Department of Chemistry
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These digital collections include theses, dissertations, faculty publications, and datasets from the Department of Chemistry.
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Browsing Department of Chemistry by Author "Ackerson, Christopher, committee member"
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Item Open Access Affinity maturation and characterization of novel binders to the HIV-1 TAR element based on the U1A RNA recognition motif(Colorado State University. Libraries, 2018) Crawford, David W., author; McNaughton, Brian, advisor; Ackerson, Christopher, committee member; Ross, Eric, committee member; Bedinger, Patricia, committee memberThe increased understanding of the importance of RNA, both as a carrier of information and as a functional molecule, has led to a greater demand for the ability to target specific RNAs, but the limited chemical diversity of RNA makes this challenging. This thesis documents the use of yeast display to perform affinity maturation for the ability of a protein to bind the TAR element of HIV-1, which is a desirable therapeutic target due to its prominent role in the HIV-1 infection cycle. To accomplish this, we used a "semi-design" strategy—repurposing a natural RNA bind- ing protein to bind a different target—by creating a library based on important binding regions (especially the β2β3 loop) of the U1A RRM. Following selection for TAR binding, a strong consensus sequence in the β2β3 loop emerged. The affinity of certain library members for TAR was measured by ELISA and SPR, and it was determined that the best binder (TBP 6.7) had remarkable affinity (KD = ~500 pM). This TAR binding protein also proved capable of disrupting the Tat–TAR interaction (necessary for HIV-1 replication) both in vitro and in the context of extracellular transcription. Through collaboration, we were able to obtain a co-crystal structure of TBP 6.7 and TAR. This crystal structure showed that the overall structure of TBP 6.7 was largely unchanged from that of U1A, thereby validating our semi-design strategy. We also found that the β2β3 loop played a disproportionately large role in the binding interaction (~2⁄3 of the buried surface area). The importance of this region inspired the creation and characterization of peptide derivatives of the TBP 6.7 β2β3 loop. These β2β3 loop derived peptides maintain affinity for TAR RNA (KD = ~1.8 μM), and can disrupt Tat/TAR-dependent transcription. Ultimately, the project has yielded the most avid known binders of TAR RNA, a potential novel platform of TAR binding peptides, and a crystal structure which will hopefully inform future targeting efforts.Item Open Access Carbon-based electrodes for environmental health applications(Colorado State University. Libraries, 2019) Berg, Kathleen E., author; Henry, Charles, advisor; Ackerson, Christopher, committee member; Krummel, Amber, committee member; Lear, Kevin, committee memberEnvironmental risk factors of air pollution and unsafe water are leading contributors to human morbidity and mortality, causing millions of deaths and diseases annually worldwide. Fine particulate matter (PM2.5) air pollution is linked to millions of deaths worldwide annually along with millions of cardiovascular and respiratory diseases. Unsafe water can contain heavy metals, including manganese (Mn), which high doses are linked to a variety of neurological and developmental diseases in humans. Analytical methods for testing for environmental risk factors such as fine PM and Mn still need improving. The primary focus of the dissertation here was to use carbon-based electrodes for improvements on environmental risk factor applications. An electrochemical assay was developed and used to measure Mn(II) in aqueous samples with stencil printed carbon paste electrodes. Stencil printed carbon paste electrodes are a mixture of graphite and organic liquid; they are easy to fabricate, portable, and disposable. These electrodes also do not require modification before detecting Mn in aqueous samples, but 1,4-benzoquinone was added to the background electrolyte for improved precision. Mn was then detected in complex matrices of tea and yerba mate samples. The focus is shifted from Mn detection to air pollution applications. A commercially available stencil printed carbon electrode was used for the dithiothreitol (DTT) assay, which is an assay commonly used to estimate the health effects of air pollution samples. The presented, improved DTT assay reduces reagents and increases sample throughput, both of which will help enable larger scale air pollution studies to be executed in the future. The DTT assay was then further improved with a semi-automated system that further increases the sample throughput and reduces reagent volumes while reducing the required manual labor associated with liquid handling. The semi-automated system uses a custom carbon composite thermoplastic electrode (TPE). Changes were observed in the TPE response over time and are studied further. The dissertation shifts focus to a more fundamental electrode characterization of high performing TPEs that were previously used because TPEs have a vast array of potential analytical applications, including environmental risk factor applications. Atomic force microscopy (AFM) and scanning electrochemical microscopy (SECM) were used for a thorough investigation of the local surface topography and electrochemistry of TPEs, which is needed to assess the cause of the excellent electrochemical properties. The evidence suggests that the TPEs behave as microelectrodes, which gives rise to their high electrochemical activity. The amount of potential applications from TPEs is then increased by modifying the surface. TPEs, while being high performing and easy to pattern, have previously been limited by their solvent compatibility to aqueous solvents. Presented here is an alternative fabrication, which makes TPEs polar organic solvent compatible, that greatly increases the number of applications. The TPEs were then modified and functionalized in acetonitrile as a proof of concept that TPEs can be used in non-aqueous solvents and can have modified surfaces, which can lead to more applications. The research here uses different carbon electrodes to advance method development of environmental risk factor quantification. Advances to Mn(II) detection and fine PM health impacts were made. Fundamental understandings were developed of carbon composite TPEs and then modified to show a large potential number of future applications for continual improvement of electrochemical sensing.Item Open Access Engineered co-crystals as scaffolds for structural biology(Colorado State University. Libraries, 2022) Orun, Abigail R., author; Snow, Christopher D., advisor; Ackerson, Christopher, committee member; Kim, Seonah, committee member; Ho, P. Shing, committee memberBiomolecules, like protein and DNA, serve as the foundation of life. The structure of biomolecules can give insight to their functions. X-ray crystallography is a cornerstone of structural biology, revealing atomic-level details of macromolecular structures. Even with advances in X-ray diffraction technology, haphazard and tedious crystal preparation remains the bottleneck of routine structure determination. An alternative to the crystal growth challenge is a scaffold crystal. Hypothetically, if one had a high-quality crystal already prepared with large enough pores for diffusion of a macromolecule, a biomolecule of interest could join the scaffold crystal for scaffold- assisted X-ray diffraction. An ideal scaffold crystal must be highly porous for guest addition, modular for installation of various guest molecules, and robust in changing solution conditions. A crystal with guest anchoring sites for post-crystallization guest addition may provide a high-throughput technique for guest DNA-binding protein structure determination. The overarching goal of this work is to design a novel scaffold crystal capable of scaffold-assisted X-ray crystallography. The scaffold crystals we designed are co- crystals of DNA and DNA-binding protein. In the co-crystal, the DNA serves as the anchoring point for guest DNA-binding guest targets while the protein acts as connective tissue to hold the DNA structure together. The scaffold co-crystal we engineered, Co-Crystal 1 (CC1), is the first example of a porous host crystal for DNA-binding guests. Ultimately, the expanded co-crystals may serve as a revolutionary figurative "lens" for routine structure determination. In addition to scaffold crystal development, we advanced methods to enhance scaffold stability and solution-independence, thereby augmenting the bioconjugation toolkit for crystals containing stacking DNA-DNA junctions. Specifically, we optimized a known bioconjugation technique, carbodiimide chemical DNA ligation, templated by crystals with stacking DNA junctions. Furthermore, crystal crosslinking chemistries were optimized to provide crystal strength at both the nanoscale and the macroscale. Post- crosslinking, co-crystal nanostructures were preserved as assessed using X-ray diffraction and co-crystal macrostructures were bolstered in harsh solution conditions. The crosslinking chemistry and protocol guidelines may advance the progress of DNA crystals and protein-DNA co-crystals utility in biomedical applications and structural biology. We are on the cusp of using designed co-crystals to host guest DNA-binding proteins for structural biology, bio-sensing, and bio-therapeutic delivery. Successful engineering of a designed porous co-crystal will open numerous application possibilities and scientific questions. For example, a future study could focus on quantifying guest protein diffusion rates and adsorption strength inside the porous scaffold crystals. The technology presented here may advance the study of DNA-binding proteins and advance our understanding of key proteins for cancer and disease.Item Open Access Fluorinated materials synthesis and characterization for energy storage and energy conversion applications(Colorado State University. Libraries, 2015) Bukovsky, Eric V., author; Strauss, Steven H., advisor; Ackerson, Christopher, committee member; Crans, Debbie, committee member; Barisas, B. George, committee member; Sutton, Sally, committee memberThe synthesis and characterization of multiple fluorinated, p-block, cage, and organic compounds will be presented. The research effort is split up in to main topics, (i) fluorinated superweak anions based on B12 cages, and (ii) perfluoroalkylation of polycyclic aromatic hydrocarbon (PAH) and fullerene compounds. In the first three chapters, superweak anion research is presented; a new purification method for the synthetic intermediate K2B12F12, synthesis and thermal and physical characterization of highly purified (H3O)2B12F12·nH2O, Li2B12F12 and Na2B12F12 (synthesized from K2B12F12), and an HF-free, improved synthesis method and characterization of KB12F11NH3. Furthermore, the unanticipated, rapid fluorination of KB12H11NH3 in the presence of HF, contrary to, previously observed, slowed fluorination of K2B12H12 in the presence of HF, will also be described. Single crystal X-ray structures of three new isomers of C60(CF3)10 are discussed, and one putative isomer of C60(CF3)10 is confirmed along with comparisons of their crystal packing properties compared to 1,9-C60(cyclo-CF2(2-C6F4)), and industry-standard fullerene acceptor phenyl-C61-butyric acid methyl ester (PCBM). Discussion of how the structural and electrochemical data of the new C60(CF3)10 isomers and 1,9-C60(cyclo-CF2(2-C6F4)) agree with currently accepted literature will also be discussed. A new metal reactor design for the radical reactions of CF3I and polycyclic aromatic hydrocarbons (PAH) and fullerenes, and initial results will be discussed and compared to previous reaction methods. Single crystal X-ray structures of four separate compounds believed to be "trapped intermediates" formed from the radical substitution reaction isolated from radical reactions with CF3I using different PAHs and different reactions conditions will be discussed as well as the implications these trapped intermediates have on the proposed mechanism of CF3• radical substitution reactions. Crystal packing and nearest molecule analysis of five PAH(CF3)n will be compared to a single crystal X-ray structure of triphenylene with a C4F4 substitution. Insights into the structural effects of CF3 substitutions compared to the flat C4F4 substitutions, and, how those effects would translate into electronic communication in the solid state will be discussed. Finally, wet milling of metallurgical grade silicon in an attritor mill, under anaerobic and aerobic conditions with and without surface passivating additives to study the affects oxygen and additives can have on milled particle properties such as, crystallinity by powder X-ray diffraction, surface bonds by X-ray photoelectronspectroscopy, dynamic light scattering particle size, N2 gas uptake BET surface area and reactivity towards oxygen will be discussed. Under anaerobic conditions silicon was found to form Si–C bonds in the presence of dry- air-free heptane. Additionally, the extensive effect oxygen has on the comminution of silicon and the surprising result that, even in aerobic conditions, formation of Si–C bonds is observed. All of the research described in this dissertation has applications in one or multiple energy storage or energy conversion devices. The superweak anion salts as electrolyte salts in battery or fuel cell, C60(CF3)10 and 1,9-C60(cyclo-CF2(2-C6F4)), as electron acceptor materials in organic photovoltaic devices, and multiple PAH(CF3)n compounds as OLED active layer materials.Item Open Access Organic cation dynamics and property relationships in layered perovskite derivatives(Colorado State University. Libraries, 2022) Koegel, Alexandra A., author; Neilson, James R., advisor; Ackerson, Christopher, committee member; Kennan, Alan, committee member; Sites, James, committee memberLayered hybrid halide perovskites are materials with applications in solid-state lighting due to their intrinsic white light emission. Layered hybrid perovskite derivates typically have the composition, (A')2 (A)n − 1BnX3n + 1, where A' = R−NH + 3 containing organic cation, A = methylammonium (CH3NH + 3, MA), B = Sn, Pb, X = Cl, Br, I, and n = number of inorganic octahedral layers. They are called "hybrid" materials because of the inclusion of both organic and inorganic moeities in the material. Studies on the three-dimensional perovskite family have shown correlations between restricted rotational motion of the organic cation and structural phase transitions, and electronic properties. However, several questions remain about the coupling between structure, optoelectronic properties, and organic cation dynamics in layered perovskites. Here, I show that the restriction of the organic cation dynamics influences the static inorganic structure. The relevant excited states that produce the observed white light emission are also impacted by the cation dynamics. Chapter One is an overview of layered perovskites and how their structural diversity influences myriad properties. The excited state dynamics proposed in the literature are examined with respect to broad emission. Chapter Two goes in depth and describes the interplay between organic cation dynamics and broadband emission. Quasi-elastic neutron scattering elucidates the dynamic radii of the organic cation ammonium head groups and their role in tilting the inorganic octahedral structure. The smaller crystallographic ii volumes resulting from restricted cation dynamics induces further out-of-plane octahedral tilting. This tilting gives rise to the observed white light emission by the formation of self-trapped excitons. The ammonium headgroup rotations happen on a time-scale that is faster than the recombination of the self-trapped excitons, providing multiple environments for the excited state to sample, leading to inhomogeneous broadening of the white light. In perovskite derivatives, chemical substitution provides an opportunity to change the physical structure. Chapter Three demonstrates how changing the number of inorganic layers influences the cation dynamics. The methylammonium residence times, determined from quasi-elastic neutron scattering, are shorter in the layered perovskite with more inorganic layers. The dielectric screening provided by the increased number of methylammonium cations in the material with thicker inorganic enables the faster molecular motions to occupy larger crystallographic volumes. The inorganic layer hosts the relevant frontier electronic states necessary for broad emission. The population of these frontier states is influenced by a number of factors, namely the out-of-plane tilt angle. Chemical substitution of the inorganic layer affects the out-of-plane tilting; therefore, it is necessary to control the tilt angle as a variable in order to determine a more direct correlation between cation dynamics and white light. Chapter Four discusses the effect of isotopic substitution of the organic cation as a way to understand the influence of dynamics independent of tilt angle. Calculations using a harmonic oscillator approximation show the deuteration of the ammonium headgroup is iii closely coupled to the inorganic lattice, does not have much effect on the residence times of hydrogen motion. Halide substitution in the three-dimensional perovskites leads to reduced organic cation rotation residence times and further correlates to changes in electronic properties. Neutron spectroscopy presented in Chapter Five demonstrates how substitution of the halide site influences the cation dynamics and broadband emission in layered perovskites. Materials with broad emission have a lesser extent of hydrogen rotational motion, which follows previous trends in the literature. Chapter Six further demonstrates the effect of chemical substitution on broad emission and cation dynamics. The formation of solid solutions in the three-dimensional materials influence cation dynamics and phase transitions. White light emission at room temperature is achievable with solid solutions of layered perovskite derivatives. The extent of hydrogen motion determined from neutron scattering does not follow what is previously discussed in Chapter Two. Cation dynamics modify the static inorganic structure and optoelectronic properties in complex, excited state-mediated pathways. The identity of the organic cation dictates the overall perovskite structure and influences the tilting of the octahedra. The cation dynamics influence the broad emission in layered perovskite derivatives. Characterization of these coupled behaviors enable design principles for solid-state lighting applications.Item Open Access Protein engineering strategy for the stabilization of HIV-1 α-helical peptides(Colorado State University. Libraries, 2019) Tennyson, Rachel Lee, author; Kennan, Alan, advisor; Ackerson, Christopher, committee member; Snow, Christopher, committee member; Gustafson, Daniel, committee memberMany disease-relevant protein-protein interactions (PPIs) contain an alpha helix and helical binding cleft at their interface. Disruption of these interactions with helical peptide mimics is a validated therapeutic strategy. However, short peptides typically do not fold into stable helices, which significantly lowers their in vivo stability. Researches have reported methods for helical peptide stabilization but, these approaches rely on laborious, and often expensive, chemical synthesis and purification. The research I have preformed aims to stabilize disease-relevant helices through protein engineering. In contrast to chemically constrained helical peptides, a protein can be expressed in a cellular system on a much larger scale. Recently, we reported a new strategy termed "helix-grafted display" that overcomes the traditional hurdles of helical mimics and applied it to the challenge of suppressing HIV entry. Our helix grafted proteins, potently inhibits formation of the extracellular PPI involving C-peptide helix, and HIV gp41 N-peptide trimer, as tested in HIV CD4+ cells. Further optimization of the helical sequence by yeast display yielded new proteins that suppress HIV-1 entry and express substantially better in E. coli. Furthermore, fusion proteins designed to improve the serum stability of these helix grafted proteins have been made that potently suppress HIV-1 entry. Collectively, I report a potential cocktail of evolved HIV-1 entry inhibitors that are functional against an Enfuvirtide-resistant strain and are designed for serum stabilities that rival current monoclonal antibody drugs.Item Open Access Using X-ray photoelectron spectroscopy to understand the solid electrolyte interphase formation in sodium ion batteries(Colorado State University. Libraries, 2022) Gimble, Nathan Jacob, author; Prieto, Amy, advisor; Ackerson, Christopher, committee member; Rappe, Anthony, committee member; Popat, Ketul, committee memberSodium-ion batteries offer a more sustainable energy storage alternative to lithium while maintaining many of lithium's important characteristics. The solid electrolyte interphase (SEI) forms on the surface of the anode in both sodium and lithium-ion batteries. The SEI effects battery performance, particularly in sodium batteries, and understanding how it forms is critical for developing sodium ion batteries. Chapter I of this dissertation motivates sodium ion batteries, outlines the important differences between sodium and lithium, introduces the SEI, and establishes how the SEI is studied, ultimately placing this work in context with the field. As the SEI is derived from the electrolyte and is affected by electrolyte additives, the small molecule electrolyte additive fluoroethylene carbonate (FEC) is introduced as it is investigated throughout the dissertation. Chapter II explains how X-ray photoelectron spectroscopy can be used to study the SEI, providing examples of important protocols and pitfalls. Chapter III examines SEI formation by correlating electrochemistry from differential capacity with X-ray photoelectron spectroscopy (XPS). It is revealed that SEI species appear as a result of applied chemistry when the small molecule additive FEC is present. Without FEC, the SEI is present without significant electrochemistry in the differential capacity. Chapter IV builds off the results in Chapter III, identifying the conditions of spontaneous SEI formation due to sodium metal reactivity with the electrolyte. The spontaneous formation of the SEI is mitigated by FEC, the role of which is understood to be pre-passivation of sodium metal to prevent further electrolyte decomposition. Chapter V summarizes the work in this dissertation and outlines different directions the work can take moving forward.