Chemistry Commons^™

Elucidating The Role Of The Secondary Coordination Sphere In Tuning Reactivity Of Synthetic Heme Superoxide Complexes And Other Biologically Relevant Intermediates, Garrett B. Tolbert

All ETDs from UAB

Tryptophan catabolizing human heme-dioxyganase enzymes have been linked to a multitude of disease conditions; therefore, understanding the mechanistic details of their function is of great interest to facilitate the design of effective inhibitors for therapeutic applications. Synthetic model systems have demonstrated dioxygenation of indole moieties, elucidating key mechanistic details of the overall reaction. However, the contrastingly low reactivity of the synthetic heme-superoxide intermediates compared to those of dioxygenase enzymes necessitates the revaluation of these models with direct relevance to their biological mode of action. Herein, we report detailed mechanistic studies on the reactivity of model porphyrin systems with installed non-covalent …

Development Of Interface-Specific Two-Dimensional Vibrational-Electronic (I2d-Ve) Spectroscopy For Vibronic Couplings At Interfaces, Yuqin Qian, Zhi-Chao Huang-Fu, Jesse B. Brown, Yi Rao

Chemistry and Biochemistry Faculty Publications

Bulk 2D electronic–vibrational (2D-EV) and 2D vibrational–electronic spectroscopies (2D-VE) were previously developed to correlate the electronic and vibrational degrees of freedom simultaneously, which allow for the study of couplings between electronic and vibrational transitions in photo-chemical systems. Such bulk-dominated methods have been used to extensively study molecular systems, providing unique information such as coherence sensitivity, molecular configurations, enhanced resolution, and correlated states and their dynamics. However, the analogy of interfacial 2D spectroscopy has fallen behind. Our recent work presented interface-specific 2D-EV spectroscopy (i2D-EV). In this work, we develop interface-specific two-dimensional vibrational–electronic spectroscopy (i2D-VE). The fourth-order spectroscopy is based on a …

Development And Characterization Of Sodium Alginate-Based Active Edible Films Functionalized With Olive Mill Wastewater Extract, Nassima Hadri, Mohamed Didi Ould El-Hadj, Zineb Mahcene, Fatih Bozkurt, Rusen Metin Yildirim, Youcef Rahmani, Aicha Tedjani, Muhammet Arici

Karbala International Journal of Modern Science

Phenolic compounds from olive mill wastewater (PCO) of Algerian origin were used to produce sodium alginate-based active films using the casting method. The effects of adding various concentrations of PCO (0%, 0.1%, and 0.2% w/v) were evaluated regarding the molecular, morphological, thermal, physicochemical, optical, barrier, biodegradability, antimicrobial, and antioxidant properties of the alginate films. The FTIR and SEM results elucidated the development of a coherent cross-linked structure attributed to hydrogen bonding interactions between PCO and alginate chains. Consequently, the films exhibited enhanced crystallinity and thermal stability, as revealed by DSC analysis. Moreover, PCO addition positively influenced several film properties, including …

Analysis Of Phytochemicals In Watercress Leaves Using Chromatographic, Spectroscopic And In-Vitro Approaches, Bidisha Roy Sengupta

Faculty Publications

No abstract provided.

Biofilm-Based Biomonitoring Of Treated Wastewater Using Bacillus Thuringiensis: Toward Sustainable Water Reuse, Bidisha Roy Sengupta, Kefa K. Onchoke, Olabisi O. Ogunlewe, Robert Friedfeld

Faculty Publications

No abstract provided.

Mechanism Of Napthenic Acid Binding To Dissolved Organic Matter, Clarissa Jules

Theses and Dissertations

The oil sands in Alberta, Canada are being destroyed by oil extraction because remediation methods have proven largely ineffective. One toxic byproduct of oil extraction is a family of cyclical surfactant organic acids known as naphthenic acids (NAs). They are toxic to aquatic life, including fish, frogs, and aquatic birds. It is suspected that NAs bind to humic acid, a major organic component of soil, in dissolved organic matter in natural water, making them difficult to remove by conventional remediation methods. This problem prompts the following question: what is the binding mechanism between NAs and humic acid when dissolved in …

Protein-Metal Interactions Of A-Synuclein And Bioactive Transition Metals Via Molecular Dynamics, Gonzalo R. Vazquez

Theses and Dissertations

Parkinson’s Disease (PD) is a neurodegenerative movement disorder which has been found to target the dopaminergic neurons of the substantia nigra. It is characterized by the formation of masses known as Lewy Bodies, formed by aggregates of the intrinsically disordered protein (IDP) -synuclein (asyn). Research suggests that alpha synuclein can undergo aggregation in the presence of heavy metals, which may accumulate in the body through a variety of mechanisms. To study how metals may play a role in wildtype (WT) asyn aggregation, MD simulation of the protein was performed in the presence of bioactive transition metals including Fe2+, Fe3+, Cu+, …

Electrochemical And Conformational Patterns Of S-Glycosides And The Synthesis Of Schistosoma Mansoni Antigens, Bhavesh Rajendra Deore

Theses and Dissertations

This thesis dives into two relevant fields in carbohydrate science: reactivity and conformation. We centered our attention on S-glycosides, a common class of glycosyl donors and glycomimetics, to study the influence exerted by the structural architecture over the conformational properties about flexible bonds and the reactivity towards electrochemical activation. Studying the conformational properties of sugars is key to understanding the molecular recognition mechanisms underlying their biological functions. Moreover, a well understanding of how the molecular components affect free rotation about bonds can be valuable information to design improved glycomimetic drug candidates. On the other hand, electrosynthesis is a promising application …

Synthesis And Characterization Of Novel Coumarin Derivatives, Jeanmeil M. Nestor

Theses and Dissertations

An optimized approach toward the synthesis of representative coumarin derivatives is described. In addition to standard heat application methods, microwave-assisted coupling has proven beneficial in generating the targeted molecular hybrids which will serve as key templates in the development of new drugs to address resistance and specificity challenges. The coumarin moiety is a fantastic scaffold for molecular hybridization and has gained much warranted attention due to its efficacy in anticancer, antibacterial, and antitumor activity. In this research, novel molecular hybrids of umbelliferone were synthesized and fully characterized as new potential players in the anticancer, antitumor and antibiotic race, as well …

Adsorption And Recovery Studies Of Cadmium And Lead Ions Using Biowaste Adsorbents From Aqueous Solutions, Liang Feng

Theses and Dissertations

The use of low-cost biowaste adsorbents for the removal of toxic metal ions from aqueous solutions offers significant environmental benefits and demonstrates strong potential. This study evaluated luffa peels and chamomile flowers as low-cost biosorbents for the adsorption and recovery of Cd2+ and Pb2+ ions in both batch and column modes. To enhance adsorption capacity, the biosorbents were treated with 0.4 M HNO3 or 0.4 M NaOH. Fourier transform infrared spectroscopy (FTIR) characterization showed that surface OH, C=O, CO and COO groups played a role in the adsorption process. Batch adsorption studies indicated an order of adsorption capacity as follows: …

Developing Phenanthroimidazole-Based Fluorescent Sensors For Efficient Analyte Detection, Brian Kellogg

Masters Theses & Specialist Projects

The highly efficient design and synthesis of organic fluorophores with an excellent quantum yield have received extensive attention. Compared with instrumental techniques, fluorescent sensors derived from organic small molecules offer many impressive benefits, such as selective detection, lower cost, and higher efficiency. Various detection mechanisms such as colorimetric, ratiometric, and fluorescence turn on/off have been reported for single analyte detection. Developing molecular probes that are capable of detecting two (or more than two) different analytes (cations, anions, and/or biomolecules) had emerged as a new research area and attracted considerable attention in the field of chemo- and biosensors.

Phenanthroimidazole represents a …

Determining The Concentrations Of Trace Metals In Caffeinated Beverages By Icp-Aes, Lillian B. Gruss, James O'Donoghue, Maya Schram

Research and Creativity Symposium

A myriad of different caffeinated beverages are advertised and readily available to consumers. Previous research has identified the presence of elevated levels of metals unsafe for consumption in many of these beverages, energy drinks in particularly. We aim to analyze concentrations of chromium, aluminum, and lead, three such metals, in a variety of different caffeinated beverages. A calibration curve relating concentration of chromium, lead and aluminum to corrected peak height for five solutions of standardized concentration was created using a ThermoFisher iCAP 6000 Series. The same instrument was then used to analyze samples of eight different caffeinated beverages. The corrected …

Artificial Intelligence In Enzyme Engineering, Margret Pagare

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

Review Of Protein-Protein Interaction Prediction Using Artificial Intelligence, Brian Ng

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

Artificial Intelligence In Aptamer Design: Current Research In Machine Learning, Jennifer L. Matthews

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

Note From The Editor, Gregory Wiedman Ph.D.

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

How Ai Has Improved And Built Upon Previous Methods In Determining Protein Structures And Folding, Alexander J. Bulsiewicz

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

Biological And Chemical Evaluation Of Amide-Based Cjoc42 Derivatives As Potential Gankyrin-Inhibitors For The Treatment Of Breast, Lung, And Liver Cancer, Benita Britton-George

Theses and Dissertations

Gankyrin is an ankyrin-repeat protein overexpressed in certain cancers and is responsible for cell growth and proliferation. Gankyrin is important to the development of many types of cancer, including breast, lung, and liver cancer. Consequently, gankyrin and its various protein-protein interactions, are prospective therapeutic targets for inhibiting the progression of certain cancers. In 2016, the first small molecule inhibitor of gankyrin, cjoc42, was discovered and subsequently demonstrated modest antiproliferative activity against liver cancer cells. Previous work from our lab demonstrated that replacing the sulfonate ester of cjoc42 with an amide group significantly improved gankyrin binding while enhancing antiproliferative activity against …

Investigation Of The Binding Mechanisms Between Naphthenic Acids And Humic Acid Using Raman Spectroscopy And Computational Modeling, Jaelyn N. Palmer

Theses and Dissertations

The oil sand regions in Alberta, Canada have proven to be costly to the environment despite its economic benefits. The toxins produced during oil processing are sent to tailing ponds to be recycled, though often leaking into nearby waterways and soil. Naphthenic acids, NAs, are one of the most common toxins produced and have shown to be toxic to aquatic life, animals, and humans. As there is dissolved organic matter in tailing ponds and surrounding environments, tailing ponds often lead to NAs coming in contact with organic material. Humic acid, HA, is a major soil component that has been suspected …

Qualitative Analysis Via Network Models Of Human Dynamin-1 Throughout Gtp Hydrolysis, Kevin Brian Schulman

Theses and Dissertations

This thesis aims to elucidate the molecular mechanisms by which nucleotide binding dictates the intrinsic dynamics and to understand the functional conformational changes of Human Dynamin-1 during the GTP hydrolysis cycle through the use of Elastic Network Models (ENM). A comprehensive understanding of this process is crucial given dynamin's role in clathrin-mediated endocytosis (CME). The research utilized both experimentally derived crystal structures and AlphaFold-predicted structures of dynamin, specifically examining the GTPase and Bundle Signaling Element (BSE) domains across nucleotide-free, GTP-bound, GDP-bound, and transition states. The essential features of the research methodology involved a multi-scale computational approach. Qualitative analyses were performed …

Cold Atmospheric Plasma Induced Degradation Of Organophosphate Pesticides On Kevlar Swatches, Ta Chun Lin, Victor Somtochukwu Mbanugo, Boluwatife Stephen Ojo, Yue-Wern Huang, Marek Locmelis, Frank Daoru Han

Biological Sciences Faculty Research & Creative Works

Cold atmospheric plasma (CAP) was evaluated for degrading organophosphate pesticide (OP) residues (acephate, malathion, and dimethoate) from Kevlar fabrics. Fourier transform-Infrared (FTIR) spectroscopy, scanning electron microscope (SEM) imaging and tensile strength testing confirmed that CAP treatment preserved Kevlar's structural integrity and mechanical properties. Results show degradation efficiency increased with higher power, shorter discharge gaps, and longer exposure duration. Hyperspectral imaging supported the detection of plasma-induced spectral changes, reinforcing the presence of reactive species. The strong oxidative potential of CAP facilitated the rapid breakdown of OPs into nontoxic byproducts. These findings demonstrate the potential of CAP as a portable, energy-efficient solution …

Syntheses And Characterization Of Isomeric 3-Bromopropanol Capped Oligoviologens, Marcus Anthony White

Theses, Dissertations and Capstones

The work described in this thesis has generated new oligoviologen structures designed to facilitate the formation of supermolecules that incorporate photoactive and redox-active groups. These viologens have several potential uses; for example, the 4+ oligoviologen (viologen 5) exhibits solvatochromic properties in various polar protic and polar aprotic solvents, indicating suitability for use as a solvatochromic dye. The syntheses of bis(4,4’-bipyridine)ortho-xylene, bis(4,4’-bipyridine)meta-xylene, and bis(4,4’-bipyridine)para-xylene were demonstrated through ¹H NMR characterization and confirmed through literature. Bis(4,4’-bipyridine)ortho-xylene, bis(4,4’-bipyridine)meta-xylene, and bis(4,4’-bipyridine)para-xylene were produced in 68%, 72%, and 54% yields, respectively. 4,4’-Bipyridine-1-[4-(bromomethyl)phenylmethyl]-1’- …

Joanne Stubbe And The Mechanistic Study Of Ribonucleotide Reductases, Madysen York

Natural Sciences Student Research Presentations

To catalyze the formation of deoxyribonucleotides from ribonucleotides, the enzyme has to remove an hydroxyl from the ribose sugar part of the molecule (circled in in green) (“Ribonucleotide Reductase”).

The problem is that hydroxyl doesn’t naturally want to break from the base it is attached to, leaving many researchers unable to discern the chemical process going on inside these enzymes that make the bond break possible (Strauss).

Mary Lowe Good And The Development Of Catalytic Solutions For Industrial Processes, Eleanor Heller-Walker

Natural Sciences Student Research Presentations

To study catalysts, Good used Mössbauer spectroscopy, a nuclear technique that measures how atoms absorb and emit gamma rays (“Mössbauer Spectroscopy”). This method helps scientists identify oxidation states, chemical environments, and structural changes in metal containing materials, especially iron.

This data revealed exactly how active metal sites in catalysts behave when exposed to exhaust gases, for example, when carbon monoxide (CO) or nitrogen oxides (NOₓ) contact the surface of the metal.

Transition Metal Alkoxide Complexes Synthesis Using Thallium Reagents And Design Of Iron(Ii)-Alkoxide Carbene Complexes And Their Reactivity, Lakshani Wathsala Kulathungage

Wayne State University Dissertations

ABSTRACTTRANSITION METAL ALKOXIDE COMPLEXES SYNTHESIS USING THALLIUM REAGENTS AND DESIGN OF IRON(II)-ALKOXIDE CARBENE COMPLEXES AND THEIR REACTIVITY by LAKSHANI WATHSALA KULATHUNGAGE May 2025 Advisor: Dr. Stanislav Groysman Major: Chemistry (Inorganic) Degree: Doctor of Philosophy

This dissertation focuses on the synthesis and reactivity of transition metal and main group metal alkoxide complexes. The dissertation began with exploring a novel, efficient synthetic route towards transition metal alkoxides involving thallium reagents. A novel dimeric Tl2(OCtBu2Ph)2 complex was synthesized in the reaction between a lithium alkoxide and thallium precursor TlPF6. Tl2(OCtBu2Ph)2 served as a convenient precursor to the formation of old and new transition …

Structural Impacts Of Canonical And Non-Canonical Oligonucleotide Modifications, Deepak Shrestha

Wayne State University Dissertations

Nucleic acids, including DNA (deoxyribonucleic acid) and RNA (ribonucleic acids), are the fundamental building blocks of living organisms. The events that cause modification of DNA/RNA are of interest because they impact the nucleic acid function. Targeting DNA is important for treating diseases such as cancer. Cisplatin (cisPt) is a well-studied drug that targets DNA and blocks replication, but its use is limited by adverse side effects and cellular resistance. Prevoius research addressed some of these challenges through development of platinum analogues such as carboplatin and oxaliplatin. Amino acid-linked platinum analogues (AAPt) are the focus of this thesis work. AAPt complexes …

Mass Spectrometry Combined With Chemical Biology To Study Human Ailments, Eric Thomas Jacquerio Davis

Wayne State University Dissertations

Post-translational modifications (PTMs) are essential as chemical changes that regulate protein function, activity, stability, interactions, and localization after protein synthesis. PTMs, such as phosphorylation, acetylation, and ubiquitination, can activate or deactivate proteins, influence their interactions with other molecules, and determine their cellular location. This regulation is vital for numerous biological processes, such as cell cycle control, signal transduction, and gene expression. Abnormal PTMs are linked to various diseases in humans, including parasitic infection, blood disorders, cancers, and neurodegenerative diseases, making their study crucial for understanding disease mechanisms and developing targeted therapies. In the Pflum lab, we are interested in the …

Identifying The Constituents Of Pyrolysis Oil Using Supercritical Fluid Chromatography- Fraction Collection (Sfc-Fc) And Gas Chromatography- Mass Spectrometry/Vacuum Ultraviolet Spectroscopy (Gc-Ms/Vuv), Sadid Morshed

2025 Fall Honors Capstones Projects - Archive

Plastic waste continues to accumulate as production increases and disposal methods remain insufficient. Even with recycling programs in place, much of the discarded plastic still ends up in landfills or waterways, eventually breaking down into harmful microplastics. One promising solution is the conversion of plastic waste into pyrolysis oil, which can also serve as an alternative feedstock for chemicals. Pyrolysis oil is produced by heating plastics to approximately 800 °C in the absence of oxygen, resulting in a complex mixture of hydrocarbons that includes paraffins, isoparaffins, olefins, naphthenes, and aromatics. Analyzing the amount of oxygen, nitrogen, and sulfur in these …

Direct Partial Oxidation Of Methane To Methanol Using Dioxygen Over Superhydrophobic Modified Catalysts, Oluchukwu V. Igboenyesi

Chemistry & Biochemistry Dissertations - Archive

Various methods for enhancing catalysts activity and productivity in gas to liquid synthesis like Direct Methane to Methanol Conversion and Fischer Tropsch Synthesis have been studied over the years. Some of these methods include the use of promoters, bifunctional catalysts, introducing steam, optimizing reaction conditions and catalyst modification. The choice of catalysts and their modification plays a critical role in improving the overall productivity in gas to liquid synthesis.

This research explored the superhydrophobic modification of heterogenous catalysts used in Direct Methane to Methanol Conversion (DMTM) and Fischer Tropsch Synthesis (FTS). The catalysts were modified with Perfluoro alkyls (PFSMA). The …

Copper-Based Oxide Semiconductors: Transparent Conductors And Ternary Alloys, Abhishek Rawat

Chemistry & Biochemistry Dissertations - Archive

This dissertation explores the strategic design and development of copper-based metal oxide semiconductors for photoelectrochemical (PEC) and optoelectronic applications, with a focus on advancing materials for sustainable energy technologies. Through a comprehensive investigation into copper vanadates and copper oxides, the work aims to understand and enhance charge transport, light-harvesting capabilities, and electronic structure modulation. The research integrates fundamental materials chemistry with applied photoelectrochemical studies to uncover the role of copper's d-electrons in mid-gap state formation, multifunctionality through electronic structure tuning, and the development of low-temperature transparent conductive oxides.

In chapter 2, we have discussed the attributes of copper metavanadate (CuV …