Chemistry Commons^™

Biochemical Analysis Of Dual T-Loop Rna Motifs That Perform Shape Recognition Of The Trna Elbow, John Aparicio Aguirre

Master's Theses (2009 -)

T-loops are highly abundant, structurally conserved five nucleotide motifs that facilitate long range intra- and intermolecular interactions and function to stabilize the tertiary fold of RNA. Interlocked or dual T-loop motifs provide additional thermodynamic stability and perform long-range docking of other RNA molecules. Dual T-loop RNA structures are present within the multi-turnover ribonuclease P-based ribozyme, the ribosome, and the bacterial tRNA-sensing riboswitch genetic element. In all three systems, a dual T-loop structure recognizes TYC/D-loop region of tRNA. Interestingly, sequence conservation at specific positions in the T-loops suggest a conserved interlocked RNA architecture. While X-ray crystallography provides insight into the putative …

Biophysical Characterization Of The Par-4 Tumor Suppressor: Evidence Of Structure Outside The Coiled Coil Domain And Interactions With Platinum Chemotherapeutics, Andrea Megan Clark

Chemistry & Biochemistry Theses & Dissertations

Prostate apoptosis response-4 (Par-4) is an apoptosis-inducing tumor suppressor protein. Full-length Par-4 has previously been shown to be a predominantly intrinsically disordered protein (IDP) under neutral conditions, with significant regular secondary structure evident only within the C-terminal coiled coil domain. However, IDPs can gain ordered structure through the process of induced folding, which often occurs under non-neutral conditions. Previous work has shown that the Par-4 leucine zipper, which is a subset of the C-terminal coiled coil domain, is disordered under neutral conditions, but forms a dimeric coiled coil at acidic pH. Increase in ionic strength was also shown to increase …

Development Of Mqct Method For Calculations Of Collisional Energy Transfer For Astrochemistry And Planetary Atmospheres, Bikramaditya Mandal

Dissertations (1934 -)

A mixed quantum/classical methodology and an efficient computer code, named MQCT, were developed to model molecular energy transfer processes relevant to astrochemical environments and planetary atmospheres and applied to several real systems. In particular, the rotational energy transfer in N2 + Na collisions was studied with the focus on quantum phase, differential cross-sections, and scattering resonances, and excellent agreement with full quantum results was found. For H2O + H2, detailed calculations were carried out with the focus on allowed vs. forbidden transitions between the ortho/para states of both collision partners. Again, excellent agreement with full quantum calculations was achieved. Calculations …

Toward Understanding The Origin Of Mass-Independent Fractionation In Sulfur Allotropes And In Ozone, Igor Gayday

Dissertations (1934 -)

Mysterious isotope effects, found in atmospheric ozone, cannot be explained by the standard mass-dependent statistical model. Similar mass-dependent isotope effects were also uncovered in sulfur deposits older than 2 billion years. In an effort to pinpoint possible reasons of these isotope effects, we build a theoretical description of the recombination reactions in sulfur allotropes and in ozone. No potential energy surface exists for the sulfur allotropes, so electronic structure calculations are also required. Ab initio calculation of two dimensionally reduced (2D and 3D) models of the potential energy surface for the tetrasulfur molecule at CCSD(T)-F12 and MRCI levels of theory …

Design And Synthesis Of Selective Estrogen Receptor Agonists, Edward Edward Wetzel

Dissertations (1934 -)

Estrogens are hormones that regulates many different physiological functions. A decline in estrogen leads to significant issues that decrease the quality of life. Past treatments of menopausal symptoms included the administration of estrogen. However, side effects such as an increased risk of breast cancer, made this an unattractive therapeutic option. When a new estrogen receptor (ERβ) was discovered, it provided new hope for hormone replacement therapy (HRT). ERβ was shown to inhibit tumor growth, whereas ERα regulates breast cancer proliferation in certain types of breast cancer. The therapeutic benefits of targeting ERβ are vast; herein we focus on the benefits …

Synthetic And Mechanistic Studies Of Ruthenium Catalyzed C-C, C-H And C-N Bond Activation Reactions, Nuwan Asanka Pannilawithana

Dissertations (1934 -)

Transition metal-catalyzed selective CH, CC and CN bond activation reactions represent a challenging and synthetically important field in organic chemistry. In particular, transition-metal catalytic unreactive bond activation protocols are applicable in various stereoselective and atom economical complex organic molecule synthesis. Recently, significant research efforts have been made for utilizing catalytic CH and CC bond cleavage methods in the further development of commercially valuable pharmaceuticals and agrochemicals. The well-defined cationic Ru–H complex was found to be an effective catalyst for mediating the coupling reaction of 1,2-disubstituted indoles with α,β-unsaturated aldehydes and ketones, in which the regioselective Cα–Cβ activation of the carbonyl …

Scope And Mechanistic Studies Of Ruthenium Catalyzed C-N Bond Activation Reactions, Pandula Taepith Kirinde Arachchige

Dissertations (1934 -)

Primary aliphatic amines which are ubiquitous in natural products, traditionally considered as inert to substitution reactions. Recent studies clearly demonstrated that the aliphatic deaminative coupling chemistry can be used to make valuable scaffolds through C–N bond activation on transition metal complexes. The catalytic system generated in situ from the tetranuclear Ru–H complex with a catechol ligand (2-9/2-16) and independently synthesized ruthenium catecholate complex 2-11 was found to be effective for the direct deaminative coupling of primary amines. The catalytic system formed in-situ from the reaction of cationic Ru–H complex 2-10 with 3,4,5,6-tetrachloro-1,2-benzoquinone 2-12 was found to mediate a regioselective deaminative …

Fabrication Of Chemically-Functionalized 3dprinted Porous Scaffolds For Biomedical Applications, Eiman Hamed Alblooshi

Theses

Hard tissues, such as bone and teeth, are natural composites of collagen nanofibers that are reinforced by inorganic calcium phosphate Nano crystallites, in the form of nanocomposites. The interlocking between these components in hard tissues explains their unique characteristics. Bone is mainly classified into two major types; compact and cancellous depending on the extent of porosity. Fractures in the compact bone can be treated using bone fixation implants, such as rods, screws, and plates, or can be totally replaced by bone implants if complete substitution is required. Cancellous bone, on the other hand, is highly porous and its substitution with …

Conservation Of Polyester-Urethane Magnetic Audio Tapes And Discrimination Of Textile Fiber Dyes Using Spectroscopy And Chemometrics, Nilmini Hemanthika Ratnasena

Theses and Dissertations

This dissertation explores and discusses conservation of magnetic audio tapes and discrimination of fiber dyes employing spectroscopic techniques and chemometrics.

Conservation of polyester urethane magnetic audio tapes has become a major challenge since they are susceptible to degradation via hydrolysis. The world’s modern cultural history is vastly recorded in this media, and now conservationists need a non-destructive technique to determine the playability status of these tapes. Once conservationists identify degraded tapes, they can be subjected to the baking process. This process temporarily reverses hydrolysis and provides enough time to digitize tapes, preserving information for future generations. The first three chapters …

Molecular Basis Of Xenobiotic Metabolism And Resistance In Tetranychus Urticae, Leily Daneshian

Theses and Dissertations

Invasive pest species are a major cause of crop loss around the world and adversely affect the agricultural industry. We are focusing on Tetranychus urticae (two-spotted spider mite; TSSM), which is a polyphagous pest that targets more than 1100 plant species. The TSSM alone causes a loss of roughly $1.6 billion per year globally due to acaricide resistance. It is developing resistance to most acaricides due to rapid growth and reproduction. Therefore, new acaricides are needed to combat TSSM resistance and infestation [1]. To address this problem, four enzymes of TSSM, intradiol ring cleavage dioxygenases, a glutathione S-transferase, a β …

Bibliometric Analysis Of Named Entity Recognition For Chemoinformatics And Biomedical Information Extraction Of Ovarian Cancer, Vijayshri Khedkar, Charlotte Fernandes, Devshi Desai, Mansi R, Gurunath Chavan Dr, Sonali Tidke Dr., M. Karthikeyan Dr.

Library Philosophy and Practice (e-journal)

With the massive amount of data that has been generated in the form of unstructured text documents, Biomedical Named Entity Recognition (BioNER) is becoming increasingly important in the field of biomedical research. Since currently there does not exist any automatic archiving of the obtained results, a lot of this information remains hidden in the textual details and is not easily accessible for further analysis. Hence, text mining methods and natural language processing techniques are used for the extraction of information from such publications.Named entity recognition, is a subtask that comes under information extraction that focuses on finding and categorizing specific …

Fate Of Persistent Contaminants And Emerging Algal Toxins In Drinking Water And The Environment, Danielle Christine Westerman

Theses and Dissertations

Population growth and global climate change has resulted in the degradation of pristine water sources, causing issues like saltwater intrusion, persistent harmful algal blooms, and drought from population growth. Future reliance on alternative sources of drinking water to is expected globally, therefore, nontraditional sources of drinking water are becoming increasingly vital sources of potable water around the world. For example, desalination (typically by reverse osmosis), despite its high energy demands and high cost, is being utilized all over the world to meet drinking water demand. Wastewater reuse, the additional treatment of wastewater to produce drinking water, either directly or indirectly, …

Studies Of The Chemistry Of Pentaruthenium Carbido Carbonyl Cluster Complexes With Aldehydes, Azobenzene And Alkynes, Humaiara Akter

Theses and Dissertations

Polynuclear metal carbonyl complexes serve as the bridging model between heterogeneous catalysis and homogeneous catalysis for the activation of small molecules. Ru5(m5-C)(CO)15 has been found to exhibit superior reactivity due to its unusual polynuclear metal geometry. possibilities of interconversions of ligand bonding modes, and the formation of the electronically unsaturated metal species. C-H activation in aldehydes and azobenzene of pentaruthenium cluster complexes is described in chapters 2 and 3 respectively. The formation of new hydrocarbyl zwitterions and C – C coupling ethyne to the carbido carbon in the complex, and the alkyne insertion reactions with pentaruthenium cluster complexes are described …

Cationic Metallo-Polyelectrolytes: Synthesis And Application In Self-Assembly And Mechanochemistry, Yujin Cha

Theses and Dissertations

In this dissertation, cationic metallocene-containing polyelectrolytes were investigated for the construction of nano-objects by CDSA and the mechanical force-responsive polymer. The self-assembly behavior and mechanically induced polymer deformation were characterized and discussed.

In Chapter 1, the overall background and recent development of metallocene-containing polymers as well as their applications in self-assembly and polymer mechanochemistry were introduced. Primary research objectives were described.

The first section of the dissertation on the CDSA of cationic metallocene-containing block copolymers was provided in Chapter 2. The preparation of PCL-b-PCoAEMAs was achieved through ring-opening polymerization (ROP) of ε-caprolactone and reversible addition-fragmentation chain-transfer (RAFT) polymerization of cobaltocenium …

Sparse Modeling For Predicting Class Assignments For Trace Forensic Evidence, Dayla Christine Rich

Theses and Dissertations

Numerous disciplines in forensic science utilize various types of spectral data when analyzing evidence. Spectral techniques are particularly critical for the analysis of trace evidence, as these methods are normally non-destructive. Preserving evidence, especially trace evidence, is of high priority in a forensic laboratory setting. Once a piece of evidence has been fully consumed, no more analyses can be performed. Typically, visual comparison, or spectral overlay, is performed to compare questioned samples (evidence) to standards or knowns. However, such an approach may not be optimal in distinguishing the subtle, yet highly important, discriminating characteristics present in the spectra. As statistical …

Characterization And Hydrogenation Activity Of Supported Palladium Particles, Narayan Acharya

Theses and Dissertations

In this project, the hydrogenation activity of palladium (Pd) particles supported on different carbon and oxide supports was investigated. Supported Pd particles were prepared using strong electrostatic adsorption (SEA) technique, which is known to produce metal particles with narrow and uniform distribution. The scanning transmission electron microscopy (STEM), X-ray diffraction (XRD), and chemisorption methods were used to characterize the Pd particle size in this project. The Pd particles on different supports were annealed at a specific temperature, and the particle size was studied as a function of annealing temperature. Propylene hydrogenation to propane was conducted in a flow reactor to …

Functional Supramolecular Materials And The Design And Synthesis Of Triple Negative Breast Cancer Pharmaceuticals, Dustin Wayne Goodlett

Theses and Dissertations

Organization of benzophenone in the solid-state facilitates the formation of persistent and regenerable radicals at room temperature upon exposure to light. Upon incident irradiation, the triplet sensitizer rapidly undergoes intersystem crossing to a triplet excited state. Structural investigation of four distinct benzophenone supramolecular assemblies gives insight into the different processes these materials can undertake once in the triplet excited state such as persistent radical formation, phosphorescence, and self-quenching.

Self-assembly of brominated triphenyl amine bis-urea macrocycles forms a host material with unidirectional pores. Separations of xylene constitutional isomers via adsorption within this crystalline host material at ambient temperature are shown to …

Effect Of Oil And Gas Extraction On Disinfection By-Product Formation In Drinking Water, Dallas Graham Abraham

Theses and Dissertations

Certain industrial processes, such as energy extraction and utilization, generate massive amounts of wastewater with various geogenic and synthetic contaminants. Oil and gas wastewaters are characterized by elevated halide levels, particularly geogenic bromide and iodide. Concentrations in produced wastewaters have been reported as high as thousands of mg/L of bromide and tens of mg/L of iodide. Large volumes of these wastewaters are stored, transported, and disposed of, potentially impacting drinking water sources. Because conventional wastewater treatment fails to remove halides, oil and gas wastewater disposal, even after treatment, facilitates the formation of brominated and iodinated disinfection by-products (DBPs) at downstream …

Automating And Implementing Complex, Multistep Sample Preparation Processes To Generate Reproducible Proteomic And Phosphoproteomic Data, Brian Todd Mullis

Theses and Dissertations

Phosphorylation is the most common post-translational modification that occurs within the cell and is intricately involved in many biological processes. It is important to understand the roles that protein kinases and phosphatases play by mapping protein phosphorylation as many disease states stem from aberrant signaling events. With the advent of modern mass spectrometry (MS), researchers are now provided with more complex phosphorylation patterns from thousands of proteins in each mass spectrometric analysis. Further developments in quantification techniques, such as stable isotope labeling with amino acids in cell culture (SILAC) and label-free quantitation, have allowed researchers to reliably quantify changes to …

Molten Alkali Halide Salt-Flux Crystal Growth And Physical Property Determination Of Complex Oxides And Chalcogenides Supported By First Principles Density Functional Theory Calculations, Mohammad Usman

Theses and Dissertations

The primary objective of this dissertation is to inform the reader about more thansixty new materials with potentially attractive physical properties obtained via molten alkali halide flux methods as X-ray diffraction quality crystals. Flux crystal growth carries several advantages over other synthetic methods, including low reaction temperatures and straightforward post-reaction workup. This dissertation consists of 11 chapters, including an introductory chapter, which are organized into two parts, each corresponding to the general structure type of the family of oxides and chalcogenides being investigated. Part 1, which encompasses chapters 2–6, is dedicated to the discussion of crystal growth of complex chalcogenides …

Reversing The Regioselectivity Of Indole Addition To Cyclic Unsymmetrical Oxyallyl Cations: Construction Of Diaryl Quaternary Centers, Thomas Davis Curry Ii

Honors Capstones

No abstract provided.

Evaluating The Role Of The Stringent Response Mechanism In Clostridioides Difficile Survival And Pathogenesis, Astha Pokhrel

Chemistry & Biochemistry Theses & Dissertations

The human pathogen Clostridioides difficile is increasingly tolerant of multiple antibiotics and causes infections with a high rate of recurrence, creating an urgent need for new preventive and therapeutic strategies. The stringent response, a universal bacterial response to extracellular stresses, governs antibiotic survival and pathogenesis in diverse organisms but has not previously been characterized in C. difficile. This dissertation explores the ability of C. difficile to mount the stringent response. The bacteria encode a full-length, canonical bifunctional Rel/Spo Homolog or RSH enzyme. C. difficile RSH is incapable of utilizing GTP as a substrate but readily synthesizes putative 5’-pGpp-3’ alarmones. …

Biophysical And Structural Studies On Telomeric G-Quadruplexes From Tetrahymena Thermophila, Dana Beseiso , '21

Senior Theses, Projects, and Awards

G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized guanine tetrads (G-tetrads). GQs are highly diverse structures that can be categorized by their strand directionality, number of G-tetrads, and loop types among other parameters. Due to their high guanine content, GQs are expected to fold in regions such as telomers or oncogene promoters. They are thus firmly established as biologically viable targets for the development of anticancer therapeutics. In order to harvest GQs’ therapeutic potential, extensive structural studies are required to elucidate the structures’ diverse topologies alone and in complex with selective ligands. Towards this goal, this thesis …

Synthesis And Characterization Of Α-Diimine Complexes Of Aluminum, Judah B. Raab , '21

Senior Theses, Projects, and Awards

Conventional aluminum complexes are incapable of one- and two-electron redox chemistry. As a result, despite being the most abundant metal on Earth, aluminum is seldom used in redox catalysis—one of chemistry’s most impactful fields. We are motivated to break this barrier to provide a green alternative to the countless redox catalysts built around the toxic, mining-intensive platinum-group metals. To create aluminum complexes that do desirable redox chemistry, we coordinate redox-active α-diimine ligands to the metal center. These ligands are stable across multiple oxidation states, allowing for multi-electron redox chemistry for their aluminum complexes. This thesis will report the synthesis of …

Kinetics Studies On Isomerization And Unimolecular Decay Processes Of The Criegee Intermediate, Methacrolein (Macr) Oxide, Hyun Kyung Lee , '21

Senior Theses, Projects, and Awards

Alkenes are one of the major components of hydrocarbons in our atmosphere. One of the most common alkenes in our atmosphere is isoprene (2-methyl – 1,3 – butadiene). Currently, it is known that isoprene ozonolysis can lead to the production of Criegee intermediates CH2OO, methacrolein (MACR) oxide, and methyl vinyl ketone (MVK) oxide. In part, we were interested in studying one specific Criegee intermediate, MACR oxide. The competition between the isomerization reactions and the unimolecular reactions became the focus of our study. Rate constants for the relevant reactions were calculated by implementing RRKM theory and using Master Equation modeling to …

Food Security As A Factor Of Sustainable Development Of The Country, Timur Nurimbetov

Karakalpak Scientific Journal

The article examines the state of the food market and the trends in ensuring the country’s food security. The article also analyzes the regional characteristics of the agricultural products market in the Republic of Karakalpakstan. The saturation level of regional food markets has been studied. Scientific conclusions and practical recommendations on the supply of food to the population have been made.

Influence Of Laterial State Of Pair Impurity Complex On Recombination Processes In Semiconductors, L Yu Leyderman, R A. Ayukhanov, Abat Uteniyazov, E S. Esenbaeva, Sh X. Annayeva

Karakalpak Scientific Journal

The paper analyzes the question of the possible influence of the lateral state of a paired impurity complex on the recombination processes. It is shown that the lateral state of the paired impurity complex does not affect the recombination processes of nonequilibrium carriers - they go through that component of the impurity complex that exchanges carriers with both bands (in this particular case, through the component). The second component of the complex () can apparently play some role in the processes of carrier attachment.

Exploring The Roles Of Herc2 And The Nedd4l Hect E3 Ubiquitin Ligase Subfamily In P53 Signaling And The Dna Damage Response, Nicholas A. Mathieu, Rafael H. Levin, Donald E. Spratt

Chemistry

Cellular homeostasis is governed by the precise expression of genes that control the translation, localization, and termination of proteins. Oftentimes, environmental and biological factors can introduce mutations into the genetic framework of cells during their growth and division, and these genetic abnormalities can result in malignant transformations caused by protein malfunction. For example, p53 is a prominent tumor suppressor protein that is capable of undergoing more than 300 posttranslational modifications (PTMs) and is involved with controlling apoptotic signaling, transcription, and the DNA damage response (DDR). In this review, we focus on the molecular mechanisms and interactions that occur between p53, …

Polymer Based Triboelectric Nanogenerator For Cost‐Effective Green Energy Generation And Implementation Of Surface‐Charge Engineering, Diana Lopez, Aminur Rashid Chowdhury, Abu Masa Abdullah, Muhtasim Ul Karim Sadaf, Isaac Martinez, Brishty Deb Chowdhury, Serena Danti, Christopher J. Ellison, Karen Lozano, Mohammed Jasim Uddin

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Performance of triboelectric nanogenerators for harvesting mechanical energy from the ambient environment has been limited by structural complexity, cost-effectiveness, and mechanical weakness of materials. Herein, a cost-effective vertical contact separation mode triboelectric nanogenerator using polyethylene (PE) and polycarbonate (PC) in a regular digital versatile disc is reported. This cost-effective nanogenerator with simplified structures is able to generate an open-circuit voltage of 215.3 V and short-circuit current of 80 μA. The effects of the distance of impact and the air gap between the triboelectric layers have also been tested from 3 to 9 cm, and 0.25 to 1 cm, respectively. It …

Organization Of Compact Spinning Technology In Textile Clusters, Baxtiyar Aralbaevich Paluanov, Abdimalik Pirmatovich Pirmatov

Karakalpak Scientific Journal

The article proposes a system of continuous supply of raw cotton in continuous spinning technology and methods of maximizing the preservation of the natural properties of the fiber and obtaining high-quality yarn.