Chemistry Commons^™

Rapid And Accurate Determination Of Atomistic Rna Dynamic Ensemble Models Using Nmr And Structure Prediction, Honglue Shi, Atul Rangadurai, Hala Abou Assi, Rohit Roy, David A. Case, Daniel Herschlag, Joseph D. Yesselman, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Biomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining ensembles is challenging because the information required to specify atomic structures for thousands of conformations far exceeds that of experimental measurements. We addressed this data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a con- formation library. Refinement of this library with NMR residual dipolar couplings provided an atomistic ensemble model for HIV-1 TAR, and the model accuracy was independently sup- ported by comparisons …

A Luminescence-Based System For Identification Of Genetically Encodable Inhibitors Of Protein Aggregation, Travis J. Nelson, Shuo Liang, Cliff I. Stains

Department of Chemistry: Faculty Publications

Molecules that disrupt protein aggregation represent potential tool compounds for the investigation of numerous human disease states. However, the identification of small molecules capable of disrupting protein aggregation has proven challenging. Larger biomolecules such as antibodies and proteins are promising alternatives due to their increased size. Despite the promise of protein-based inhibitors, generalizable assays are needed to more readily identify proteins capable of inhibiting aggregation. Herein, we utilize our previously reported self- assembling NanoLuc luciferase fragments to engineer a platform in which both detection reagents are expressed from the same plasmid, enabling facile co-transformation with a genetically encodable inhibitor. This …

Constructing Stable And Potentially High-Performance Hybrid Organic-Inorganic Perovskites With “Unstable” Cations, Qing Yang, Menghao Wu, Xiao Cheng Zeng

Department of Chemistry: Faculty Publications

A new family of functional hybrid organic-inorganic perovskites (HOIPs) is theoretically designed based on the following chemical+ insights: when a proton is adhered to molecules like water or ethanol, the newly formed larger-sized cations (e.g., H5O2 ,++ C2H5OH2 , and CH3SH ) entail low electron affinities mimicking superalkalis; they are conjugated acids of weak bases that cannot survive in solution, while their chemistry behavior in the HOIP frameworks, however, may be markedly different due to greatly enhanced cohesive energies of the proton, which facilitate the formation of new HOIPs. First-principles computations show that the putative formation reactions for these newly …

Domain Wall Conduction In Calcium-Modified Lead Titanate For Polarization Tunable Photovoltaic Devices, Chong-Xin Qian, Hong-Jian Hong-Jian, Qiang Zhang, Jiawei He, Zi-Xuan Chen, Ming-Zi Wang, Xiao Cheng Zeng

Department of Chemistry: Faculty Publications

Ferroelectric domain wall (DW) conduction, confirmed in recent experiments, has attracted intense attention due to its promising applications in optoelec- tronic devices. Herein, we provide theoretical evidence of electric conduction in Pb0.8Ca0.2TiO3 (PCT) DWs. The separation of charge accumulation in DWs, corresponding to the electronic conduction-band minimum (CBM) and valence-band maximum (VBM), weakens the tendency for the electron-hole recombination, thereby providing more efficient channels for charge transfer. We fabricate PCT-based functional photovoltaic devices with polarization tunable charge transfer to exploit the combined conduction and ferroelectric properties of the DW. The photovoltaic performance of the devices can be regu- lated by …

Mechanistic Insights Into The Acetate-Accelerated Synthesis Of Crystalline Ceria Nanoparticles, Tamra J Fisher, Deepa Choudhry, Kaitlynn Derr, Soodabeh Azadehranjbar, Dan Stasko, Chin Li Cheung

Department of Chemistry: Faculty Publications

Recent increasing uses of ceria in research and industrial applications have fostered continuing developments of efficient routes to synthesize the material. Here we report our investigation of the effects and the mechanistic roles of lithium acetate to accelerate the growth of crystalline ceria nanoparticles in ozone-mediated synthesis. By increasing the mole ratio of the acetate to cerium nitrate in the reactions, the reaction yields of ceria nanoparticles were observed to increase from ca. 10% to up to over 90% by cerium content in 30 min reactions. Microscopy images and Raman spectra of the assynthesized nanoparticles revealed that increasing the acetate …

A Click-Based Modular Approach To Introduction Of Peroxides Onto Molecules And Nanostructures, Alissa Horn, Patrick H. Dussault

Department of Chemistry: Faculty Publications

Copper-promoted azide/alkyne cycloadditions (CuAAC) are explored as a tool for modular introduction of peroxides onto molecules and nanomaterials. Dialkyl peroxide-substituted alkynes undergo Cu(I)- promoted reaction with azides in either organic or biphasic media to furnish peroxide-substituted 1,2,3- triazoles. Heterolytic fragmentation of the peroxide to an aldehyde, a side reaction that appears to be related to the formation of the triazole, can be suppressed by use of excess alkyne, the presence of triethylsilane, or by use of iodoalkyne substrates. Complementary reactions of simple alkynes with azidosubstituted peroxides are much less efficient. Click reactions of alkynyl peroxyacetals are also reported; reductive fragmentation …

Agbis2 As A Low-Cost And Eco-Friendly All-Inorganic Photovoltaic Material: Nanoscale Morphology– Property Relationship†, Ming-Gang Ju, Jun Dai, Liang Ma, Yuanyuan Zhou, Xiao Cheng Zeng

Department of Chemistry: Faculty Publications

Solar cells made of low-cost solution-processed all-inorganic materials are a promising alternative to conventional solar cells made of high-temperature processed inorganic materials, especially because many high-temperature processed inorganic materials contain toxic element(s) such as lead or cadmium (e.g., CsPbI₃ perovskite, PbS, CdTe and CdS(Se)). AgBiS₂ nanocrystals, consisting of earth-abundant elements but without lead and cadmium, have already emerged as a promising candidate in highperformance solar cells. However, the nanoscale morphology–optoelectronic property relationship for AgBiS₂ nanocrystals is still largely unknown. Herein, we investigate the electronic properties of various AgBiS₂ nanocrystals by using first-principles computation. We show that …

Ionic Liquid Functionalized Β-Cyclodextrin Modified Electrode As Electrochemical Sensor For 2,4-Dichlorophenol, Fairuz Liyana Mohd Rasdi

Student Works (2020-2029)

This thesis described the synthesis and characterization of ionic liquid monofunctionalized β-cyclodextrin (β-CD-1-BIMOTs) and ionic liquid difunctionalized β-cyclodextrin (β-CD-2-BIMOTs) for sensor applications. The physical characterizations of these compounds have been conducted using nuclear magnetic resonance (NMR), Fourier transform infra-red (FTIR), energy dispersive x-ray (EDX), x-ray diffraction (XRD) and Brunauer-Emmet-Teller (BET) analyses. These compounds were used as modifiers for carbon paste electrode (CPE). Cyclic voltammetry and chrono-amperometry methods were employed to examine the electrochemical responses of all prepared CPEs. All prepared electrodes show responses towards the target analyte of 2,4-dichlorophenol (2,4-DCP). Both β-CD-1-BIMOTs/CPE and β-CD-2-BIMOTs/CPE give higher current (i) responses compared …

Development And Validation Of Advanced Analytical Methods For Pesticides, Per- And Polyfluoroalkyl Substances, And Opioids In Soil And Drinking Water, Christopher Skaggs

Electronic Theses and Dissertations

Environmental pollution from contaminants is a serious concern in a world where more and more pesticides and pharmaceuticals are being used, sometimes improperly and in excess. Since pesticides are used on practically every crop on Earth, it’s no surprise that these compounds are detected in soil, water, and processed agricultural commodities meant for human consumption. Additionally, because of the ubiquity of pharmaceuticals, specifically opioids, and their inherent addictive properties, these compounds are being over-consumed. Because current waste-water treatments can be insufficient to remove them from water sources, this consumption has led to the detection of these compounds in drinking water. …

Structural Annotation Of Electro- And Photochemically Generated Transformation Products Of Moxidectin Using High-Resolution Mass Spectrometry, Lisa Kotthoff, Sarah-Louise O'Callaghan, Jan Lisec, Tanja Schwerdtle, Matthias Koch

Articles

Moxidectin (MOX) is a widely used anthelmintic drug for the treatment of internal and external parasites in food-producing and companion animals. Transformation products (TPs) of MOX, formed through metabolic degradation or acid hydrolysis, may pose a potential environmental risk, but only few were identified so far. In this study, we therefore systematically characterized electro- and photochemically generated MOX TPs using high-resolution mass spectrometry (HRMS). Oxidative electrochemical (EC) TPs were generated in an electrochemical reactor and photochemical (PC) TPs by irradiation with UV-C light. Subsequent HRMS measurements were performed to identify accurate masses and deduce occurring modification reactions of derived TPs …

Capillary Electrophoresis Analysis Of Proteins Using Phospholipid Based Materials, Cassandra L. Crihfield

Graduate Theses, Dissertations, and Problem Reports (ETD)

Capillary electrophoresis has many advantages that make it a powerful technique for the analysis of proteins, which is challenging due to the natural heterogeneity of proteins. The small sample volume required for each analysis (nano- and pico-liter), fast separation times (<30 >min), and ability to couple the separation to mass spectrometry are all factors that make capillary electrophoresis an ideal technology for protein separations. Capillary zone electrophoresis and capillary gel electrophoresis are the two most commonly employed modes for protein analysis and allow for rapid, high resolution separations that can be automated. This makes capillary electrophoresis ideal for meeting the …

Development And Implementation Of A Novel Voltage-Free Interface For Capillary Electrophoresis-Mass Spectrometry Separations Of Proteins, Courtney J. Kristoff

Graduate Theses, Dissertations, and Problem Reports (ETD)

Capillary electrophoresis-mass spectrometry is a powerful technique for high-throughput and high efficiency separations combined with structural identification. Electrospray ionization is the primary interface used to couple capillary electrophoresis to mass analyzers; however, improved designs continue to be reported. A new interfacing method based on vibrating sharp-edge spray ionization is presented in this work to overcome the challenges of decoupling applied voltages and to enhance the compatibility with separations performed at near-neutral pH. The versatility and ease of use of this ionization source is demonstrated using β-blockers, peptides, and proteins. The cationic β-blocker pindolol was injected electrokinetically and detected at concentrations …

Genetic And Biochemical Characterization Of Ergot Alkaloid Synthesizing Fungi And Their Symbionts, Matthew Duane Maust

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ergot alkaloids are fungal tryptophan derived toxins which affect mammalian circulation and neurotransmission. These compounds are biosynthesized by a conserved genetic pathway, known as the ergot alkaloid synthesis (EAS) pathway by fungi belonging to the ascomycete families Trichocomaceae and Clavicipitaceae. Several Ipomoea species and related plants in the morning glory family harbor vertically transmitted symbiotic fungi in the genus Periglandula, also members of Clavicipitaceae, that produce ergot alkaloids. Metabolomic analysis of seeds identified a previously uncharacterized glycoside form of the pharmaceutically important ergot alkaloid, ergonovine. Several species belonging to the fungal genus Metarhizium have recently been shown to have the …

Protein/Peptide Characterization Using Mass Spectrometry And Molecular Dynamics Simulations, Ahmad Kiani Karanji

Graduate Theses, Dissertations, and Problem Reports (ETD)

Mass spectrometry (MS) based-techniques and molecular dynamics (MD) simulations have been used to characterize protein/peptide structure as well as their interactions with lipid vesicles and detergents. Chapter 1 introduces an introduction to the concepts and tools that were used in this work. In Chapter 2, the dominant gas-phase conformer of [M+3H]3+ ions of the model peptide Acetyl-PSSSSKSSSSKSSSSKSSSSK are examined with ion mobility spectrometry (IMS), gas-phase hydrogen deuterium exchange (HDX), and mass spectrometry (MS) techniques. This section furthers the development of a protein structural prediction tool by providing information about gas-phase ion conformers of two model peptides having different solution conformational …

The Effects Of Membrane Physicochemical Properties On Huntingtin Membrane Association And Downstream Aggregation, Maryssa Beasley

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s Disease (HD) is a fatal neurodegenerative disorder caused by an expanded glutamine repeat region (polyQ) within the huntingtin protein (htt). As a result of the expanded polyQ domain, htt associates into a variety of toxic aggregate species. The polyQ domain of htt is flanked at the N-terminal end by 17 amino acids (Nt17) that adopt an amphipathic α-helical structure in the presence of binding partners such as lipid membranes. In addition to comprising a lipid binding domain, the Nt17 amphipathic α -helix has been directly implicated in htt aggregation initiation via self-association with other Nt17 α -helices. Due to …

Phytochemical Investigations Of Goniothalamus Tapis And G. Tapisoides, And Kinetic Mechanism Studies Of Goniothalamin, Pei Theng Rosalind Kim

Student Works (2020-2029)

Phytochemical studies on two species of Annonaceae; Goniothalamus tapis and Goniothalamus tapisoides have been carried out. Isolation and purification of the crude extract of stem bark of G. tapis and G. tapisoides yielded seventeen compounds. G. tapis gave nine compounds; goniothalamin 1, isoaltholactone 41, 3-acetylisoaltholactone 151, cheliensisin A 22, garvensintriol 4, goniopyyprone 26, 7-epi-goniofufurone 49, stigmasterol 133 and β-sitosterol 134. Out of nine compounds, 3-acetyl-isoaltholactone 151 was identified as a new styryl-lactone. The skeleton is similar as the major compound, isoaltholactone 41. But 3-acetylisoaltholactone 151 have different functional group compared to hydroxyl group in isoaltholactone 41, which is acetyl group. …

Derivatization Of Stable, Soluble Redox-Active Organic Materials For Non-Aqueous Redox Flow Batteries, Thilini Malsha Suduwella

Theses and Dissertations--Chemistry

In screening active materials for redox flow batteries (RFBs) – in which solubility is important to raise the volumetric energy density – scientists are slave to trial and error, modifying organic molecules in an attempt to optimize (increase) solubility without compromising other important properties such as stability and redox potential. A trained chemist can often predict the trends of solubility with the structural modifications in the neutral state of the materials, but when it’s come to the charged state of the materials, it doesn’t follow the same trend as the neutral species and relative values are hard to predict. The …

Applications Of Drones In Atmospheric Chemistry, Travis J. Schuyler

Theses and Dissertations--Chemistry

The emission of greenhouse gases (GHGs) has changed the composition of the atmosphere during the Anthropocene. A major technical and scientific challenge is quantifying the resulting fugitive trace gas fluxes under variable meteorological conditions. Accurately documenting the sources and magnitude of GHGs emission is an important undertaking for discriminating contributions of different processes to radiative forcing. Therefore, the adverse environmental and health effects of undetected gas leaks motivates new methods of detecting, characterizing, and quantifying plumes of fugitive trace gases. Currently, there is no mobile platform able to quantify trace gases at altitudes(UASs), or drones, can be deployed on-site in …

Flavodoxin, The Hydrogen Atom Of Flavoproteins: A 19f Nmr Study Of Dynamics And Conformational Changes Utilizing Flavodoxin From Rhodopseudomonas Palustris, Taylor Varner

Theses and Dissertations--Chemistry

Flavodoxin is a small, highly stable protein that contain a single FMN cofactor used to transfer single electrons at low potentials. The organism Rhodopseudomonas palustris contains a long-chain flavodoxin. Long-chain flavodoxins are characterized by a 20 amino acid loop that is proposed to allow interactions with partner proteins. We plan to utilize this protein as a model to build our repertoire with protein fluorination and fluorine NMR in flavoproteins. This tool kit will then be applied to the study of a partner protein of interest that is capable of performing electron bifurcation. We have incorporated m-fluoro tyrosine into flavodoxin and …

Interfaces In Lead-Free Tin Perovskite Photovoltaics: An Investigation Of Energetics, Ion Mobility, Surface Modification, And Performance, Alex Boehm

Theses and Dissertations--Chemistry

Halide perovskites have generated tremendous interest as low-cost semiconductors for optoelectronics, such as photovoltaics, lasers, and light emitting diodes due to their extraordinary optical and transport properties. Perovskite photovoltaics in particular have demonstrated a meteoric rise in power conversion efficiencies and drawn considerable interest as a next-generation solar energy technology. The rapid development has centered around lead-based derivatives, and concerns regarding the toxicity of lead has sparked interest in low toxicity and more environmentally friendly perovskite derivatives. In this regime tin (Sn) is regarded as a prominent alternative owing to the ideal bandgap and reduced toxicity exhibited by Sn-halide perovskites. …

Tools To Evaluate Nanodiamond-Mediated Delivery Of Tiopronin For Cataract Prevention, Justin Beltz

Doctoral Dissertations

”There is a growing demand for non-surgical means of cataract treatment. This dissertation presents three bodies of work that reflect the early-stage development of eye drop formulations aimed at delaying cataract progression. These formulations consist of the antioxidant 2-mercaptopropionylglycine (MPG) loaded onto nanodiamond particles.

Cataractogenesis is linked to oxidative damage to lens proteins. To investigate the potential of MPG for protection against oxidative damage, A549 cells were incubated in 0.6 mM tert-butylhydroperoxide (tBHP). Cells exposed to tBHP without MPG exhibited elevated levels of reactive oxygen species, which led to the depletion of the vital antioxidant glutathione and, ultimately, apoptosis. Co-administration …

Structural Characterization Of Emerging Synthetic Drugs, Jay Tyler Davidson

Graduate Theses, Dissertations, and Problem Reports (ETD)

The identification of well-characterized seized drugs is performed thousands of times a day in the United States; however, the expanding use of emerging synthetic drugs is creating a growing problem for both toxicological and seized drug analyses. Two of the most rapidly growing areas of emerging synthetic drugs are synthetic cathinones and fentanyl-related compounds (FRCs). In this work we demonstrate the combination of multi-stage mass spectrometry (MSⁿ), accurate mass measurements with high-resolution mass spectrometry (HRMS), and isotopic labeling for the structural characterization of synthetic cathinones and fentanyl analogs. The deliverables of this research include the identification of conserved …

Metal Ions Impact On Shewanella Oneidensis Mr-1 Adhesion To Ito Electrode And The Enhancement Of Current Output, Aisha Awad Alshahrani

Dissertations

The goal of this study is to enhance the efficiency of bacterial extracellular electron transfer (EET) in Shewanella oneidensis MR-1 by enhancing adhesion to the electrode's surface. Our results clearly show a major difference in the attachment and behavior of Shewanella oneidensis MR-1 for Ca2+, Pb2+, Cd2+, and Mg2+, compared to the control. the final microbial coverage, as measured by confocal microscopy and cathodic peak charge in cyclic voltammetry (Qpc), increases with increasing metal ion concentrations. We found the cells attached to the electrode increased more with the addition of metal ion concentrations in the following order of metals: Ca2+ …

Development Of Methods For The Removal Of Selected Pollutants From Several Matrices And Identification Of Unknown Pollutants Adsorbed Onto Plastics Collected From Freshwater, Kathryn Marie Renyer

Dissertations

Plastic pollution represents one of greatest anthropogenic threats to the environment. Five to ten billion tons of plastic are manufactured every year. Currently, Earth's ecosystem is contaminated with billions of tons of plastic debris, much of which cannot be recycled. Over time, this plastic debris decomposes into small particles. Small plastic particles are known to adsorb toxic compounds in marine environments. My research is concerned with creating novel methods for the detection and quantification of selected persistent organic pollutants from several media. Specifically, I developed methods for the detection and quantification of endosulfan sulfate (ESS) from Lumbricus terrestris tissue and …

Electron Transfer Of Shewanella Oneidensis Mr-1 At Clay-Modified Ito Electrode, Reem Faez Alshehri

Dissertations

Various strategies have been established to enhance the extracellular electron transfer and energy output capability of microbial fuel cells, with the majority being aimed at anode modification. The anode has a significant impact on the electricity generation performance of MFCs because it is in direct contact with the microorganisms. The materials of the anode should be favorable for the bacterial cell and capable to facilitate the electron transfer. Developing of an electrode using low-cost and effective materials assists to enhance the bacterial cell attachment and extracellular electron transfer. This provides a significant improvement in MFC performance. In this study, clay …

Fabrication And Characterization Of Multicomponent Gradients Containing Weakly Acidic And Basic Functional Groups, Kallol Roy

Theses and Dissertations

Multicomponent synthetic chemical gradients containing amine (NH₂) and carboxylic acid (COOH) groups have been prepared on the silanol (Si-OH) containing a base-layer substrate by the controlled-rate infusion (CRI) method. The spatial variation of weakly acidic COOH and basic NH₂ functional groups on weakly acidic Si-OH surface was created in such a way that the two antagonist groups at high concentrations were in close proximity (aligned gradient) and were separated (opposed gradient). The difference in concentration of different components (acid, base, or silanol) along the length of aligned or opposed resulted in significantly different physicochemical properties …

Determination Of Samarium And Dysprosium Solubility, Seana Brennan

Theses and Dissertations (Comprehensive)

In recent years, the use of Rare Earth Elements (REE) has rapidly increased, resulting in numerous potential anthropogenic inputs to the environment. As a result, these metals are emerging as microcontaminants and pose a potential threat to aquatic life. However, the toxicity of REE are largely unknown due, in part, to the limited information on their chemical speciation. The purpose of this project was to gain an understanding of REE precipitate formation and solubility as the foundation for the development of the chemical equilibrium component of toxicity prediction models. Solubility experiments were conducted with Samarium, (Sm), a light REE, and …

Ratiometric Near-Infrared Fluorescent Probes For The Sensitive Detection Of Intracellular Ph And Bio-Thiols In Live Cells, Shuai Xia

Dissertations, Master's Theses and Master's Reports

In the past twenty years, fluorescence sensing and imaging based on fluorescent probes has been developed as an imperative technique due to the merits including excellent sensitivity, operational simplicity, instant time effectiveness and outstanding selectivity in the research areas such as mineralogy, gemology, biological medicine, materials and environmental engineering. Protons act as a significant role in a variety of pathological and physiological processes, and there are obvious differences in the pH among organelles: the pH in lysosomes is acid within the range of 4.5–5.5, whereas mitochondrial pH is basic that can be as high as 8.0. Abnormal intracellular pH is …

Reduction In Salt Deposition On Carbon Nano-Tube Immobilized Membrane During Desalination Via Membrane Distillation, Madihah Saud Humoud

Dissertations

As water scarcity increases globally under the stresses of increasing demand, aquifer depletion, and climate change, the market for efficient desalination technologies has grown rapidly to fill the void. One such developing technology, membrane distillation (MD), has found much interest in the scientific community. MD has also been powered by solar energy and waste heat resources because it can be operated at relatively low temperatures. Recent studies indicate that MD could potentially achieve the efficiencies of state-of-the-art mature thermal desalination technologies, although additional engineering and scientific challenges must first be overcome.

MD can be used to treat high salinity water …

Transient Electrochemical Surface-Enhanced Raman Spectroscopic Study In Electrochemical Reduction Of P-Nitrothiophenol, Yun Ling, Jing Tang, Guo-Kun Liu, Cheng Zong

Journal of Electrochemistry

P-nitrothiophenol (PNTP) is one of the most common probe molecules studied by surface-enhanced Raman spectroscopy (SERS). The research in electrochemical reduction behavior of PNTP will help understanding the mechanism for the nitrobenzene reduction. In this paper, we used transient electrochemical surface-enhanced Raman spectroscopy (TEC-SERS) to study the SERS of PNTP with cyclic voltammetry and chronoamperometry on gold electrodes. The results show that the TEC-SERS provide a time resolution that equals the transient electrochemical methods, and we concluded that the reaction was so quick that we did not observe the spectral information of intermediate species described in the literatures with a …