Chemistry Commons^™

A Critical Inter-Subunit Interaction For The Transmission Of The Allosteric Signal In The Agrobacterium Tumefaciens Adp-Glucose Pyrophosphorylase, Hiral Patel, Gabriela Martinez-Ramirez Ms., Emily Dobrzynski, Alberto A. Iglesias, Dali Liu, Miguel Ballicora

Chemistry: Faculty Publications and Other Works

ADP-glucose pyrophosphorylase is a key regulatory enzyme involved in starch and glycogen synthesis in plants and bacteria, respectively. It has been hypothesized that inter-subunit communications are important for the allosteric effect in this enzyme. However, no specific interactions have been identified as part of the regulatory signal. The enzyme from Agrobacterium tumefaciens is a homotetramer allosterically regulated by fructose 6-phosphate and pyruvate. Three pairs of distinct subunit-subunit interfaces are present. Here we focus on an interface that features two symmetrical interactions between Arg11 and Asp141 from one subunit with residues Asp141 and Arg11 of the neighbor subunit, respectively. Previously, scanning …

Fabrication And Imaging Of Highly Ordered Plasmonic Au Nano-Prism And Self-Assembled Supramolecular Nanostructure, Ridwan Tobi Ayinla

Theses and Dissertations

The precise control of the resonance frequency of plasmonic nanostructures is critical and depends on the size, composition, shape, and dielectric nature of the environment. The ability to control the shape and size of nanomaterials acutely depends on the fabrication technique and material design. We used a cheap and scalable method known as nanosphere lithography (NSL) to fabricate plasmonic nano-prism (NP) on glass and indium tin oxide substrate (ITO). The methods involve substrate hydrophilicity treatment, polystyrene nanosphere masking, metal deposition, and mask removal. The array and specific morphology of the fabricated NP was established using scanning electron microscope (SEM) and …

Improved Stoichiometric Synthesis Of Ccc-Nhc Pincer Rh Complexes And Catalytic Activity Towards Dehydrogenative Silylation And Hydrosilylation Of Alkenes, Enock Amoateng

Theses and Dissertations

N-Heterocyclic carbenes (NHCs) have attracted growing interest not only as successful ancillary ligands in a wide variety of transition-metal-catalyzed reactions but have also shown to offer photophysical and electrochemical properties. The metalation/transmetalation strategy using [Zr(NMe₂)₄] as initial metalating reagent offers an efficient approach to the preparation of CCC-NHC pincer complexes of the late transition metals such as Rh and Ir. In the process of investigating an intermediate and the mechanism of the metalation/transmetalation to Rh sequence, a mixed valent bimetallic CCC-NHC pincer Rh complex with two chloro ligands bridged between a [(CCC-NHC)Rh(III)] and a [Rh(I)(COD)] fragment …

Synthesis And Characterization Of Redox-Noninnocent Pyrazine(Diimine) Iron Complexes And An Inverted Pyridine(Diimine) Ligand, Jaylan Billups

Theses and Dissertations

Cooperativity between the metal center and the ligand has been shown in nature to be an important feature of systems that catalyze two-electron processes that first-row transition metals usually cannot catalyze on their own. In these cases, the ligand acts as a site of reactivity that in many instances can store electrons or react directly with substrates in solution. The design and study of systems where there is synergy between the metal and the ligand have been leveraged to catalyze polymerization and hydrogenation-type reactions as well as the activation of small molecules such as dihydrogen. Specifically, the pyridine(diimine) ligand scaffold …

Identifying Student Challenges In Organic Chemistry: Supporting Student Understanding Through Eye-Tracking, Think-Aloud Interviews And Alternative Questions, Lisa Ann Smith

Theses and Dissertations

Think-aloud interviews are a strategy used to identify misconceptions held by students. We incorporated think-aloud interviews and studied representational competence of novice and expert participants with identifying alkyl halides with multiple representations. We hypothesized that the participants would approach representations differently and think-aloud interviews would reveal misconceptions. Eye-tracking results showed that novice and expert participants differ in their approaches to representations and that novice participants spend more time on representations. Think-aloud interviews revealed that novice participants contain misconceptions on alkyl halide identification. This research provided insights on student understanding in identifying alkyl halides and representations, allowing instructors to use student …

Uncoupling System And Environment Simulation Cells For Fast-Scaling Modeling Of Complex Continuum Embeddings, G. Medrano, E. Bainglass, O. Andreussi

Chemistry and Biochemistry Faculty Publications and Presentations

Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all atomistic simulations. However, some challenges with the implementation of these models in plane-wave simulation packages still persists, especially when the goal is to simulate complex and heterogeneous environments. Among these challenges is the computational cost associated with large heterogeneous environments, which in plane-wave simulations has a direct effect on the basis-set size and, as a result, on the cost of the electronic structure calculation. Moreover, the use of …

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. …

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 …

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 …