Chemistry Commons^™

High Order Structures Formed By The Natural Aromatic Amino Acids, Gabriel Alexander Kupovics, Zeina Alraawi

Inquiry: The University of Arkansas Undergraduate Research Journal

Excessive concentrations of the natural aromatic amino acids phenylalanine and tyrosine are characteristic of the severe genetic abnormalities known as phenylketonuria (PKU) and tyrosinemia, respectively. Within this context, this feature article authenticates claims that tryptophan can form amyloid-like supramolecular structures in vitro and is the first to propose potential mechanisms of tryptophan self-assembly, including hydrophobic and electrostatic interactions. Thioflavin T (ThT) fluorescence kinetics and transmission electron microscopy (TEM) data suggest the formation of amyloid-like fibrillar structures by natural aromatic amino acids in vitro. Additionally, the propensity of amino acid aggregation increases in the presence of sodium dodecyl sulfate (SDS). The …

Green And Non-Green Extraction Of Eugenol From Cloves Using Steam Distillation, Bek Yuldashbaev

Science University Research Symposium (SURS)

Eugenol is commonly found in many plants such as cloves. It is one of the most used natural anesthetics in dentistry. Indonesia is one of the places indigenous to clove trees. Its people take advantage of the pain numbing properties in cloves to aid their tooth pain. The extraction of eugenol itself can be performed through steam distillation. With the process of distillation, the steam carries the oils extracted from the clove buds and recondenses into a cloudy distillate containing polar and non-polar molecules. To separate the eugenol from the distillate, green and non-green solvents were used. The green solvent …

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) …

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 …

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 …

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 …

Paek- And Pes-Like Perarylated Phosphonium Ionenes: Synthesis, Thermal Properties, And Conductivity, Samantha Sims

Murray State Theses and Dissertations

Ionic liquids (ILs) are useful for many applications due to the tunability of their characteristic properties making these salts ideal for many applications. To further increase possible areas of application for these materials, some ILs can be incorporated into polymer structures to form poly ionic liquids (PILs) or ionenes. The specific ions used within the material will determine the thermal, mechanical, and chemical stability properties exhibited by the polymer. Adjustments can be made to the ion structures during the synthetic process to influence these observed properties.

Fuel cells, batteries, solar cells, and capacitors, all require materials that can withstand high …

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 …

Natural Product Co-Metabolism And The Microbiota–Gut–Brain Axis In Age-Related Diseases, Mark Obrenovich, Sandeep Kumar Singh, Yi Li, George Perry, Bushra Siddiqui, Waqas Haq, V. Prakash Reddy

Chemistry Faculty Research & Creative Works

Complementary alternative medicine approaches are growing treatments of diseases to standard medicine practice. Many of these concepts are being adopted into standard practice and orthomolecular medicine. Age-related diseases, in particular neurodegenerative disorders, are particularly difficult to treat and a cure is likely a distant expectation for many of them. Shifting attention from pharmaceuticals to phytoceuticals and "bugs as drugs" represents a paradigm shift and novel approaches to intervention and management of age-related diseases and downstream effects of aging. Although they have their own unique pathologies, a growing body of evidence suggests Alzheimer's disease (AD) and vascular dementia (VaD) share common …

Design, Synthesis, And Evaluation Of Acetyl Coa Synthetase Inhibitors, Michael Emmett Heene

Graduate Research Theses & Dissertations

Invasive fungal species provide a challenge to the current drug landscape, only partiallymet by approved drugs. The Acetyl Coenzyme Synthetase (ACS) enzymes are an attractive target for antifungal compounds because normal mammalian cells do not rely on ACS for energy metabolism while fungal cells do rely on ACS. This work focuses on the design and synthesis of inhibitors of various fungal ACS enzymes. The first class of inhibitors is based on the 2-aminothiazole scaffold originating from a saturation transfer difference (STD) nuclear magnetic resonance (NMR) study and previous whole-organism assays. Ultimately, the 2-aminothiazole core compounds were found to not be …

Investigation Of Factors Affecting Reverse-Phase High Performance Liquid Chromatography, Rida A. Syed

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

This study focused on the application of reverse-phase high-performance liquid chromatography (RP-HPLC). RP-HPLC is used for the purification of organic molecules, including pharmaceuticals, natural products, and proteins. We developed a modified version of a United States Pharmacopeia (USP) procedure to separate and purify the chemical components found in Excedrin tablets. The goal was to investigate the relationship between retention time (Tr) and the capacity factor (k') of solutes. By varying the composition of the mobile phase and stationary phase, we experimentally determined the capacity factor of acetaminophen (APAP), caffeine, and aspirin. Our results show that the capacity factor (k') of …

Synthetic Studies Of Dragonamide E And Its Potential Treatment Of Leishmaniasis, Sarah E. Glaesemann

Chemistry Theses

Leishmaniasis is a parasitical infection categorized as one of about twenty Neglected Tropical Diseases. Spread by the female sand fly, it can become very severe if left untreated. Symptoms include skin lesions, which may cause scarring, and mucosal membrane infection, which may lead to facial deformity. The most severe form of leishmaniasis can infect organs such as the liver and spleen, possibly leading to death. The current treatments for leishmaniasis are becoming limited due to an increase in drug resistant parasites. Furthermore, the side effects of these treatments can be very problematic.

In the search for new treatments for tropical …

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

Graduate Theses/Dissertations

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 …

One-Pot Enol Silane Formation-Allylation Of Ketones Promoted By Trimethylsilyl Trifluoromethanesulfonate, Elizabeth D. Heafner, Xuechun Lin, Alexa Connors, Hanyu Zhong, R. J. Coyle, Yiqi Liu, C. Wade Downey

Chemistry Faculty Publications

Ketones and related substrate classes undergo enol silane formation in the presence of trimethylsilyl trifluoromethanesulfonate (TMSOTf) and triethylamine, reaction conditions that also promote the in situ ionization of allyl propionates. When these two processes are performed in one pot, allylation of the ketone is observed in high yields. Aldehydes, esters, and thioesters also serve as enol silane precursors under these conditions. When unsymmetrical allyl cations are employed, regioselectivity depends upon the electronic and steric properties of the substituents.

Synthesis And Evaluation Of Sorbicillinoids, Noah Devolve

Honors Program Theses

Sorbicillinoids are a rich family of natural products that have intrigued and inspired scientists since their initial discovery in 1948. A recent report by Zhang et al. detailed the discovery of several new monomeric sorbicillinoids that are particularly interesting as they show nitric oxide (NO) inhibition in RAW264.7 monocyte cell assays and thus possess potential as anti-inflammatory agents. Based on this information, obtaining more of these novel compounds and establishing a preliminary structure activity relationship (SAR) could be achieved by modulating the substitution pattern on the molecules’ benzene ring and varying the alkyl chain length. To this end, a flexible …

Design, Synthesis, And Biological Evaluation Of Novel Steroidal Analogs: Potential Anticancer Agents, Trevor Ostlund

Electronic Theses and Dissertations

Cancer is a malicious disease with low survivability rates primarily due to lack of reliable treatment options. Treatments are often non-specific for patients, and cancer resistance to treatment is becoming more prevalent as fast as new therapies are created. Previous studies in our laboratory have focused on the Epidermal Growth Factor Receptor (EGFR) and its downstream kinase family members as a key target for cancer. This cascade controls cell proliferation, anti-apoptotic effects, cell regulation, and other survival factors. Additionally, ABC transporters, responsible for efflux of chemotherapeutic material from cells, are key targets to combat drug resistance. We first evaluated a …

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 …

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, …

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 …

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 …

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 …

Natural Product Co-Metabolism And The Microbiota–Gut–Brain Axis In Age-Related Diseases, Mark Obrenovich, Sandeep Kumar Singh, Yi Li, George Perry, Bushra Siddiqui, Waqas Haq, V. Prakash Reddy

Chemistry Faculty Research & Creative Works

Complementary alternative medicine approaches are growing treatments of diseases to standard medicine practice. Many of these concepts are being adopted into standard practice and orthomolecular medicine. Age-related diseases, in particular neurodegenerative disorders, are particularly difficult to treat and a cure is likely a distant expectation for many of them. Shifting attention from pharmaceuticals to phytoceuticals and "bugs as drugs" represents a paradigm shift and novel approaches to intervention and management of age-related diseases and downstream effects of aging. Although they have their own unique pathologies, a growing body of evidence suggests Alzheimer's disease (AD) and vascular dementia (VaD) share common …

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.

Structural And Functional Modulation Of Metal-Organic Supercontainers (Moscs) And Their Applications In Supramolecular Catalysis, Shrijana Dc

Dissertations and Theses

Metal-organic supercontainers (MOSCs), a breakthrough development in our laboratory since 2012, have emerged as promising enzyme mimics, showcasing their prowess in encapsulating guest molecules and catalyzing confined chemical reactions. The intrigue surrounding MOSCs stems from their extraordinary traits, encompassing multiple binding domains, high stability, large surface area, tunable pore size, and structural modularity. Primarily comprising sulfonylcalix[4]arenes, divalent metal ions, and carboxylate linkers, MOSCs' quintessential architecture comprises both endo- and exo- nano-cavities, amenable to guest interaction, with geometry and functionality manipulation achievable through precise precursor selection. Nonetheless, early MOSC models exhibit limited reactivity, often necessitating more potent nucleophiles or electrophiles. This …

Discovery Of Acetyl Coa Synthetase And Sars-Cov-2 Protease Inhibitors, Taiwo Elijah Esan

Graduate Research Theses & Dissertations

There is an urgent need for new antifungal drugs. Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. This body of work focuses on the inhibition of the Acetyl CoA synthetase enzyme in fungal species. This work has involved designing and synthesizing compounds that are potential fungal ACS1 …

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 …

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 …

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 …

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 …