Chemistry & Biochemistry Theses and Dissertations
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Item Development of single-neuron proteomics by mass spectrometry for the mammalian brain.(2021) Choi, Bok Dong; Nemes, Peter; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Single-neuron proteomics holds the potential to advance our understanding of important biological processes during neuron maturation and development. However, to characterize proteins from single neurons, further technological advances are still required. This dissertation discusses the development and application of single-cell mass spectrometry (MS) technologies to investigate proteins and its role in different neurons. The work presented herein demonstrates the strategies to develop and advance single-neuron analysis using capillary electrophoresis (CE)-MS. In addition, this work features several contributions to our understanding of neuron-to-neuron heterogeneity, providing new information to advance cell biology and neuroscience.Item Development of Next Generation Living Coordinative Chain Transfer Polymerization and New Polyolefin Materials Obtained Therefrom(2021) Wallace, Mark Alexander; Sita, Lawrence R; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The living polymerization of ethene, propene, higher carbon-number linear and branched chain α-olefins, and α,ω-nonconjugated dienes has provided the basis for the development of modern technological advances and achievements. The use of polyolefin materials is ubiquitous through the many plastic products produced on an over 300-million-metric-ton global scale annually. The sheer range and scope of these products is further underscored by the fact that such diversity is achieved from a very limited number of industrially relevant olefin monomer feedstocks. As such, continued advancement of polyolefin materials has been achieved through the design and validation of new polymerization methods and transition-metal catalysts that allow for the controlled production of polyolefins with tailored architectural features and physical properties. Furthermore, these methods and materials must generate the desired products in a fashion that is both cost effective and amenable to large scale production.Towards this goal, the work herein presents the design, validation, and implementation of ‘next generation’ living coordinative chain transfer polymerization (LCCTP) through five new polymerization methods for the synthesis of polyolefin materials with new functionalities, stereochemical configurations, optical activities, and with tailored molecular weight distribution profile and dispersity. These new methods include the design of a novel homochiral group 4 cyclopentadienyl, caproamidinate (CPAM) hafnium pre-initiator that exhibits unprecedented configurational stability. Most importantly, these new LCCTP methods allow for the generation of different classes of polyolefin materials in a controlled and scalable manner. Discussions concerning the design and application of these new methods, the materials they produce, and the future of these new advances will be presented.Item CHARACTERIZATION OF THE STRUCTURE AND BINDING OF BRANCHED K6/K48-LINKED AND BRANCHED K6/63-LINKED POLYUBIQUITIN CHAINS(2021) Abeykoon, Dulith Maduwantha Bandara; Fushman, David; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Ubiquitin (Ub) is an important post-translational protein modifier in eukaryotes. Post-translational modification with Ub is an essential process for eukaryotic cellular signaling including protein degradation, DNA repair, antigen-peptide generation and endocytosis. This post-translational modification with Ub occurs through ubiquitination where Ub attach as monoUb or polyUb chains. Ub form polyUb chains by forming covalent linkages between the C-terminus of one Ub and any of seven lysines or the N-terminus of other Ubs. Polyubiquitin chains can form homogeneous, heterogeneous, linear or branched chains, leading to diversity in polyubiquitin chain signaling outcomes. This diversity in signaling is due to the variety of conformations that arise based on the linkage specificity of the polyUb chains. Recently, branched K6/K48-linked polyubiquitins were shown to enhance deubiquitinating activity of UCH37 in the presence of Rpn13. To better understand the underlying structural mechanisms, here we determined the NMR structures of branched K6/K48-linked triubiquitin (Ub3) and discovered a previously unobserved interdomain interface between each of the distal ubiquitins and the proximal domain. We performed NMR binding assays to study the interactions of branched K6/K48-linked Ub3 with hHR23a UBA2, Rap80 tUIM and UCH37/Rpn13 complex. Binding studies of branched K6/K48-linked Ub3 to the UBA2 domain of the proteasomal shuttle protein hHR23A resulted in negligible differences between branched K6/K48-linked Ub3 and related dimers (K6-Ub2 and K48-Ub2). Interestingly, introducing hydrophobic patch surface residue mutations led to stronger affinity with both distal domains suggesting a change in the binding mode. Stronger binding affinity for K6/K48-linked branched Ub3 was observed with Rap80 tUIM. Moreover, deubiquitinating enzyme UCH37 (with Rpn13) showed strong affinity for both K6-linked and K48-linked distal domains, thereby suggesting a functional impact of this interdomain interface towards enhanced deubiquitinating activity of UCH37. Moreover, mutation studies of the hydrophobic patch residues of the proximal ubiquitin have shown the importance of the hydrophobic patch surface to maintain the interdomain interface of this branched trimer and for interactions with binding partners. Finally, initial studies done with the regulatory domain of the DNA repair protein p53 (p53c) have shown that p53c is a promising candidate for ubiquitination via non-enzymatic ubiquitination method introduced by our lab.Item INVESTIGATION OF ORDERED POROUS MATERIALS FOR LITHIUM AND MAGNESIUM IONS ELECTROCHEMICAL ENERGY STORAGE(2021) Henry, Hakeem Kimani; Lee, Sangbok; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)As portable electronics and electric vehicles become a more integral part of everyday life, rechargeable electrical energy storage devices (batteries) capable of providing greater energy and power densities will soon be necessary. Lithium-ion batteries (LIBs) have dominated this area of rechargeable energy storage devices since their commercialization in 1990. However, as electronic devices continue to advance, battery technology will have to go beyond conventional lithium-ion battery systems to power these devices. Among the many possible alternatives to lithium, magnesium is a promising candidate. In comparison to lithium, magnesium is more abundant, lower in cost, and more environmentally friendly. Magnesium batteries can also utilize a Mg metal anode which offers a high volumetric capacity and low standard reduction potential. Despite the potential benefits, Mg batteries suffer from several drawbacks. The three main issuesplaguing Mg batteries are (1) a lack of practical cathodes due to slow insertion kinetics of the divalent Mg2+ ion, (2) incompatibility between Mg electrolytes and high voltage cathodes, (3) and parasitic and passivating reactions occurring at the Mg metal anode surface. The work of this dissertation aims to address the Mg2+ insertion issue by developing modified cathodes with enhanced electrochemical performance. In the first study, the effect of structure and hydration on Mg2+ intercalation into amorphous and crystalline V2O5 films was systematically investigated by electrochemical methods. It was determined that the high water content of electrodeposited V2O5 films was the primary factor impacting Mg2+ intercalation, while the crystal structure played a secondary role. In the second study, an ordered mesoporous carbon (OMC) structure was grown on the surface of carbon nanotubes (CNT) to achieve a novel electrode architecture. The hybrid carbon structure allowed for fast ion diffusion and high electronic conductivity. The porous structure also served as an excellent host for the deposition of high-capacity cathode materials for an all-in-one electrode design. In the final study, the OMC synthesis method was paired with electrodeposited V2O5 protocol to further investigate the OMC electrochemical performance. Overall, the work of this dissertation contributes to the development and commercialization of rechargeable Mg batteries by elucidating a portion of this complex chemistry.Item LIGHT CONTROL OF CHEMICAL SYSTEMS: PHOTOCHEMICAL ELECTRON TRANSFER METHODS FOR RELEASING CALCIUM IONS AND THE PHOTOISOMERIZATION OF ALKENES TO MODULATE RHEOLOGICAL CHANGES.(2021) Heymann Loor, Romina R; Falvey, Daniel E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Our research combines organic photochemistry with the engineering principles of rheology through the study of photorheological fluids (PR). The two photochemical systems researched show changes in the rheological properties brought about by the addition of light. The investigated systems are the photoisomerization of cinnamic acid derivatives in the surfactant, Cetyltrimethylammonium bromide (CTAB), and calcium release through degradation ethylenediaminetetraacetic acid (EDTA) caused by an electron transfer mechanism. The CTAB system shows how a change in molecular conformation can cause significant changes in the bulk property of a solution. The calcium EDTA system employs targeted electron transfer to cause calcium release, which gels the biopolymer alginate with inexpensive, readily available materials. Chapter 2 details how the orientational binding, intermolecular interactions, and molecular geometry of cinnamic acid derivatives contribute to the rheological changes in CTAB. 1H NMR titration studies in CTAB identified binding patterns of the additives in CTAB. From those studies orientational binding models were developed for trans-ortho-methoxycinnamic acid (tOMCA), cis-ortho-methoxycinnamic acid (cOMCA), meta-methoxycinnamic acid (mMCA), para-methoxycinnamic (pMCA), ortho-hydroxycinnamic acid (oCoum), meta-hydroxycinnamic acid (mCoum), and para-hydroxycinnamic acid (pCoum). 1H-1H 2D NOESY spectra identified through space intermolecular interactions occurring within the micelle. Preliminary data into possible π-anion interaction between tOMCA molecules within the micelle is presented. Photolysis confirmed the creation of cis isomers for all additives but also identified coumarin by-products for oCoum. B3LYP calculations indicated out-of-plane geometry for all the cis isomers and possible intramolecular hydrogen bonding of oCoum. Finally, a model of binding interactions that lead to changes in the packing parameter of the surfactant and, therefore, a change into wormlike micelles for tOMCA versus cOMCA is introduced. In chapters three and four, we investigated calcium release using sensitizers that promote photoinduced electron transfer. Anthraquinones derivatives were shown in Chapter 3 to release calcium in stoichiometry amounts with UV light irradiation. In Chapter 4, flavins produced 1000-fold calcium release to sensitizer concentration in the visible light spectrum. In both chapters, there are detailed calcium release studies, degradation studies, and alginate experiments. We present calcium release studies at acidic and neutral pH, quantum yields, degradation of EDTA, sensitizer reoxidation studies, sensitizer degradation data, fluorescence, and transient spectra. While enough calcium was released to produce alginate gels, none were made in vitro at neutral and acidic pH.Item Mechanistic Studies of Photochemical Reactions: Photoacid Generators, Photoreleaseable Protecting Groups, and Diarylnitrenium Ions(2021) Zeppuhar, Andrea; Falvey, Daniel E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of light to drive chemical reactions is becoming increasingly popular due to the enhanced spatial and temporal control provided. Because of this, it is important to understand how these photochemical transformations occur from a mechanistic viewpoint in order to aid in the improvement of existing systems as well as in the development of new systems. The work presented in this dissertation will examine the mechanisms of several photochemical systems including photoacid generators, photoreleaseable protecting groups, and diarylnitrenium ions. Chapter 1 will begin with an introduction to organic photochemistry and describe some of the excited state reactions that will be encountered throughout this text. It will also describe laser flash photolysis, a technique critical to studying the reactive intermediates generated in photochemical reactions. Chapter 2 will describe the design and synthesis of photoacid generators that are activated via sequential two-photon absorption. The experiments conducted support a mechanism involving triplet re-excitation providing a more favorable bond scission. Chapter 3 will explore the applications of these newly developed photoacid generators, specifically for photopolymerization. It is shown that these compounds are capable of initiating both cationic and radical polymerizations depending on the intensity of visible light irradiation used. Chapter 4 will examine the 9-phenyl-9-tritylone photoreleaseable protecting group for alcohols to understand the details of its release mechanism. It is shown that the tritylone anion radical is required for alcohol photorelease. Chapters 5 and 6 will explore the behavior of diarylnitrenium ions in aqueous media. Chapter 5 will examine the reactivity of diarylnitrenium ions toward guanosine and it is shown that there is a rapid reaction to generate the C8 adduct, suggesting potential carcinogenicity. Chapter 6 will examine the reactivity of diarylnitrenium ions under acidic aqueous conditions. Under these conditions, a long-lived species is formed, and the experiments conducted indicate this species is the cation radical derived from the diarylnitrenium ion. Mechanistic analysis supports formation via a pathway separate from the nitrenium ion, suggestive of a triplet mechanism.Item SYNTHESIS OF PNAG ANALOGS TO PROFILE BIOFILM GLYCOSIDASES(2021) Wang, Shaochi; Poulin, Myles; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Bacteria biofilms consisting of surface-attached bacterial communities embedded in an extracellular matrix serve as a defense mechanism for many medically important bacterial species. Exopolysaccharides of partially de-N-acetylated poly-β-D-(1->6)-N-acetyl-glucosamine (dPNAG) are key structural components in the biofilm of many human pathogens. Dispersin B (DspB), a family 20 glycoside hydrolase produced by the Aggregatibacter actinomycetemcomitans, catalyzes the hydrolysis of dPNAG to disrupt biofilm formation leading to its use as an aniti-biofilm agent. Yet little is known of substrate recognition by DspB.Here, we describe the synthesis of two series of PNAG trisaccharide analogs with defined N-acetylation pattern (2.1 – 2.5) or containing glucose moiety (2.32 and 2.33) prepared through an iterative one-pot glycosylation approach and used to profile the activity and substrate preference of DspB (Chapter 2). These studies suggest that DspB hydrolyzes dPNAG polysaccharides via both exo- or endoglycosidase mechanisms and has a substrate preference for cationic substrates at the +2 position of the binding site. Understanding the activity and specificity of DspB provides a valuable guide to develop biocatalyst with improved biofilm dispersal activity. Next, colorimetric (Chapter 3) and fluorogenic (Chapters 4 & 5) PNAG analogs were developed as substrates for high-throughput PNAG glycosidase assay development. PNAG disaccharide probes (3.1 and 5.1) demonstrate exclusive specificity for enzymes capable of hydrolyzing PNAG and monosaccharide analog AMC-GlcNAc (4.1) acts as a general hexosaminidases enzyme substrate. We showed that all the analogs can detect DspB activity in crude E. coli cell lysates, and thus could be applied for functional metagenomic screening to discover novel PNAG glycosidase enzyms. Finally, a series of PNAG triazinyl glycosides (6.1, 6.2 and 6.3) were designed, synthesized and evaluated as affinity labeling reagents for PNAG binding proteins, using a catalytically inactive DspB E184Q mutant as a model PNAG binding protein (Chapter 6). However, only non-specific background signal was observed. In the future, recombinant enzymes or lectins that have higher binding affinity to the PNAG might be used to revisit these labeling results.Item Controlled synthesis of carbon nanotubes: from mechanisms to applications(2021) Cheng, Xiyuan; Wang, YuHuang; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Carbon nanotubes exhibit exceptional properties in many different aspects. However, harnessing those properties in real applications is challenging mainly due to the structural heterogeneity, high impurity contents, and architectural defects that originate in the synthesis. In this dissertation, I aim to understand the nucleation and growth mechanisms of both the catalyst and carbon nanotubes in chemical vapor deposition processes and establish a relationship between the structure and properties of the synthesized carbon nanotubes. I will also discuss applications enabled by some of the nanotubes that I synthesized. First, I will discuss the structure control of vertically aligned carbon nanotube arrays to show that the nanotube diameter, density, and growth pattern are correlated with the migration and aggregation behavior of the catalyst across the substrate. Then, I will present experimental studies revealing new insights into the nucleation of the catalyst particles in the gas phase. Based on the new fundamental understanding of the nucleation and growth of both metal catalysts and carbon nanotubes, we have developed a new method to produce semi-aligned high-quality nanotube films, with a tunable number of walls, continuously at an ambient atmosphere with a record high production rate of 1400 m h-1. With this technique, we have reduced the catalyst impurity content and increased the production rate of the carbon nanotubes while simultaneously maintaining a high Raman G/D ratio of >70. The carbon-catalyst interaction during carbon nanotube growth is also studied by planting and etching the carbon nanotubes on a metal melt. We found that the carbon was readily removed by H2 from the growing front of the carbon nanotubes. Finally, we exploited the applications of these synthesized carbon nanotubes in achieving high power thin-film thermoacoustics, high power battery, and dynamic mechanical interface.Item MECHANISTIC STUDY AND THE DESIGN OF IRON-CATALYZED MULTI-COMPONENT CROSS-COUPLING REACTION(2021) Lee, Wes; Gutierrez, Osvaldo; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Cross-coupling reactions (CCRs) are one of the most versatile methods for the formation of C-C bonds. Traditionally, palladium and nickel are broadly used as the catalyst in this type of transformation. However, due to the low cost, low toxicity, and high natural abundance, iron has become an alternative metal catalyst for CCRs. The first iron-catalyzed asymmetric cross-coupling reaction was reported by Nakamura in 2015 but the mechanism remained unknown. Since then, our lab has been working on 1) the elucidation of the mechanism using quantum mechanical calculations and experimental probes; and 2) the rational design and development of new types of iron-catalyzed cross-coupling reactions. Quantum mechanical calculations were applied to study the mechanism (Chapter 1). With multiple possible pathways computed and extensive conformational search, we determined that the lowest energy pathway proceeds via radical formation by Fe(I), radical addition to Fe(II), and reductive elimination from Fe(III) to form the desired cross-coupled product. With the mechanism in hand, we then designed and developed many new types of iron-catalyzed CCRs (Chapter 2-5), that included an intra- and inter-molecular dicarbofunctionalization of vinyl cyclopropanes, a three-component difunctionalization of unactivated alkenes, and a multicomponent radical cascade/annulation reaction. Finally, in Chapter 6, we introduced the [1.1.1]propellane as the σ-type radical acceptor in the three-component difunctionalization of iron-catalyzed cross-coupling reaction. These reactions showcases the potential of iron-catalyzed CCRs and expanded the toolbox for organic synthesis.Item Human Dietary Exposure to Arsenicals in Seafood: Occurrence and Analytical Considerations(2021) Luvonga, Caleb; Lee, Sangbok; Rimmer, Catherine A; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Consumption of seafood has been on a steady rise based on reports of associated health benefits. Marine organisms are sources of staple and functional food. However, they are also the main source of total arsenic exposure in humans. Most food safety regulations are based on total arsenic. Unfortunately, total arsenic as an indicator for risk from dietary intake is inadequate. Knowledge of arsenic speciation is important as the chemical form of arsenic controls its bioavailability, mobility, and toxicity. Therefore, an accurate account for the myriads of arsenic species, naturally occurring in seafood, is required. However, this present considerable analytical challenge. Arsenic speciation in seafood is challenging owing to its existence in diverse chemical forms and oxidation states, interconversions between chemical forms, matrix complexity, lack of widely accepted analytical methods, and lack of commercially available standards and certified reference materials. Identification and quantification of the toxic arsenic species is imperative to understanding the risk associated with exposure to arsenic from dietary intake, which in turn underscores the need for speciation analysis. Setting of standards for arsenic in food is complicated, owing to the enormous metabolic diversity of organic arsenic species in humans, lack of knowledge about their toxicity, and lack of reliable speciation data on seafood. To establish human exposure to arsenic from seafood, five proxy seafood samples were selected to represent the entire food chain. The selection was based on their high consumption rate, which makes them economically important and a significant route for arsenic exposure. The seafood samples are either candidate reference materials or materials meant for interlaboratory comparisons, which require measurements for certification purposes or property values assignment. This work contributed towards that effort. Analytical methods for the determination of total arsenic and hydrophilic arsenic species were developed and optimized for analysis of the seafood samples. A structural library was developed based on in silico fragmentation data of extant lipophilic arsenicals that are reported in literature. The library aims to enhance the screening and identification of the novel lipophilic arsenicals for which very little is known, standards are not available, and whose toxicological profiles are of interest.