Other Chemistry Commons^™

Esipt-Enabled Alkyne Migration Provides Rapid Access To Benzoxazinones, Andrés G. Muñoz

Electronic Theses and Dissertations

Benozoxazinones have long been of interest to agrochemical scientists and medicinal chemists because of their widespread biological activity. These scaffolds are also of interest to synthetic chemists, who recognize the utility of benzoxazinones for accessing functionalized heterocycles. The use of efavirenz, a benzoxazinone-based reverse transcriptase inhibitor used in the treatment of HIV-1, has brought increased attention to this privileged pharmacophore. While there exist numerous strategies for synthesizing benzoxazinones, methods that do not require the use of acutely toxic and environmentally hazardous reagents are lacking. Consequently, there is a need to develop new methods for constructing this valuable scaffold. Herein, we …

Dynamics And Turnover Of Lipid And Protein Domains In Cells And Supported Bilayers, Alan Weisgerber

Electronic Theses and Dissertations

Protein and lipid clustering is an important mechanism for cell processes such as exo- and endo-cytosis and creating functional signaling complexes. It has been seen that both lipids and proteins are involved with the formation of cluster domains on cell membranes, yet little is known about the interplay between the two. In this work I began with visualizing lipid sorting to artificially induced curvature in supported lipid bilayers, with lipid tails affecting the sorting differently to curvature. These results demonstrate that lipids sort to curvature on curved, supported lipid bilayers. The sorting depends on the number of lipids in the …

Web-Based Platform For Analysis Of Rna Folding From High Throughput Chemical Probing Data, Christopher Jurich, Amir Brivanlou, Silvi Rouskin, Joseph D. Yesselman

Department of Chemistry: Faculty Publications

RNA structures play critical roles in regulating gene expression across all domains of life and viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the RNA structure field by enabling the assessment of many structures in their native, physiological context. Previously, we developed Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in the RNA. We used this approach to determine the genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which permitted uncovering new biology and identifying therapeutic targets. Due to the simplicity and …

Peptidomics Analysis Reveals Changes In Small Urinary Peptides In Patients With Interstitial Cystitis/Bladder Pain Syndrome, Md Shadman Ridwan Abid, Haowen Qiu, Bridget Tripp, Aline De Lima Leite, Heidi E. Roth, Jiri Adamec, Robert Powers, James W. Checco

Department of Chemistry: Faculty Publications

Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic and debilitating pain disorder of the bladder and urinary tract with poorly understood etiology. A definitive diagnosis of IC/BPS can be challenging because many symptoms are shared with other urological disorders. An analysis of urine presents an attractive and non-invasive resource for monitoring and diagnosing IC/BPS. The antiproliferative factor (APF) peptide has been previously identified in the urine of IC/BPS patients and is a proposed biomarker for the disorder. Nevertheless, other small urinary peptides have remained uninvestigated in IC/BPS primarily because protein biomarker discovery efforts employ protocols that remove small endogenous peptides. …

Developing A New Treatment For Superficial Fungal Infection Using Antifungal Collagen-Hsaf Dressing, Jing Zhong, Xiayi Yan, Xin Zuo, Xuan Zhao, Jiahui Yang, Qin Dou, Lulu Peng, Yuxiang Zhu, Yichen Xiao, Zeran Bian, Dalian He, Qiushuang Xu, Stephen Wright, Yaoyao Li, Liangcheng Du, Yan Wang, Jin Yuan

Department of Chemistry: Faculty Publications

Fungal pathogens are common causes of superficial clinical infection. Their increasing drug resistance gradually makes existing antifungal drugs ineffective. Heat stable antifungal factor (HSAF) is a novel antifungal natural product with a unique structure. However, the application of HSAF has been hampered by very low yield in the current microbial producers and from extremely poor solubility in water and common solvents. In this study, we developed an effective mode of treatment applying HSAF to superficial fungal infections. The marine-derived Lysobacter enzymogenes YC36 contains the HSAF biosynthetic gene cluster, which we activated by the interspecific signaling molecule indole. An efficient extraction …

Identifying And Minimizing Sources Of Variability Within Modern Spectroscopic Techniques For The Forensic Analysis Of Glass, Oriana Christy Ovide

Graduate Theses, Dissertations, and Problem Reports (ETD)

Broken glass is a trace material frequently found at crime scenes such as hit-and-runs, burglaries, assaults, and homicides. Existing research encompassing the forensic analysis of glass evidence is vast. Published studies cover the analysis and interpretation of various types of glass. However, organizations such as the National Institute of Justice (NIJ), National Institute of Standards and Technology Organization of Scientific Area Committees (NIST-OSAC), and American Society of Trace Evidence Examiners (ASTEE) continue to identify glass-specific research needs to strengthen the scientific foundations of the field. Current gaps within the forensic glass community involve understanding modern glass formulations, re-evaluating the performance …

Development Of Peg-B-Pla Based Micelles For Neutralization Of A Toxic Peptide, Giselle Campos

Graduate Theses/Dissertations

I herein report the preparation and characterization of PEG-b-PLA block copolymer micelles and PEG-b-PLA/PLA mixed micelles as potential “plastic antidotes” for a toxic peptide, melittin. PEG-b-PLA micelles have been used in a number of biomedical applications for their biodegradability and biocompatibility. Along these lines, I investigated the colloidal stability and the peptide absorption properties of PEG-b-PLA/PLA mixed micelles. A series of PEG-b-PLA block copolymer micelles and PEG-b-PLA/PLA mixed micelles were prepared, and their colloidal stability was studied. The hydrodynamic diameters of stable micelles were determined by using Dynamic …

Electron Spin Relaxation Of Nitroxide Spin Labels And Relaxation Processes, Thacien Ngendahimana

Electronic Theses and Dissertations

MTSL is the nitroxide spin label that is most commonly used in site-directed spin labeling. However, due to rotation of its gem-dimethyl groups that average anisotropic interactions, T_m becomes short above about 70 K and this makes DEER experiments difficult at these temperatures. Strategies for decreasing spin echo dephasing and electron spin lattice relaxation rates are important for design of nitroxide spin labels and molecular qubits.

In searching for labels with longer T_m, new nitroxide spin labels devoid of gemdimethyl groups or with more rigid structures were synthesized at the University of Nebraska and pulsed EPR measurements …

Binding Interactions Between Mixed-Monlayer Functionalized Gold Nanoparticles (Aunps) And The Serum Protein Albumin, Jennifer Hanigan-Diebel

All Master's Theses

This study investigated the protein adsorption interactions of bovine serum albumin (BSA) with three different functionalized 5 nm gold nanoparticles (AuNPs) in order to determine the binding affinity and total amount of protein adsorbed to each AuNP surface chemistry. AuNPs were synthesized using two different capping agents to display three different surface chemistries: a neutral ω-functionalized thiol ligand (mercapto-ethoxy-ethoxy-ethanol, MEEE), a thiol ligand that is negatively charged at pH 7.4 (mercaptohexanoic acid, MHA), and a mixture of the two ligands (mixed-ligand AuNPs). The interactions of this library of AuNPs with bovine serum albumin (BSA) were investigated using UV-visible absorbance spectroscopy, …

Purification And Activity Assay Optimization Of Bacterial Catalase From Psychrobacter Koprana, Sydney Willis

Honors Program Theses

To date, catalase protein from bacterial species is not the most widely used commercial catalase. Catalase, the enzyme that breaks down hydrogen peroxide in most living organisms, is an invaluable enzyme in the food, agriculture, and pharmaceutical industries. In 2019, a novel species of a psychrotolerant bacterium was discovered in Cold Harbor, NY. This species, Psychrobacter koprana, exhibits highly active catalase. Preliminary data from activity assays demonstrates that P. koprana catalase has the same activity as commercially available catalase. After purification and activity assay optimization, the activity of this catalase has the potential to be more active than other easily …

Electrochemical Impedance Spectroscopy Analysis Of Corrosion Of Reinforcing Steel In Fly Ash Mortar By Means Of Transmission Line Modeling, Padraig Stack

Williams Honors College, Honors Research Projects

Electrochemical impedance spectroscopy (EIS) is an important non-destructive tool that allows for a deeper understanding of the electrochemical processes and mechanisms occurring in an electrochemical cell. Equivalent electrical circuits (EECs) are used to model the impedance data into electrical components, such as resistors and capacitors, on a circuit. Current potentiostat offers software packages that can analyze the frequency response, but the software only supports “simple” EEC that can be written as fixed electrical components in some combination of series and parallel. Park and Macdonald propose a transmission line model (TLM) that does not use lumped-element models, instead, the values of …

Analysis Of Blue Fountain Pen Ink By Uv-Vis Spectroscopy, Atr-Ftir Spectroscopy, And Thin Layer Chromatography Enhanced With Rgb Spot Evaluation To Construct A Database For Comparison And Identification., Elliot D. Quinteros

Dissertations and Theses

Pen ink can be a crucial piece of physical evidence in the area of Forensic Science. For example, evidence such as notes, letters, printed documents, checks, currency, ransom notes, and books may contain ink. Analysis of ink is typically done for identification or differentiation purposes. To improve existing methods, it was proposed to create a database with many samples and experimental information. The methods used and evaluated were thin-layer chromatography (TLC) enhanced with RGB spot evaluation, UV-Vis spectroscopy, and ATR-FTIR spectroscopy. All three methods were used to analyze 89 fountain pen ink samples. All three methods were able to discriminate …

Oxidative Damage To Brain Cells Underlies: (I) Resistance To Radiation And Increased Tumor Cell Growth In Glioblastoma; (Ii) Apoe Allele Status And Pentose Phosphate Pathway Proteins In Alzheimer Disease Mouse Models, Nicole Rummel

Theses and Dissertations--Chemistry

Oxidative phosphorylation occurs within the inner mitochondrial membrane producing ATP for the cell’s energy needs. The Electron Transport Chain carries out the transfer of electrons from electron carriers through a series of proteins to form a proton gradient across the inner mitochondrial membrane. This gradient acts as the energy source needed to put a phosphate onto ADP and form ATP. With the large amounts of free electrons and oxygen within the mitochondria, an inevitable by-product of free radicals in the form of superoxide are produced. Superoxide (O^-̇₂) is a reactive radical that can react further to …

Advancing Competency In Managing Risk And Knowledge: Steps Toward Operationalisation Of The Risk-Knowledge Infinity Cycle (Rki Cycle) - Part 1: Improving Effectiveness Of Risk-Based Decision Making (Rbdm), Martin Lipa, Paige Kane, Anne Greene

Articles

To date, literature on the Risk-Knowledge Infinity Cycle (RKI Cycle) has mainly been theoretical. This paper series intent is to focus on the operationalisation of the RKI Cycle by describing a series of steps – the “How to” – for RKI Cycle deployment, to help move the RKI Cycle from theory to practice. The first paper in this series focuses on how the RKI Cycle can support effective Risk-Based Decision Making (RBDM).

Analysis Of Forensically Relevant Evidence Using Electrochemistry, Spectroscopy, And Mass Spectrometry Tools, Colby Edward Ott

Graduate Theses, Dissertations, and Problem Reports (ETD)

Forensic science relies on the use of multiple techniques in the assessment of evidence to increase the accuracy and reliability of the results. However, with the rapidly changing drug landscape due to the introduction of novel psychoactive substances, many traditional screening methods are no longer sensitive or selective enough for use. Additionally, many screening methods such as chemical color tests are prone to false positive and negative results and are subjective. Therefore, the goal of this dissertation was to develop a novel analytical scheme that can provide a more efficient, rapid, and sensitive method that will facilitate adoption in the …

Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih

Makara Journal of Science

Black cumin is commonly used as traditional medicine due to its wide range of pharmacological potential. Black cumin oil (BCO) was often prepared as nanoemulsion to improve its solubility, stability, and bioavailability. This study was conducted to investigate the molecular behavior as well as structural evolution of BCO-surfactant systems during self-assembly micellization using molecular dynamics (MD) simulations. Several BCO constituents and variations of surfactants were employed to model BCO-surfactant systems. 50 ns of MD simulations were performed to elucidate their evolution of structures and physicochemical properties during formation. Results showed that BCO-tween20 and BCO-lecithin were able to form spherical-shaped micelles …

Uniting Non-Empirical And Semi-Empirical Density Functional Approximation Strategies Using Constraint-Based Regularization, Trine K. Quady

University Honors Theses

In this work, we present a general framework that unites the two primary strategies for constructing density functional approximations (DFAs): non-empirical (NE) constraint satisfaction and semi-empirical (SE) data-driven optimization. The proposed method employs B-splines--bell-shaped spline functions with compact support--to construct each inhomogeneity correction factor (ICF). This choice offers several distinct advantages over a polynomial basis by enabling explicit enforcement of linear and non-linear constraints as well as ICF smoothness using Tikhonov regularization and penalized B-splines (P-splines). As proof of concept, we use this approach to construct CASE21--a Constrained And Smoothed semi-Empirical global hybrid generalized gradient approximation that completely satisfies all …

Computational Analysis Of The Spin Trapping Properties Of Lipoic Acid And Dihydrolipoic Acid, Matthew Bonfield

Electronic Theses and Dissertations

While the spin trapping properties of thiols have been investigated through EPR analysis and kinetics studies, few groups have studied these properties using strictly computational methods. In particular, α-lipoic acid (ALA) and its reduced form, dihydrolipoic acid (DHLA), one of the strongest endogenously produced antioxidants, show potential for being effective, naturally occurring spin traps for the trapping of reactive oxygen species. This research covers electronic structure calculations of ALA, DHLA, and their corresponding hydroxyl radical spin adducts, performed at the cc-pVDZ/B3LYP/DFT level of theory. The effects on DHLA introduced by other radicals such as ·OOH, ·OCH₃, …

Amilorides Inhibit Sars-Cov-2 Replication In Vitro By Targeting Rna Structures, Martina Zafferani, Christina Haddad, Le Luo, Jesse Davila-Calderon, Liang-Yuan Chiu, Christian Shema Mugisha, Adeline G. Monaghan, Andrew A. Kennedy, Joseph D. Yesselman, Robert J. Gifford, Andrew W. Tai, Sebla B. Kutluay, Mei-Ling Li, Gary Brewer, Blanton S. Tolbert, Amanda E. Hargrove

Department of Chemistry: Faculty Publications

The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, emphasized the urgent need for development of novel antivirals. Small-molecule chemical probes offer both to reveal aspects of virus replication and to serve as leads for antiviral therapeutic development. Here, we report on the identification of amiloride-based small molecules that potently inhibit OC43 and SARS-CoV-2 replication through targeting of conserved structured elements within the viral 5′-end. Nuclear magnetic resonance–based structural studies revealed specific amiloride interactions with stem loops containing bulge like structures and were predicted to be strongly bound by the lead amilorides in retrospective docking studies. Amilorides represent the …

Nuscon: A Community-Driven Platform For Quantitative Evaluation Of Nonuniform Sampling In Nmr, Yulia Pustovalova, Frank Delaglio, D. Levi Craft, Haribabu Arthanari, Ad Bax, Martin Billeter, Mark J. Bostock, Hesam Dashti, D. Flemming Hansen, Sven G. Hyberts, Bruce A. Johnson, Krzysztof Kazimierczuk, Hengfa Lu, Mark Maciejewski, Tomas M. Miljenović, Mehdi Mobli, Daniel Nietlispach, Vladislav Orekhov, Robert Powers, Xiaobo Qu, Scott Anthony Robson, David Rovnyak, Gerhard Wagner, Jinfa Ying, Matthew Zambrello, Jeffrey C. Hoch, David L. Donoho, Adam D. Schuyler

Department of Chemistry: Faculty Publications

Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and …