Physical Sciences and Mathematics Commons^™

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

Sensitized Photooxidation Of Prenylated Compounds: Mechanisms Of Downstream Dark Effects And Phototoxicity Priming, Shakeela Jabeen

Dissertations, Theses, and Capstone Projects

This thesis consists of four chapters as detailed below.

Chapter 1 discusses a singlet oxygen priming mechanism. Airborne singlet oxygen derived from photosensitization of triplet dioxygen is shown to react with an alkene surfactant (8-methylnon-7-ene-1 sulfonate) leading to ‘ene’ hydroperoxides that in the dark inactivate planktonic E. coli. The ‘ene’ hydroperoxide photoproducts are not toxic on their own, but they become toxic after the bacteria are pretreated with singlet oxygen. The total quenching rate constant (k_T) of singlet oxygen of the alkene surfactant was measured to be 1.1 × 10⁶ M⁻¹ s^{− …}

A Comparison Of Methods Used For The Elimination Of Organics From Soil Prior To Analysis By Ftir-Atr And Sem-Eds, Argeliz Pomales

Student Theses

This project suggests improvements to the treatment methods utilized for the sample preparation and evaluation of minerals in soil samples encountered in forensic science casework and research. The evaluation of pre-treated and post-treated soil samples were performed using Fourier-Transform Infrared Spectroscopy with Attenuated Total Reflection (FTIR-ATR) and Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS). Because soil samples contain a significant amount of organic matter and water which interfere with examination of these minerals while using these instruments, pretreatment methods are necessary to isolate the mineral fraction for examination and analysis.

Soil samples were first sieved with various size stainless steel mesh …

Investigating The Mechanisms Driving Mercury Reduction And Emissions In Soil, Hamil Patel

Student Theses

The water-induced emission of mercury from soil has been studied, but a complete understanding of the mechanisms driving mercury reduction and emission in soil has not been reached. The current understanding is an immediate expulsion of soil gaseous mercury upon water treatment and an upward transport of dissolved soil ionic mercury as the water evaporates. We analyzed emissions from several types of samples using various methods to further our understanding on the mechanisms involved. Light-induced emissions from aqueous samples of humic acid (HA) spiked with mercury (II) chloride (HgCl₂) showed that at higher concentrations of HA, less mercury …

Biomimetic And Medical Applications Of Hollow Nanoscale Structures, Justin Fang

Dissertations, Theses, and Capstone Projects

Materials whose structure incorporates nanoscale void spaces have multiple possible uses, whether in a bulk form or as individual particles, due to the combination of high surface area ratios and nanoscale material properties. This thesis will explore a few of these possibilities, concentrating on potential biomimetic and biomedical applications, for two materials: metal- organic frameworks and superparamagnetic iron oxide nanocages.

Metal-organic frameworks consist of metal ions such as Cu2+ which have highly porous lattice structures allowing them to absorb and release guest molecules such as peptides like diphenylalanine; this stored chemical energy can be turned into kinetic energy and used …

Understanding The Proton Transport In Non-Aqueous Histidine-Based Nanostructures, Jiang Bian

Dissertations, Theses, and Capstone Projects

Over the past two decades, proton transport has been extensively studied because of the many applications to the development of new technological devices. In particular, understanding proton transport permits the design of new materials with desired properties for constructing effective proton exchange membranes (PEM) in fuel cells. Current PEM technology involves biocummulative perfluorinated membranes that operate under hydrated conditions, for which the proton conductivity is limited by the usually high temperature that fuel cells operate. Therefore, it is of great interest to study the alternative systems that have the potential to conduct protons, in particular, those that are able to …

Water-Based Lead Generation, Brian Olson

Dissertations, Theses, and Capstone Projects

Water-based Lead Generation. The opioid epidemic and the SARS-CoV-2 pandemic are current serious challenges whose devastating effects could be assuaged through the development of new drugs. Opioids that are functional painkillers, that are less likely to cause overdose, and small molecule drugs that could inhibit the life cycle of SARS-CoV-2 would be useful. The work herein investigated the use of water molecules for lead generation in drug development against opioid receptors and SARS-CoV-2 viral proteins. In opioid receptor binding sites, purported bridging waters were obtained from crystal waters or from molecular dynamics simulations, as Hydration Site Analysis was used to …

Evolution Of Microscopic Heterogeneity And Dynamics In Choline Chloride-Based Deep Eutectic Solvents, Stephanie Spittle, Derrick Poe, Brain Doherty, Charles Kolodziej, Luke Heroux, Md Ashraful Haque, Henry Squire, Tyler Cosby, Yong Zhang, Carla Fraenza, Sahana Bhattacharyya, Madhusudan Tyagi, Jing Peng, Ramez A. Elgammal, Thomas Zawodzinski, Mark Tuckerman, Steve Greenbaum, Burcu Gurkan, Clemens Burda, Mark Dadmun, Edward J. Maginn, Joshua Sangoro

Publications and Research

Deep eutectic solvents (DESs) are an emerging class of non-aqueous solvents that are potentially scalable, easy to prepare and functionalize for many applications ranging from biomass processing to energy storage technologies. Predictive understanding of the fundamental correlations between local structure and macroscopic properties is needed to exploit the large design space and tunability of DESs for specific applications. Here, we employ a range of computational and experimental techniques that span length-scales from molecular to macroscopic and timescales from picoseconds to seconds to study the evolution of structure and dynamics in model DESs, namely Glyceline and Ethaline, starting from the parent …

Stoichiometry Question Sets, Myungshim Kang

Open Educational Resources

This is a question pool for general chemistry. This consists of question sets, each of which contains variations of questions for topics, including the mole, molar mass, balancing chemical equations, and quantitative relationships in chemical reactions.

Biomedical Applications Of Lanthanide Nanomaterials, For Imaging, Sensing And Therapy, Qize Zhang, Stephen O'Brien, Jan Grimm

Publications and Research

The application of nanomaterials made of rare earth elements within biomedical sciences continues to make significant progress. The rare earth elements, also called the lanthanides, play an essential role in modern life through materials and electronics. As we learn more about their utility, function, and underlying physics, we can contemplate extending their applications to biomedicine. This particularly applies to diagnosis and radiation therapy due to their relatively unique features, such as an ultra-wide Stokes shift in the luminescence, variable magnetism and potentially tunable properties, due to the library of lanthanides available and their multivalent oxidation state chemistry. The ability to …

Analysis Of Blue Fountain Pen Ink By Uv-Vis Spectroscopy, Atr-Ftir Spectroscopy, And Thin Layer Chromatography Enhanced With Rgb Spot Evaluation To Construct A Database For Comparison And Identification., Elliot D. Quinteros

Dissertations and Theses

Pen ink can be a crucial piece of physical evidence in the area of Forensic Science. For example, evidence such as notes, letters, printed documents, checks, currency, ransom notes, and books may contain ink. Analysis of ink is typically done for identification or differentiation purposes. To improve existing methods, it was proposed to create a database with many samples and experimental information. The methods used and evaluated were thin-layer chromatography (TLC) enhanced with RGB spot evaluation, UV-Vis spectroscopy, and ATR-FTIR spectroscopy. All three methods were used to analyze 89 fountain pen ink samples. All three methods were able to discriminate …

Poly(Β-Gal-Thr): A New Scalable Synthetic Mucin, Manuel A. Lema

Dissertations and Theses

A method for the preparation of glycosylated polypeptides via the nucleophilic ring-opening polymerization of a glycosylated N-carboxyanhydride (NCA) monomer is reported. The synthesis of 2,3,4,6-tetraacetyl-β-galactose-threonine N-carboxyanhydride (β-AcO-Gal-Thr-NCA) monomer in 5 steps with an 8 % overall yield is described, and the single-crystal X-ray structure is provided. The effect of a series of Ni⁰-based organometallic initiators, nucleophilic amine initiators, co-catalysts, and solvents on the polymerization were explored. The kinetics of the three most promising conditions were studied in greater detail. The conditions that provided the highest yield, low polydispersity (Ð), and …

Probing The Production Of Intracellular Vesicles Containing Reactive Oxygen And Nitrogen Species By Electrochemical Resistive-Pulse Sensing, Rui Jia

Publications and Research

No abstract provided.

High-Resolution Cryo-Electron Microscopy Structure Of Photosystem Ii From The Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, Christopher J. Gisriel, Jimin Wang, Jinchan Liu, David A. Flesher, Krystle M. Reiss, Hao-Li Huang, Ke R. Yang, William H. Armstrong, M. R. Gunner, Victor S. Batista, Richard J. Debus, Gary W. Brudvig

Publications and Research

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the …

Quantum Mechanics-Based Computational Chemistry Has Become A Powerful Partner In The Scientific Research Of Nitrogen-Rich Compounds, Paving The Way For Important Advances In Biochemical, Pharmacological And Other Related Fields, Dobrushe Denburg

Student Theses and Dissertations

The Computational Chemistry of Nitrogen-Rich Compounds; Insight into Pioneering Research

Nitrogen-rich functional groups have long been studied for their diversity; nitrogen can form single, double and triple bonds with itself, and will therefore exist in a very broad range of molecular arrangements. Poly-nitrogen compounds are highly energetic and electron rich, and many compounds display unique properties that allow participation in very specialized chemical reactions. Of import is their ubiquity in biological systems, and throughout the past century and currently, their biological relevance is deeply and widely explored in biochemistry and biomedicine, from their involvement in natural biological processes and complex …

Me3al-Mediated Domino Nucleophilic Addition/Intramolecular Cyclisation Of 2-(2-Oxo-2-Phenylethyl)Benzonitriles With Amines; A Convenient Approach For The Synthesis Of Substituted 1-Aminoisoquinolines, Krishna M. S. Adusumalli, Lakshmi N.S. Konidena, Hima B. Gandham, Krishnaiah Kumari, Krishan R. Valluru, Satya K.R. Nidasanametla, Venkateswara R. Battula, Hari K. Namballa

Publications and Research

A simple and efficient protocol for the construction of 1-aminoisoquinolines was achieved by treating 2-(2-oxo-2- phenylethyl)benzonitriles with amines in the presence of Me 3 Al. The reaction proceeds via a domino nucleophilic addition with subsequent intramolecular cyclisation. This method provides a wide variety of substituted 1-aminoisoquinolines with good func- tional group tolerance. Furthermore, the synthetic utility of this protocol was demonstrated in the successful synthesis of the anti- tumor agent CWJ-a-5 in gram scale.

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Physical Chemistry, Ruth E. Stark

Open Educational Resources

This is a provisional syllabus for Physical Chemistry I (Thermodynamics), to be taught using an OER Textmap in Fall, 2021.

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Synthesis, Characterization And Applications Of Europium Based Perovskite Oxide Nanoparticles, Nasim Farahmand

Dissertations, Theses, and Capstone Projects

The synthesis and characterization of nanocrystalline transition and rare-earth metal oxides have been studied widely over the past years. These materials possess unique physical, chemical, magnetic and dielectric properties which make them potential candidates for a wide range of applications such as electronics, energy storage and photocatalysis. There are a number of synthesis methods for preparing these materials, where most of them require stringent conditions such as high pressure and high temperature. However, in this study, a modified sol-gel synthesis has been used with a lower calcination temperature to make uniform nanocrystals of the transition/rare-earth metal oxide family. The focus …

Development Of An Lcms Analytical Method With Applicability To Determination Of Trace Level Explosives In Environmental Waters, Cristina I. Veresmortean

Dissertations, Theses, and Capstone Projects

Traces of explosives and their degradation products present in explosives contaminated sites from military sources, such as training facilities, impose a great concern over the public health and our eco-system. This work is centered around finding an efficient way to extraction of these chemicals from water samples and their analysis using advanced separation technology: LC-MS/MS Shimadzu Prominence 8050 and AB Sciex Trap 4000 LC-MS/MS. Different extraction methods will be proposed, along with chromatographic and mass spectroscopy method development. Dependent on the target analyte polarity, thermal degradation, solubility and type of matrix, an appropriate method of analysis will be established. The …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Automated Code Engine For Tensor Hypercontraction: Derivation, Optimization And Implementation Of Rank-Reduced Coupled Cluster Theories, Yao Zhao

Dissertations, Theses, and Capstone Projects

The ultimate goal of electronic structure theory is solving the electronic Schr¨odinger Equation. However, even accurate approximations of solving Schr¨odinger Equation, such as high order coupled cluster theories, require computational efforts that are too demanding to be applied on large chemical systems. This thesis tackles the problem of curse of dimensionality: how to reduce the time complexity of high-accuracy coupled cluster methods in order to accelerate computations of molecular energy. On one hand, we believe that low-rank approximation (i.e. Tensor HyperContraction) of high-order tensors appearing in coupled cluster theory is a promising way to achieve rank-reduced coupled cluster theory. On …

Enhanced Platinum (Ii) Drug Delivery For Anti-Cancer Therapy, Marek T. Wlodarczyk

Dissertations, Theses, and Capstone Projects

Over the years, anti-cancer therapies have improved the overall survival rate of patients. Nevertheless, the traditional free drug therapies still suffer from side effects and systemic toxicity, resulting in low drug dosages in the clinic. This often leads to suboptimal drug concentrations reaching cancer cells, contributing to treatment failure and drug resistance. Among available anti-cancer therapies, metallodrugs are of great interest. Platinum (II)-based agents are highly potent and are used to treat many cancers, including ovarian cancer (OC). Cisplatin (cis-diaminedichloroplatinum (II)) is the first Food and Drug Administration (FDA)-approved metallodrug for treatment of solid tumors, and its mechanism …

Evaluation Of The Potential Of Automated Sem-Eds Analysis For The Discrimination Of Inorganic Soil Particles, Anna S. Duggar

Dissertations, Theses, and Capstone Projects

Soil, that complex mixture of minerals, organic particles, chemicals, and anthropogenic materials, is ubiquitous and easily transferred, which gives it forensic relevance. Forensic soil analysis has traditionally included the identification and comparison of both organic and inorganic components, the inorganic portion being most commonly examined by light microscopy and other instrumental techniques. Predominantly, the inorganic materials in soil are naturally-occurring minerals, contributed as grains from the surrounding bedrock, which gives a soil its regional character. That parent material then undergoes physical, chemical, and anthropogenic changes producing wide geographic variation within a single region. This variation forms the basis for potential …

Designing Atomic Edge Structures In 2d Transition Metal Dichalcogenides For Improved Catalytic Activity, Raymond R. Unocic, Xiahan Sang, Guoxiang Hu, Victor Fung, Jingsong Huang, Matthew G. Boebinger, Kai Xiao, Panchapakesan Ganesh

Publications and Research

Designing new materials for functional applications depends upon our ability to understand and correlate the materials structure and chemistry to functional material properties. This is even more important for two-dimensional (2D) materials where thicknesses are on the order of a single atom to a few-atomic layers; therefore, any structural or chemical modification at these length scales can have a profound effect on modifying physical and chemical properties. 2D transition metal dichalcogenides (TMDs) such as MoS2 have emerged as a promising catalyst for the hydrogen evolution reaction with defects such as vacancies and edges being linked to high catalytic active sites …

Evaluation Of Log P, Pka, And Log D Predictions From The Sampl7 Blind Challenge, Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, M. R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley

Publications and Research

The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pK_a for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pK_a challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was …

Emergent Photophysics In Diketopyrrolopyrrole Superstructures, Andrew Levine

Dissertations, Theses, and Capstone Projects

Organic semiconductors have received substantial attention as active components in optoelectronic devices because of their processability and customizable electronic properties. Tailoring the organic active layer in these devices to exhibit desirable optoelectronic properties requires understanding the complex and often subtle structure-property relationships governing their photophysical response to light. Both structural organization and frontier molecular orbitals (FMO) play pivotal roles in energy relaxation processes, and complex interplay between organization and orbital energies are difficult to anticipate based upon the molecular structure of the components alone, especially in systems comprised of multiple components. In pursuit of design rules, there is a need …

Photosensitization And Analytical Study On Reactive Oxygen Intermediates: Self-Sorting Surface Radicals And “On-Off” Sensitizer Function Mechanisms, Sarah J. Belh

Dissertations, Theses, and Capstone Projects

This thesis consists of four chapters which are detailed below. Chapter 1 is an introductory chapter, which lays out the background and purpose of the research.

Chapter 2 describes a study of the mobility of alkoxy radicals on a surface by detection of their recombination product. A novel method called symmetrical product recombination (SRP) utilizes an unsymmetrical peroxide that upon sensitized homolysis recombines to a symmetrical product [R'OOR → R'O•↑ + •OR → ROOR]. This allows for self-sorting of the radical to enhance the recombination path to a symmetrical product, which has been used to deduce surface migratory aptitude. SPR …