Chemistry Commons^™

Representing Quantum Spins In Different Coordinate Systems For Modelling Rigid Body Orientation, Nadjet Zioui, Aicha Mahmoudi, Mohamed Tadjine

Karbala International Journal of Modern Science

Various methods for representing the spatial orientation and rotation of objects are presented and compared with the quantum bit state representation. By contrasting spherical, Euler angle, quaternion, and quantum spin coordinate systems, this work highlights important concepts regarding the rotation axis of the X gate. Several ambiguities and incomplete definitions associated with the qubit state representation are discussed, such as the spin around the qubit itself and the explanation of the considered rotation angles and signs. A mathematical analysis of the physical meaning of each eigenstate is provided along with a new comprehensive and meaningful YPR-based 3D representation of a …

Quercetin As An Anticancer Candidate For Glioblastoma Multiforme By Targeting Akt1, Mmp9, Abcb1, And Vegfa: An In Silico Study, Muhammad Hermawan Widyananda, Setyaki Kevin Pratama, Arif Nur Muhammad Ansori, Yulanda Antonius, Viol Dhea Kharisma, Ahmad Affan Ali Murtadlo, Vikash Jakhmola, Maksim Rebezov, Mars Khayrullin, Marina Derkho, Emdad Ullah, Raden Joko Kuncoroningrat Susilo, Suhailah Hayaza, Alexander Patera Nugraha, Annise Proboningrat, Amaq Fadholly, Mada Triandala Sibero, Rahadian Zainul

Karbala International Journal of Modern Science

Quercetin, a natural compound present in various fruits and vegetables, shows promise as a potential inhibitor for glioblastoma multiforme (GBM) development. This study aims to examine the anti-GBM potential of Quercetin. The protein target of Quercetin is identified and analyzed using databases such as NCBI, SEA, CTD, and STRING. Protein-protein interaction (PPI) and functional annotation are carried out based on the obtained target proteins. Molecular docking and dynamics simulations are employed using AutoDock Vina and WebGro tools to analyze the interaction between Quercetin and its target proteins. The prediction of protein targets reveals that Quercetin directly targets four proteins associated …

Improving The Burt’S Sensitivity Using Noise Calibration Unit Via Crab Nebula Observations, Uday E. Jallod, Lana T. Ali, Hareth S. Mahdi, Kamal M. Abood

Karbala International Journal of Modern Science

Radio observations from astronomical sources like supernovae became one the most important sources of information about the physical properties of those objects. However, such radio observations are affected by various types of noise such as those from sky, background, receiver, and the system itself. Therefore, it is essential to eliminate or reduce these undesired noise from the signals in order to ensure accurate measurements and analysis of radio observations. One of the most commonly used methods for reducing the noise is to use a noise calibrator. In this study, the 3-m Baghdad University Radio Telescope (BURT) has been used to …

Bioinformatic Analysis Of The Interaction Of Evc And Evc2 Proteins, Md Atikul Islam Mamun

Electronic Theses and Dissertations

Protein to protein interactions are significant to various biological processes, functioning, and the regulation of cells and organisms. Proteins perform essential cellular tasks and often work together in complexes, enabling specific functions like enzymatic activity, signal transduction, DNA replication, and cell division. These interactions are important in signaling pathways, allowing proteins to interact sequentially, leading to specific cellular responses. Some proteins rely on chaperones to fold correctly, and protein to protein interactions enhance stability, preventing degradation.

Researchers at Stanford University School of Medicine discovered that EvC syndrome is related to a malfunction in the Hedgehog (Hh) signaling pathway. They found …

[3+2]-Cycloadditions Of Tertiary Amine N-Oxides And Dipolarophiles Providing An Efficient Route To Heterocyclics And 1,2-Diamines, And Nickel Catalayzed Transformations, Sarah Hejnosz

Electronic Theses and Dissertations

Nitrogen containing compounds are ubiquitous in nature as well as pharmaceuticals. These structures exhibit rich bioactive and chemical properties boasting an array of practical applications. As a result, the synthetic methods of forming nitrogen containing compounds are highly sought after. More efficient syntheses of these structures could result in less expensive industrial processes, particularly in the pharmaceutical industry. Roussi and coworkers established a highly efficient synthetic route forming nitrogen containing heterocycles in a single step from commercially available reagents, however this chemistry has not be used since its discovery in the 1980. Herein, this work greatly expanded Roussi’s method and …

Investigating The Impact On Private Water Supply Of Hydraulic Fracturing Communication With An Abandoned Conventional Gas Well In New Freeport, Pa, Kiley Miller

Electronic Theses and Dissertations

In June of 2022 a “frac out” occurred in New Freeport, PA when an unconventional gas well under development by hydraulic fracturing, communicated with an abandoned gas well to the surface. An initial “zone of impact” encompassed much of the town’s main thoroughfare. Water samples were obtained from 17 private water wells, 5 springs and 1 pond (31 total samples) and analyzed for cations, anions, and light hydrocarbons. Methane was found in 18 of the samples, both located within and outside of the “zone of impact”. Mass ratio analyses indicated contamination from both unconventional and conventional wells. Interferometric Synthetic Aperture …

Design Of Stormwater Bmps For Surface And Groundwater Protection Based On Site-Scale Soil Properties: Phase I, Kelly Kibler, Lisa Chambers, Melanie Beazley

Florida DOT

Much of Earth’s nutrient cycling takes place in soils. Characteristics of soils control physical, chemical, and biological processes that determine rates of nutrient fluxes, storage, or transformation. As remediation of excess nutrients in stormwater runoff is one function of stormwater Best Management Practices (BMPs), the soil profile constitutes one of the most important factors of BMP design. Variation observed in BMP effectiveness (e.g., why one BMP design works effectively in one place and not another) can often be explained by variations in the soil profile, either through direct means or by a soil’s influence on hydraulics of stormwater flow through …

Developing Strategies For The Integration Of Metal–Organic Frameworks (Mofs) Into E-Textiles For Chemical Sensing, Filtration, And Detoxification, Aileen Mary Eagleton

Dartmouth College Ph.D Dissertations

Metal-organic frameworks (MOFs) are crystalline porous materials that offer modularity through diverse combinations of metal nodes and linkers, as well as tailorable surface chemistry and structure, along with tunable conductivity. The integration of these framework materials onto fibers can result in robust and flexible MOF-based textiles with enhanced functionality and applicability. This thesis illustrates the versatility of multifunctional MOF-integrated textile systems, showcasing their unique properties and the advantages of installing MOFs at the fiber level.

Probing Conformational Landscapes Of Binding And Allostery In The Sars-Cov-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations And Perturbation-Based Profiling Approaches: Hidden Role Of Omicron Mutations As Modulators Of Allosteric Signaling And Epistatic Relationships, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 spike protein complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which can be contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using the dynamics-based mutational scanning of spike residues, we identified structural stability and binding affinity hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational …

Dinitroxides In Rapid Scan Electron Paramagnetic Resonance Imaging, Lukas B. Woodcock

Electronic Theses and Dissertations

Local tissue physiology is an important parameter in understanding disease behavior. Rapid Scan (RS) electron paramagnetic resonance (EPR) offers a unique, non-invasive tool for investigation of these so-called microenvironments through EPR Imaging (EPRI). Research into advancement of EPRI falls into many categories. Not least among those are advances in instrumentation and methodology. Presented here are updates to a benchtop EPRI instrument operating at 1 GHz targeted at pre-clinical EPRI applications. Newly developed methods for reducing RS-EPR background through inversion of the magnetic field are also demonstrated. EPR applications are limited in native biological systems due to the miniscule concentration of …

Towards Deposition Of Iron & Nickel Onto Cadmium Selenide/Cadmium Sulfide Nanorods, Rajib Nath

Masters Theses & Specialist Projects

Metal-semiconductor hybrids have been studied extensively as photocatalysts for the watersplitting reaction to generate hydrogen gas and oxygen gas to use as a renewable energy source. The semiconductor component converts light into electrochemical energy, while the metal component provides a site for chemical reactions with water. Here, the choice of metal can have a significant impact on the efficiency of the catalyst. Platinum efficiently catalyzes the watersplitting reaction and is therefore commonly used in metal-semiconductor hybrids to generate hydrogen. Platinum is very expensive, which motivates research into improving less costly metals like iron or nickel that do not have nearly …

Activation Of The Renin–Angiotensin–Aldosterone System Is Attenuated In Hypertensive Compared With Normotensive Pregnancy, Robin C. Shoemaker, Marko Poglitsch, Hong Huang, Katherine Vignes, Aarthi Srinivasan, Cynthia Cockerham-Morris, Aric Schadler, John Anthony Bauer, John O'Brien

UK CARES Faculty Publications

Hypertension during pregnancy increases the risk of adverse maternal and fetal outcomes, but the mechanisms of pregnancy hypertension are not precisely understood. Elevated plasma renin activity and aldosterone concentrations play an important role in the normal physiologic adaptation to pregnancy. These effectors are reduced in patients with pregnancy hypertension, creating an opportunity to define the features of the renin–angiotensin–aldosterone system (RAAS) that are characteristic of this disorder. In the current study, we used a novel LC-MS/MS-based methodology to develop comprehensive profiles of RAAS peptides and effectors over gestation in a cohort of 74 pregnant women followed prospectively for the development …

On The Chemistry Of Aqueous Ammonium Acetate Droplets During Native Electrospray Ionization Mass Spectrometry, Lars Konermann, Zeyuan Liu, Yousef Haidar, Methew J. Willians, Nicholas A. Bainbridge

Chemistry Publications

Ammonium acetate (NH₄Ac) is a widely used solvent additive in native electrospray ionization (ESI) mass spectrometry. NH₄Ac can undergo proton transfer to form ammonia and acetic acid (NH₄⁺ + Ac^- → NH₃ + HAc). The volatility of these products ensures that electrosprayed ions are free of undesired adducts. NH₄Ac dissolution in water yields pH 7, providing “physiological” conditions. However, NH₄Ac is not a buffer at pH 7 because NH₄⁺ and Ac^- are not a conjugate acid/base pair (L. Konermann, J. Am. Soc. Mass Spectrom. 2017 …

Site-Specific Glyco-Engineering Of Recombinant Thrombomodulin, Joseph M. Keil

ETD Archive

Thrombomodulin (TM), a membrane glycoprotein predominately expressed on endothelium, plays essential roles in regulating local hemostatic balance. Particularly, TM modulates the activity of thrombin from a procoagulant to an anticoagulant protease. When bound to TM, thrombin activates plasma protein C, which selectively inactivates coagulation factors Va and VIIIa. At the same time, TM-bound thrombin is unable to cleave fibrinogen or to activate platelets diminishing its procoagulant activity. recombinant TM456 is a promising anticoagulant candidate, but it has a very short half-life. TM is a proteoglycan and its O-linked glycosaminoglycan (GAG), chondroitin sulfate (CS), on the D3 domain contributes to TM’s …

Long Non-Coding Rnas In Inflammation, Macrophage Activation, And Inflammatory Human Diseases, Avisankar Chini

Chemistry & Biochemistry Dissertations - Archive

Inflammation and immune signaling is central to infection and diseases. Growing evidence suggests that along with protein coding genes, long non-coding RNAs (lncRNAs) play a critical role in disease onset, combat, and recovery against pathogen, damaged and self-altered cells. Our lab has been extensively studying the role of lncRNA HOTAIR (HOX transcript antisense intergenic RNA) in gene regulation and epigenetics, and eventually discovered its hidden function regulating inflammation and immune signaling in macrophage, a major type of cell involved in immunity. Previous scholars in our lab have successfully demonstrated lncRNA HOTAIR’s regulatory molecular mechanism elucidating its specific role in cellular …

Reactive Atmosphere Pyrolysis(Rap) Of Silicon Carbo Nitride (Sicn), Akshada Bharat Hande

Chemistry & Biochemistry Theses - Archive

Polymer Derived Ceramics (PDCs) are synthesized by converting liquid polymer precursors into ceramics through controlled pyrolysis. This study focuses on silicon carbonitride (SiCN) ceramics obtained from Ceraset Polysilazane (Durazane1800) precursor. The influence of pyrolysis atmospheres, including inert (Ar, N2) and reactive (H2) environments, on the thermal conversion of Durazane1800 into SiCN ceramics is investigated. The resulting ceramics' chemical variations are explored through phase analysis using X-ray diffraction (XRD), Raman spectroscopy, and thermogravimetric analysis (TGA). Notably, the impact of hydrogen versus nitrogen atmospheres on the conversion process is analyzed, shedding light on their distinct contributions to the composition and properties of …

Identification Of Acidic Residues In Proteins By Selective Chemical Labeling And Tandem Mass Spectrometry, Fnu Ashima

Chemistry & Biochemistry Theses - Archive

Proteins play important role in carrying out a wide range of cellular activities. They are subjected to various post-translational modifications (PTMs) by the addition of functional groups such as acetyl, phosphoryl, and methyl which leads to changes in their biological functions, localization, activity, and structure. The growth of MS technology has immensely facilitated the identification of PTMs comprehensively. This dissertation focuses on mapping these changes using covalent labeling techniques by tagging carboxylic acid residues, which undergo various kinds of PTMs. The second chapter focuses on the methods designed for Affinity Purification Mass Spectrometry (AP-MS) chemical cross-linking (CXL) of protein complexes. …

Atomically Dispersed Cu-N3 On Hollow Spherical Carbon Nitride For Acetaminophen Degradation: Generation Of 1o2 From H2o2, Shuoyuan Tian, Yu Yin, Mengxuan Liu, Lei Shi, Shu Zhang, Abdul Hannan Asif, Xuan Li, Mengqiong Liu, Xiaoguang Duan, Shaobin Wang, Hongqi Sun

Research outputs 2022 to 2026

Discharge of recalcitrant pharmaceuticals into aquatic systems has caused severe impacts on public health and ecosystem. Advanced oxidation processes (AOPs) are effective for eliminating these refractory pollutants, for which single-atom catalysts (SACs) become the state-of-the-art materials owing to the maximized exposure of active metal sites. In this work, hollow spherical graphitic carbon nitride (hsCN) was fabricated to incorporate copper species to develop Fenton-like catalysts for acetaminophen (ACT) removal. Through pyrolysis of supramolecular assemblies derived from melamine-Cu complex and cyanuric acid, single atom Cu-N3 sites were anchored on hsCN by N-coordination to obtain SACu-hsCN. In virtue …

Functional Nanocomposite Coatings For Use In Food Packaging, Camden N. Webb

Master's Theses

Plastics are a class of materials known for their cost and property advantages, increasing significantly in their usage worldwide. Unfortunately, these benefits come with an increasingly concerning environmental impact. A combination of inadequate disposal options and combinations of materials have led to environmental disasters that will impact generations. One of the worst areas for plastic waste is food packaging. Plastic as a material generally excels at durability and longevity, but as food packaging, it outlives its intended purpose by several orders of magnitude. This leads to plastic food packaging materials sitting in landfill or leading to the environment for hundreds …

Synthesis And Characterization Of Cobalt(Iii) Complexes And A Vanadium(Iv) Complex With Flavonoids As Ligands, Ethan Schroeder

Chemistry & Biochemistry Theses & Dissertations

For many years now, transition metal complexes have been used as favorable additional chemotherapeutic approaches to medicine that were previously unexplored in the literature. One well-known chemotherapeutic drug, cisplatin, has been applied, but is limited in use due to its toxicity to the cells and its undesirable side effects to humans. Newly developed cobalt-based complexes with ligands known as flavonoids are being used to fight cancer. Flavonoids, compounds mainly found in fruits and vegetables, are shown to have antioxidative and anticancer properties. Use of flavonoids as ligands in transition metal complexes, e.g., those with a Ru(II) metal center, have been …

Outgassing Behavior And Heat Treatment Optimization Of Jsc-1a Lunar Regolith Simulant, Ryan P. Wilkerson, Mihail P. Petkov, Gerald E. Voecks, Catherine S. Lynch, Holly S. Shulman, Santhoshkumar Sundaramoorthy, Amitava Choudhury, Douglas L. Rickman, Michael R. Effinger

Chemistry Faculty Research & Creative Works

As NASA Strives towards a Long Duration Presence on the Moon, It Has Become Increasingly Important to Learn How to Better Utilize Resources from the Lunar Surface for Everything from Habitats, Vehicle Infrastructure, and Chemical Extraction. to that End, a Variety of Lunar Simulants Have Been Sourced from Terrestrially Available Volcanic Minerals and Glass as Apollo Regolith is Unavailable for Experimentation Needing Large Masses. However, While Mineralogy and Chemical Composition Can Approach that of Lunar Material in These Simulants, There Are Still Distinct Non-Lunar Phases Such as Hydrates, Carbonates, Sulfates, and Clays that Can Cause Simulants to Behave Distinctly Non-Lunar …

Mapping Roles Of Active Site Residues In The Acceptor Site Of The Pa3944 Gcn5-Related N-Acetyltransferase Enzyme, Cillian Variot, Daniel Capule, Xhulio Arolli, Jackson Baumgartner, Cory T. Reidl, Charles Houseman, Miguel Ballicora, Daniel P. Becker Ph.D., Misty L. Kuhn

Chemistry: Faculty Publications and Other Works

An increased understanding of how the acceptor site in Gcn5-related N-acetyltransferase (GNAT) enzymes recognizes various substrates provides important clues for GNAT functional annotation and their use as chemical tools. In this study, we explored how the PA3944 enzyme from Pseudomonas aeruginosa recognizes three different acceptor substrates, including aspartame, NANMO, and polymyxin B, and identified acceptor residues that are critical for substrate specificity. To achieve this, we performed a series of molecular docking simulations and tested methods to identify acceptor substrate binding modes that are catalytically relevant. We found that traditional selection of best docking poses by lowest S scores …

Investigating The Effects Of E219 Mutations In M. Tuberculosis Indole-3-Glycerol Phosphate Synthase, Cinthya Moran

Theses, Dissertations and Culminating Projects

Tuberculosis (TB) is a serious infectious disease caused by Mycobacterium tuberculosis. Tuberculosis drug resistance is increasingly a problem, but recent research has provided results that suggest Indole-3-Glycerol Phosphate Synthase (IGPS) could be a potential drug target. IGPS is an enzyme that catalyzes the fourth step in the tryptophan biosynthesis pathway, a crucial process for optimal Mycobacterium tuberculosis growth. In this research, we studied IGPS from Mycobacterium tuberculosis (MtIGPS) to shed light on a particular conserved residue that has not been studied in depth in any IGPS homolog. My investigation focuses on understanding the role of the active site residue E219. …

Exploiting Natural Rna 2′-5′-Linkage In Nucleic Acid Aptamers And Dna Nanostructures, Johnsi Mathivanan

Legacy Theses & Dissertations (2009 - 2024)

Developments in chemical synthesis of nucleic acid sequences and modifications have aided in the study of biomolecular interactions and the roles of modified nucleic acids in biology, medicine, and nanotechnology. This work describes some of the aspects of such developments, from synthesis of chemically modified RNA and DNA aptamers that can bind antibiotics and metal ions to the use of nucleic acids with novel backbone linkages in the construction of nanostructures. Analysis of such nucleic acid structures inform us on the basic structure of these molecules and the resulting functions that are applicable in fields such as biosensing, drug screening …

Novel Applications Of Enhanced Raman Spectroscopy For Drug Discovery, Mrna Vaccine Stability Assessment, And Forensic Purposes, Lamyaa M. Almehmadi

Legacy Theses & Dissertations (2009 - 2024)

The main focus of this dissertation was to apply enhanced Raman spectroscopy techniques to a variety of applications, ranging from drug discovery, mRNA vaccine stability, to forensic analysis. There are five chapters in this dissertation. The first chapter discusses the basics of enhanced Raman spectroscopy techniques and their relevance. The second chapter is focused on the use of surface-enhanced Raman spectroscopy (SERS) for drug discovery. The third chapter introduces the use of deep ultraviolet resonance Raman (DUVRR) spectroscopy for the detection of mRNA degradation in a mRNA vaccine model. The fourth chapter introduces the use of stand-off Raman spectroscopy in …

Distinguishing Between Living And Dead Plant Material From The Red Spruce Using Atr Ft-Ir Spectroscopy, Bailey Ann Hoplight

Legacy Theses & Dissertations (2009 - 2024)

Spectroscopic methods have recently been used to analyze plant species and maturation. However, there is a lack of research into employing spectroscopy for distinguishing living plant material and dead plant material, which is important for the agriculture and environmental health fields. Here in this study, we have shown the potential of ATR-FT IR (Attenuated total reflectance Fourier transformed infrared spectroscopy) to classify plant materials as living or dead through the help of multivariate statistical analysis methods. Plant samples were from the roots and needles of picea rubens, more commonly known as the red spruce tree. The samples were classified by …

Band Gap Engineering In Ternary Oxides And Sulfides: A Route To New Photoelectrodes For Solar Energy Conversion, Fahad Ibrahim Danladi

Chemistry & Biochemistry Dissertations - Archive

In recent years, there has been a growing interest in semiconductor photoelectrodes that can effectively split water into hydrogen and oxygen using sunlight. However, there is currently no known material that is efficient enough to be used for commercial purposes. Photoelectrodes currently have an efficiency of less than 10% in converting water under visible light irradiation. There is a need to develop an efficient semiconductor photoelectrode for photoelectrochemical water splitting that is both chemically stable and affordable, composed of earth-abundant elements and capable of operating under visible light. Metal oxides are considered promising photoelectrode materials due to their low cost, …

Studying The Stability Of Collagen/Heparin Coatings To Be Used In Cell Therapy Applications, Gavin Mussino

Biological Sciences Undergraduate Honors Theses

This honors thesis aims to investigate the reusability and performance of cell coatings for cell therapy applications. Cell therapy, which involves the use of human cells to repair or replace damaged tissues, holds immense potential for medical advancements. However, ensuring the survival and functionality of transplanted cells remains a significant challenge. We focused on studying the effectiveness of coatings applied to cells for improved cell growth and viability. The research project involved the preparation of the coatings using a layer-by-layer method and the subsequent seeding of cells. The coated cells were then subjected to a series of experiments to assess …

Probing The Mechanism Of Dna Protein Crosslink Formation By Aziridinomitosenes Through The Selective Precipitation Of Protein Salts, Michael Blair

Boise State University Theses and Dissertations

Aziridinomitosenes are synthetic chemotherapeutic agents that are analogs of Mitomycin C, as well as other mitomycins. They are known for their ability to form DNA interstrand cross-links (ICLs), and more recently have been observed to form DNA-protein cross-links (DPCs). In this work, three synthetic aziridinomitsenes were prepared and studied to better understand the role of the C6 and C7 positions in the formation of DNA-protein cross-links. In addition, two separate methods, the advanced recovery of K-SDS precipitates and the K-SDS assays were utilized and compared to assess the advancements in the analysis of DPC formation. H AZM, C6 AZM, Dimethyl …

Intra-Gendered Perceptions And Adoption Of Climate-Smart Agriculture: Evidence From Smallholder Farmers In The Upper East Region Of Ghana, Kwabena Antwi, Philip Antwi-Agyei

Student Publications [Scholarly]

Climate-smart agriculture (CSA) remains a key strategy for sustaining agricultural systems and achieving food security and nutrition. Despite this, uncertainty remains on how intra-gendered dynamics influence its adoption in dryland farming systems. This study implements both quantitative and qualitative approaches including household surveys, key informant interviews, and focus group discussions to explore how intra-gender dynamics shape the perceptions and adoption of climate-smart agriculture in three selected communities (Katanga, Dakio, and Zonno) in the Bolgatanga East District of the Upper East Region of Ghana. Specifically, the study answers the following research questions: (i) What is the degree of change in rainfall …