Chemistry Commons^™

Exploration Of Metal-Carbonyl Complexes For Decarbonylation Reactions, Rebekah C. Krupa

Graduate Theses, Dissertations, and Problem Reports (ETD)

In recent years, transition metal-mediated decarbonylation reactions have emerged as an alternative to conventional cross-coupling methods due to the advantages associated with the use of carbonyl-containing functionalities as coupling electrophiles instead of organohalides found in traditional cross-coupling reactions. This, coupled with the ubiquity of carbonyl-containing compounds in pharmaceuticals and non-biodegradable chemicals, has led to the interest in developing efficient systems for transition metal-catalyzed decarbonylation. However, these reactions are commonly limited to stoichiometric amounts of metal reagents due to the strong metal-carbonyl bond formed during transition metal-mediated decarbonylation. With the goal of gaining a better mechanistic understanding of CO dissociation in …

Ambient Ammonia Synthesis Via Microwave-Catalytic Materials And Plasma Chemistry, Siobhan Brown

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ammonia is critical to supporting human life on earth because of its use as fertilizer. The Haber-Bosch process to produce ammonia has been practiced for over 100 years. This process operates at high pressure and temperature to overcome the thermodynamic and kinetic limitations of the ammonia synthesis reaction thus researchers have tried to overcome it for decades. At present this process represents 1% of global energy usage and 2.5% of global CO₂ emissions. The proposed chemical looping ammonia synthesis approach seeks to reduce the environmental impact of this critical process and to elucidate microwave-catalytic principles.

This research aims to …

Analysis Of ‘Touch’ Dna Recovered From Metal Substrates: An Investigation Into Cfdna-Metal Interactions And The Efficacy Of Different Collection Techniques On Dna Yield, Jessica E. Thornton

Graduate Theses, Dissertations, and Problem Reports (ETD)

While several improvements have been made in recent years to optimize the recovery of ‘touch’ DNA, relatively little research has been conducted to understand the relationship between ‘touch’ DNA and the binding affinity of that DNA to metal surfaces, specifically those with a significant copper presence. Furthermore, characterization of cell-free DNA (cfDNA) and its contribution to ‘touch’ samples and those cfDNA-metal interactions from objects commonly identified at crime scenes (cartridge casings, knives, doorknobs) have been lacking. Research has identified the tendency of copper ions to intercalate with DNA helices, resulting in sample degradation among other damaging conformational changes; however, while …

Room-Temperature Crystallography Reveals Altered Binding Of Small-Molecule Fragments To Ptp1b, Tamar Skaist Mehlman, Justin T. Biel, Syeda Maryam Azeem, Elliot R. Nelson, Sakib Hossain, Louise Dunnett, Neil G. Paterson, Alice Douangamath, Romain Talon, Danny Axford, Helen Orins, Frank Von Delft, Daniel A. Keedy

Advanced Science Research Center

Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of …

Strengthening The Interpretation Of Glass And Paint Evidence Through The Study Of Random Frequency Of Occurrence And Analytical Information, Lauryn C. Alexander

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glass and paint particles are frequently discovered at crime scenes as valuable trace evidence. Often, these fragments are transferred from a crime scene to a victim or person-of-interest, and can subsequently be evaluated, analyzed, and classified according to their physical and optical measurements, and chemical properties, each of which can provide important information to the analyst to assist in the determining if a recovered particle is distinguishable or indistinguishable from a known source. Moreover, these minute materials can provide information about how the events took place, leading to the reconstruction of crime scenes and the identification of valuable clues for …

The Affect Of Dha Concentration On Lipid Membrane Fluidity, Elise Rezabeck

Williams Honors College, Honors Research Projects

My proposed project will be creating large unilaminar vesicles with varying concentrations of DHA in the vesicles. The diffusion in and out of these vesicles will be tracked by using singular lipid molecules. These singular lipid molecules will be tagged with fluorescence and viewed using an internal reflection fluorescence microscope. The data collected over the course of this project will then be analyzed using Matlab. The result of the project will be to find the specific lipid diffusion constant of these unilaminar vesicles. The relationship between the concentration of DHA and lipid diffusion and membrane fluidity will be found as …

Global Minimum Search For The Largest Ge Cage Stabilized By A Single Interstitial Metal Atom, Alexis Kiefer

Williams Honors College, Honors Research Projects

Recent joint experimental and theoretical studies showed that the largest Ge cage-like cluster features 14 Ge atoms that encapsulate a single transition metal atom in the [Nb@Ge₁₄]^3- cluster. The next larger experimentally confirmed Ge cluster exhibiting a cage-like geometry was found to be viable only when stabilized by two transition metal atoms in the [Co₂@Ge₁₆]^4- cluster. So, as of now, it is not clear whether a cage-like cluster made out of 15 Ge atom stabilized by a single transition metal is viable. Hence, the aim of this project is to find the …

Intergranular And Pitting Corrosion Mechanisms Of Sensitized Aluminum Alloy Aa5083, Clayton Egleston

Williams Honors College, Honors Research Projects

The motivation and objectives of this project is to examine the mechanisms of intergranular corrosion (IGC) and pitting corrosion of sensitized AA5083. In this regard, different characterization techniques were used, including optical analysis of microstructure, cyclic potentiodynamic polarization with Tafel fitting, electrochemical impedance spectroscopy with electrical equivalent circuit (EEC) fitting, and potentiostatic current transient monitoring. The transition from IGC to pitting corrosion occurs when the grain boundaries become saturated with the β-phase (Mg₂Al₃). It was found that AA5083 becomes more vulnerable to pitting corrosion as the degree of sensitization increases.

Nmr Study Of Co2 Capture By Butylamine And Oligopeptide Kdde In Aqueous Solution: Capture Efficiency And Gibbs Free Energy Of The Capture Reaction As A Function Of Ph**, Kaidi Yang, Joseph Schell, Fabio Gallazzi, Wei Wycoff, Rainer Glaser

Chemistry Faculty Research & Creative Works

We Have Been Interested in the Development of Rubisco-Based Biomimetic Systems for Reversible CO₂ Capture from Air. Our Design of the Chemical CO₂ Capture and Release (CCR) System is Informed by the Understanding of the Binding of the Activator CO₂ (^ACO₂) in Rubisco (Ribulose-1,5-Bisphosphate Carboxylase/oxygenase). the Active Site Consists of the Tetrapeptide Sequence Lys-Asp-Asp-Glu (Or KDDE) and the Lys Sidechain Amine is Responsible for the CO₂ Capture Reaction. We Are Studying the Structural Chemistry and the Thermodynamics of CO₂ Capture based on the Tetrapeptide CH₃CO−KDDE−NH₂ ("KDDE") in Aqueous …

Nanostructured Ternary Nickel-Based Mixed Anionic (Telluro)-Selenide As A Superior Catalyst For Oxygen Evolution Reaction, Ibrahim Munkaila Abdullahi, Siby Thomas, Alessio Gagliardi, Mohsen Asle Zaeem, Manashi Nath

Chemistry Faculty Research & Creative Works

Developing Protocols for Designing High-Efficiency, Durable, Cost-Effective Electrocatalysts for Oxygen Evolution Reaction (OER) Necessitates Deeper Understanding of Structure–property Correlation as a Function of Composition. Herein, It Has Been Demonstrated that Incorporating Tellurium into Binary Nickel Chalcogenide (NiSe) and Creating a Mixed Anionic Phase Perturbs its Electronic Structure and Significantly Enhances the OER Activity. a Series of Nanostructured Nickel Chalcogenides Comprising a Layer-By-Layer Morphology Along with Mixed Anionic Ternary Phase Are Grown in Situ on Nickel Foam with Varying Morphological Textures using Simple Hydrothermal Synthesis Route. Comprehensive X-Ray Diffraction, X-Ray Photoelectron Spectroscopy, and in Situ Raman Spectroscopy Analysis Confirms the Formation …

Epitaxial Electrodeposition Of Ordered Inorganic Materials, Jay A. Switzer, Avishek Banik

Chemistry Faculty Research & Creative Works

Conspectus The quality of technological materials generally improves as the crystallographic order is increased. This is particularly true in semiconductor materials, as evidenced by the huge impact that bulk single crystals of silicon have had on electronics. Another approach to producing highly ordered materials is the epitaxial growth of crystals on a single-crystal surface that determines their orientation. Epitaxy can be used to produce films and nanostructures of materials with a level of perfection that approaches that of single crystals. It may be used to produce materials that cannot be grown as large single crystals due to either economic or …

Nuclear Magnetic Resonance Study Of Co2 Capture By Fluoroalkylamines: Ammonium Ion Pka Depression Via Fluorine Modification And Thermochemistry Of Carbamylation, Brian Jameson, Kari Knobbe, Rainer Glaser

Chemistry Faculty Research & Creative Works

We are developing energy-efficient and reversible carbon capture and release (CCR) systems that mimic the Lys201 carbamylation reaction in the active site of ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO). The multiequilibria scenario ammonium ion Xa ⇌ amine Xb ⇌ carbamic acid Xc ⇌ carbamate Xd requires the presence of both free amine and CO2 for carbamylation and is affected by the pKa(Xa). Two fluorination strategies aimed at ammonium ion pKa depression and low pH carbamylation were analyzed with (2,2,2-trifluoroethyl) butylamine 2b and 2,2-difluoropropylamine 3b and compared to butylamine 1b. The determination of K1 and ΔG1 of the carbamylation reactions requires the solution of …

Inter-Rater Agreement For The Annotation Of Neurologic Signs And Symptoms In Electronic Health Records, Chelsea Oommen, Quentin Howlett-Prieto, Michael D. Carrithers, Daniel B. Hier

Chemistry Faculty Research & Creative Works

The extraction of patient signs and symptoms recorded as free text in electronic health records is critical for precision medicine. Once extracted, signs and symptoms can be made computable by mapping to signs and symptoms in an ontology. Extracting signs and symptoms from free text is tedious and time-consuming. Prior studies have suggested that inter-rater agreement for clinical concept extraction is low. We have examined inter-rater agreement for annotating neurologic concepts in clinical notes from electronic health records. After training on the annotation process, the annotation tool, and the supporting neuro-ontology, three raters annotated 15 clinical notes in three rounds. …

Using Catalysis To Control The Morphology And Stiffness Of Shape Memory Poly(Isocyanurate-Urethane) (Pir-Pur) Aerogels, A. B.M. Shaheen Ud Doulah, Chandana Mandal, Hojat Majedi Far, Vaibhav A. Edlabadkar, Rushi U. Soni, Stephen Y. Owusu, Nicholas Leventis, Chariklia Sotiriou-Leventis

Chemistry Faculty Research & Creative Works

A large array of anhydrous metal ions were tested as catalysts in the preparation of shape memory poly(isocyanurate-urethane) (PIR-PUR) aerogels from the reaction of 1,3,5-tris(6-isocyanatohexyl)-1,3,5-triazinane-2,4,6-trione (Desmodur N3300A: a well-known isocyanurate-based aliphatic triisocyanate) and triethylene glycol (TEG) in anhydrous acetonitrile. The reaction yielded wet gels that were dried into aerogels in an autoclave with supercritical fluid CO2. The catalytic activity was mostly identified among CH3CN-soluble salts (mainly chlorides) of third-row d-block elements from iron to zinc, group 13 elements from aluminum to thallium, as well as cadmium, bismuth, and tin. Tin (119Sn) NMR indicated that the metal ion complexes with TEG, …

Rovibrational States Calculations Of The H2o-Hcn Heterodimer With The Multiconfiguration Time Dependent Hartree Method, Hervé Tajouo Tela, Ernesto Quintas-Sánchez, Marie Lise Dubernet, Yohann Scribano, Richard Dawes, Fabien Gatti, Steve Ndengué

Chemistry Faculty Research & Creative Works

Water and hydrogen cyanide are two of the most common species in space and the atmosphere with the ability of binding to form dimers such as H₂O-HCN. In the literature, while calculations characterizing various properties of the H₂O-HCN cluster (equilibrium distance, vibrational frequencies and rotational constants) have been done in the past, extensive calculations of the rovibrational states of this system using a reliable quantum dynamical approach have yet to be reported. In this work, we intend to mend that by performing the first calculation of the rovibrational states of the H₂O-HCN van der …

Extracellular Poly(Hydroxybutyrate) Bioplastic Production Using Surface Display Techniques, Kevin Beaver, Ashwini Dantanarayana, Willisa Liou, Markus Babst, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

Poly(hydroxybutyrate) is a biocompatible, biodegradable polyester synthesized naturally in a variety of microbial species. A greener alternative to petroleum-based plastics and sought after for biomedical applications, poly(hydroxybutyrate) has failed to break through as a leading material in the plastic industry due to its high cost of production. Specifically, the extraction of this material from within bacterial cells requires lysis of cells, which takes time, uses harsh chemicals, and starts the process again with growing new living cells. Recently, surface display of enzymes on bacterial membranes has become an emerging technique for extracellular biocatalysis. In this work, a fusion protein lpp-ompA-phaC …

Food Waste Storage Gaseous Emissions Detection And Quantification Using Infrared Spectroscopy, Ryley A. Burton-Tauzer

Cal Poly Humboldt theses and projects

A growing interest in sustainable waste management and the implementation of new policies have prompted a shift towards alternative resource recovery methods for organic waste, including food waste. To effectively assess alternative food waste treatment scenarios, it is important to evaluate the life cycle impacts associated with each scenario. The storage phase of food waste, encompassing its accumulation in kitchens, and storage in bins for collection and transportation, has been overlooked as a source of greenhouse gases in previous studies. This investigation aimed to identify the greenhouse gases emitted during the initial five-day period of low-oxygen storage. An open dynamic …

Neutral And Charged Bis(Triarylamines) For Use In Grid Scale Battery Technologies, Taylor Matthews

Online Theses and Dissertations

Energy storage systems allow flexibility in control and maintenance of the electric grid while integrating renewable energy resources to mitigate carbon emissions. Redox flow batteries (RFBs) are stationary energy storage systems that convert chemical energy to electrical energy by charge-transfer reactions. Designing molecules that are capable of stable multi-electron redox reactions per active-species molecule can increase the efficiency of future systems. Spectroelectrochemistry, the combination of spectroscopy and electrochemistry, allows for quantitative and qualitative analyses of electron-transfer processes. The focus of this research is to use optical and electrochemical properties obtained from spectroelectrochemistry to determine the stability of neutral and charge …

Method Development For The Quantification Of Heavy Metals In Biological Matrices And Its Application To Clinical And Environmental Samples, Michelle Catherine Gende

Dissertations

A three-fold approach was taken to develop a method for the detection of heavy metals in different matrices and had to be performed sequentially. The first was to develop a method capable of quantifying lead in complex matrices by graphite furnace atomic absorption (GFAA). The developed method needed to meet specific analytical requirements, namely, to be robust, sensitive, and accurate. Initially, four different sample preparation methods were explored for the quantification of lead using Escherichia coli (E. coli) as a sample matrix. The sample preparation procedures attempted were acidic dilution, matrix modification, conventional heating digestion, and microwave assisted acid digestion …

Wetting Transition Of Texturized Surfaces, Jenna Stephens

Williams Honors College, Honors Research Projects

Building on previous research, this project aims to continue the investigation of the wettability of various liquids on a uniform, texturized surface. Different surface energies can impact the wettability of a surface. The surface can be hydrophilic, hydrophobic, or in between. The goal of this project is to research how features of texturized surfaces affect the wetting transition of water, oil, and a mixture of both. Additionally, this project aims to improve the quality of the 3D printed surfaces. The surfaces that will be studied are constructed using UV cured resin 3D printing and are made up of an array …

Expanding Our Grasp Of Two-Component Signaling In Clostridioides Difficile, Orlando Berumen Alvarez, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

The intestinal pathogen Clostridioides difficile encodes roughly 50 TCS, but very few have been characterized in terms of their activating signals or their regulatory roles. A. G. Pannullo, B. R. Zbylicki, and C. D. Ellermeier (J Bacteriol 205:e00164-23, 2023, https://doi.org/10.1128/jb.00164-23) have identified both for the novel C. difficile TCD DraRS. DraRS responds to antibiotics that target lipid-II molecules in the bacterial cell envelope, and regulates the production of a novel glycolipid necessary for bacitracin and daptomycin resistance in C. difficile.

Uhplc/Ft-Ms Non-Targeted Screening Approach For Biomass Burning Organic Aerosol And Liquid Smoke As Biomass Burning Organic Aerosol Surrogate, D.M.R. Thusitha Dinusha Kumarihami Divisekara

Dissertations, Master's Theses and Master's Reports

Biomass combustion contributes a large amount of aerosol particles to the atmosphere impacting the climate system and human health. Identifying the molecular composition of biomass burning organic aerosol (BBOA) is challenging because of its complex nature. Liquid chromatography mass spectrometric non-targeted screening (NTS) methods provide a comprehensive analysis. However, the instrumentation and data analysis are challenging due to the extreme complexity of environmental samples. In the first part of this study, we implemented a new LC/FT-MS data processing approach by combining existing open-source data processing tools, MZmine2.53 and MFAssignR. The method's validity was checked using the standard polyacrylic acid (PAA) …

Enhancing The Forensic Comparison Process Of Common Trace Materials Through The Development Of Practical And Systematic Methods, Meghan Nicole Prusinowski

Graduate Theses, Dissertations, and Problem Reports (ETD)

An ongoing advancement in forensic trace evidence has driven the development of new and objective methods for comparing various materials. While many standard guides have been published for use in trace laboratories, different areas require a more comprehensive understanding of error rates and an urgent need for harmonizing methods of examination and interpretation. Two critical areas are the forensic examination of physical fits and the comparison of spectral data, which depend highly on the examiner’s judgment.

The long-term goal of this study is to advance and modernize the comparative process of physical fit examinations and spectral interpretation. This goal is …

Enabling Technologies For Chemical Synthesis: I. Selective Microwave Heating; Ii. Synthesis And Regioselective Cyclotrimerizations Of Tethered 1,6-Diynes, Amir Tavakoli

Graduate Theses, Dissertations, and Problem Reports (ETD)

Reaction discoveries, method developments, and technology advancements lie at the heart of synthetic organic chemistry. These innovations are essential for creating and manipulating complex molecules, which are the building blocks of many important chemical compounds, including pharmaceuticals, materials, and agrochemicals. Here, we first describe new methods to prepare neopentylene-tethered (NPT) 1,6-diynes which are valuable substrates for reaction discovery and target-oriented synthesis, especially in benzannulation strategies toward illudalane natural products. NPT 1,6-diynes have been employed as coupling partners in cyclotrimerization reactions for the synthesis of highly substituted benzene rings which present a persistent challenge in chemical synthesis and are underrepresented scaffolds …

Enantioselective Dearomatization Facilitated By Non-Covalent Interactions Of N-Heterocyclic Carbene Catalysts And Pyridinium Salts, Jack A. Patterson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Dihydropyridines are a practical organic scaffold commonly used for their pharmaceutical properties. Nucleophilic dearomatization of pyridines has proven to be a useful method in obtaining dihydropyridines. By using N-heterocyclic carbene (NHC) organocatalysts, dihydropyridines can be synthesized with high regioselectivity of the 1,4 regioisomer over the 1,2- regioisomer but often with low enantioselectivity. By incorporating non-covalent interaction contact points, we hypothesize that enantioselectivity can be enhanced. By synthesizing numerous NHCs, each proposed to exhibit a different type of non-covalent interaction (i.e., hydrogen bonding or ion pairing), an understanding of the secondary interactions within this reaction system can be studied and …

Synthesis And Pharmacology Of Illudalic Acid And Analogous Chemical Structures, Robert Gaston Jr

Graduate Theses, Dissertations, and Problem Reports (ETD)

Natural products are the foundation of modern medicine and an inspiration for chemical innovation. Developing new synthetic strategies to complex natural products drives synthetic innovation and promotes pharmacological exploration. As bioactive secondary metabolites of fungi, illudalic acid and associated analogs have unrealized medicinal potential due to synthetic limitations. Illudalic acid is notably the first selective covalent inhibitor of the LAR-PTPs, a class of enzymes linked to many human illnesses, including stimulant addiction. The chemistry herein focuses on optimizing synthetic routes to illudalic acid and associated analogs toward exploring their pharmaceutical potential. We report a second-generation synthesis of illudinine (55% overall …

Exogenous Factors That Impact Huntingtin Aggregation, Adam Skeens

Graduate Theses, Dissertations, and Problem Reports (ETD)

While expansion of a polyglutamine (polyQ) domain is the immediate cause of huntingtin (htt) aggregation associated with Huntington’s Disease (HD), other cellular factors modify aggregation. These include interactions with cellular membranes, protein biding partners, molecular crowding, and proteinaceous seeds. Here, two important factors are biophysically characterized: 1) the interaction of htt with endomembranes and 2) proteinaceous seeds obtained from a variety of htt-derived peptides. In the first project, the aggregation of htt at bilayer interfaces and in the presence of divalent cations was investigated. A major cellular factor implicated in altered htt aggregation is the binding of lipids. Furthermore, the …

Investigation Of Early Complex Formation Of Huntingtin Protein With And Without Lipids, Alyssa R. Stonebraker

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s disease (HD) is a fatal neurodegenerative disease caused by the expansion of the polyglutamine (polyQ) domain of the huntingtin protein (htt). The expansion of the polyQ domain beyond a threshold of approximately 35 repeats triggers complex toxic aggregation mechanisms and results in altered interactions between htt and lipid membranes. Many factors modulate these processes. One such modulator includes sequences flanking the polyQ domain, most notably the first 17 amino acids at the N-terminus of the protein (Nt17), and environmental factors including the presence of membranous structures. Nt17 has the propensity to form an amphipathic a-helix in the presence of …

Copper-Catalyzed Dehydrogenative Decarboxylation Reactions Of Carboxylic Acids To Alkenes, Michael P. Stanton

Graduate Theses, Dissertations, and Problem Reports (ETD)

Linear alpha olefins (LAOs) are important building blocks in the production of linear low-density polyethylene, a plastic used in products such as shrink wraps, plastic bags, tubing, plasticizers, among others. Commercial methods for generating LAOs utilize ethylene oligomerization, but this method is reliant on fossil fuels and leads to unselective product formation. Synthesis of LAOs from renewable resources, namely carboxylic acids, by decarbonylative dehydration strategies has been well studied, however, this method has inherent drawbacks rooted in the formation of internal olefin side-products through isomerization pathways. With the goal of avoiding internal isomerization, this thesis explores a dehydrogenative decarboxylation strategy …

Interpretation Of The Tandem Mass Spectrum Of The Novel Psychoactive Substance 5f-App-Pinaca, Px-2, Christopher S. Poulos

Graduate Theses, Dissertations, and Problem Reports (ETD)

Designer drugs and novel psychoactive substances (NPSs) are continuously entering the black market and causing serious health problems among users. NPSs present an especially difficult challenge to forensic chemists and toxicologists because they are not well characterized and often involve families of structurally related analogs. In crime laboratories, mass spectrometry is commonly used as a part of an analytical scheme to characterize and identify unknown analytes. Towards this end, tandem mass spectra of questioned analytes are often compared to reference spectra of standards that are either collected contemporaneously with the analyte or collected previously and stored in a database. However, …