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Renewable Fuels: Molecular Dynamics Investigations Into Pyrolysis Of Methyl Linoleate, Elson Osakpolor Eguaosa

MSU Graduate Theses

With the rapid depletion of the world’s supply of fossil fuels, especially petroleum products, petroleum prices have risen by approximately 800% between the 1970s and now and are projected to continue rising. It is also expected that the world’s consumption of energy will increase commensurate with its growing population. Although biodiesel is a good renewable alternative, it has its limitations including high production costs and poor low-temperature performance. We seek to improve conventional biodiesel with pyrolysis to produce low molecular-weight compounds with high energy densities. Understanding the pyrolysis path on the atomic scale is key as it will allow us …

Systemic Analyses Of Radiocarbon Ages Of Coexisting Planktonic Foraminifera, Jörg Lippold, Julia Gottschalk, Jean Lynch-Stieglitz, Matthew W. Schmidt, Sönke Szidat, Andre Bahr

OES Faculty Publications

We compare radiocarbon (¹⁴C) ages of coexisting planktonic foraminifera species from sediment cores VM12-107 and KNR166-2-26JPC from the Equatorial Atlantic Ocean for three time periods (Holocene, Heinrich Stadial 1, last glacial maximum). We find a maximum inter-species difference of 1200 ¹⁴C yr. On average, the ¹⁴C ages deviate by ∼300 yr between Globigerinoides ruber and other species. In most cases, this exceeds the analytical uncertainty range of the measurements and thus renders the choice of species for generating age models as important as sample weight. While modern stratified water-column profiles imply an increase in ¹⁴C …

Telp Theory: Elucidating The Major Observations Of Rieger Et Al. 2021 In Mitochondria, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The transmembrane-electrostatically localized protons (TELP) theory may represent a complementary development to Mitchell's chemiosmotic theory. The combination of the two together can now excellently explain the energetics in mitochondria. Our calculated transmembrane-attractive force between an excess proton and an excess hydroxide explains how TELP may stay within a 1-nm thin layer at the liquid-membrane interface. Consequently, any pH sensor (sEcGFP) located at least 2–3 nm away from the membrane surface will not be able to see TELP. This feature as predicted from the TELP model was observed exactly in the experiment of Rieger et al., 2021. In contrast to their …

The Effect Of Metalation On Antimicrobial Piscidins Imbedded In Normal And Oxidized Lipid Bilayers, Ana Dreab, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

Metalation of the N-terminal Amino Terminal Cu(II)- and Ni(II)-binding (ATCUN) motif may enhance the antimicrobial properties of piscidins. Molecular dynamics simulations of free and nickelated piscidins 1 and 3 (P1 and P3) were performed in 3 : 1 POPC/POPG and 2.6 : 1 : 0.4 POPC/POPG/aldo-PC bilayers (POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPG, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol; aldo-PC, 1-palmitoyl-2-(9′-oxo-nonanoyl)-sn-glycero-3-phosphocholine) bilayer models. Nickel(II) binding decreases the conformation dynamics of the ATCUN motif and lowers the charge of the N-terminus to allow it to embed deeper in the bilayer without significantly changing the overall depth due to interactions of the charged half-helix …

Ultrasensitive Tapered Optical Fiber Refractive Index, Erem Ujah, Meimei Lai, Gymama Slaughter

Electrical & Computer Engineering Faculty Publications

Refractive index (RI) sensors are of great interest for label-free optical biosensing. A tapered optical fiber (TOF) RI sensor with micron-sized waist diameters can dramatically enhance sensor sensitivity by reducing the mode volume over a long distance. Here, a simple and fast method is used to fabricate highly sensitive refractive index sensors based on localized surface plasmon resonance (LSPR). Two TOFs (l = 5 mm) with waist diameters of 5 µm and 12 µm demonstrated sensitivity enhancement at λ = 1559 nm for glucose sensing (5-45 wt%) at room temperature. The optical power transmission decreased with increasing glucose concentration due …

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.

Para-Methoxybenzylidene Acetal-Protected D-Glucosamine Derivatives As Ph-Responsive Gelators And Their Applications For Drug Delivery, Jonathan Bietsch, Logan Baker, Anna Duffney, Alice Mao, Mary Foutz, Cheandri Ackermann, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based low molecular weight gelators (LMWGs) are compounds with the capability to self-assemble into complex molecular networks within a solvent, leading to solvent immobilization. This process of gel formation depends on noncovalent interactions, including Van der Waals, hydrogen bonding, and π–π stacking. Due to their potential applications in environmental remediation, drug delivery, and tissue engineering, these molecules have emerged as an important area of research. In particular, various 4,6-O-benzylidene acetal-protected D-glucosamine derivatives have shown promising gelation abilities. In this study, a series of C-2-carbamate derivatives containing a para-methoxy benzylidene acetal functional group were synthesized and characterized. These compounds exhibited good …

2-Aminopyridyl Functionalized Scaffold As A Tool For Systematic Investigation Of B-Glucan Binding And Dectin-1 Activation, Jasper Alinea Aquino

Graduate Student Theses, Dissertations, & Professional Papers

Tuberculosis (TB) – an infectious disease caused by Mycobacterium tuberculosis (Mtb) – remains an epidemic worldwide contributing to millions of deaths each year. Vaccination is possibly the best means of addressing this global threat. In recent years, synergistic Th1 and Th17 immune responses have emerged as the key players for a vaccine-induced protection against TB. There is currently no vaccine approved for humans that elicits a Th17-mediated immune response. C-Type Lectin Receptors (CLR), specifically Dectin-1, a pattern recognition receptor (PRR) of β-1,3-glucans (β-glucans) primarily from fungi cell walls, is known to induce a Th17-mediated response. The Th17 response upon binding …

I. Preparation Of Strategic Synthetic Building Blocks For World Health Organization Essential Medicines. Ii. Applying The Principles Of Process Intensification To The Synthesis Of Fluoroquinolone Antibiotics., Jeffrey M. Noble

Theses and Dissertations

The synthesis of active pharmaceutical ingredients is often a time-consuming and expensive process. Due to the nature of pharmaceutical manufacturing, these costs are carried forward to the final purchase price by the consumer. Although there are many factors which are involved in the final costing of a pharmaceutical, the cost associated with the synthesis is the primary one which can be managed by chemists and engineers.

This work discusses the synthetic routes of four active pharmaceutical ingredients as well as the synthetic techniques and equipment used with an emphasis on how the application of specific techniques can be applied to …

Translating Chemistry, Structure, And Processing To The Solid-State Morphology And Function Of Organic Semiconductors Through Computational Modeling And Simulations, Chamikara D. Karunasena

Theses and Dissertations--Chemistry

The immense synthetic design space and material versatility have driven the exploration and development of organic semiconductors (OSC) over several decades. While many OSC designs focus on the chemistries of the molecular or polymer building blocks, a priori, multiscale control over the solid-state morphology is required for effective application of the active layer in a given technology. However, molecular assembly during solid-state formation is a complex function interconnecting the building block chemistry and the processing environment. Insufficient knowledge as to how these aspects engage, especially at the atomistic and molecular scales, has so far limited the ability to predict …

Exploring The Role Of Ring Annulation In Polycyclic Aromatic Hydrocarbons For Organic Electronic Applications, Tanner Smith

Theses and Dissertations--Chemistry

Organic materials offer promising potential for the next generation of electronic devices, as their tunability, processability, and low-temperature manufacturing make them a cheap and versatile alternative to traditional silicon-based electronics. The ability to systematically alter the electronic properties of organic materials is vital for their incorporation into device applications. Polycyclic aromatic hydrocarbons (PAHs) are of significant interest for organic electronic applications, as relevant properties are highly dependent on their size, structure, and functionalities, and thus can be tuned to fit a wide variety of applications. Due to the enormous number of structural isomers available in larger PAHs, the development of …

Development And Biological Evaluation Of Selective Small-Molecule Inhibitors Of The Human Cytochrome P450 1b1, Austin Hachey

Theses and Dissertations--Chemistry

The human cytochrome P450 1B1 (CYP1B1) is an emerging target for small- molecule therapeutics. Several solid tumors overexpress CYP1B1 to the degree that it has been referred to as a universal tumor antigen. Conversely, its expression is low in healthy tissues. CYP1B1 may drive tumorigenesis through promoting the formation of reactive toxins from environmental pollutants or from endogenous hormone substrates. Additionally, the expression of CYP1B1 in tumors is associated with resistance to several common chemotherapies and with poor prognoses in cancer patients. However, inhibiting CYP1B1 with small molecules has been demonstrated in cellular and murine model systems to reverse this …

Application Of Mass Spectrometry For The Characterization Of Synthetic Oligomers And Natural Lignin, Poorya Kamali

Theses and Dissertations--Chemistry

As part of the ongoing effort to substitute finite fuel and chemical resources with renewable ones, biomass is emerging as one of the most promising sources. Biomass consists of three main components of cellulose, hemicellulose, and lignin. Traditionally, cellulose has been used extensively in pulping industry, while lignin has been considered waste and is burned to generate heat. Lignin, a complex aromatic polymer component of biomass, has the potential to be used as a source of aromatic chemicals and pharmaceutical synthons. The recalcitrant nature of lignin, the lack of effective lignin breakdown methods and analytical techniques to analyze it are …

Development Of An Effective Au:Pd Bimetallic Heterogeneous Catalyst For Oxidative Lignin Depolymerization To Low Molecular Weight Aromatics, Gayan P. Karunasinghe

Theses and Dissertations--Chemistry

The principal concept behind biorefining involves the transformation of lignocellulosic biomass into valuable products and energy resources. Historically, biorefinery strategies for lignocellulosic biomass have primarily focused on improving the conversion of cellulose into ethanol, often neglecting the underutilized lignin component. Lignin consists of phenolic subunits, from which it follows that value-added products can be obtained from lignin depolymerization. Unfortunately, lignin utilization is particularly challenging due to its high structural irregularity and recalcitrance. The goal of this study was to develop an AuPd/Li-Al layered double hydroxide (LDH) bimetallic catalyst for efficient lignin depolymerization, resulting in the production of high-value aromatic compounds. …

The Discovery And Characterization Of Novel Potent 5-Substituted 3, 3’, 4’, 7-Tetramethoxyflavonoid Dna Triplex Specific Binding Ligands, Vanessa Marie Rangel

University of the Pacific Theses and Dissertations

Chemotherapy works by killing fast dividing cells. Unfortunately, these drugs are not specific to cancer tissue and can damage normal cells. Chemotherapy is like taking poison and hoping it kills the cancer cells before it kills you. As an alternative, many researchers have investigated the use of antigene therapy to selectively target cancer causing genes to avoid off target effects. Although promising, the theory is limited by the stability of the triplex structure. Here, we report the discovery of potent triplex binding ligands derived from the natural product quercetin. Chemical derivatives of 5-substituted 3, 3’, 4’, 7-tetramethoxyquercetin derivatives were characterized …

Sound The (Smaller) Alarm: The Triphosphate Magic Spot Nucleotide Pgpp, Areej Malik, Megan A. Hept, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

It has recently become evident that the bacterial stringent response is regulated by a triphosphate alarmone (pGpp) as well as the canonical tetra- and pentaphosphate alarmones ppGpp and pppGpp [together, (p)ppGpp]. Often dismissed in the past as an artifact or degradation product, pGpp has been confirmed as a deliberate endpoint of multiple synthetic pathways utilizing GMP, (p)ppGpp, or GDP/GTP as precursors. Some early studies concluded that pGpp functionally mimics (p)ppGpp and that its biological role is to make alarmone metabolism less dependent on the guanine energy charge of the cell by allowing GMP-dependent synthesis to continue when GDP/GTP has been …

Abiotic Stress Mitigation: A Case Study From 21 Trials Using A Natural Organic Matter Based Biostimulant Across Multiple Geographies, Rachel L. Sleighter, Terry Hanson, David Holden, Kristen M. Richards

Chemistry & Biochemistry Faculty Publications

Crop productivity and yields can be greatly diminished by abiotic stress events including drought, extreme temperatures, excess moisture, and saline irrigation water. Multiple stressors occurring simultaneously can further exacerbate the strain on plants. Various types of biostimulants have been shown to mitigate abiotic stress and here, the results of 21 trials on corn, wheat, soybean, and various high-value crops are discussed in the context of the abiotic stress that either occurred naturally or was experimentally induced. Treatments in these trials included stressed and non-stressed plants, as well as either an untreated control or grower standard fertilizer applications alone and in …

Reduced Metal Nanocatalysts For Selective Electrochemical Hydrogenation Of Biomass-Derived 5-(Hydroxymethyl)Furfural To 2, 5-Bis(Hydroxymethyl)Furan In Ambient Conditions, Baleeswaraiah Muchharla, Moumita Dikshit, Ujjwal Pokharel, Ravindranath Garimella, Adetayo Adedeji, Kapil Kumar, Wei Cao, Hani Elsayed-Ali, Kishor Kumar Sadasivuni, Naif Abdullah Al-Dhabi, Sandeep Kumar, Bijandra Kumar

Chemistry & Biochemistry Faculty Publications

Selective electrochemical hydrogenation (ECH) of biomass-derived unsaturated organic molecules has enormous potential for sustainable chemical production. However, an efficient catalyst is essential to perform an ECH reaction consisting of superior product selectivity and a higher conversion rate. Here, we examined the ECH performance of reduced metal nanostructures i.e., reduced Ag (rAg) and reduced copper (rCu) prepared via electrochemical or thermal oxidation and electrochemical reduction process, respectively. Surface morphological analysis suggests formation of nanocoral and entangled nanowire structure formation for rAg and rCu catalysts. rCu exhibits slight enhancement in ECH reaction performance in comparison to the pristine Cu. However, the rAg …

Thermotrophy Exploratory Study, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The question of whether environmental heat energy could be utilized as a source of energy for biological metabolism is the center of this exploratory research. In 1979, this author postulated a hypothesis for the existence of thermotrophs that could isothermally utilize environmental heat energy as a source of their energy on Earth. According to this hypothesis, the thermotrophs could be the first primitive forms of life in the early Earth environment. The chemotrophs and phototrophs that we currently are all well familiar with might have been evolved somehow from the primitive thermotrophs. Furthermore, all the organisms currently regarded as the …

Halogen Bonding Interactions Of Haloaromatic Endocrine Disruptors And The Potential For Inhibition Of Iodothyronine Deiodinases, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

Halogen bonding (XB) is a potential mechanism for the inhibition of the thyroid-activating/deactivating iodothyronine deiodinase family of selenoproteins through interactions with halogenated endocrine disrupting compounds (EDCs). Trends in XB interactions were examined using density functional theory for a series of polyhalogenated dibenzo-1,4-dioxins, biphenyls, and other EDCs with methylselenolate, a simple model of the Dio active site selenocysteine. The strengths of the interactions depend upon the halogen (Br>Cl), the degree of substitution, and the position of the acceptor. In terms of donor-acceptor energies, interactions at the meta position are often the strongest, suggesting a link to the topology of THs, …

Extracting High-Molecular Weight Dna From Cyanobacteria Using Promega's Wizard® Hmw Dna Extraction Kit With A Modified Protocol, Metis, Megan A. Hept, Lesley H. Greene

Chemistry & Biochemistry Faculty Publications

Extraction of high molecular weight (HMW) DNA for long read sequencing with little to no fragmentation and high purity is difficult to acquire from cyanobacterial species. Here we describe a modified method of extraction using Promega's Wizard® HMW DNA Extraction Kit to acquire high molecular weight DNA from cyanobacterial species. The protocol used in the kit is the “3.D. Isolating HMW DNA from Gram-Positive and Gram-Negative Bacteria” protocol. During a key step in the protocol, the lingering remnants of the mucilage layer of the cyanobacterial species is removed, preventing it from sticking to the DNA pellet produced. This customized modification …

Cultivating Health, Not Wealth In The United States' Healthcare System: Comprehensive Revisions For The Orphan Drug Act Of 1983, Kayla Smith

Regis University Student Publications (comprehensive collection)

This thesis explores the way in which the Orphan Drug Act of 1983, originally instituted in response to a lack of treatments for rare diseases in the United States of America, has failed to achieve its initial objectives in the 40 years since its implementation. In evaluating various successful examples of government subsidization programs designed to intervene in private industry, this thesis composes the criterion required for funding-based legislation which maximize market outcomes while minimizing tax-payer burden. An analysis of the synthetic organic chemistry industry – and a case study into the production of a particular orphan treatment for a …

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

Graduate Theses, Dissertations, and Problem Reports

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 …

Interactions Of Bioactive Trace Metals In Shipboard Southern Ocean Incubation Experiments, Shannon M. Burns, Randelle M. Bundy, William Abbott, Zuzanna Abdala, Alexa R. Sterling, P. Dreux Chappell, Bethany D. Jenkins, Kristen N. Buck

OES Faculty Publications

In the Southern Ocean, it is well‐known that iron (Fe) limits phytoplankton growth. Yet, other trace metals can also affect phytoplankton physiology. This study investigated feedbacks between phytoplankton growth and dissolved Fe, manganese (Mn), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), and cadmium (Cd) concentrations in Southern Ocean shipboard incubations. Three experiments were conducted in September–October 2016 near the West Antarctic Peninsula: Incubations 1 and 3 offshore in the Antarctic Circumpolar Current, and Incubation 2 inshore in Bransfield Strait. Additions of Fe and/or vitamin B₁₂ to inshore and offshore waters were employed and allowed assessment of metal (M) …

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

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 …

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

Graduate Theses, Dissertations, and Problem Reports

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 …

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

Graduate Theses, Dissertations, and Problem Reports

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 …

Non-Traditional Methods For The Green Synthesis Of Fine Chemicals, Tara Renée Mooney

Graduate Masters Theses

Herein, the advancement of microwave-assisted flow synthesis is reviewed and the green nitration of arenes is investigated. First, microwave-assisted flow systems are described, followed by their synthetic and environmental applications. Microwave-assisted flow synthesis has been applied successfully in organic, inorganic, material, and biochemical syntheses as well as environmental applications such as water desalination and the removal of volatile organic compounds from the atmosphere. In the second part of the Thesis, the methodological development of the first catalyst and solvent-free nitration of m-xylene using only nitric acid is detailed. This environmentally friendly reaction proceeds without the use of harsh Brønsted acids, …

Palladium (Ii)-Catalyzed Selective Reduction Of 4’-(Phenylethynl)Acetophenone In The Presence Of A Formic Acid-Triethylamine Mixture, Suzanne Chayya, Akram Hijazi, Anis Daou, Ali Alaaeddine, Mohamad Sakr, Ghassan Younes, Mohammad El-Dakdouki

BAU Journal - Science and Technology

An efficient and straightforward palladium acetylacetonate-catalyzed hydrogen transfer of 4'- (phenylethynyl)acetophenone was developed in this study. Formic Acid was found to be the best hydrogen source in this catalytic system in the presence of triethylamine. Excellent conversions and selectivity were obtained in reducing the starting internal aromatic alkyne to either (E)-1-(4- styrylphenyl)ethanone or an interesting cyclic product, 1-(phenanthrene-3-yl)ethenone, over the ketone functional group present. Over-reduction was rarely seen. The reaction conditions were optimized in terms of the choice of the palladium catalyst, temperature, solvent, and the H-donor/base combination. Using this catalytic system, a one-step synthetic pathway of the …

Metallacycle-Mediated Cross-Coupling As An Enabling Tool For Studies In Carbocycle Synthesis And Functionalization, Adam Barry Millham

Dartmouth College Ph.D Dissertations

Natural products, specifically complex, carbocyclic natural products, have served as the inspiration for novel methods development for decades. Over that time, metallacycle-mediated cross-coupling has arisen as a powerful means for the synthesis of fused carbocycles. This work details three methods for the synthesis and functionalization of carbocyclic motifs that have been enabled by Ti-mediated cross-coupling reactions. The first of these studies include a complementary method to the Pauson–Khand reaction for the synthesis of highly substituted cyclopentenones via Ti-mediated alkyne–β-ketoester coupling. The second project, a modern approach to steroidal tetracycles, will be discussed that features: (1) an alkoxide-directed metallacycle-mediated [2+2+2] annulation …