Browsing by Author "McNally, Andy, committee member"
Now showing 1 - 7 of 7
Results Per Page
Sort Options
Item Open Access Bioengineering of cloneable inorganic nanoparticles(Colorado State University. Libraries, 2023) Hendricks, Alexander Ryo, author; Ackerson, Christopher J., advisor; Chung, Jean, committee member; McNally, Andy, committee member; Cohen, Bob, committee memberWhen a defined protein/peptide (or combinations thereof) control and define the synthesis of an inorganic nanoparticle, the result is a cloneable NanoParticle (cNP). This is because the protein sequence/structure/function is encoded in DNA, and therefore the physicochemical properties of the nanoparticle are also encoded in DNA. Thus the cloneable nanoparticle paradigm can be considered as an extension of the central dogma of molecular biology (e.g. DNA -> mRNA -> Protein -> cNP); modifications to the DNA encoding a cNP can modify the resulting properties of the cNP. The DNA encoding a cNP can be recombinantly transferred into any organism. Ideally, this enables recombinant production of cNPs with the same defined physiochemical properties. Such cNPs are of primary interest for applications in biological imaging as clonable contrast agents. The advancement of cNPs for broader and more rigorous applications in imaging (and elsewhere) requires further development through multidisciplinary approaches. Described in This Thesis is a bioengineering approach to improve the cNP platform through development of the enzymes responsible for nanoparticle formation.In the first chapter, background and significance is given to provide rationale behind the cNP platform. Among all the modalities of biological imaging, there is no 'one-size-fits-all' solution. Biological fluorescence microscopy (FM) and electron microscopy (EM) are the preferred methods of choice when imaging at cellular levels. Although the relatively recent advent of fluorescent proteins and super-resolution microscopy have ushered major scientific breakthroughs, FM is resolution-limited: only the cellular components which are labeled by fluorophores can be resolved – everything else in a cell (~99% of components) is imaged with low resolution owing to the diffraction limit of light. Biological EM comparatively can image widefield cells at atomic-level resolution yet lacks an analogous toolset to fluorescent proteins. cNPs are proposed as a multimodal, uniform, and precise means of clonable contrast for biological EM (and other modalities) analogous to fluorescent proteins. In the second chapter, a tellurium reductase is isolated and characterized from screened environmental bacterial cultures collected throughout the Colorado Mineral Belt. A strain of Rhodococcus erythropolis PR4 was found to be highly resistant to a broad range of metal(loid) species at toxic concentrations – notably 4.5 mM TeO32− determined by broth microdilution. Through screening of cell lysate in the presence of metal(loid) substrates, a mycothione reductase was characterized as a Te-specialized enzyme which reduces Te preferentially over Se. This is a surprising finding on the basis of reduction potentials for the two substrates. The standard reduction of potential for the reaction TeO32− + 3 H2O + 4e− ← → Te + 6 OH− is −0.57 V vs Hydrogen. The corresponding reduction of SeO32− is −0.366 V. Thus, SeO32− is the preferred substrate for reduction in the absence of a mechanism for substrate selectivity. We hypothesize that the R. erythropolis mycothione reductase may form the basis of a cloneable tellurium nanoparticle (cTeNP). In the third chapter, metal(loid) reductase substrate specificity is developed through directed evolution of a glutathione reductase-like metalloid reductase (GRLMR). The native substrate of GRLMR is selenodiglutathione (GS-Se-SG), where zerovalent selenium nanoparticles are formed in the presence of NADPH. Error prone polymerase chain reaction was used to create a library of ~100,000 GRLMR variants. The library was expressed in Escherichia coli with 50 mM SeO32− to select a GRLMR variant with 2 mutations. One mutation (a D to E) appears to be silent, whereas the other (L to H) resides within 5Å of the active site. Compared to the GRLMR parent enzyme, the evolved enzyme became less capable of reducing reduced glutathione (GSSG) and GS-Se-SG in favor of SeO32−. The evolved enzyme also gained an ability to reduce SeO42−. We have described this enzyme as a selenium reductase (SeR). This is the first known instance of the substrate specificity profile of a metal(loid) reductase changing as a result of directed evolution. In the fourth chapter, the cNP concept is discussed in greater detail. The cNP synthesis paradigm is loosely defined as a system of ligands, reductants, and inorganic cations – where ligands are peptides, reductants are enzyme-cofactor pairs, and inorganic cations are dietary or supplemented metal(loid) ions. This modular platform is adaptable to a wide variety of metal(loid)/enzyme/peptide systems. The story of the creation of a cloneable Se nanoparticle (cSeNP) is also retraced. Briefly, a bacterial endophyte Pseudomonas moraviensis subsp. Stanleyae was found to be capable of efficient selenium reduction under aerobic conditions. Continued characterization led to the discovery of GRLMR which unraveled the cellular mechanism for reducing SeO32−. The enzyme can endow host cells with selenium resistance through nanoparticle formation when cloned. GRLMR was further modified through the fusion of a selenium nanoparticle-binding peptide which improved overall kinetic rates, nanoparticle retention, and nanoparticle uniformity. In the fifth chapter, preliminary work is described which may enable further development of the next generation of cNPs through reduced enzyme mass/mericity and 'multicolored' nanoparticles. Work is described which investigates the plasticity of GRLMR towards reducing other metals such as bismuth. Fluorescence assisted cell sorting (FACS) was used to determine if the relative quantity of intracellular metal(loid) nanoparticles can be differentiated, which is hypothesized to correlate to relative metal(loid) reductase activity. Whereas selenium content could be discerned between active and inactive GRLMR-expressing bacteria, relative bismuth content has yet to be analogously discerned. On the other hand, work was done towards rationally designing a monomeric GRLMR; there are ongoing efforts to use machine learning to graft the active site of GRLMR into a different monomeric template. Finally, a Muchor racemosus cytochrome b5 reductase (Cb5R) was identified in the literature which may serve as an ideal candidate to develop more minimalistic cSeNPs. Initial work has revealed that the enzyme is particularly resistant to soluble expression, which may hinder its ability to function as a clonable contrast agent. However, ongoing work is being done to 'supercharge' the enzyme to enable more facile expression.Item Open Access Design and application of strongly reducing photoredox catalysts for small molecule and macromolecular synthesis(Colorado State University. Libraries, 2019) Pearson, Ryan Michael, author; Miyake, Garret, advisor; McNally, Andy, committee member; Szamel, Grzegorz, committee member; Li, Yan Vivian, committee memberThe synthesis and application of new families of strongly reducing organic photoredox catalysts are described in this dissertation. These compounds provide a platform on which catalytically relevant properties including redox potentials and absorption profiles can be tuned, as well as predicted in silico. The critical photophysical and electrochemical characteristics have been established for both dihydrophenazine and phenoxazine catalysts which enable their ability to be used as green alternatives to commonly used transition metal photocatalysts. Specifically, phenoxazines have been utilized to mediate organocatalyzed atom transfer radical polymerization (O-ATRP) for the production of well-defined polymers using visible light. To this end, a catalyst system able to synthesize acrylic polymers with predictable molecular weights and dispersities less than 1.10 has been developed. In addition, dihydrophenazines were shown to mediate trifluoromethylation and atom transfer radical addition reactions, while phenoxazines were able to mediate C-N and C-S cross coupling reactions in the presence of a nickel co-catalyst.Item Open Access Dual nickel- and photoredox-catalyzed enantioselective desymmetrization of meso anhydrides and C-O bond activation via phosphines and photoredox catalysis(Colorado State University. Libraries, 2018) Stache, Erin Elizabeth, author; Rovis, Tomislav, advisor; Doyle, Abigail G., advisor; Chen, Eugene, committee member; McNally, Andy, committee member; Reynolds, Melissa, committee member; Kipper, Matt, committee memberDescribed herein is the application of photoredox catalysis in the development of new synthetic methods. A dual nickel- and photoredox catalyzed desymmetrization of meso succinic anhydrides was developed to generate stereodefined cis keto-acids in high enantioselectivity and diastereoselectivity. The approach employed benzylic radicals as a coupling partner, generated from a photoredox catalyzed single-electron oxidation of benzylic trifluoroborates using an inexpensive organic dye. A unique epimerization event was discovered and the degree of epimerization was rendered tunable by changing catalyst loadings to ultimately form the trans diastereomer preferentially in high enantioeselectivity. A method for the C–O bond activation of aliphatic alcohols and carboxylic acids was developed using phosphines and photoredox catalysis. This novel reaction platform was used to generate aliphatic or acyl radicals directly from benzylic alcohols and aliphatic and aromatic acids, and with terminal hydrogen atom transfer, afforded the desired deoxygenated alkanes and aldehydes. Additionally, the intermediate acyl radicals could be intercepted in an intramolecular cyclization reaction to generate new lactones, amides and ketones.Item Embargo Leveraging bio-based monomers, chemical recyclability, and sustainable polymerization techniques for sustainable polymer synthesis(Colorado State University. Libraries, 2024) Bernsten, Simone Noelle, author; Miyake, Garret, advisor; McNally, Andy, committee member; Reynolds, Melissa, committee member; Reisfeld, Brad, committee memberPolymeric materials have become vital to everyday life since their commercialization. Although polymers are integral to many industries and consumers, their synthesis and use brings with them a myriad of environmental concerns. Unsustainability can arise even before polymer synthesis in that many synthetic polymers are made from petroleum-derived monomers which are inherently nonrenewable. Next, many polymers are synthesized using one or more unsustainable components such as precious metals including iridium and ruthenium. Finally, at the end of a polymer's useful life, options for recycling are limited by the inability to make virgin-quality materials that can be used for the same application as the original polymer. The work described in this thesis aims to address each of these issues. The polymerizations of several bio-based monomers are described. The use of organic photoredox catalysis to enable polymerization represents sustainable synthesis of polymers. Polymers exhibiting chemical recyclability are also investigated, wherein end-of-life materials can be depolymerized and used to produce virgin- quality materials. Ultimately, this work represents a diverse array of methodologies for increasing the overall sustainability of polymeric materials.Item Open Access New base-catalyzed processes enable new approaches to C–H functionalization reactions(Colorado State University. Libraries, 2022) Puleo, Thomas R., author; Bandar, Jeffrey, advisor; McNally, Andy, committee member; Zadrozny, Joseph, committee member; Chatterjee, Delphi, committee memberBrønsted bases are ubiquitous, inexpensive, and widely available reagents used in synthetic chemistry due to their well-studied and predictable activation mode. This thesis details the discovery and incorporation of new Brønsted base-catalyzed processes into fundamental proton transfer equilibria to enable new approaches to C–H functionalization reactions. The direct functionalization of C–H bonds represents a streamlined and attractive approach to access valuable synthetic targets, and this utility will be highlighted throughout the discussion of each method.Chapter one describes the discovery and development of a base-catalyzed α-selective styrene deuteration reaction. The mechanistic studies that led to the conceptualization and optimization of this reaction will be highlighted. α-Deuterated styrenes are compounds frequently utilized in the mechanistic studies of alkene functionalization reactions and this work represents the first method to achieve α-selective hydrogen isotope exchange on styrene derivatives. Chapter two provides an overview of existing approaches to catalytic aryl halide isomerization reactions. A particular focus on base-catalyzed aryl halide isomerization reactions will be provided, as these reports serve as the mechanistic foundation for the reactions developed throughout the remainder of the thesis. Chapter three describes our discovery and application of a general approach to base-catalyzed aryl halide isomerization. Aryl halides are valuable compounds in synthetic chemistry, and this new catalytic isomerization process unlocks a new mode of reactivity for these compounds. The scope of this process is demonstrated on several simple aryl bromides and iodides. The second part of this chapter will highlight an application of this process to enable the 4-selective nucleophilic substitution of 3-bromopyridines. Chapter four describes our approach to achieve nucleophilic C–H etherification of electron-deficient N-heteroarenes via a base-catalyzed halogen transfer mechanism. 2-Halogenated thiophenes efficiently transfer halogens to N-heteroaryl anions to generate N-heteroaryl halide intermediates that undergo nucleophilic aromatic substitution with alkoxide nucleophiles. Additionally, C–H etherification can be sequenced with a cascade base-promoted elimination to enable N-heteroarene C–H hydroxylation. The scope of process is highly general, and regioselective C–H etherification and hydroxylation is demonstrated on thiazoles, oxazoles, imidazoles, pyridines, pyrimidines, pyridazines, and polyazines. Chapter five briefly highlights two new C–H functionalization reactions currently being developed that are enabled by base-catalyzed halogen transfer. First, use of this approach to enable the C–H hydroxylation of benzenes will be described. Second, the monoselective and site-selective benzylic C–H etherification of toluenes and polyalkyl benzenes will be detailed. In the final part of the chapter, I will summarize my contributions and discuss the future outlooks on this chemistry.Item Open Access Realizing thermometric control of Cobalt-59 spin-based probes via ligand design(Colorado State University. Libraries, 2022) Ozvat, Tyler M., author; Zadrozny, Joseph M., advisor; Rappé, Anthony K., committee member; McNally, Andy, committee member; Ross, Kathryn A., committee memberCobalt-59 is an exemplary nucleus for the design of NMR thermometers through its highly responsive nuclear spin properties such as its temperature-driven chemical shift (Δδ/ΔT) and relaxation dynamics (ΔT1/ΔT and ΔT2/ΔT). Investigated through a series of low-spin d6 Co3+ octahedrally coordination complexes, the temperature dependences of the 59Co nuclear spin properties are readily affected by molecular features such as coordination geometry, ligand identity, and local environmental factors. However, precise control of these thermometric properties (i.e., Δδ/ΔT, ΔT1/ΔT, and ΔT2/ΔT) via ligand design is absent. While it is known that molecular identity, defined by the coordinating ligand, ultimately dictates the thermometric properties of the 59Co-containing complex, it is neither known how it is governed nor how it may be improved. Thus, the goal of this dissertation aims to explore fundamental design principles that inform on the synthetic control of thermometric properties of 59Co via molecular features. Presented herein is the first comprehensive collection of experimental and computational investigations on the temperature-dependence of 59Co in a series of structurally similar coordination complexes with progressively encapsulating ligands. Through a suite of spectroscopic and theoretical techniques, a critical lens has been applied to establish a variety of key structural implications. These key points include the enhancement of thermometric properties via multidentate ligand encapsulation, temperature-driven structure, symmetry, and lastly, mass-induced changes to ligand-specific vibrational modes. The identified design principles pave way for future studies of either new ligand systems, coordination geometries, or other NMR-active transition metal nuclei.Item Open Access Synthesis of biologically relevant molecules(Colorado State University. Libraries, 2023) Braasch-Turi, Margaret, author; Crans, Debbie C., advisor; McNally, Andy, committee member; Prieto, Amy, committee member; Prenni, Jessica, committee memberNatural products total synthesis and bioorganic chemistry rely on organic synthesis to produce the compounds for biological study. Natural products and some biomolecules are naturally found in extremely low concentrations. Organic synthesis made it possible to acquire the amounts needed for biological studies. The research described herein discusses both areas. In the body of this document, the bioorganic work regarding lipoquinones, particularly ubiquinones and menaquinones, is described. Appendix IV described the natural products work. Chapter 1 provides a more detailed explanation as to the circumstances that led to two different areas of research. Chapter 2 serves as the introduction to the bioorganic research. In this chapter, a review of the literature surrounding ubiquinones, plastoquinones, and menaquinones is complied with their properties at the forefront. Lipoquinones are incredibly hydrophobic molecules, and such properties are often ignored or misinterpreted in the literature. The review compares reported similarities and differences among the lipoquinones with respect to their headgroups, isoprene sidechain length, conformations, and location of lipoquinones in membrane environments. The review also highlights the need for and encourages more experimental studies to validate the computational work in the field. Chapter 3 discusses the conformation and location of ubiquinone-2 in AOT reverse micelles. Previous work with menaquinone-2 determined the truncated lipoquinone derivative adopted a folded conformation in organic solvents and in AOT reverse micelles and suggest menaquinone-2 is located near the lipid-water interface. We hypothesized ubiquinone-2 would also adopt a folded conformation in the membrane and be located near the lipid-water interface, but closer to the bulk water than menaquinone-2. We used 1D and 2D NMR spectroscopic methods to explore the solvent and membrane conformations and membrane location of ubiquinone 2. The conformations and locations of ubiquinone-2 were compared to menaquinone-2, and the location of ubiquinone-2 was found to be slightly closer to the interface than menaquinone-2. Chapter 4 provides a review of the literature regarding the synthesis of naphthoquinone derivatives. There are five main synthetic approaches that have been used to synthesize naphthoquinone derivatives. The categories are (1) nucleophilic ring methods, (2) sidechain homologations and extensions, (3) metal-mediated and radical reactions, (4) electrophilic ring, and (5) pericyclic reactions. The advantages and disadvantages of each approach are discussed regarding selectivity, number of steps, yield, and overall safety. Some approaches are simpler to carry out for the non-expert and successfully yield product, although stereospecificity and yields of the reactions are less, whereas other routes are higher yielding. Chapter 5 discusses the exploratory synthesis of menaquinone derivatives. The established Friedel-Crafts approach has poor regioselectivity, poor stereoretention of the first isoprene unit in the sidechain, and universally low yields. Using the knowledge gained in Chapter 4, a pericyclic approach using Diels-Alder adducts was used to exert regiocontrol of sidechain and maintain the stereochemistry of the sidechain. A convergent route was designed to provide access to a diverse library of sidechains to include E and Z isomers of the first isoprene unit and varying degrees of saturation along the sidechain. Appendix IV discusses the progress towards the total synthesis of versiquinazoline A and versiquinazoline B, alkaloids with anti-cancer properties and a unique pyrazinoquinazolinedione (6-6-6) and imidazoindolone (5-5-6) scaffold. Through this synthesis, the non-proteinogenic amino acid, 1-amino-1-cyclopropycarboxylic acid, was prepared to be used in the synthesis of versiquinazoline B. The synthesis of the 5-5-6 ring system explored the use of many peptide coupling conditions to afford a sterically hindered amide bond. After frequent unsuccessful trials, steps toward the total synthesis of versiquinazoline A were taken using alanine instead of 1-amino-1-cyclopropylcarboxylic acid. After successful amide coupling, the reoxidation of the aromatic sing system was explored using 2,3-dichloro-5,6-dicyanoquinone. This project ended prematurely due to the advent of COVID-19 and the passing of my advisor, Dr. Robert M. Williams.