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A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap For Methyl Reactivity In Acetyl Coenzyme A Synthase, A. C. Manesis, B. W. Musselman, Breena C. Keegan, Jason M. Shearer, N. Lehnert, H. S. Shafaat

Chemistry Faculty Research

Nickel-containing enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical role in global energy conversion reactions, with significant contributions to carbon-centered processes. These enzymes are implied to cycle through a series of nickel-based organometallic intermediates during catalysis, though identification of these intermediates remains challenging. In this work, we have developed and characterized a nickel-containing metalloprotein that models the methyl-bound organometallic intermediates proposed in the native enzymes. Using a nickel(I)-substituted azurin mutant, we demonstrate that alkyl binding occurs via nucleophilic addition of methyl iodide as a methyl donor. The paramagnetic Ni …

Oxidative Degradation Of Lignin And Investigation Of Utilization Of Lignin-Derived Materials As Building Blocks For Epoxy Resins, Zhen Fang

Theses and Dissertations--Chemistry

Lignin, the second most abundant biopolymer on earth, is potentially a replaceable source for bulky fuels and chemical feedstocks. There have been numerous reports on methods for the oxidative cleavage of β-O-4 linkages but relatively few reports of how those methods affect other linkages that are present in lignin. We investigated how the β-1 and β-5 linkages respond under oxidative conditions proposed for lignin deconstruction based on their effect on β-O-4 linkages. Mechanochemical treatment of lignin can greatly improve the yield of monomer products and we applied a mechanochemical approach, using powerful ring-and-puck milling to promote lignin degradation. Along with …

Oxidative Depolymerization Of Lignin To Low Molecular Weight Aromatics, Yang Song

Theses and Dissertations--Chemistry

To date, most lignocellulosic biorefinery strategies have focused on optimizing conversion of cellulose to ethanol, leaving lignin as an underutilized biomass constituent. Lignin is engineered by nature with the intent to protect plants from chemical and biological attack; this leaves lignin with high structural irregularity and recalcitrance, rendering conversion of the lignin macromolecule to valuable products particularly challenging. Nevertheless, given that the economics of cellulosic ethanol production are strongly dependent on the value that can be obtained for the lignin co-product, the successful valorization of lignin is a crucial step in the transition towards a bio-based economy.

This thesis focuses …

Bottom-Up Lignomics: Towards The Development Of Adduct Electrospray Ionization Mass Spectrometric Methods To Characterize And Sequence Lignin Oligomers, Shardrack O. Asare

Theses and Dissertations--Chemistry

Lignin, the second most abundant naturally occurring polymer found in plant cell wall has the potential of becoming an alternative source for the production of chemical synthons for the pharmaceuticals and other chemical industries. While much gain has been made towards the development of degradation methods to break down lignin, effective analytical methods are still required to rapidly and accurately identify the products of lignin breakdown experiments. The goal of this work was to develop mass spectrometric methods for the characterization of lignin oligomers based on the study of model lignin compounds.

Unlike peptides and oligosaccharides, lignin model compounds that …

Synthesis And Characterization Of Carbonaceous Particles From Xylose And Soybean Residuals, Shanshan Wang

Theses and Dissertations--Chemistry

Carbonaceous materials, especially in micro and nanoscale, are useful in optical, energy storage, electronic, and biomedical devices or technologies. Techniques have been developed for preparation and modification of the carbonaceous materials, while it is still challenging to tailor the properties of carbonaceous materials effectively and economically. Laser is a powerful tool in academic and industrial laboratories, which also plays important roles in the preparation and modification of high-performance carbonaceous nanomaterials.

In this study low-cost hydrothermal synthesis, high-temperature annealing, and Laser ablation (LAL) methods are developed to prepare functionalized carbon nanomaterials and modify their electrochemical and optical properties.

Sub-micro hollow carbon …

Investigation Of Amyloid Β Oligomer Dissociation Mechanisms By Single Molecule Fluorescence Techniques, Hope Cook Abdalla

Theses and Dissertations--Chemistry

Alzheimer’s disease (AD) is currently considered the most prevalent neurodegenerative disease and places a large financial burden on society as healthcare resources are limited and the disease does not have a cure. Alzheimer’s disease is characterized by the presence of amyloid beta (Aβ) plaques and neurofibrillary tangles; however current literature suggests Aβ oligomers are the main aggregating species leading to AD symptoms. Therefore, the underlying cause of Alzheimer’s, accumulation of amyloid beta, is currently being studied in hopes of developing treatment options. Our research aims at determining the mechanism and kinetics of Aβ oligomer dissociation into non-toxic monomers in the …

Development Of Chromatography And Mass Spectrometry Methods For Enzyme Kinetics And Inhibition In Glycolysis And The Methylerythritol Phosphate (Mep) Pathways, Allison Fabino Carr

Graduate Research Theses & Dissertations

This dissertation focuses on method development for enzymatic activity and inhibition assays for use in screening potential antibacterial compounds. Infection by antibiotic-resistant pathogens in on the rise globally and several enzymes, including the those in the methylerythritol phosphate (MEP) pathway and fructose bisphosphate aldolase, as strong targets for novel pharmaceuticals because they are not present in humans. Several assays exist for the MEP pathway and aldolase, but there is always work to be done to improve sensitivity, increase throughput, and lower cost. This dissertation describes the development of several methods – hydrophilic interaction chromatography (HILIC), liquid chromatography-mass spectrometry (LC-MS), and …

New Synthetic Methods Using Superelectrophiles, Sean Kennedy

Graduate Research Theses & Dissertations

The work outlined in this dissertation describes new synthetic methods in the synthesis of heterocyclic compounds mediated by superacid catalysis. Superacids are powerful reagents that enhance the reactivity of electrophiles, thereby opening the door to new reactive pathways with very weak nucleophiles. In this work, trifluoromethanesulfonic acid (triflic acid, CF3SO3H) is employed as a superacid catalyst to effect new transformations. These concepts are summarized in chapter 1. Chapter 2 describes a new acid-catalyzed cascade leading to the indolizidine ring system, which is present in a number of natural products. Experiments support a proposed mechanism involving vinylogous keto-enol tautomerization. The synthesis …

Lewis Base Promoted Annulations Of Allenoates With 1,4-Naphthoquinones, Nicole Marie Shoup

Electronic Theses and Dissertations

Lewis base promoted cyclization of allenoates with electron deficient olefins open up the possibility to generate more complex organic structures. By generating more complex molecules, we are able to produce new compounds for biomedical and material applications. Both phosphine and amine Lewis bases offer interesting annulations with allenoates resulting in Lu or Morita–Baylis–Hillman type reactions. Once the Lewis base engages with the allenoate there can be several modes of nucleophilic reactivity that allows for the allenic ester to act as a two or three carbon synthon. The allenoate can then react with varying electron deficient olefins generating more complex molecules …

Utilization Of Superelectrophiles In Organic Synthesis, Hien Quoc Vuong

Graduate Research Theses & Dissertations

This dissertation describes the use of triflic acid as a catalyst in organic synthesis. The first chapter is an introduction of reaction classes, reactive intermediate, and superacids.

Chapter 2 discusses a series of compounds have been prepared by the Fischer indole synthesis and Friedel–Crafts reactions, using a single acid catalyst in a one-pot conversion. The reactions have worked best with pyridyl-substituted hydrazones/indoles. Chlorination and bromination products are formed in good yields and high regioselectivities. Acylation products have also been prepared by the two-stage reaction. In the case of alkylation, the expected alkyl-substituted indoles are obtained however they are accompanied by …

Coupling Reactions Of Triaryl Carbocations Via Cationic Charge Delocalization, Hongfang Xue

Graduate Research Theses & Dissertations

This thesis describes a coupling reaction involving cationic charge delocalization. This work began as a study of the Piancatelli rearrangement, a reaction involving furan-based triaryl methyl cations. A new synthetic reaction has been discovered using these furan-based triaryl methyl cations as electrophilic intermediates. Zinc chloride has been found to be an effective Lewis acid catalyst for the ionization of the triaryl methanols to the carbocations. It has been found that furan-based triaryl methyl cations react with nucleophiles such as enol silyl ethers and silyl ketene acetals. Similar to the Piancatelli reaction, nucleophilic reactions are found to occur at the 5-position …

Oleic Acid Vesicles: Formation, Mechanisms Of Reactivity, And Uses In Determination Of Terpene Activity, Laura A. Walther

Theses and Dissertations--Chemistry

This dissertation will focus on the volatile compounds released upon the burning of incense which are numerous and varied. The first part of this dissertation is the gas chromatography-mass spectral (GC-MS) analysis of burning incense collected via solid phase microextraction (SPME) with the aim of developing a library of compounds found in incense as used in the Orthodox church.

The second part of this dissertation has the aim of developing a method for forming oleic acid bilayer vesicle membranes and a fluorescence spectroscopy method by which the reactivities of these vesicles can be analyzed. These reactivities include permeability, fluidity, aggregation, …

Modeling The Condensed-Phase Behavior Of Π-Conjugated Polymers, Walker Mask

Theses and Dissertations--Chemistry

It is well established that the morphology and physical properties of an organic semiconducting (OSC) material regulate its electronic properties. However, structure-function relationships remain difficult to describe in polymer-based OSC, which are of particular interest due to their robust mechanical properties. If relationships among the molecular and bulk levels of structure can be found, they can aid in the design of improved materials. To explore and detail important structure-function relationships in polymer-based OSC, this work employs molecular dynamics (MD) simulations to study various π-conjugated polymers in different environments. Two independent investigations are discussed in this work. One investigation examines how …

Development Of Synthetic Methodologies Of Nucleophile-Electrophile Chemistry, Michael R. Stentzel

Graduate Research Theses & Dissertations

The work outlined in this dissertation describes the development of synthetic methodologies utilizing a wide electrophilicity range of substrates towards the synthesis of new compounds. Substitution, addition, and superelectrophilic chemistry are powerful tools to afford potentially important compounds. These concepts are summarized in chapter 1.

Chapter 2 describes the capture of superacid catalyzed fluorenyl cations with nitriles (Ritter reaction) and alcohols. Optimization of reaction conditions and extensive scope studies were performed.

In chapter 3, the Michael addition of organometallic reagents with N-heterocyclic substituted olefins is explored. The nucleophilic carbanion intermediate species is shown to have reactivity towards strong electrophiles. With …

The Design, Synthesis, And Evaluation Of Inhibitors Of The Ispf Enzyme In The Mep Pathway, Christopher G. Stewart

Graduate Research Theses & Dissertations

Isoprenoids are a class of over 50,000 compounds that serve as key precursors for many compounds in plants and animals. These compounds play critical roles in many biological functions such as cellular growth, respiration, and go on to form critical compounds such as steroids and vitamins. Despite their overall necessity to life their biosynthesis only follows two synthetic pathways. These pathways are the Mevalonic Acid (MVA) Pathway and the 2-C-Methyl-D-Erythritol-4-Phosphate (MEP) Pathway also known as the non-mevalonate pathway. The MVA pathway is found primarily in humans and some higher plants while the MEP pathway is found in bacteria and some …

Investigation Of Thiol-Containing Biomarkers And Their Role In The Exposome, Tracy Gastineau-Stevens

Theses and Dissertations--Chemistry

Exposomics is an emerging area of study that looks at how the environment around a person or persons affects their overall health. Biomarkers have emerged as useful tools to better understand how the exposome affects a person. In this work, we investigate two potential endogenous biomarkers, homocysteine and glutathione that have been previously implicated in a number of diseases that have been linked to environmental causes. We also investigated an environmental exposure, the fungicide Ziram, which epidemiologically has been linked to diseases. In our investigation, we utilized capillary electrophoresis and capillary electrophoresis-mass spectrometry to develop a method for homocysteine and …

Silicone Wristbands As Passive Samplers For Quantitative Measurement Of Wood Smoke Exposure, Hannah J. Wright

Graduate Student Theses, Dissertations, & Professional Papers

Human exposure to biomass smoke is a health concern worldwide. Although many studies have measured particulate matter in wood smoke as a health concern, exposure to mutagenic and carcinogenic volatile and semivolatile compounds remains understudied. This research introduces a novel method of quantitative measurement of exposure to these compounds using silicone wristbands. The study developed a method to extract analytes of interest from the wristbands and quantify a few volatile organic compounds and polycyclic aromatic hydrocarbons with known ill health effects, and then performed linear regressions between extracted levels and exposure to those analytes using controlled exposure studies. Results indicate …

Evaluating Methods Of Obtaining Male Pheromone From Hymenochirus Sp. Using Analytical Chemistry, Vincent Wing-Kun Leung

University of the Pacific Theses and Dissertations

Male Hymenochirus sp. frogs are known to release pheromone that attracts females of the same species. Four methods for collecting secretions containing pheromone in Hymenochirus sp. were tested: norepinephrine injection, gonadotropin-releasing hormone injection, homogenization of gland tissue, and electrostimulation of the skin over the breeding gland area. The samples collected were analyzed using high-performance liquid chromatography (HPLC) and mass spectrometry. The HPLC chromatograph for the male norepinephrine sample contained a peak at 6.4 min that was not in the female norepinephrine sample HPLC chromatograph. The male norepinephrine sample mass spectrum had a peak of m/z 292.0 not in the female …

Development And Characterization Of Ldv Peptide Targeted Nanocarriers For Paclitaxel Delivery: A Comparative Study Of Micelles, Liposomes And Solid Lipid Nanoparticles, Poonam Dattani

University of the Pacific Theses and Dissertations

Nanocarriers have been established as delivery vehicles to target cancer tumors. However, premature drug leakage is one of the major reasons for inefficient drug delivery of nanocarriers to the tumor. Drug diffusion out of the nanocarriers or destabilization of drug loaded nanocarriers by physiological interactions with blood cells, serum proteins, and cell membranes upon systemic administration contribute to premature drug release. In this study, targeted micelles, liposomes and solid lipid nanoparticles (SLNs) of similar composition were prepared and characterized to compare physicochemical characteristics, in vitro stability, in vitro release rates in release media and in vivo performance. Peptide Amphiphiles (PAs) …

Construction Of A Cross-Layer Linked G-Octamer Via Conformational Control: A Stable G-Quadruplex In H-Bond Competitive Solvents, Ying He, Yanbin Zhang, Luksaz Wojtas, Novruz G. Akhmedov, David Thai, Heng Wang, Xiaopeng Li, Hao Guo, Xiaodong Shi

Faculty & Staff Scholarship

Methanol soluble and stable guanosine octamers were successfully achieved via H-bond self-assembly. Through structural conformational design, we developed a new class of guanosine derivatives with modification on guanine (8-aryl) and ribose (20 ,30 -isopropylidene). This unique design led to the formation of the first discrete G8-octamer with its structure characterized by single crystal X-ray diffraction, MS and NMR spectroscopy. The G8-octamer showed unique cation recognition properties, including the formation of a stable Rb+ templated G-quadruplex. Based on this observation, further modification on the 8-aryl moiety was performed to incorporate a cross-layer H-bond or covalent linkage. Similar G-octamers were obtained in …

Unexpected Outcomes During The Attempted Iodination Of Biphenol, Henry Nguyen

Honors Theses

The goal of this research was to create a new procedure to iodinate 4,4- biphenol using a ball miller. Iodination of 4,4-biphenol was first attempted in solution using electrophilic aromatic substitution. Several attempts were made to iodinate 4,4-biphenol, but the general insolubility of crude products inhibited progress. Interestingly, NMR analysis of the aqueous ammonia product suggested that 4,4-biphenol dimerized or polymerized with itself to make an ether. The exact mechanism by which the ether dimer was created is unknown, but the reaction may have occurred using a radical mechanism. Though the original goal of the project is left unmet, a …

Inhibition Of The Self-Assembly Of Aβ And Of Tau By Polyphenols: Mechanistic Studies, Qiuchen Zheng, Micheal T. Kebede, Merc M. Kemeh, Saadman Islam, Bethany Lee, Stuart D. Bleck, Liliana A. Wurfl, Noel D. Lazo

Chemistry

The amyloid-β (Aβ) peptide and tau protein are thought to play key neuropathogenic roles in Alzheimer’s disease (AD). Both Aβ and tau self-assemble to form the two major pathological hallmarks of AD: amyloid plaques and neurofibrillary tangles, respectively. In this review, we show that naturally occurring polyphenols abundant in fruits, vegetables, red wine, and tea possess the ability to target pathways associated with the formation of assemblies of Aβ and tau. Polyphenols modulate the enzymatic processing of the amyloid-β precursor protein and inhibit toxic Aβ oligomerization by enhancing the clearance of Aβ42 monomer, modulating monomer–monomer interactions and remodeling oligomers to …

The Benefit Of Precise Chemical Shift And Concentration Referencing In Nmr Applications, Ming Huang

Doctoral Dissertations

“In Nuclear Magnetic Resonance (NMR) spectroscopy, the chemical shift and intensity of NMR signals provide critical information about a sample's molecular structure, reaction conditions, and material properties. For the precise determination of structures and properties, it is critical to know sample or reaction conditions such as temperature, pH, concentration, or absolute amount of material. Chemical-shift and signal-intensity calibrations play a key role for extracting the maximum amount of information from NMR experiments. In this dissertation, internal and external reference standards are used to calibrate NMR spectra with respect to chemical shift and signal intensity. Sealed capillary tubes filled with specific …

Analysis Of Bodily Fluids Using Vibrational Spectroscopy: A Direct Comparison Of Raman Scattering And Infrared Absorption Techniques For The Case Of Glucose In Blood Serum, Drishya Prachalil, Clément Bruno, Franck Bonnier, Helen Blasco, Igor Chourpa, Matthew Baker, Jennifer Mcintyre, Hugh Byrne

Articles

Analysis of biomarkers present in the blood stream can potentially deliver crucial information on patient health and indicate the presence of numerous pathologies. The potential of vibrational spectroscopic analysis of human serum for diagnostic purposes has been widely investigated and, in recent times, infrared absorption spectroscopy, coupled with ultra-filtration and multivariate analysis techniques, has attracted increasing attention, both clinical and commercial. However, such methods commonly employ a drying step, which may hinder the clinical work flow and thus hamper their clinical deployment. As an alternative, this study explores the use of Raman spectroscopy, similarly coupled with ultra-filtration and multivariate analysis …

Cross Faculty Collaboration In The Development Of An Integrated Mathematics And Science Initial Teacher Education Program, Sharon P. Fraser, Kim Beswick, Margaret Penson, Andrew Seen, Robert Whannell

Australian Journal of Teacher Education

This paper describes a collaborative project involving mathematicians, scientists and educators at an Australian university where an innovative initial teacher education (ITE) degree in mathematics/science was developed. The theoretical frameworks of identity theory and academic brokerage and their use in understanding the challenges associated with the early stages of collaborative projects is described. Data from reflections and interviews of the participants after involvement in the project from one to three years are presented to illustrate these challenges. The paper concludes with a description of the importance of the academic broker in overcoming identity challenges and facilitating cultural change for academics …

Metallophthalocyanine-Based Electrode For Sodium-Ion Batteries, Apinut Chongphanitkul

Chulalongkorn University Theses and Dissertations (Chula ETD)

In this study, metallophthalocyanine-modified electrodes were fabricated and investigated for their electrochemical properties and energy storage performance. Six kinds of electrodes were prepared from indium tin oxide-coated glass (ITO-coated glass) substrates coated with titanium dioxide nanotube (TNT), poly(3,4-ethylenedioxythiophene) (PEDOT) and reduced graphene oxide (rGO) to improve conductivity of the substrates and surface area for the phthalocyanine-based materials. Target phthalocyanine monomers possess amino groups and Co(II) or Ni(II) central metals. On surface of each electrodes, films of the monomers were coated by a drop-casting technique, while those of their polymers were formed by electropolymerization. According to study on electrochemically active surface …

Interactions Of Pyrrolidinyl Peptide Nucleic Acid With Oligodeoxyguanosine And Biosensing Applications, Chayan Charoenpakdee

Chulalongkorn University Theses and Dissertations (Chula ETD)

Pyrrolidinyl peptide nucleic acid is a DNA mimic consisting of proline-2-aminocyclopentane carboxylic acid (acpcPNA) as a core structure. It binds to DNA to form a more stable hybrid while showing greater selectivity and affinity than the conventional DNA and PNA probes. In this study, we aim to develop novel DNA sensing systems based on the acpcPNA probe. In the first part, graphene oxide (GO) was used as an external quencher which could effectively quench the fluorescein-labeled PNA probe. A remarkable fluorescence restoration was achieved after the addition of a complementary DNA target. This acpcPNA-GO combination was successfully used to monitor …

Chemical Constituents Of Knema Angustifolia Stem And Biological Activities, Dung Le Thi Kim

Chulalongkorn University Theses and Dissertations (Chula ETD)

The medicinal plant Knema angustifolia has been used in Thai folk medicine for the treatment of various diseases, especially related to body tonic or blood tonic agent. Chemical data on this plant are scarce. A novel para-benzoquinone, angustiquinone (3), along with ten known compounds, rapanone (1), embelin (2), quercetin (4), kaempferol (5), bergenin (6), 11-O-acetyl bergenin (7), catechin (8), isovanillic acid (9), protocatechuic acid (10) and gallic acid (11) were isolated from the n-hexane and EtOAc extracts of the stems of K. angustifolia. Their structures were unambiguously elucidated using extensive 1D and 2D NMR analyses, high-resolution mass spectrometry along with …

Synthesis And Development Of Nanocomposites Of Magnetic Nanoparticles-Silica-Mannan As Vaccine Adjuvants, Kamonlatth Rodponthukwaji

Chulalongkorn University Theses and Dissertations (Chula ETD)

Over the past years, vaccination has been considered as an effective treatment against a wide range of pathogens and diseases. Despite a promising outcome, the lack of strong immune response of some types of vaccines is still challenging. Therefore, targeting and activating dendritic cells (DCs) using nanomaterial-based vaccine adjuvant is of our interest. Herein, superparamagnetic iron oxide nanoparticles (SPIONs) have been exploited as directing agents to the targeted dendritic cells (DCs). In addition, mannan extracted from Saccharomyces cerevisiae was used as targeting molecules for targeting DCs. Nanocomposites of silica-magnetic nanoparticles-mannan (S-SPION-MN) were successfully fabricated. The synthesized particles were morphologically and …

Development Of Portable Electrochemical Sensors For Determination Of Heavy Metals, Nitrogen Oxides And Thiocyanate Ion, Kingkan Pungjunun

Chulalongkorn University Theses and Dissertations (Chula ETD)

This dissertation focused on the development of portable electrochemical sensors using the paper-based analytical device (ePAD) for the determination of the important compounds/biomarkers in various applications. Considering the target applications, this dissertation can be divided into three main parts including food safety application, environmental analysis and clinical application, respectively. In the first part, two sub-sections relating to the detection of heavy metals contaminated in food will be discussed. For the first sub-section, an ePAD coupled with a boron-doped diamond electrode was developed for the determination of total arsenic. The device was performed using the origami paper device for the preparation …