Chemistry Commons^™

Directly Polymerizable Co Releasing Molecules, Jackson Snow

Electronic Theses and Dissertations

Despite the commonly held consensus that carbon monoxide (CO) is toxic, it has been shown to be an essential signaling molecule in the human neuronal system and has been noted to have anti-inflammatory properties, act as a vasodilator, have anti-proliferative impacts on tumors, and many other beneficial effects. The current limitation to using CO as a therapeutic molecule is delivering the proper dosages using CO releasing molecules (CORMs) without exhibiting toxicity. The first chapter of this thesis will review the biological significance of CO in biological systems, the limitations of existing CORMs, and the properties of diphenylcyclopropenone (DPCP) that make …

Lipophilic Probes For Cellular Ethylene Detection, Morgan R. Brown

Electronic Theses and Dissertations

The structure of ethylene is simple, yet its biological effects are significant. When considering its role in biology it is almost exclusively regarded as a plant hormone. Research on ethylene from plants was progressed by several advancements in analytical instrumentation, from its discovery to elucidation of its signaling pathway. There is currently limited understanding of ethylene’s role in mammals, but evidence suggests that it may be a biomarker for oxidative stress! Additional tools and technology are crucial to study this surprising and important signaling role in mammals. Our group has developed molecular ethylene probes as a strategy to detect ethylene …

Measurements Of Atmospheric Radicals, Heather L. Runberg

Electronic Theses and Dissertations

Atmospheric particulate matter (PM) is a global health concern. PM_2.5 is formed primarily through combustion processes such as automobile use and industrial activity. Natural sources of PM_2.5 result from events like volcanos and wildfires. Upon inhalation, PM_2.5 is small enough to travel deep into the lungs where it can form reactive oxygen species (ROS), such as hydroxyl radical (OH), causing oxidative damage to pulmonary tissues. PM_2.5 has been linked to cardiopulmonary diseases such as asthma, chronic obstructive pulmonary disease (COPD), and high blood pressure.

PM_2.5 is small enough to remain aloft and travel many hundreds …

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 …

Thin Liquid Films On A Rotary Bell Atomizer In Surface-Following Coordinates, Mark Doerre, Nelson Akafuah

Institute of Research for Technology Development Faculty Publications

This article analyzes a published formulation of the Navier–Stokes equations cast into surface-following coordinates and provides some additional mathematical background to follow the article. Ubiquitous in the paint shops of automotive plants around the world, a high-speed rotary bell is succinctly described as a rapidly spinning concave axisymmetric surface with liquid paint supplied from a port coinciding with the center of rotation. The spinning surface transfers momentum to the paint film causing it to flow outward. Upon reaching the bell periphery, it is flung off, subsequently forming an atomized spray transferred to an automotive body through advection and electrostatics. Common …

Protonation And Non-Innocent Ligand Behavior In Pyranopterin Dithiolene Molybdenum Complexes, Cassandra Gates, Haley Varnum, Catherine Getty, Natalie Loui, Ju Chen, Martin L. Kirk, Jing Yang, Sharon J. Nieter Burgmayer

Chemistry Faculty Research and Scholarship

The complex [TEA][Tp*MoIV(O)(S2BMOPP)] (1) [TEA = tetraethylammonium, Tp* = tris(3,5-dimethylpyrazolyl)hydroborate, and BMOPP = 6-(3-butynyl-2-methyl-2-ol)-2-pivaloyl pterin] is a structural analogue of the molybdenum cofactor common to all pyranopterin molybdenum enzymes because it possesses a pyranopterin-ene-1,2-dithiolate ligand (S2BMOPP) that exists primarily in the ring-closed pyrano structure as a resonance hybrid of ene-dithiolate and thione-thiolate forms. Compound 1, the protonated [Tp*MoIV(O)(S2BMOPP-H)] (1-H) and one-electron-oxidized [Tp*MoV(O)(S2BMOPP)] [1-Mo(5+)] species have been studied using a combination of electrochemistry, electronic absorption, and electron paramagnetic resonance (EPR) spectroscopy. Additional insight into the nature of these molecules has been derived from electronic structure computations. Differences in dithiolene C–S bond …

Modelling Quinones Using Density Functional Theory, David Ruiter, Madeleine Callan, Elijah Gruszecki, Maya Nambisan, Dr. K. V. Lakshmi

Summer Research

We modelled benzoquinone (BQ), dichlorobenzoquinone (DCBQ), and dimethylbenzoquinone (DMBQ) using the ORCA quantum chemistry computation suite. We obtained singlepoint energies, electron and spin densities, and the hyperfine coupling values for each molecule suspended in dimethyl sulfoxide (DMSO) and isopropyl alcohol (IPA). In most cases, we find close agreement with published literature values.

Cysteine-Tyrosine Crosslink Synthesis In Bf4112 From B. Fragilis, Alex Van Uffelen, Sophie Hruska, David Benson

Summer Research

Redox-active crosslinked amino acids are a class of post-translational modifications that extend protein chemistry. These cofactors occur in fifteen known proteins with high resolution Xray crystallography as the primary method for confirmation. One of those proteins is cytochrome c oxidase (complex IV), where HisTyr (figure 1) is responsible for the high-valent oxidative intermediate in O2 reduction to 2H2O. Cys-Tyr was the first of these cofactors to be identified and is characterized in galactose oxidase (coordinated to a Cu ion) and cysteine dioxygenase (distal to a mononuclear non-heme iron ion).

An Approach To The Synthesis Of 3-Quinazolinedione Carboxylic Acids: Putative Antibiotics, Colton J. Stonehouse, Michael Barbachyn

Summer Research

Bacterial resistance to antibiotics is a growing public health threat. Each year, more than 2.8 million antibioticresistant infections occur in the United States and 35,000 people die as a consequence. Fluoroquinolone (FQ) agents targeting the essential bacterial type II topoisomerases DNA gyrase and topoisomerase IV, exemplified by ciprofloxacin, have been in clinical use since the 1980’s and shown to be useful antibiotics. Unfortunately, heavy use of the FQs has inevitably led to the development of FQ-resistant pathogens

Purification And Evaluation Of Manganese Superoxide Dismutase, Madison Detullio

Senior Honors Projects

The goal of this research is to evaluate the mechanism by which p53 and SOD2 interact • Develop purification protocols for both p53 and SOD2 • Evaluate DNA binding affinity of SOD2 and p53 • Conduct a series of assays to evaluate aggregation state of p53 and SOD2 under various conditions.

Micro-Rna And Proteomic Profiles Of Plasma-Derived Exosomes From Irradiated Mice Reveal Molecular Changes Preventing Apoptosis In Neonatal Cerebellum, Simonetta Pazzaglia, Barbara Tanno, Ilaria De Stefano, Paola Giardullo, Simona Leonardi, Caterina Merla, Gabriele Babini, Seda Tuncay Cagatay, Ammar Mayah, Munira Kadhim, Fiona Lyng, Christine Von Toerne, Zohaib N. Khan, Prabal Subedi, Soile Tapio, Anna Saran, Mariateresa Mancuso

Articles

Cell communication via exosomes is capable of influencing cell fate in stress situations such as exposure to ionizing radiation. In vitro and in vivo studies have shown that exosomes might play a role in out-of-target radiation effects by carrying molecular signaling mediators of radiation damage, as well as opposite protective functions resulting in resistance to radiotherapy. However, a global understanding of exosomes and their radiation-induced regulation, especially within the context of an intact mammalian organism, has been lacking. In this in vivo study, we demonstrate that, compared to sham-irradiated (SI) mice, a distinct pattern of proteins and miRNAs is found …

Advancing Competency In Managing Risk And Knowledge: Steps Toward Operationalisation Of The Risk-Knowledge Infinity Cycle (Rki Cycle) Part 3: Uncovering Knowledge For Qrm Through Knowledge Mapping At Node 1, Martin Lipa, Valerie Mulholland, 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 third paper in this series focuses on ensuring the best available knowledge flows into QRM through a case study demonstrating knowledge mapping to support effective quality risk assessment during commissioning and qualification activities.

The Value Of Peer Mentoring Networks For Developing Leaders And Inspiring Change, Chrystal D. Bruce, Patricia M. Flatt, Sarah R. Kirk, Elizabeth Roberts-Kirchhoff, Hala G. Schepmann

2022 Faculty Bibliography

A peer-mentoring network, funded by the National Science Foundation ADVANCE program, profoundly impacted the career trajectory of five women chemistry faculty at predominantly undergraduate institutions. By providing each other support, encouragement, information, and accountability, we advanced our careers, became leaders in our own right, and implemented change at our institutions. To extend this benefit to more women STEM faculty, we have developed and implemented a model to support 74 faculty and administrators representing 51 institutions across the country.

Cooperative Allosterism In Avidin And Streptavidin Upon Biotin Binding As Observed By Changes In Intrinsic Fluorescence, Alycia Murphy

Senior Honors Projects

Avidin is a homotetrameric protein known for its high binding affinity and specificity for biotin which gives it great functionality in many biotech applications. Prior research on the bacterial analog, streptavidin found cooperative allosterism exhibited in the binding process. This research was aimed at investigating whether this same cooperative allosterism accompanies the binding of biotin to avidin. This work measured intrinsic tryptophan fluorescence as biotin was titrated into avidin. A blueshift in the wavelength of maximum fluorescence as well as quenching of the overall fluorescence intensity, similar to the streptavidin was observed. The saturation point for 335 nm emission (tryptophans …

Chemical Proteomic Identification And Functional Studies Of Cardiac Protein Glutathionylation, Maheeshi Yapa Abeywardana

Wayne State University Dissertations

Elevated intracellular levels of reactive oxygen species (ROS) are associated with induction of oxidative stress. Increased levels of ROS participate in development of cardiovascular diseases by modifying proteins reversibly or irreversibly. Especially, the cysteine residues can undergo oxidative post-translational modifications such as glutathionylation. Glutathionylation is an important regulatory reversible thiol oxidation. Identification and quantification of glutathionylated proteins is important for the understanding of the molecular mechanisms behind initiation and progression of many diseases. Our lab previously developed a click chemistry-based method to detect and identify glutathionylation in cells by synthesizing clickable-glutathione.We established a mass spectrometry-based strategy coupled with clickable glutathione …

Visualizing The Electronic Structure Of Atoms, Ryan Bouman, Henry Baldacci, Roger Dekock

Summer Research

There are three aspects of the electronic structure of atoms that confront the university student. All three arise in Hartree-Fock (HF) theory, which is foundational to understanding the periodic table. These aspects are: 1) Electron probability distributions of oneelectron atomic orbitals. 2) One-electron orbital energies. 3) How 1) and 2) relate to the total atomic energy and the total electron probability distribution. The goal of our work is to build a website that will employ a long-neglected model, first introduced by Slater and Zener (SZ). HF theory requires a knowledge of calculus, differential equations, and the ability to solve many …

Using Circular Dichroism Spectroscopy To Study Secondary Structure Of Horseradish Peroxidase: A Laboratory Experiment In Biochemistry, Shemaiah Kamran, Sarah E. Bultje, Kumar Sinniah

Summer Research

• We present a laboratory experiment in biochemistry to study the Far-UV Visible secondary structure of a protein (horseradish peroxidase, HRP) that can be adapted for a single-session laboratory experiment or a multiple-session laboratory project.
• A Circular Dichroism (CD) spectrometer provides structural information of proteins as a function of environmental changes such as pH and temperature. We present secondary structural information for the protein, horseradish peroxidase, at pH 3 and pH 7 in the temperature range 30-80° C in phosphate buffered solution (PBS).
• HRP has many applications in biochemistry and biotechnology. It is frequently used as a reporter enzyme in diagnostics …

Catalytic Enantioselective Birch–Heck Sequence For The Synthesis Of Phenanthridinone Derivatives With An All-Carbon Quaternary Stereocenter, Mary Elizabeth Sexton, William Paul Malachowski, Glenn P. A. Yap, Diana Rachii, Greg Feldman, Andrew T. Krasley, Zhilin Chen, My Anh Tran, Kalyn Wiley, Alexandra Matei, Samantha Petersen, Sabrina Tran Tien

Chemistry Faculty Research and Scholarship

Novel phenanthridinone analogues with an all-carbon quaternary stereocenter have been enantioselectively synthesized using the Birch–Heck sequence. Flat phenanthridinone structures have extensive bioactivity but consequently also suffer from poor therapeutic selectivity. The addition of a quaternary center to the phenanthridinone skeleton has the potential to generate more complex analogues with improved selectivity. Unfortunately, no general synthetic pathway to such derivatives exists. Herein we report a four-step process that transforms inexpensive benzoic acid into 22 different quaternary carbon-containing phenanthridinone analogues with a variety of substituents on all three rings: alkyl groups at the quaternary center; methyl, methoxymethyl, or para-methoxybenzyl on the …

Generation Of Nanomaterials By Reactive Laser Synthesis In Liquid, Laysa M. Frias Batista, Ashish B. Nag, Victoria K. Meader, Katharine M. Tibbetts

Chemistry Publications

Nanomaterials with tailored structures and surface chemistry are in high demand, as these materials play increasingly important roles in biology, catalysis, energy storage, and manu- facturing. Their heightened demand has attracted attention towards the development of syn- thesis routes, particularly, laser-synthesis techniques. These efforts drove the refinement of laser ablation in liquid (LAL) and related methods over the past two decades, and have led to the emergence of reactive laser-synthesis techniques that exploit these methods’ character- istic, non-equilibrium conditions. Reactive laser-synthesis approaches foster unique chemical reactions that enable the formation of composite products like multimetallic nanoparticles, supported nanostructures, and complex …

Inflammatory Response To Sleep Fragmentation In Skeletal, Cardiac, And Smooth Muscle Tissues In Female Mice, Patton Allen

Mahurin Honors College Capstone Experience/Thesis Projects

Sleep is a critical process that the body undergoes. When sleep is interrupted, so that an individual is awakened for some period before going back into sleep, the sleep can be described as fragmented. Studies in the past have shown that sleep fragmentation (SF) promotes an inflammatory environment, especially in the brain and peripheral tissue. However, studies have not been conducted to observe inflammatory responses in muscle. To examine this, C57BL/6J female mice were subjected to either a control group (no SF) or a SF group which involved using an automated SF chamber to disrupt sleep every 2 min over …

Affinity Of Cadmium Versus Zinc For The Carbonic Anhydrase Active Site, Rachel Phan

Honors Scholars Collaborative Projects

Cadmium is a heavy metal found in tobacco plants, nickel-cadmium batteries, and as a byproduct of metal mining. The similarities between the properties of zinc ions and cadmium ions in proteins due to their 2+ charges may cause displacement of zinc by cadmium if encountered and has been shown to do so in several transcription factors. Cadmium’s ability to replace zinc- a metal found in around 3,000 human proteins- is a cause for concern, especially due to its toxicity, long half-life in the body, and larger size.

Carbonic anhydrase is an important metalloprotein protein that relies on a central zinc(II) …

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 …

The Impacts Of The Molecular Education And Research Consortium In Undergraduate Computational Chemistry On The Careers Of Women In Computational Chemistry, Kelly Anderson, Sarah Arradondo, K Aurelia Ball, Chrystal D. Bruce, Maria A. Gomez, Kedan He, Heidi Hendrickson, Lindsey Madison, Ashley Ringer Mcdonald, Maria C. Nagan, Carol Parish, Caitlin E. Scott, Patricia Soto, Aime'e Tomlinson, Mychel Varner

2022 Faculty Bibliography

The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has supported a diverse group of faculty and students for over 20 years by providing computational resources as well as networking opportunities and professional support. The consortium comprises 38 faculty (42% women) at 34 different institutions, who have trained nearly 900 undergraduate students, more than two-thirds of whom identify as women and one-quarter identify as students of color. MERCURY provides a model for the support necessary for faculty to achieve professional advancement and career satisfaction. The range of experiences and expertise of the consortium members provides excellent networking opportunities …

S-Glutathionylation Of Chicken Breast Extract, Isabella Fransisco

Senior Honors Projects

The purpose of this experiment was to analyze chicken breast fractions through affinity chromatography for protein modifications by glutathione disulfide (GSSG). The fractions were incubated with different concentrations of GSSG to determine potential modified proteins. There were proteins modified with GSSG at 33 kDa in fraction I, at 16 kDa, 36 kDa, and 44kDa in fraction II, and at 36 kDa in fraction III for the concentration dependent reactions. In the time dependent reaction for fraction II, there were two major proteins at 65 kDa and 176 kDa that were modified by GSSG. Lastly, we suggest that the major modified …

Development Of Scent Detection And Categorization Algorithm Using Gas Chromatography And Machine Learning, Alex Driehaus

Mahurin Honors College Capstone Experience/Thesis Projects

There are many looking to connect human senses to quantifiable data. Scents are categorized by their descriptions into scent families. These include citrus, floral, and woody. Similar descriptors designate similar families, while different descriptors correlate with different families. Dravnieks compiled an Atlas of chemical descriptors [1]. Such descriptors are cinnamon, fruity, and cadaverous. By analyzing the applicability of these descriptors, the chemicals will be sorted into their scent families.

Gas chromatography generates sample-specific signals of voltage over time. Chromatograms of known scents will serve as a basis for a convolutional neural network. This algorithm will be trained on these signals …

Soil Project, Gabriella Hopkins

Natural Sciences Student Research Presentations

What are soil-borne diseases?

- Soil-borne diseases are diseases that can infect plants, animals, and human via soil.

- There are multiple different pathogens that contaminate soil and cause disease including bacteria, fungi, and helminths (parasitic worms). Most of these lay dormant (inactive) in the soil until they come in contact with a host.

- A host such as an animal can become infected by inhaling dormant spores or eggs in the case of helminths or by the pathogen coming in contact with an open wound. These situations are also the case for humans, but humans can also become infected …

Soil Health And The Effects Of Nanoparticles, Elijah Mock

Natural Sciences Student Research Presentations

I researched the effects of soil on human health. Specifically, I was interested in nanoparticles that reside in soil and how they affect humans as well as crops that are planted in the soil. This topic is relevant because nanoparticles can be used to deliver drugs for doctors, create specific properties for material scientists, sensors for the military, and in a plethora of other fields (“What Are Nanoparticles? Definition, Size, Uses and Properties.”).

A Kinetic Analysis Of Bleaching Synthetic Indigo In Solution, Emily Fry

[Archive] Belmont University Research Symposium (BURS)

Indigo's ability to dye a wide variety of fabric types gives it a prominent place in the textile industry. As a vat dye, indigo must be reduced to leuco-indigo to dissolve in water and dye fabric. It is common practice in the textile industry to bleach indigo-dyed denim to alter the final appearance of the garment. This research aims to determine the kinetic order of this bleaching process, using hydrogen peroxide as a bleaching agent for synthetic indigo. Vat solutions of synthetic indigo were made using fructose as the reducing agent and sodium hydroxide to create a reducing environment. Four …

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. …