences of Pt(II) accumulation within RNA, and RNA processes affected following drug treatment. Chapter II reports our thorough investigation of the distribution of Pt species throughout messenger and ribosomal RNA, with the discovery that Saccharomyces cerevisiae ribosomes act as a de facto cellular Pt sponge. In Chapter III, we report the synthesis of an azide-functionalized platinum (II) species, picazoplatin, for post-treatment click labeling and isolation of drug targets in vivo. Picazoplatin was designed to circumvent mislocalization and misprocessing of Pt typically encountered when trying to track small molecules tethered to large, charged fluorophores. This chapter contains several proof-of-principle studies validating the use of this class of reagents for future purification and sequencing of Pt-bound nucleic acids. Chapter IV describes the first application of the click-capable Pt reagent technology: the demonstration of significant in-gel fluorescent detection of Pt-bound ribosomal RNA and transfer RNA extracted from picazoplatin-treated S. cerevisiae and the first evidence that cellular tRNA is a platinum substrate. Chapter V summarizes these data, which suggest a potential ribotoxic mechanism for cisplatin cytotoxicity and broadly describe a convenient click chemistry methodology that can be applied to identify other metal or covalent modification-based drug targets. This dissertation includes previously published and unpublished co-authored material.