Chemistry Commons^™

Avidin Cooperative Allosterism Upon Binding Biotin Observed By Differential Changes In Intrinsic Fluorescence, Mark J. Waner, Gianna Ellis, Meghan Graeca, Nicholas Ieraci, Cole Morell, Alycia Murphy, David P. Mascotti

2023 Faculty Bibliography

Similar to streptavidin, the binding of biotin by avidin does not appear to be cooperative in the traditional sense of altered binding strength, though it appears to be cooperative in terms of ligand induced structural communication across subunits in the protein as previously shown for streptavidin. In this work we provide data from intrinsic tryptophan fluorescence as evidence of a cooperative structural change. The technique involves examination of the changes in fluorescence emission corresponding to the various tryptophan populations accompanying avidin-biotin binding. We note that the 335 nm emission population (i.e. more hydrophobic local environment) saturates prior to full ligation …

Determined Mechanism For The Formation Of 2-Bromo-3-Methylbutane, Gabriele Cross

Senior Honors Projects

Carbocation rearrangements are particularly interesting mechanistic steps in organic reactions. Carbocations form when a carbon atom within a molecule is electron deficient, giving it a positive charge. A rearrangement occurs when either a hydrogen atom or methyl group from an adjacent carbon atom in the molecule moves to the carbocation, thus moving the carbocation to the adjacent carbon. This rearrangement only occurs if the newly formed carbocation is more stable than the previous carbocation. These concepts are typically taught in organic chemistry courses. Researchers from Villanova University, the University of Wisconsin-River Falls, and Bethel University designed an experiment to help …

Novel Application Of Graphene Oxide In Conjunction With Dna Binding Dcas9 For Detecting Antibiotic Resistance Genes, Langley Williams

Mahurin Honors College Capstone Experience/Thesis Projects

The frequent emergence of antibiotic resistance genes poses a stumbling block to prompt treatment of pathogen-originating diseases and therefore spurs the demand for a simple, rapid diagnostic device that can outcompete the time and cost of traditional methods such as PCR and cell culturing. The proposed method for detecting pathogenic DNA utilizes the binding properties of deactivated CRISPR-associated protein9 (dCas9) complexed with fluorescein-labeled single-guide RNA (sgRNA) and the fluorescence quenching properties previously demonstrated in graphene oxide (GO). For our assay, we designed sgRNAs to target specific 20 nucleotide sequences extracted from the tetracycline resistance (tetM) gene sequence and covalently modified …

Synthesis Of Cysteine-Tyrosine Crosslinks In Β-Hairpin Peptide Models, C.D. Tatko, David Benson, Sophie A. Hruska

Summer Research

The Cysteine-Tyrosine crosslink (Cys-Tyr) is - A unique Post-Translational Modification - Redox-active - Found in a handful of proteins, including Cysteine Deoxygenase (CDO), whose malfunction has been linked to Alzheimer’s Disease

In Vitro Corrosion And Biocompatibility Behavior Of Cocrmo Alloy Manufactured By Laser Powder Bed Fusion Parallel And Perpendicular To The Build Direction, Masoud Atapour, Saber Sanaei, Zheng Wei, Mohammadali Sheikholeslam, Jeffrey D. Henderson, Ubong Eduok, Yara K. Hosein, David W. Holdsworth, Yolanda S. Hedberg, Hamid Reza Ghorbani

Chemistry Publications

Biomedical cobalt-chromium-molybdenum alloys (CoCrMo) are frequently used for orthopedic implant and dental materials exposed to mechanical stressors, such as wear and cyclic load. Due to the high demand for customizable implant shapes, these alloys are increasingly manufactured by additive manufacturing methods such as laser powder bed fusion (LPBF). LPBF results in different microstructures and surface roughness as a function of the building direction. This study investigated the corrosion resistance, bioactivity, biocompatibility, and microstructure of LPBF CoCrMo (low carbon content, heat-treated) in the XY (perpendicular) and XZ (parallel) plane of the building direction for as-printed (as-received) and abraded surfaces. A distinct …

Chemistry And Public Policy: Equipping Advocates, Herbert R. Fynewever, I. Bos, C. Demlow, G. Fulkerson

Summer Research

No abstract provided.

Progress In 7sk Ribonucleoprotein Structural Biology, Momodou B. Camara, Amr M. Sobeh, Catherine D. Eichhorn

Department of Chemistry: Faculty Publications

The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the noncoding 7SK RNA, core proteins, and numerous accessory proteins, the most wellknown 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK …

Synthesis Of A Novel Terbium(Iii) Complex For Application In Metal Nanoparticle Surface Modification, Lauralee E. Hurst, Davon Ferrara, Justin Stace

Science University Research Symposium (SURS)

Lanthanide ions, such as terbium(III), exhibit bright luminescence when bound to organic ligands which strongly absorb light. This property has been used in creating chemical sensors or luminescent tags for microscopy. Complexes centered with terbium(III) exhibit a yellow-green luminescence upon excitation by shortwave ultraviolet light. In this work, a bifunctional ligand, 4-mercaptobenzoic acid (4mba), was chosen to selectively coordinate terbium(III) to the oxygens of the acid functional group, leaving the thiol group available for another compound. Thiol groups are effectively used in surface coordination to noble metal nanoparticles (NP). In efforts to create a novel 4mba-terbium(III)-NP system, a one pot …

Facile Synthesis And Characterization Of Multi-Walled Carbon Nanotubes Decorated With Hydroxyapatite From Cattle Horns For Adsorptive Removal Of Fluoride, Walter Ojok, James P. Bolender, John Wasswa, Emmanuel Ntambi, William Wanasolo, Brenda Moodley

Chemistry and Biochemistry: Faculty Scholarship

Developing a new adsorbent for fluoride removal from cattle horn waste materials by a facile chemical method has shown great potential for fluoride removal. This paper reports the synthesis of multi-walled carbon nanotubes decorated with hydroxyapatite from cattle horns (MWCNT-CH) using a facile chemical method. Characterization studies using standard techniques showed that the composite is mesoporous with a rough morphology and contained MWCNTs uniformly encapsulated by the hydroxyapatite forming a crystalline MWCNT-CH composite. Optimization of fluoride adsorption by the as-synthesized composite using Response Surface Methodology (RSM) showed that a maximum fluoride removal efficiency of 80.21% can be attained at initial …

Exploration Of Electron Dynamics In A Strong Field By Time Dependent Configuration Interaction With A Complex Absorbing Potential, Paul Hoerner

Wayne State University Dissertations

Strong field electron dynamics are a quickly developing field of study in physical chemistry. In order to better understand experimental observations, there is a need for computational tools to simulate electron dynamics in a strong field. Due to the nature of strong electric fields, this requires the solving of the time dependent Schrödinger equation (TDSE). Various methods have been used to solve the TDSE in a strong field. In order to look at molecular systems while accurately treating the underlying physics, a method that balances computational affordability with theoretical rigor is necessary. The chosen method that matches these criteria is …

Modulating Photochemical Properties To Enhance The Stability Of Electronically Dimmable Eye Protection Devices, Sruthy Baburaj, Jayachandran Parthiban, Sarvar Aminovich Rakhimov, Rasheedah Johnson, Ludmila Sukhomlinova, Paul Luchette, Steffen Jockusch, Malcolm D. E. Forbes, Jayaraman Sivaguru

Chemistry Faculty Publications

The study evaluates compatibility of stabilizers with dye doped liquid crystal (LC) scaffolds that are used in electronically dimmable materials. The photodegradation of the materials was investigated and suitable stabilizers were evaluated to slow the degradation process. Various types of benzotriazole-based stabilizers were evaluated for stabilizing the liquid crystals. Based on spin trapping experiments, radicals generated upon UV exposure is likely responsible for the degradation of the system. The radical generation is competitively inhibited by the addition of stabilizers.

Abbreviations: LC, liquid crystal; STB, stabilizers.

Alternating Current Electrolysis For Amine Functionalization And Hydrogen Isotope Exchange, Disni Gunasekera

Wayne State University Dissertations

Electrochemical organic synthesis is experiencing a renaissance driven by the increasing demand for green chemistry and engineering in the pharmaceutical industry. Synthetic organic electrochemical methods can be divided into three types: anodic, cathodic, and paired electrolysis. Paired electrolysis, in which two desirable half-reactions are performedsimultaneously at the two electrodes, is mostly underdeveloped. However, paired electrolysis can be technologically significant because it not only improves energy efficiency by using both electrodes but also provides a unique reaction environment where two redox-opposite reactions of substrates take place in the same pot. A major challenge for paired electrolysis is that the difficulties associated …

Synthesis Of Putative Microcystin-Lr Degradation Products And Full Macrocyclic Cyanopeptide, Mahesh Kumar Yadab

Wayne State University Dissertations

This thesis primarily focuses on synthesizing fragments of microcystin-LR, which is a natural product, with the aim of establishing them as analytical standards for investigating the biodegradation pathways of MC-LR. Despite of the substantial interest in synthesizing, isolating, and degrading Microcystins over the past few decades, the availability of high-purity microcystin standards at known concentration for quantitative analysis of using LC-MS/MS remains limited. The synthesis of the proposed MC-LR fragments employs the Fmoc/t-Bu protecting group strategy to prevent isomerization. Additionally, novel methods for the total synthesis of N-Boc-Adda are explored, incorporating atom-economic approaches, cross-metathesis, and oxidative boron Heck reactions. The …

Inkjet Printing Of Sers-Based Inks For Covert Anti-Counterfeiting Labels, Erin E. Schnetzer

Dissertations and Theses

Millions of counterfeit products are produced every year, which negatively impacts the global economy, public health, and human safety. Current anti-counterfeiting methods include holograms, watermarks, microprinting, and QR codes. QR codes are a two-dimensional version of a barcode, thus they can store more information. Different types of inks such as thermochromic ink and invisible UV ink are widely used in making anti-counterfeiting labels. Most of these inks have specific changes in optical properties with external stimulations, and these changes are usually associated with broad bands in the visible region. Such broad bands result in a low information capacity that can …

High Order Structures Formed By The Natural Aromatic Amino Acids, Gabriel Alexander Kupovics, Zeina Alraawi

Inquiry: The University of Arkansas Undergraduate Research Journal

Excessive concentrations of the natural aromatic amino acids phenylalanine and tyrosine are characteristic of the severe genetic abnormalities known as phenylketonuria (PKU) and tyrosinemia, respectively. Within this context, this feature article authenticates claims that tryptophan can form amyloid-like supramolecular structures in vitro and is the first to propose potential mechanisms of tryptophan self-assembly, including hydrophobic and electrostatic interactions. Thioflavin T (ThT) fluorescence kinetics and transmission electron microscopy (TEM) data suggest the formation of amyloid-like fibrillar structures by natural aromatic amino acids in vitro. Additionally, the propensity of amino acid aggregation increases in the presence of sodium dodecyl sulfate (SDS). The …

Evaluating The Effect Of Resveratrol On Sirt1 With Different Peptide Substrates, Yujin Hur

Master's Theses

SIRT1 is an NAD+-dependent lysine deacetylase that is involved in many important cellular pathways. The protein has an extended N-terminal domain that seems to play a role in regulating its activity. Sirtuin Activating Compounds (STACs) are allosteric activators, such as resveratrol, that regulate the activity of SIRT1. STACs bind to the N-terminal STAC Binding Domain (SBD) in SIRT1. Past literature has found that SIRT1 activity can be increased, decreased, or remain unchanged by resveratrol depending on the identity of the peptide substrate. The goal of this study is to clarify the mechanism for substrate-specific allosteric regulation by resveratrol. The interactions …

Selective Melt Recrystallization Of Acetaminophen Polymorphs Through Environmental Control, Eleanor Lowe

Honors Theses

Polymorphism is the ability for a molecule to crystallize into multiple different structures in the solid state. The preparation of one polymorph over another is practically important to pharmaceutical development, as properties of polymorphs can vary and impact the drug delivery method. Polymorph outcomes depend heavily on the environment in which the crystal is nucleated, or initially formed. Acetaminophen, the active ingredient in Tylenol, is one example of a polymorphic compound. Here we use acetaminophen as a model system to better understand primary factors controlling polymorph selection and interconversion. We hypothesize a specific atmospheric environmental factor plays large role in …

Dynamic Luminescence Of Lead Doped Calcium Zinc Germanate For Anti-Counterfeiting, Levi Spencer

Dissertations and Theses

As counterfeited goods appear in the consumer market through various trade routes, unsuspecting buyers are left with products that are potentially dangerous and in poor quality. Products intended for the automotive and aerospace industry are often counterfeited due to their easy market accessibility. Once these products make their way into the supply chain, it leaves the end users with a significant risk due to voided warranties and inferior product quality and design. Therefore, advanced anti-counterfeiting measures need to be developed to assure the products are genuine, as well as allow the end users to authenticate the product. Luminescent materials have …

Instrumental Approaches For High Resolution Photoluminescence Spectroscopy And Its Applications To Environmental Analysis, Anthony Santana

Electronic Theses and Dissertations, 2020-2023

Photoluminescence phenomena provide valuable information for the direct analysis of target chemicals in complex samples. To take full advantage of the information content of fluorescence and phosphorescence phenomena, the analyst should have access to instrumentation capable to record data formats in the wavelength and time domains. Previous efforts in our lab have developed laser-based instrumentation to combine spectral and lifetime information into data formats known as wavelength time matrices (WTMs) and time-resolved excitation emission matrices (TREEMs). Recording WTMs during the emission decay of the sample makes it possible to unambiguously identify chemicals on the bases of spectral and lifetime information. …

Chemical Approach To Tire Mark Analysis, John Lucchi

Graduate Thesis and Dissertation 2023-2024

Fatal accidents on the road are an unfortunate daily occurrence, with almost 30,000 deaths resulting from hit-and-runs in the USA between 2006 and 2021. The identification of the driver responsible for this road crime can become a challenge. Nonetheless, the accident scene provides a large amount of trace evidence that can prove critical to this matter, one of them being the tire marks. While traditional tire mark analysis is full of physical information helping the reconstruction of the event, additional information can be extracted from the rubber left during the braking event. Each tire model is manufactured with a specific …

Error Rate Determination Of Latent Print Chemistry Via 1d And 2d Gas Chromatography, Jessica Kindell

Electronic Theses and Dissertations, 2020-2023

Latent print evidence collected from crime scenes are analyzed and compared by examiners using the ACE-V protocol (Analysis, Comparison, Evaluation-Verification) to identify potential suspects. However, smudged and poor-quality prints, usually deemed inconclusive, could be utilized for source association or discrimination based on the chemistry of the oils and sweat that comprises the latent print residue (LPR). For this research, LPRs were collected from various places on the face and analyzed via two-dimensional gas chromatography-mass spectrometry (2D GC-MS), one-dimensional (1D) GC-MS, and direct analysis in real time-high resolution mass spectrometry (DART-HRMS). LPR recovery with two common sample preparation methods, derivatization and …

Lanthanide-Based Responsive Contrast Agents For Magnetic Resonance Imaging, Md Mamunur Rashid

Wayne State University Dissertations

This thesis is a collection of seven chapters that discuss the contributions to the field oflanthanide-based contrast agents for magnetic resonance imaging (MRI), particularly in the context of imaging hypoxia and extracellular pH. These physiological changes play a significant role in life-threatening conditions such as cancer, making it essential to develop effective imaging tools to aid in diagnosis and treatment. The thesis provides insights for the rational development of lanthanide-based contrast agents for MRI. A comprehensive review of divalent europium as a tool for imaging hypoxia using magnetic resonance imaging and how coordination chemistry can be used to tune the …

The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers

Robert Powers Publications

DJ-1 is a homodimeric protein that is centrally involved in various human diseases including Parkinson disease (PD). DJ-1 protects against oxidative damage and mitochondrial dysfunction through a homeostatic control of reactive oxygen species (ROS). DJ-1 pathology results from a loss of function, where ROS readily oxidizes a highly conserved and functionally essential cysteine (C106). The over-oxidation of DJ-1 C106 leads to a dynamically destabilized and biologically inactivated protein. An analysis of the structural stability of DJ-1 as a function of oxidative state and temperature may provide further insights into the role the protein plays in PD progression. NMR spectroscopy, circular …

Investigation Of Oleic Acid As A Dispersant For Hydroxyapatite Powders For Use In Ceramic Filled Photo-Curable Resins For Stereolithography, Brendan Kennedy, Eamonn De Barra, Stuart Hampshire, Maura Kelleher

Articles

Stereolithography allows production of porous hydroxyapatite scaffolds for bone regeneration but is limited by the challenging rheology of ceramic filled resins. Oleic acid, a natural fatty acid, was applied in concentrations of 0.0–0.3 wt% to improve the rheological properties of HAp resins for the fabrication of solid cylinders and scaffolds by digital light processing (DLP) printing in a wiperless system. Bonding by chemisorption was confirmed by FTIR analysis. The powders were then incorporated into a photo-curable resin of 1–6 hexanediol diacrylate at 18–30 vol%. The shear viscosity and sedimentation rates of photocurable resins containing HAp powder decreased with increasing concentration …

Synthesis And Reactivity Of Xanthene-Based Heterobimetallic Systems For Co Oxidation, Umesh Kaluarachchige Don

Wayne State University Dissertations

Nature provides a useful guideline for the design of an efficient earth-abundant catalyst for CO oxidation that relies on bimodal heterobimetallic cooperativity. Molybdenum-copper carbon monoxide dehydrogenase (Mo-Cu CODH) is an enzyme of the xanthine oxidoreductase family that catalyzes reversible oxidation of CO; it is inhibited by cyanide CN- and inserts isocyanide CNR between Cu and O/S. The active site contains molybdenum(VI) in a square pyramidal configuration with apical oxo and basal dithiolene, oxo, and sulfide ligands. The two-coordinate Cu(I) is coordinated by cysteinate and Mo-sulfide to form Mo-S-Cu bridge.While several groups have reported structural models of the active site of …

Surface-Engineered Mineral Particles For Gated Drug Delivery, Gene Transfer And Sunscreen Formulations, Mahadi Hasan

Dissertations and Theses

Surface-engineered nanomaterials have recently garnered wide attention for their huge biomedical applications. The surface functionalization of nanoparticles by desired chemical groups and coatings imparts unique properties to be used in therapeutic applications. Herein, we reported the biological and biomedical applications of three mineral particles: calcium carbonate nanoparticles, hydroxyapatite nanoparticles and mesoporous silica nanoparticles. The ability of pristine and surface-modified calcium carbonate particles to scatter UV-light significantly depends on the particle’s size, its surface chemical composition, and can be close to the SPF values of commercial sunscreens. These nontoxic particles are a promising component of biocompatible sunscreens free of the traditional …

Neutral And Charged Bis(Triarylamines) For Use In Grid Scale Battery Technologies, Taylor Matthews

Online Theses and Dissertations

Energy storage systems allow flexibility in control and maintenance of the electric grid while integrating renewable energy resources to mitigate carbon emissions. Redox flow batteries (RFBs) are stationary energy storage systems that convert chemical energy to electrical energy by charge-transfer reactions. Designing molecules that are capable of stable multi-electron redox reactions per active-species molecule can increase the efficiency of future systems. Spectroelectrochemistry, the combination of spectroscopy and electrochemistry, allows for quantitative and qualitative analyses of electron-transfer processes. The focus of this research is to use optical and electrochemical properties obtained from spectroelectrochemistry to determine the stability of neutral and charge …

Green And Non-Green Extraction Of Eugenol From Cloves Using Steam Distillation, Bek Yuldashbaev

Science University Research Symposium (SURS)

Eugenol is commonly found in many plants such as cloves. It is one of the most used natural anesthetics in dentistry. Indonesia is one of the places indigenous to clove trees. Its people take advantage of the pain numbing properties in cloves to aid their tooth pain. The extraction of eugenol itself can be performed through steam distillation. With the process of distillation, the steam carries the oils extracted from the clove buds and recondenses into a cloudy distillate containing polar and non-polar molecules. To separate the eugenol from the distillate, green and non-green solvents were used. The green solvent …

Identification Of Rickettsia Prowazekii Methionine Aminopeptidase Inhibitors And Development Of Thermal Shift Assays For Burkholderia Pseudomallei Ispf And Sars-Cov-2 3cl Protease, Ishpriya Sharma

Graduate Research Theses & Dissertations

There is a crucial need for new antibacterial agents to combat the increase in antibiotic resistance. Methionine aminopeptidase (MetAp) is an enzyme that removes the amino-terminal methionine residue from newly synthesized proteins, an important step in the maturation of proteins. As such, MetAp is a target for the development of antibacterial and anticancer agents. One such bacterial target is Rickettsia prowazekii (Rp), the causative agent of epidemic typhus. To discover new inhibitors of RpMetAp1, the MMV Malaria Box, which is a collection of 400 compounds with drug-like and probe-like compounds, was screened using a high throughput fluorescence-based RpMetAp1 enzyme inhibition …

Homopurine Guanine-Rich Sequences In Complex With N-Methyl Mesoporphyrin Ix Form Parallel G-Quadruplex Dimers And Display A Unique Symmetry Tetrad, Ming Ye , '23, Erin V. Chen , '23, S. H. Pfeil, Kailey N. Martin, Tamanaa Atrafi , '23, Sara Yun , '23, Zahara Martinez , '23, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

DNA can fold into G-quadruplexes (GQs), non-canonical secondary structures formed by π-π stacking of G-tetrads. GQs are important in many biological processes, which makes them promising therapeutic targets. We identified a 42-nucleotide long, purine-only G-rich sequence from human genome, which contains eight G-stretches connected by A and AAAA loops. We divided this sequence into five unique segments, four guanine stretches each, named GA1-5. In order to investigate the role of adenines in GQ structure formation, we performed biophysical and X-ray crystallographic studies of GA1-5 and their complexes with a highly selective GQ ligand, N-methyl mesoporphyrin IX (NMM). Our data indicate …