Chemistry Commons^™

Effect Of Polyacrylamide Gel Elasticity On Collagen Type Ii Fibril Assembly, Kathryn G. Wilcox, Stephanie Kramer, Surajit Chatterjee, Adam Linscott, Sneha Suresh, Lydia Kisley, Svetlana Morozova

Faculty Scholarship

Collagen type II fibrils provide structural integrity to the articular cartilage extracellular matrix. However, the conditions that control the fibril radial size scale, distribution, and formation inside of dense networks are not well understood. We have investigated how surrounding elastic networks affect fibril formation by observing the structure and dynamics of collagen type II in model polyacrylamide gels of varying moduli. Cryogenic transmission electron microscopy (cryo-TEM) is used to image the fibril structure and is verified qualitatively with optical microscopy of fluorescently-tagged collagen within the gels. Using fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI), the diffusion dynamics of the …

Computational Logp Calculations And Determination Of Lipophilicity Values Of Fluorinated Morphine Derivatives, Mirabella Romano, Allison Vu, Emily Chen

Student Scholar Symposium Abstracts and Posters

The addictive effect of opioids impacted 60 million people globally in 2023. This opioid crisis necessitates the development of opioid derivatives that maintain analgesic efficacy while minimizing addictive effects from opioid use. The present work focuses on morphine, a commonly prescribed opioid with high affinity to the mu-opioid receptor (MOR). Morphine binds non-selectively within both healthy and inflamed tissue. By modifying morphine’s structure through fluorination to counteract its non-selective binding, the drug’s pharmacological ability to provide effective pain relief comes with a lower risk of addiction. Specifically, the addition of fluorine to differing beta positions of the main binding site …

Rings Of Power: Controlling Sod Mimic Activity By The Addition Of Pyridine Rings Within The Pyridinophane Scaffold, Katherine J. Smith, Timothy M. Schwartz, David M. Freire, Cameron Bowers, Sarah K. Dunn, Jackson F. Bonnell, Magy A. Mekhail, Giridhar Akkaraju, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Superoxide dismutase enzymes are a major defense against superoxide, which is a potent reactive oxygen species. Misregulation of reactive oxygen species and subsequent neuronal damage are etiological hallmarks of neurodegenerative disease. Macrocyclic small molecules have offered inroads toward functional SOD1 mimics. Herein, we report a series of five tetra-aza macrocyclic ^RPy₂N₂ ligands, varied by 4-position substitution of the pyridine ring with both electron-donating (R = OMe) and withdrawing groups (R = Cl, I, and CF₃) to offer the first comparison to well-studied ^RPyN₃ congeners and other mimics in the literature. New ligands …

D101n: A Unique And Ill-Understood Familial Als-Related Sod1 Mutant, Analisa Lott

Honors Program Theses and Research Projects

Background: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease, with 90% of documented cases considered sporadic and about 10% showing a hereditary link; such cases are deemed as familial ALS (fALS). Superoxide dismutase (SOD), a copper-zinc binding enzyme that protects cells from damaging free radicals, has been linked to fALS with certain toxic gain of function mutations, such as the D101N mutant. The human SOD1 D101N mutant has been shown to be associated with rapidly progressing neurodegeneration yet is less prone to aggregation than similar mutants, but its deviation from wild-type (WT) SOD1 remains misunderstood.

Objective: Although the D101N …

Nanofabrication Of Tetraphenyl Porphyrin Surface Assemblies Linked With Tin Tetrachloride: A Scanning Probe Microscopy Investigation, Quynh Do

LSU Doctoral Dissertations

Scanning probe microscopy (SPM) and colloidal lithography methods were used to study the covalent coupling of porphyrins to surfaces. In this dissertation, experimental methods for SPM operation, techniques, and applications are described. Measurement of tip-sample interactions between a sharp tip and surface is translated into digital image data maps with x-, y-, and z-data. Colloidal lithography can be used to fabricate test platforms for AFM studies. The periodicity and arrangement of the designed nanostructures is determined by the size of the colloidal particles used for surface masks. Data processing is required to obtain images and topography information from raw AFM …

Alphafold2-Based Characterization Of Apo And Holo Protein Structures And Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics And Ligand-Induced Conformational Changes, Nishank Raisinghani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2, which combines randomized alanine sequence masking with shallow multiple sequence alignment subsampling to expand the conformational diversity of the predicted structural ensembles and capture conformational changes between apo and holo protein forms. Using several well-established datasets of structurally diverse apo-holo protein pairs, the proposed approach enables robust predictions of apo and holo structures and conformational ensembles, …

Reaction Of A Chiral Platinum Triamine Compound With Key Amino Acid And Guanine Analog, Onu Emmanuel Chukwu

Masters Theses & Specialist Projects

Platinum compounds can exhibit cytotoxic activity through reaction with DNA; however, interaction with proteins and DNA bases, especially with methionine residues and Guanine analogs, is another common biological reaction. Our lab has synthesized Chloro[2-(4-Methyl-1,4- diazepan-1-yl) ethanamine]platinum(II) chloride ([Pt(L)Cl]Cl), which has a tridentate binding mode for the amine ligand. This study focused on the reaction of the chiral platinum triamine with key amino acids (methionine and 2-hydroxybutyric acid) and guanine analogs under different pH and temperature conditions. The mass spectrometry of N-AcMet Interaction with [Pt(L)Cl]+ showed a m/z of 542 and 579 for reactions at pH 4. The m/z of 542 …

Photogeneration, Characterization, And Kinetic Study Of A New Phthalocyanine Species, Sobenna Onyeso

Masters Theses & Specialist Projects

In the search for green chemistry, the development of synthetic metal complexes that model enzyme function has been extensively studied. Phthalocyanine metal complexes, closely related to these heme-containing macrocycles, have gained continued interest due to their ease of direct synthesis, efficient redox, and optical properties. Despite the significant progress in phthalocyanine metal complexes, much more work needs to be done in the characterization and identification of their metal-oxo species, as well as mechanistic insights into their catalytic oxidations. To date, the reactivity of metal-oxo species on phthalocyanine platforms has not been probed.

In this study, metal phthalocyanine complexes have been …

Investigation Of Polybenzoxazine Vitrimers Based On Dynamic Transesterification Exchange, Jaylen Davis

Dissertations

With the ever-increasing issue of plastic waste production, a greener approach to synthetic processes and increased sustainability in plastic materials is still a high demand. Thermosets, which find uses in applications such as coatings, adhesives, and aerospace composites account for 15% of global plastics production, are particularly problematic in this context, as covalent crosslinks within the material serve both as a source of high-performance stability during use and as a barrier to conventional recycling after use. Therefore, our efforts focus on the incorporation of dynamic transesterification exchange chemistry into polybenzoxazine thermosets, which allows these materials to undergo reprocessing. This investigation …

The Disordered Negatively Charged C-Terminus Of The Large Hect E3 Ubiquitin Ligase Herc2 Provides Structural And Thermal Stability To The Hect C-Lobe, Kelly L. Waters, Kayla J. Rich, Noah D. Schwaegerle, Tianyi Yang, Shuanghong Huo, Donald E. Spratt

Chemistry

Homologous to the C-terminus of E6AP (HECT) and RCC1-like domain (RLD)-containing protein 2 (HERC2) is a large, 528 kDa E3 ubiquitin ligase that is associated with cancer, oculocutaneous albanism type 2, Prader-Willi syndrome, and other neurological diseases. HERC2 has been found to contribute to double-stranded DNA break repairs, tumor suppression, maintaining centrosome architecture, and ubiquitylation. The C-terminal portion of the HECT domain (C-lobe) of HERC2 is responsible for transferring ubiquitin to a substrate but the precise function of the other eight domains in HERC2 are unknown. Interestingly, HERC2 contains a unique and negatively charged C-terminal …

Selective Hydroxyl Functionalization Using Novel Bifunctional Macrocyclic Catalysts And Sufex-Based Methodologies, Austin Seilkop

All Dissertations

The research behind this dissertation explores innovative strategies for the functionalization of alcohols. Alcohols are abundant in biologically relevant molecules and pharmaceutical drugs, so designing new methods for modifying them has gained significant interest over the years. The first and second chapters of this dissertation focus on the selective functionalization of a particular class of alcohols, amino alcohols, a well-represented functional handle in biomolecules. The hydroxyl functionalization of amino alcohols often demands multiple synthetic steps. We developed a new class of macrocyclic catalysts to enable precise and efficient transformations of amino alcohols, advancing the scope and efficiency of amino alcohol …

Hydrothermal Synthesis, Characterisation, And Magnetic Study Of First-Row Transition Metal Molybdates And First-Row Transition Metal Vanadates, Mahsa Foroughian Foroughian

All Dissertations

Growing high-quality single crystals of transitional metal oxides have been of interest over the last two centuries because of the many applications of these transparent materials in various industries, such as optics, magnetism, semiconductors, and batteries. During this period, a variety of crystal growth techniques have been utilized, each offering unique advantages and disadvantages to the solid-state community.

Traditionally, metal oxides such as molybdates and vanadates are produced using high-temperature techniques (700 to 1200 °C). These methods can cause oxygen to be expelled, resulting in the creation of lattice defects and lower-valence metal ions and complicate precise measurements of physical …

Recyclable Composites Prepared From Animal Coproducts And Industrial Waste Sulfur, Perla Y. Sauceda-Oloño

All Dissertations

Pursuing sustainable and environmentally friendly materials has become a significant objective in materials science, particularly flame retardants and construction materials. This dissertation explores the development and evaluation of novel composites and high sulfur-content materials (HSMs) as potential alternatives to conventional, environmentally harmful materials.

Chapter one reviews recent advancements in environmentally benign flame-retardant additives, highlighting the potential of bio-derived phenols, polysaccharide derivatives, and greener phosphorus sources. The review discusses how green additives can enhance the flame retardancy, thermal stability, and smoke suppression properties of various polymers while addressing the challenges and future directions in the field.

Chapter two investigates the production …

Comparison Of Autoclaving And Γ-Radiation Impact On Four Spices Aroma Profiles And Microbial Load Using Hs-Spme Gc–Ms And Chemometric Tools, Mostafa H. Baky, Nora M. Elkenawy, Heba A.S. El-Nashar, Bishoy Abib, Mohamed A. Farag

Faculty Journal Articles

Herbal spices are widely consumed as food additives owing to their distinct aroma and taste as well as a myriad of economic and health value. The aroma profile of four major spices including bay leaf, black pepper, capsicum, and fennel was tested using HS-SPME/GC–MS and in response to the most widely used spices´ processing methods including autoclaving and γ-radiation at low and high doses. Additionally, the impact of processing on microbial contamination of spices was tested using total aerobic count. GC–MS analysis led to the identification of 22 volatiles in bay leaf, 34 in black pepper, 23 in capsicum, and …

Co2 Capture Utilizing Novel Deep Eutectic Solvents: Modeling, Process Simulation, And Cost Analysis, Nazneen Aspi Kolah

Masters Theses

One of the most pressing global issues that humans face is climate change caused by anthropogenic greenhouse gas emissions, especially carbon dioxide (CO2). Conventional solvents utilized for CO₂ capture, such as amines, are widely used in industrial applications due to their high CO2 absorption capacity. However, deep eutectic solvents (DES) have attracted a lot of academic attention recently due to their biodegradability and low energy for regeneration.

This research serves as a foundational proof-of-concept for using DESs in industrial gas separation processes. Five DES are evaluated for CO2 removal from flue gases. Aspen Plus is utilized to simulate the performance …

Lessons Learned From Establishing And Running A Mössbauer Laboratory In Industry, Paulo De Souza

Research outputs 2022 to 2026

Mössbauer spectroscopy offers unique capabilities for primary industry sectors such as mining, mineral processing, and steelmaking, as well as in environmental services and advanced manufacturing. However, there are three key limiting factors: the time required to record a single spectrum, the challenges of managing an additional radioactive source on company premises, and the lack of personnel skilled in analysing Mössbauer spectra and understanding its operation. More commonly used techniques such as XRD, SEM, or XRF have technical staff who can interpret data with support from standard libraries and user-friendly software packages. In contrast, Mössbauer spectroscopists, who often hold degrees in …

Phytoplankton Responses To Changing Irradiance And Carbon Fertilization, Alison Siersma

Graduate Theses and Dissertations (2019 - present)

Phytoplankton play a crucial role in marine ecosystems due to their innate ability to fix carbon. As atmospheric CO2 levels continue to rise from fossil fuel combustion, the resulting increase in dissolved CO2 and the concurrent decrease in ocean pH are likely to impact the phytoplankton community. The response of phytoplankton to elevated CO2 can vary significantly among species and environmental conditions (e.g. light, temperature, nutrient availability). To address these variations, an experiment was conducted using a controlled photobioreactor system, maintaining high and low light, constant temperature, nutrient levels, and two pCO2 concentrations. This study focused on two regionally relevant …

Synthesis Of Novel Chromenone Esters For Biochemical Assays, Andrew Dean Helmerich

Undergraduate Honors Thesis Collection

This project details the synthesis of a variety of novel chromenone esters to be used as enzymatic probes. A robust, initial library of 22 chromenone esters was successfully synthesized with differences in chain length, branching, and the incorporation of cyclic and heteroatomic moieties. These new chromenones were fully characterized by 1HNMR, 13CNMR, DEPT HRMS, 19FNMR, and HSQC. The utility of these compounds comes from the fact that they will fluoresce upon cleavage of the ester; thus, this property makes them ideal candidates to be used in the monitoring of enzymatic activity of esterases. Elucidating the enzyme-substrate structure activity relationship (SAR) …

Impact Of Water Ionic Chemistry On Kombucha Fermentation, Katherine A. Thompson-Witrick, Olivia Sundman, Sadie Disselkoen, Nicholas Hanson, Cheyenne Butler, Victoria Jordan, Ian Galbraith, Jada Spake, Seiler Pollock, Drew M. Budner

Chemistry

Kombucha is made by using a symbiotic culture of bacteria and yeast (SCOBY) to ferment sweetened tea. This fermentation produces a beverage with a unique aroma and acidic flavor. Kombucha has recently gained popularity in the United States and has been reported to have numerous health benefits. While there is a wide variation in kombucha composition, little is known about the impact water’s chemistry has on the fermentation and the resulting kombucha. Brewing water for kombucha was altered using the following ions: bicarbonate, chloride, calcium, magnesium, and sulfate at different concentrations. Pre-(tea) and post-(kombucha) fermentation (kombucha) products were analyzed for …

Use Of Equine H3n8 Hemagglutinin As A Broadly Protective Influenza Vaccine Immunogen, David Verhoeven, Brett A. Sponseller, James E. Crowe, Sandhya Bangaru, Richard J. Webby, Brian M. Lee

Chemistry

Development of an efficacious universal influenza vaccines remains a long-sought goal. Current vaccines have shortfalls such as mid/low efficacy and needing yearly strain revisions to account for viral drift/shift. Horses undergo bi-annual vaccines for the H3N8 equine influenza virus, and surveillance of sera from vaccinees demonstrated very broad reactivity and neutralization to many influenza strains. Subsequently, vaccinating mice using the equine A/Kentucky/1/1991 strain or recombinant hemagglutinin (HA) induced similar broadly reactive and neutralizing antibodies to seasonal and high pathogenicity avian influenza strains. Challenge of vaccinated mice protected from lethal virus challenges across H1N1 and H3N2 strains. This protection correlated with …

Theoretical Investigation Of Hydrogen Abstraction From Fluorinated Propanones And Fluorinated Propanals, Laurel Washburn

Honors Theses

Per- and polyfluoroalkyl substances (PFAS) are a class of thousands of industrially used compounds often called “forever” chemicals because of their slow degradation process that leads to accumulation in soil, dust, drinking water, and the body. PFAS are used for their grease and water resistance properties but some of these compounds are toxic at extremely low levels. To better understand the effects of these types of compounds, the main pathways of their degradation need to be further investigated. This study analyzes computationally the hydrogen abstraction reactions by both hydroxyl radical and triplet oxygen atom for all possible fluorinated propanones and …

Composites Developed By The Reaction Of Elemental Sulfur With Biologically Derived Fats And Oils, Katelyn Tisdale

All Dissertations

Human civilization’s modern infrastructure relies mainly on cement and petrochemical products. However, the production of these building materials have harmful ecological effects such as green gas emissions, therefore intensifying the need to develop alternative, sustainable structural materials from renewably sourced or waste material precursors. The work presented herein investigates various biomass derived resources that serve as the olefin source for reaction with elemental sulfur, another abundant waste source, via inverse vulcanization to form high strength composites competitive with that of traditional building materials.

Chapter one reviews various techniques that have been developed and executed in an effort towards lignin valorization …

Influence Of Glycopolymer Structure On Amphiphilic, Hybrid, Linear Branched Block Copolymer Properties For Use In Biomedical Applications, Kevin Green

Dissertations

The focus of this dissertation is evaluating and adding fundamental knowledge regarding the structure-property relations of glycopolymers used in the design of hybrid block copolymers (HBC) that are cable of self-assembling into delivery vehicles for biomedical applications. A shift to the utilization of natural materials in the design and fabrication of drug-delivery vehicles has garnered significant attention. Understanding the effects of linear glycopolymers content and composition on the resulting HBCs properties can provide valuable insight into how these materials may be tailored for use in targeted biological applications.

The first chapter introduces current literature on the need for improvement in …

Aars Online: A Collaborative Database On The Structure, Function, And Evolution Of The Aminoacyl-Trna Synthetases, Jordan Douglas, Haissi Cui, John J. Perona, Oscar Vargas-Rodriguez, Henna Tyynismaa, Claudia Alvarez Carreno, Jiqiang Ling, Lluis Ribas De Pouplana, Xiang-Lei Yang, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like …

Density Functional Theory And Machine Learning Analysis Of C—C Reductive Coupling From Terminal Cyanido And Cyaphido Complexes, Roberto Magdiel Escobar

Theses and Dissertations

Carbon–carbon (C–C) bond activation has gained increased attention as a direct method for the synthesis of pharmaceuticals and industrial chemistry. Due to the thermodynamic stability and kinetic inaccessibility of the C–C bonds, however, activation of C–C bonds by homogeneous transition-metal catalysts under mild homogeneous conditions is still a challenge. Most of the systems in which the activation occurs either have aromatization or relief of ring strain as the primary driving force. The activation of unstrained C–C bonds of phosphaalkynes does not have this advantage. This study employs Density Functional Theory (DFT) calculations using the Gaussian16 package to elucidate and compare …

Assessing Reproducibility Challenges In Clinical Metabolics, Darcy Lin Cochran

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Current metabolomics research is expanding to be multiplatform and interdisciplinary. Metabolomic analysis has the potential to provide detailed insight into any biological system of interest to analyze the underlying molecular mechanisms of variables like environment, disease, and genetics. Human clinical metabolomics is a major research area that is often focused on finding biomarkers or panels of biomarkers for different diseases. However, results are difficult to compare across different laboratories since the field of metabolomics has yet to widely adopt best practices for sample preparation, data acquisition and data processing, results are difficult to compare across different laboratories.

This thesis focuses …

Ai Is A Viable Alternative To High Throughput Screening: A 318-Target Study, Izhar Wallach, Denzil Bernard, Kong Nguyen, Gregory Ho, Adrian Morrison, Adrian Stecula, Andreana Rosnik, Ann Marie O'Sullivan, Aram Davtyan, Ben Samudio, Bill Thomas, Brad Worley, Brittany Butler, Christian Laggner

Chemistry Faculty Research & Creative Works

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, …

Development Of Uranium Fluoride Microstructures, Harry Jang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Uranium microstructured materials with controlled size and shape have found applications in several branches of the nuclear industry including as targets for medical isotopes production, fuels for nuclear reactors, standards for analytical measurements, and energy sources for space exploration. Morphological studies of actinide materials are also highly relevant to nuclear forensics-related work. Other potential applications include information storage, catalysis, sensors, and luminescent devices. Most studies on uranium microstructured materials have focused on binary oxides, nitrides, carbides, and fluorides, with the spherical shape being the dominant morphology. Prior to the work reported in this dissertation, aside from UF4 microspheres (ms) and …

Evaluation Of Polymerization Condition Reactions Of Methyl Vinyl Ketone For Hydrogen Storage, Rituborna Ghosh

Theses and Dissertations

Hydrogen is widely regarded as one of the most promising clean alternative fuel sources; however, its widespread adoption has been hindered by significant challenges related to storage and transportation. Various storage methods have been proposed and developed, with continuous advancements being made to address these issues. Among the most effective solutions is the utilization of polymers, which serve as safe and efficient hydrogen storage media. This work investigated the polymerization of methyl vinyl ketone using different ratio of monomer: initiator and monomer: crosslinker using N,N′-methylenebisacrylamide (MBA) as crosslinker and ammonium persulfate (APS) as initiator in a free radical polymerization mechanism. …

Thermal Conductivity Characterization Of High Oleic Vegetable Oils Based Hybrid Nanofluids Formulated Using Gnp, Tio2, Mos2, Al2o3 Nanoparticles For Mql Machining, Anthony Chukwujekwu Okafor, Tobechukwu Kingsley Abor, Saidanvar Esanjonovich Valiev, Ignatius Echezona Ekengwu, Abiodun Saka, Monday Uchenna Okoronkwo

Mechanical and Aerospace Engineering Faculty Research & Creative Works

This paper presents the results of thermal conductivity characterization of six high oleic soybean oil (HOSO) and four high oleic canola oil (HOCO)-based hybrid nanofluids formulated with four types of nanoparticles (Graphene nanoplatelet (xGnP), TiO2, MoS2, and Al2O3) at nanoparticles wt.% concentration from 1 % to 7 % in 1 % increment using the two-step method for use in MQL machining of difficult-to-cut metals. Thermal conductivity of the formulated hybrid nanofluids were measured using Thermtest Transient Hot Wire Liquid Thermal Conductivity Meter at temperatures from 25 °C to 75 °C in increment of 10 °C. Obtained results showed that thermal …