Chemistry Commons^™

Artemisinin And Its Derivatives Reactions: Characterization Of The Reaction Products Using Lc/Tof Ms, Kogila Vijayan

Theses and Dissertations

Artemisinin (ART) is a sesquiterpene lactone and a popular malaria drug with potential anticancer properties. In this work, LC/TOF MS was used to investigate the reaction of ART with DNA bases and estradiol. ART-deoxyadenosine and ART-deoxycytidine interactions were studied in the presence of Fe (II) ions. ART-deoxyadenosine and ART-deoxycytidine reaction mixtures gave chromatographic signatures that remained unchanged at room temperature but grew after incubation at 37°C. The change in temperature from room temperature to 37°C was the main driver of adduct formation in these reactions. ART was found to react with Fe (II) ions as observed from several new chromatographic …

Diffusion Of Ionic Liquid-Modified Polymer Nanoparticles Through Nasal Mucus, Mary Vanlandingham

Honors Theses

Mucosal barriers are a natural defense system for preventing the entry of foreign objects into the body; however, they pose as obstacles for effective drug delivery. Coated polymer nanoparticles have been proven to possess improved rates of diffusion across mucus compared to their uncoated, or bare, counterparts. When choline-based ionic liquids (ILs) are introduced to an aqueous system, their dissociation leads to an increase in solution conductivity which ultimately reduces the viscosity of mucus without significantly affecting its structure. Additionally, ILs are highly tunable, so they work well in a range of pHs and conductivities, making ILs an ideal choice …

Photocatalyzed Hydrogen Evolution Using Nickel-Bound Metallothionein Protein, Windfield Swetman

Honors Theses

The continued burning of fossil fuels is not only a cause of increasing deterioration of the environment but also a financially unsustainable source of energy. Advances in energy production must be investigated to avoid the long-term effects of this current main source of energy. One of the avenues being explored is the use of metalloenzymes to catalyze hydrogen evolution via water splitting that occurs during the reductive half of artificial photosynthesis. Metalloenzyme catalysts with a single Ni(Cys)₄ active site have been previously studied, and this study explores the possibility of increasing hydrogen production by using metalloenzyme catalysts with multiple …

Structural Integrity And Stability Of Dna In Ionic Liquid And Near-Infrared Indolizine Squaraine Dye, Ember Yeji Suh

Honors Theses

Luminol, the most common presumptive test for blood at a crime scene, has multiple issues, such as false positive results with chemical agents, no luminescence due to “active oxygen” cleaning agents on bloodstains, and inability to penetrate textile materials. A combination of indolizine squaraine dye and ionic liquid (IL), or Dye Enhanced Textile Emission for Crime Tracking (DETECT), have shown potential to address these issues. The purpose of this study was to assess the binding mechanism of CG (1:1) and SO₃SQ dye to HSA and how the mechanism can explain the W214 fluorescence quenching effect and to determine …

A Synthetic Approach To The Optimization Of Silicon-Rosindolizine Swir Fluorophores, Timothy Lewis

Honors Theses

Fluorophores emitting within the near-infrared (700 – 1000 nm) or shortwave-infrared (1000 – 1700 nm) regions of the electromagnetic spectrum are of particular interest for their potential to supplement or even outright replace commonly used biological imaging techniques, such as magnetic resonance imaging and computed tomography scanning. Various characteristics make these molecules particularly appealing to researchers, such as their ease of synthetic tunability, generally low toxicity, and high solubility in biological media in comparison to other NIR- and SWIR-emissive fluorophores. Different molecular skeletons have been examined for use as the core of these imaging agents, such as squaraine, cyanine, and …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols

DU Undergraduate Research Journal Archive

DU Undergraduate Showcase: Research, Scholarship, and Creative Works

Studies Of The Reaction Of Rongalite With Epoxides, Anuj Aryal

Theses, Dissertations and Culminating Projects

Reactions between Rongalite (Na⁺O^-SOCH₂OH) and epoxides were studied with the aim of developing new synthetic routes for the procurement of sulfone diols. This class of compounds contains essential building blocks in the construction of sulfur heterocycles, which have been implied in the development of several medicinal compounds. Thus far, the desired diols have not been isolated. During control experiments with bromo alcohols, an unknown product was isolated but remains to be identified.

The Interconnected Roles Of Residues N189, E168, And S220 In M. Tuberculosis Indole-3-Glycerol Phosphate Synthase Catalysis, Erik Domlija

Theses, Dissertations and Culminating Projects

Tuberculosis (TB) is an infectious disease caused by the bacteria Mycobacterium tuberculosis that primarily attacks the lungs. Drug resistance for M. tuberculosis is emerging and therefore new drug targets need to be identified. One way to target TB is through the inhibition of the tryptophan biosynthetic pathway of M. tuberculosis since production of tryptophan is essential for the replication of M. tuberculosis. The enzyme Indole-3-glycerol phosphate synthase (MtIGPS) was chosen as a potential drug target due to its role in tryptophan biosynthesis. Residue N189 interacts with active site residues E168 and S220. It is inferred from previous studies done with …

Spatial Metabolomics Reveals Glycogen As An Actionable Target For Pulmonary Fibrosis, Lindsey R. Conroy, Harrison A. Clarke, Derek B. Allison, Samuel Santos Valenca, Qi Sun, Tara R. Hawkinson, Lyndsay E. A. Young, Juanita E. Ferreira, Autumn V. Hammonds, Jaclyn B. Dunne, Robert J. Mcdonald, Kimberly J. Absher, Brittany Dong, Ronald C. Bruntz, Kia H. Markussen, Jelena A. Juras, Warren J. Alilain, Jinze Liu, Matthew S. Gentry, Peggi M. Angel, Christopher M. Waters, Ramon C. Sun

Saha Cardiovascular Research Center Faculty Publications

Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high- dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed …

College Of Natural Sciences Newsletter, March - May 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 4, Issue 2

Page 1 Dean's Message
Page 2-7 Awards and Recognition
Page 8 March 3rd Corothers Seminar
Page 9 54th Geography Convention
Page 10 Spring 2023 Day of Scholars
Page 11 2023 URSCAD Snaps
Page 12-14 Media Coverage of CNS
Page 15 Open PRAIRIE Data

Developing And Applying Computational Methods On Biomolecules, Shengjie Sun

Open Access Theses & Dissertations

Computational biophysics is an interdisciplinary subject that uses numerical algorithms to study the physical principles underlying biological phenomena and processes. Electrostatic interactions play an important role in computational molecular biophysics and their potential impact on disease mechanisms. At distances larger than several Angstroms, electrostatic interactions dominate all other forces, while the alteration of short-range electrostatic pairwise interactions can also have significant effects. The dual nature of electrostatic interactions, being dominant at long-range and specific at short-range, underscores their profound implications for wild-type structure and function. Any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could …

Quantum Chemistry–Machine Learning Approach For Predicting Properties Of Lewis Acid–Lewis Base Adducts, Hieu Huynh, Thomas J. Kelly, Linh Vu, Tung Hoang, Phuc An Nguyen, Tu C. Le, Emily Jarvis, Hung Phan

Chemistry and Biochemistry Faculty Works

Synthetic design allowing predictive control of charge transfer and other optoelectronic properties of Lewis acid adducts remains elusive. This challenge must be addressed through complementary methods combining experimental with computational insights from first principles. Ab initio calculations for optoelectronic properties can be computationally expensive and less straightforward than those sufficient for simple ground-state properties, especially for adducts of large conjugated molecules and Lewis acids. In this contribution, we show that machine learning (ML) can accurately predict density functional theory (DFT)-calculated charge transfer and even properties associated with excited states of adducts from readily obtained molecular descriptors. Seven ML models, built …

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

Determination Of Cadmium Uptake In Crassostrea Virginica Shell Under Controlled Conditions, Joseph John Pavelites Ii

Graduate Theses and Dissertations (2019 - present)

The objective of this thesis was to meet growing demand for the development of environmental biomonitors that protect ecosystems and public health. To do this, I determined the potential of oyster shell as a bioindicator of cadmium (Cd) in the environment by determining the mode of Cd uptake and relationships between Cd concentrations in the environment, shell, and soft tissues of juvenile eastern oysters (Crassostrea virginica Gmelin). I performed a review of the literature on the ability of oyster shell to retain metal contaminants and the factors that could affect this process (Chapter 2). I then reared C. virginica …

Non-Destructive Imaging Of Phytosulfokine Trafficking In Plants Using Fiber-Optic Fluorescence Microscopy, Bernard Abakah

Electronic Theses and Dissertations

Plants secrete peptide ligands and use receptor signaling to respond to stress and control development. Understanding these phenomena is key to improving plant health and productivity for food, fiber, and energy applications. Phytosulfokine (PSK), a sulfated peptide hormone, regulates plant cell division, growth, and stress tolerance via specific phytosulfokine receptors (PSKRs). This study uses fiber-optic fluorescence microscopy to elucidate trafficking of PSK in live plants. The microscope features two-color optics and an objective lens connected to a 1-m coherent imaging fiber mounted on either a conventional upright microscope body or 5-axis positioning system (X–Y–Z plus pitch and yaw). PSK and …

The Role Of Sars-Cov-2 Orf8 Protein Arks Motif On Novobiocin Binding, Si Chun Chiu, My T. Nguyen

Celebrating Scholarship and Creativity Day (2018-)

The discovery of the SARS-CoV-2 virus during the COVID-19 pandemic required scientists to develop medical solutions to reduce infectivity, severity of symptoms, and death. Although vaccines and drugs provided urgent assistance, the need to continue developing better drugs is necessary long term, and understanding the structure of the virus and finding potential inhibitors would prove vital to discovering solutions to this worldwide health problem. This experimental project focuses on targeting the unique accessory protein, Open Reading Frame 8 (ORF8) in SARS-CoV-2 through studying its interactions with a repurposable drug, novobiocin. Importantly, ORF8 specializes in helping evade immune system checks by …

Toward The Design, Synthesis, And Characterization Of Abiotic Coiled-Coil Peptides Via Solid-Phase Copper-Catalyzed Azide-Alkyne Cycloaddition (Sp-Cuaac) Click Reaction For The Preparation Of Controlled Self-Assembly Molecular Building Block, Liaquat Ali

Chemistry Theses

The production of cutting-edge materials, the development of novel medications, drug delivery systems, technological advancements, and biosynthesizing all depend on molecular building blocks. Proteins are required for the creation of intricate, well-organized structures, and coiled-coil protein domains are vital subunits for the oligomerization of protein complexes, gene expression, and the structural components of biological materials. The numerous interactions between a wide variety of amino acids make it difficult to assemble protein complexes with a particular shape. In the current study, we successfully designed and synthesized four different 32-residue peptides, each of which had two modified amino azide residues. These peptides …

Study Of Protein Extraction Techniques For M. Foliorum Phages, Lola Sibaud, Anna Elgersma

Student Academic Conference

Characterizing phages is becoming increasingly important in biochemistry and biotechnology due to their potential to treat bacterial infections without need for antibiotics. Last year, students attempted to isolate proteins from Microbacterium foliorum infecting phages Babydotz and Rosadiaz. Proteins were successfully extracted; however, after further analysis it was shown that the obtained proteins belonged to the host bacteria and not the phages. The purpose of this study was to find a method to separate phage from host bacterial debris to successfully isolate phage proteins and analyze them later. Isolating phage proteins could help us characterize more phages and know more about …

Activation Of Nrf2 Pathway By Natural Products, Genesis Schat, Madelyn Sedlachek

Liberty University Research Week

Undergraduate

Basic

Investigation Of Cofactor Activities Of Endothelial Microparticle- Thrombomodulin With Liposomal Surrogate, Valentinas Gruzdys, Lin Wang, Dan Wang, Rachel Huang, Xue-Long Sun

Chemistry Faculty Publications

Thrombomodulin (TM) is a type I transmembrane glycoprotein mainly expressed on the endothelial cells, where it binds thrombin to form the thrombin-TM complex that can activate protein C and thrombin-activable fibrinolysis inhibitor (TAFI) and induce anticoagulant and anti-fibrinolytic reactions, respec-tively. Cell activation and injury often sheds microparticles that contain membrane TM, which circulate in biofluids like blood. However, the biological function of circulating microparticle-TM is still unknown even though it has been recognized as a biomarker of endothelial cell injury and damage. In comparison with cell membrane, different phospholipids are exposed on the microparticle surface due to cell membrane "flip-flop"upon …

Simulating A Flexible Water Model As Rigid: Best Practices And Lessons Learned, Raymond Weldon, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model’s Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more straightforward to create, it leads to relatively poor performance. The EG model behaves similarly to the corresponding flexible model (the FL model) and, in some cases, agrees even better with experiments. While the difference between the EG and the FL models is mostly a result of flexibility, the MG and EG models …

Toward The Yeast Surface Display Of Microviridin B, Jillian Leigh Stafford

Chemistry and Chemical Biology ETDs

Humans have turned to natural products for medicinal therapeutics for millennia. In recent years, the ribosomally synthesized and post-translationally modified peptide (RiPP) class of natural products have garnered a lot of attention due to their ability for heterologous expression, relative ease of mutation, and vast biological activates. Microviridins are a family of RiPPs that contain a tricyclic cage-like structure through the formation of two lactone rings and one lactam ring catalyzed by two ATP-grasp ligase family enzymes. Microviridins are potent inhibitors of serine proteases and mutational studies of a small number of residues indicates the potential of peptide engineering protease …

Traffic Lights For Catalysis: Stimuli-Responsive Molecular And Extended Catalytic Systems, Grace C. Thaggard, Johanna Haimeri, Roland A. Fischer Prof. Dr., Kyoung Chul Park, Natalia B. Shustova Prof. Dr.

Faculty Publications

The advances made in the field of stimuli-responsive catalysis during the last five years with a focus on the novel recently-emerged directions and applications have been surveyed. Metal-free catalysts and organometallic complexes, as well as biomimetic systems and extended structures, which display switchable catalytic activity for a variety of organic transformations, are discussed. Light-activated systems comprised of photochromic molecules capable of modulating reaction rate, yield, or enantioselectivity based on geometric and electronic changes associated with photoisomerization are the focus of the detailed discussion. Alternative stimuli, including pH and temperature, which could be applied either alone or in combination with light, …

Stabilizing G-Quadruplex Dna And Rna Structures With Ionic Liquids, Timothy Vaden

College of Science & Mathematics Departmental Research

Stabilizing DNA and RNA for long-term room-temperature storage is important for many biotechnological applications including oncology pharmaceuticals and mRNA-based vaccines (e.g. Covid vaccines). This poster shows that ionic liquids can improve the thermal stability of G-quadruplex DNA and RNA structures, and motivates further studies of ionic liquid-based materials for DNA / RNA stabilization.

Damped Oscillating Phosphoryl Transfer Reaction In The Cyanobacterial Circadian Clock, Hye In Jang, Pyonghwa Kim, Yongick Kim

Chemistry Faculty Research

Most organisms have circadian clocks to ensure the metabolic cycle to resonate with the rhythmic environmental changes without “damping,” or losing robustness. Cyanobacteria is the oldest and simplest form of life that is known to harbor this biological intricacy. Its KaiABC-based central oscillator proteins can be reconstituted inside a test tube, and the post-translational modification cycle occurs with 24 h periodicity. KaiC’s two major phosphorylation sites, Ser-431 and Thr-432, become phosphorylated and dephosphorylated by interacting with KaiA and KaiB, respectively. Here, we mutate Thr-432 into Ser to find the oscillatory phosphoryl transfer reaction damps. Previously, this mutant KaiC was reported …

Synthesis, Characterization, And Cytotoxicity Studies Of A Copper(Ii) Complex With Vanillin 3-Ethyl-Thiosemcarbazone A Ligand, Novia Mann, Ifeoluwa Oyeyemi, Duaa R. Alajroush, Elizabeth A. Tonsel-White, Stephen J. Beebe, Alvin Holder

Undergraduate Research Symposium

Triple-negative breast cancer (TNBC) is one of the most aggressive and challenging breast cancer subtypes to treat, as these cancer cells lack three common receptors: estrogen, progesterone, and human epidermal growth factor receptor 2. The multiple oxidation states transition metals can occupy have made this narrowly explored group popular for anti-cancer research in recent decades. Furthermore, the success of cisplatin, which has platinum as a metal center, while being a cancer-fighting agent with serious side effects, has caused other metal centers to be investigated as possible alternatives as chemotherapeutic drugs. Copper, as a biologically essential metal, makes an attractive candidate …

Apkcs Role In Neuroblastoma Cell Signaling Cascades And Implications Of Apkcs Inhibitors As Potential Therapeutics, Sloan Breedy

USF Tampa Graduate Theses and Dissertations

Neuroblastoma (NB) is a cancer that develops in the neuroblasts. It is the most common cancer in children under the age of 1 year, accounting for approximately 6% of all cancers. The prognosis of NB is linked to both age and degree of cell differentiation. This results in a range of survival rates for patients, with outcomes ranging from recurrence and mortality to high survival rates and tumor regression. Our previous work indicated that PKC-ι promotes cell proliferation in NB cells through the PKC-ι/Cdk7/Cdk2 cascade. We report on two atypical protein kinase inhibitors as potential therapeutic candidates against BE(2)-C and …

In Silico Binding Of 2-Aminocyclobutanones To Sars-Cov-2 Nsp13 Helicase And Demonstration Of Antiviral Activity, Thahani S. Habeeb Mohammad, Yash Gupta, Cory T. Reidl, Vlad Nicolaescu, Haley Gula, Ravi Durvasula, Prakasha Kempaiah, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted α-aminocyclobutanones from an α-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus …

College Of Natural Sciences Newsletter, February 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 4, Issue 1

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3-4 Nobel Recipient Visits Campus
Page 4 Adopting the Pantry
Page 5 Growing a Recruitment Mindset
Page 6 February Outreach Events
Page 7 Media Coverage of CNS
Page 8 Open PRAIRIE Data
Page 9 54th Geography Convention, and Tom Loveland EROS Geography Scholarship
Page 10 Photos of Dr. Carolyn Bertozzi's Visit

Ultrasound-Assisted Air-Jet Spinning Of Silk Fibroin-Soy Protein Nanofiber Composite Biomaterials., Futian Yang, Fang Wang, Janine Mazahreh, Xiao Hu

College of Science & Mathematics Departmental Research

Ultrasound utilizes a non-radiation technology that can meet modern standards to gain access to cheap, reliable and sustainable modern energy. Ultrasound technology can be implemented in the field of biomaterials for its exceptional potential in controlling the shape of nanomaterials. This study presents the first example of the production of soy and silk fibroin protein composite nanofibers in various ratios via combining ultrasonic technology with air-spray spinning. Characterization of ultrasonic spun nanofibers was performed by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric (TG) analysis, water contact angle, water retention, enzymatic …