Browsing by Author "Fisher, Ellen R., committee member"
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Item Open Access Air quality implications from oxidation of anthropogenic and biogenic precursors in the troposphere(Colorado State University. Libraries, 2019) Link, Michael F., author; Farmer, Delphine, advisor; Fisher, Ellen R., committee member; Neilson, James R., committee member; Jathar, Shantanu H., committee member; Ravishankara, Akkihebbal R., committee memberOxidation chemistry in the troposphere drives the formation of air pollutants, harmful to human health and the natural world. Emissions from both anthropogenic and biogenic sources control the ways in which air pollution is formed and thus understanding the chemistry of the oxidation of these emissions enhances our ability to predict how air quality evolves in the future. Experiments simulating tropospheric oxidation chemistry on anthropogenic point sources show that identifying unique chemical processes resulting in air pollution allow for a greater specificity in how to pursue strategies for pollution mitigation policy with regional and hemispheric implications. This thesis focuses on the implementation of advancements in instrumentation and experimental techniques to understand how tropospheric oxidation of anthropogenic and biogenic precursors can produce air pollution. First, we subject vehicle exhaust to simulated tropospheric oxidation and quantify the formation of particulate matter and a toxic gas, isocyanic acid. We estimate how important oxidation of vehicle emissions are for these atmospheric pollutants for the South Coast Air Basin of California and the Seoul Metropolitan Region. Second, we investigate the propensity for isoprene to produce formic and acetic acid in laboratory oxidation experiments. We find that isoprene is likely a major source of formic acid in biogenically-influenced environments, however the exact mechanisms for formation remain unclear. Lastly, we use chemical ionization mass spectrometer measurements to quantify the fraction of oxidized carbon allocated to gas-phase organic acids from isoprene oxidation in laboratory experiments. Through comparison with field measurements from a forest in Alabama to a forest in Colorado we determine high levels of isoprene in Alabama are responsible for high levels of organic acids compared to Colorado. We also observe that influences of anthropogenic NOₓ suppress the formation of gas-phase organic acids suggesting as NOₓ levels decrease throughout the US in the future organic acids produced from oxidation from isoprene are likely to increase.Item Open Access Analytical spectroscopy method development to study mechanisms of Alzheimer's and tuberculosis diseases(Colorado State University. Libraries, 2020) Beuning, Cheryle Nicole, author; Crans, Debbie C., advisor; Levinger, Nancy E., committee member; Barisas, George, committee member; Fisher, Ellen R., committee member; Zabel, Mark, committee memberThis dissertation covers the analytical method development created to study and enhance the knowledge of two specific disease mechanisms important to Alzheimer's disease and Mycobacterium tuberculosis. There are two parts in this dissertation where Part 1 is entitled Measurement of The Kinetic Rate Constants of Interpeptidic Divalent Transition Metal Ion Exchange in Neurodegenerative Disease. Part 2 is entitled The Electrochemistry of Truncated Menaquinone Electron Transporters with Saturated Isoprene Side Chains Important in Tuberculosis. These diseases appear on the World Health Organization's top 10 leading causes of death worldwide. The amyloid-beta (Aβ) peptides are associated with Alzheimer's disease, where neurodegeneration is caused by the aggregation of the peptide into senile plaques within neuronal synaptic cleft spaces. Alzheimer's disease currently has no cure due to its multi-causative pathology. One disease mechanism is the coordination of divalent metal ions to the peptide. Specifically, Aβ coordinates Cu(II) and Zn(II) ions that can enhance the aggregation of Aβ into plaques. These metal ions are highly regulated within the human body and are usually found bound to peptides and not as free ions. Therefore, the Aβ must sequester the metals from other proteins and peptides. The primary research in this dissertation advances fluorescence method development to measure interpeptidic Cu(II) exchange kinetics to be able to measure this type of disease mechanism. The small peptides GHK (Gly – His – Lys) and DAHK (Asp – Ala – His – Lys) both chelate Cu(II) with nM affinity, have biological relevance as they are motifs found in human blood like Aβ, and chelate Cu(II) with similar nitrogen-rich binding ligands as Aβ. By substituting non-coordinating lysine residues with fluorescent tryptophan, the interpeptidic exchange rates can be measured since tryptophan fluorescence is statically quenched when within 14 angstroms of a paramagnetic bound Cu(II). Thus Cu(II) transfer from Cu(H-1GHW) to either GHK or DAHK can be monitored by recovered GHW fluorescence as the Cu(II) is exchanged and second-order kinetic rate constants were determined. This methodology was then used to monitor the Cu(II) exchange from truncated Cu(Aβ1-16) and Cu(Aβ1-28) complexes to GHW and DAHW, where second-order reaction kinetic rate constants were determined. While in the exchanges between Cu(H-1GHW) with GHK/DAHK the second-order rate constants were on the magnitude of 102 or 101 M-1s-1, respectively, the exchanges from Cu(Aβ) complexes were 2-3 orders of magnitude larger, 104 M-1s-1 (to GHW and DAHW). These differences in rate constant magnitude arise from the fact that the affinity of GHW (KA = 1013 M-1) for Cu(II) is larger than Aβ (KA =1010 M-1). This method development is an important step to an accurate measurement of the interpeptidic exchange between Aβ peptides, including in their fibril and plaque formations. Since senile plaques are found in synaptic cleft spaces with nanometer distances between neurons, a model system was generated to study coordination reactions at the nanoscale. In order to do this, the metal ion would need to be released in a controlled manner. Studies of metal ion burst reactions through the use of photocages can simulate bursts of ions like those seen in the synaptic cleft. Zn(II) is often released in its ionic form within the synapse in its function as a neurotransmitter, so we simulated a burst of Zn(II) ions by using a photocage, [Zn(NTAdeCage)]- which releases Zn(II) when irradiated with light. The photocage was irradiated to release Zn(II) then we followed its reaction progress with an in situ chelator, Zincon, in reverse micelles and in bulk aqueous buffer. The coordination reaction was 1.4 times faster in an aqueous buffer than in reverse micelles, despite the Zn(II) and Zincon being closer in the nanoparticle. These observations suggested that there is an impact on coordination reactivity within a highly heterogeneous environment with a cell-like membrane, which is due to the partitioning of each ligand. We observe that the photocage stays in the water pool of the reverse micelle and the Zincon partitions into the membrane interface. Thus, the coordination reactivity is diminished, likely due to the need for Zn(II) to diffuse to the Zincon, crossing a highly organized Stern layer to encounter the Zincon. Whereas in aqueous buffer, these are free to encounter each other despite being hundreds of nanometers apart. These proof of concept studies are integral to studying initial binding dynamics of metal ions with peptides at the nanoscale present in cells and neuronal synapses. Tuberculosis is a pathogenic bacterium which despite having a curable medication, can be drug-resistant. Menaquinone (MK) analogs with regiospecific partial saturation in their isoprenyl side chain, such as MK-9(II-H2), are found in many types of bacteria, including pathogenic Mycobacterium tuberculosis and function as electron transport lipids cycling between quinone and quinol forms within the electron transport system. While the function of MK is well established, the role of regiospecific partial saturation in the isoprenyl side chain on MK remains unclear and may be related to the redox function. Recently, an enzyme in M. tuberculosis called MenJ was shown to selectively saturate the second isoprene unit of MK-9 to MK-9(II-H2). The knockout expression of this enzyme was shown to be essential to the survival of the bacterium. A series of synthesized truncated MK-n analogs were investigated using a systematic statistical approach to test the effects of regiospecific saturation on the redox potentials. Using principal component analysis on the experimental redox potentials, the effects of saturation of the isoprene tail on the redox potentials were identified. The partial saturation of the second isoprene unit resulted in more positive redox potentials, requiring less energy to reduce the quinone. While full saturation of the isoprene tail resulted in the most negative potentials measured, requiring more energy to reduce the quinone. These observations give insight into why these partially saturated menaquinones are conserved in nature.Item Open Access Approaches towards the synthesis of saxitoxin alkaloids(Colorado State University. Libraries, 2013) Pearson, Aaron Daniel, author; Williams, Robert M., advisor; Wood, John L., committee member; Kennan, Alan J., committee member; Fisher, Ellen R., committee member; Woody, Robert W., committee memberZetekitoxin AB is a toxin isolated from the Panamanian golden frog (Atelopus zeteki). The structure and activity of zetekitoxin AB was a mystery for 30 years until 2004 when it was elucidated by Yamashita and coworkers. It was found to be a potent analog of Saxitoxin, a marine neurotoxin. Saxitoxin is a sodium channel blocker and has been used extensively as a research probe. Zetekitoxin AB shows an affinity profile similar to saxitoxin, but is considerably more potent. Due to the endangerment of the Panamanian golden frog there is no source of zetekitoxin AB, preventing further studies. Presented herein is a concise synthesis of 4,5-epi-11-hydroxy-saxitoxinol, which utilizes D-ribose to direct an asymmetric Mannich reaction. This approach allows many modes of reactivity, which can be used to potentially access various analogs of saxitoxin with novel bioactivity.Item Open Access Hyperpolarized and thermally polarized quadrupolar noble gas nuclei studied by nuclear magnetic resonance spectroscopy and magnetic resonance imaging(Colorado State University. Libraries, 2010) Stupic, Karl Francis, author; Meersmann, Thomas, advisor; Fisher, Ellen R., committee member; Szamel, Grzegorz, committee member; Prieto, Amy L. (Amy Lucia), committee member; Roberts, Jacob Lyman, committee memberThis dissertation consists of several studies of two quadrupolar nuclei, 83Kr and 131Xe, with nuclear spin states of I = 9/2 and I = 3/2, respectively. These nuclei possess a nuclear electric quadrupole moment that strongly interacts with the surrounding electric field gradient (EFG). The quadrupolar interactions in these noble gas atoms dominate the longitudinal (T1) spin relaxation. To fully study these nuclei, high non-equilibrium nuclear spin polarization, referred to as hyperpolarization (hp), is generated using spin exchange optical pumping (SEOP). By employing this technique, enhanced nuclear magnetic resonance (NMR) signals many orders of magnitude above that of a thermally polarized (Boltzmann distribution of spin states) sample are possible and allow for experiments where signal averaging over long periods of time is prohibited (i.e. in vivo). The gas phase 83Kr T1 is shown to be sensitive to the surface composition/chemistry and the surface-to-volume ratio in an ideal system of closest packed glass beads. Understanding the behavior of 83Kr in these conditions allows for its development as a surface sensitive probe that could provide information in opaque porous media environments. Similar relaxation behavior can be observed in 131Xe; however, the quadrupolar interactions experienced by 131Xe also induce an observable splitting in the NMR spectrum. This quadrupolar splitting is extremely sensitive to surfaces during periods of adsorption as well as to the magnetic field strength when a 131Xe atom is present in the bulk gas phase. As the influence on the quadrupolar splitting can be more readily observed than the relaxation of either 83Kr or 131Xe, the observed splitting in 131Xe NMR can provide helpful insights into quadrupolar behavior experienced by both nuclei. To develop a better understanding of the quadrupolar behavior, both 131Xe quadrupolar splitting and 83Kr relaxation are explored as functions of magnetic field strength, gas phase composition and co-adsorbing species. In closing, improvements in polarization of 83Kr from line-narrowed diode array lasers as well as new delivery techniques have provided improvements that allow for the implementation of variable flip angle FLASH imaging sequence in an excised, intact rat lung. Additionally, initial evidence suggests the T1 of 83Kr can differentiate between the regions of the lung (the trachea, the bronchi and bronchioles, and the alveoli), which has potential as a diagnostic tool for the biomedical community. Improvements in signal intensity are needed to achieve in vivo studies, additional enhancements are possible through improved SEOP and by using isotopically enriched gases.Item Open Access Improvement in dye sensitized solar cell efficiency through functionalization of redox mediators and passivation of the photoanode using a home-built atomic layer deposition system(Colorado State University. Libraries, 2017) Thomas, Joshua D., author; Prieto, Amy L., advisor; Fisher, Ellen R., committee member; Menoni, Carmen S., committee member; Sampath, Walajabad S., committee memberThe efficiency of dye sensitized solar cells (DSSCs) is driven based on the contributions of a vast array of kinetic and thermodynamic processes which must all function in sync with one another. The redox mediator factors into a majority of these processes and thus its proper function is vital to adequate function of the DSSC as a whole. The function of the redox mediator can be altered in two ways: changing the identity of the redox couple used and modifying one of the components which the redox couple is interacting with. Herein, both methods have been performed to optimize the properties and processes involved in efficient DSSC function. Several cobalt bipyridine coordination complex type mediators have been synthesized and differentiated through the modification of the ligand structure. The purpose of the modification was to generate complexes with more positive redox potentials to increase the open circuit voltage of the cells. Subsequently, attempts were made to further modify the ethyl ester substituted ligands which yielded the highest redox potential in order to provide higher stability for the resulting mediator. While the outcome of the synthesis was unsuccessful at this point, promising results have been shown. Further, an apparatus was constructed in order to cheaply perform atomic layer deposition of aluminum oxide on the surface of the mesoporous titanium dioxide photoanodes for DSSCs. Atomic layer deposition has been shown to reduce the rate of recombination with the oxidized mediator. In this case, improvement in the open circuit voltage of the cell was shown. However, the overall improved performance of the DSSCs shown in the literature could not be replicated. It is hoped that more high resolution analytical techniques could be used to elucidate the deficiencies still present in the use of this technique.Item Open Access Low temperature solution synthesis of ZnSb, MnSb, and Sr-Ru-O compounds(Colorado State University. Libraries, 2011) Noblitt, Jennifer Lenkner, author; Prieto, Amy L., advisor; Dandy, David S., committee member; Elliot, C. Michael, committee member; Fisher, Ellen R., committee member; Van Orden, Alan K., committee memberIncreasing energy demands are fueling research in the area of renewable energy and energy storage. In particular, Li-ion batteries and superconducting wires are attractive choices for energy storage. Improving safety, simplifying manufacturing processes, and advancing technology to increase energy storage capacity is necessary to compete with current marketed energy storage devices. These advancements are accomplished through the study of new materials and new morphologies. Increasing dependence on and rising demand for portable electronic devices has continued to drive research in the area of Li-ion batteries. In order to compete with existing batteries and be applicable to future energy needs such as powering hybrid vehicles, the drawbacks of Li-ion batteries must be addressed including (i) low power density, (ii) safety, and (iii) high manufacturing costs. These drawbacks can be addressed through new materials and morphologies for the anode, cathode, and electrolyte. New intermetallic anode materials such as ZnSb, MnSb, and Mn2Sb are attractive candidates to replace graphite, the current industry standard anode material, because they are safer while maintaining comparable theoretical capacity. Electrodeposition is an inexpensive method that could be used for the synthesis of these electrode materials. Direct electrodeposition allows for excellent electrical contact to the current collector without the use of a binder. To successfully electrodeposit zinc and manganese antimonides, metal precursors with excellent solubility in water were needed. To promote solubility, particularly for the antimony precursor, coordinating ligands were added to the deposition bath solutions. This work shows that the choice of coordinating ligand and metal-ligand speciation can alter both the electrochemistry and the film composition. This work focuses on the search for appropriate coordinating ligands, solution pH, and bath temperatures so that high quality films of ZnSb, MnSb, and Mn2Sb may be electrochemically deposited on a conducting substrate. Increasing use of natural resources for energy generation has driven research in the area of energy storage using superconducting materials. To meet energy storage needs the materials must have the following features: (i) safety, (ii) superconductivity at or above liquid nitrogen temperature (77 K), (iii) low cost manufacturing processes, and (iv) robustness. The search for materials that meet all of these criteria is on-going, specifically in the area of high temperature superconductivity. The precise mechanism of superconductivity is not known. A few theories explain some of the phenomenological aspects, but not all. In order to logically select and synthesize high temperature superconductors for industrial applications, the precise mechanism must first be elucidated. Additionally, a synthetic method that yields pure, high quality crystals is required because transition temperatures have been shown to vary depending on the preparation method due to impurities. Before measuring properties of superconductors, the development of a synthesis method that yields pure, high quality crystals is required. Most superconductors are synthesized using traditional solid state methods. This synthesis route precludes formation of kinetically stable phases. Low temperature synthesis is useful for probing thermodynamic verses kinetic stability of compounds as well as producing high quality single crystals. A novel low temperature hydrothermal synthesis of Sr-Ru-O compounds has been developed. These materials are important because of their interesting properties including superconductivity and ferromagnetism. Sr2RuO4 is particularly interesting as it is superconducting and isostructural to La2CuO4, which is only superconducting when doped. Therefore, Sr2RuO4 is a good choice for study of the mechanism of superconductivity. Additionally, new kinetically stable phases of the Sr-Ru-O family may be formed which may also be superconducting. Sr-Ru-O compounds were previously synthesized via the float zone method. There is one report of using hydrothermal synthesis, but the temperatures used were 480-630 °C. In general, hydrothermal methods are advantageous because of the potential for moderate temperatures and pressures to be used. Additionally, the reaction temperature, precursor choice, and reaction time can all be used to tune the composition and morphology of the product. Hydrothermal methods are inexpensive and a one-step synthesis which is very convenient to scale up for industrial application. This work shows how a hydrothermal method at temperatures between 140 °C and 210 °C was developed for the synthesis of the Sr-Ru-O family of compounds.Item Open Access Part 1: Synthesis and characterization of magnetic Cr5Te8 nanoparticles. Part 2: Local atomic structure studies using theory to simulate polarons in superconducting cuprates and experiment to analyze alternative energy nanomaterials(Colorado State University. Libraries, 2012) Martucci, Mary B., author; Prieto, Amy L., advisor; Elliott, C. Michael, committee member; Fisher, Ellen R., committee member; Rickey, Dawn, committee member; Patton, Carl E., committee memberThe field of spintronics, the development of spin-based devices that utilize the spin degree of freedom to increase memory capacity, has emerged as a solution to faster more efficient memory storage for electronic devices. One class of materials that has been extensively studied is the half-metallic ferromagnets, compounds that are 100% spin-polarized at the Fermi level. One material in this group that has been investigated is chromium telluride (Cr1-xTe), whose family of compounds is known to exhibit a wide range of interesting magnetic and electronic properties. We have developed a hot injection solution synthesis of Cr5Te8 nanoplatlets which show similar magnetic behavior to the bulk material. It has also been shown that selenium and sulfur analogues can be obtained without changing the reaction conditions, making progress toward a better understanding of the reaction as well as an interesting family of compounds. Using real-space simulations, the effect of polarons in the high-Tc superconducting cuprates has been studied. The simulations demonstrate energetically favorable sites for the defects and show evidence of longer-range pairing interactions. Variations of the stripe show similar energetic results. X-ray absorption fine structure spectroscopy and neutron scattering have been utilized to examine the local structure of Ni-doped Mg nanoparticles, a hydrogen storage material as well as Cu2ZnSnS4 (CZTS) nanoparticles, a photovoltaic material. The Mg-Ni material shows much local disorder upon hydrogen cycling. The CZTS data demonstrate a loss of sulfur from around the copper sites upon annealing, helping to explain the changes observed in the optical absorption properties resulting from the annealing process.Item Open Access The enantioseletive rhodium catalyzed [2+2+2] cycloaddition of alkenyl isocyanates with diaryl acetylenes and 1,2-disubstituted alkenyl isocyanates(Colorado State University. Libraries, 2010) Oinen, Mark Emil, author; Rovis, Tomislav, 1968-, advisor; Kipper, Matthew J., committee member; Williams, Robert Michael, committee member; Fisher, Ellen R., committee memberElaborating upon the recent discovery of a [2+2+2] rhodium-catalyzed cycloaddition of alkenyl isocyanates with various alkynes, the scope of this rhodiumcatalyzed cycloaddition with diaryl acetylenes was explored. The reaction with pentenyl isocyanate and diaryl acetylenes utilizing [Rh(C2H4)Cl]2 and 3,3'-substituted BINOL phosphoramidites as a catalyst predominantly affords vinylogous amide type products. Investigation into product selectivity reveals that both electronic and steric factors of the ligand have an influence on the product selectivity. Information gleaned from these studies allowed for a change in product selectivity for formation of lactam products with diaryl acetylenes. Selectivity for lactam product is at best 1:1.5 with BINOL phosphites. Vinylogous amide products are formed selectively (>20:1) in the cycloaddition using a variety of BINOL based phosphoramidites. Using 3,3' substituted BINOL based phosphoramidites promising enantioselectivies are obtained in the cycloaddition of diaryl acetylenes and pentenyl isocyanate. In the course of this investigation an interesting effect of substrate on the enantioselectivity was noticed. The ee of the reaction is highly dependent upon the nature of the diaryl acetylene. It was revealed that substrate affects the enantioselectivity by playing the role of spectator ligand in the reaction. Elucidation of the mechanism of the role of this spectator ligand was done by characterization of intermediates, kinetic analysis of the reaction rate and competition experiments between substrates. This effect of spectator ligands was exploited in a synthetically viable way to yield products with high and consistent enantioselectivities. By employing methyl nicotinate, a non-participating spectator ligand, as a stoichiometric additive synthetically useful enantioselectivities can be achieved. Finally, limitations existed within the scope of both alkynes and alkenyl isocyanates on the scope of the rhodium catalyzed [2+2+2] cycloaddition. Acetylene dicarboxylates, and 1,2-disubstituted alkenyl isocyanates were reaction partners that failed to provide cycloadducts under current reaction conditions. In both cases, the resultant cycloadduct would be interesting as they could provide additional synthetic handles for further manipulation of cycloadducts. Identification of undesired byproducts in these reactions allowed for the development of reaction conditions to reduce their formation of these by-products. The reduction in the formation of benzenoids formed from alkyne trimerization allowed for the production of mixtures of lactam and vinylogous amide products using acetylene dicarboxylates. With 1,2-disubstituted alkenyl isocyanates the implementation of reaction conditions which lead to the suppression of 2- pyridone lead to successful formation of the lactam products.Item Open Access Tracking ammonia volatilization and fate from emission source to pristine ecosytem(Colorado State University. Libraries, 2014) Stratton, Joshua James, author; Borch, Thomas, advisor; Prieto, Amy, committee member; Bernstein, Elliott, committee member; Fisher, Ellen R., committee member; Collett, Jeffrey L., committee memberAmmonia has been widely documented as a contributor to negative impacts on natural ecosystems. Agricultural related management has been closely tied to ammonia emission and therefore negative impacts of ammonia pollution. The aim of this research is to improve our current understanding of how ammonia is lost from native and agricultural soils and if nitrogen isotopes can be used to elucidate what sources of ammonia pollution affect native ecosystems the most. Rocky Mountain National Park (RMNP) has undergone ecosystem changes due to excessive nitrogen deposition in the forms of ammonium, nitrate and organic nitrogen. Due to uncertainty in source apportionment; the efficacy of nitrogen isotopes of ammonia to distinguish sources of ammonia deposited in RMNP was investigated. This study shows average δ¹⁵N isotopes of certain sources (beef cattle, dairy cattle production, wastewater treatment, cropland, urban) were distinguishable at this study's emission sites; however, the average δ¹⁵N isotope values measured at a RMNP site were not useful for identification of specific ammonia sources. Supplemental information (weekly integrations of gaseous and particulate reduced nitrogen, oxidized nitrogen, sulfur measurements, and HYSPLIT modeling) was needed to help pinpoint the likely sources of ammonia, such as agriculture and biomass burning, affecting RMNP. Moreover, this supplemental information was used to support the most likely reasons δ¹⁵N isotope values observed in gaseous ammonia and wet deposition were indistinguishable compared to emission sources. Little is known about the potential local contribution of ammonia from soils within RMNP. Thus, the goal of this study was also to develop a method for analysis of ammonia emissions from intact soil cores sampled from a sub-alpine grassland and forest within RMNP. Nitrogen wet deposition was monitored at the sampling location to investigate possible impacts on soil emissions of ammonia. Lastly, method development and analysis of formation of ammonia (urea hydrolysis), pH speciation (ammonia and ammonium), and vapor pressure (Henry constant) were investigated in beef and dairy feedlots to reveal important controls on ammonia emission. This research provides new information on the importance of post emission physical and chemical processes, such as source mixing, isotopic fractionation, and dry deposition, preventing the use of δ¹⁵N isotopes for source tracking without the use of complementary techniques, such as atmospheric modeling. Moreover this work provides further evidence indicating that natural emissions within RMNP are not major sources of reduced nitrogen in the RMNP airshed. Lastly, this work provides new chemical values for the Henry constant, acid dissociation constant, and urea hydrolysis rate constants in animal production systems and can be used to better estimate ammonia emissions from animal production to improve our current emission inventories.