Chemistry Commons^™

Detection Of Cathinone And Mephedrone In Plasma By Lc-Ms/Ms Using Standard Addition Quantification Technique, Theron W. Ng-A-Qui

Student Theses

Designer drugs are structural analogs of Drug Enforcement Agency (DEA) Schedule I and II substances. They are synthesized to mimic the effects of illegal drugs of abuse and to bypass the provisions of drug regulations. Despite the increased availability of designer drugs, few studies have focused on specific analytical extraction techniques for their detection and quantification in biological samples. Solid phase extraction (SPE) is the most commonly used technique for sample preparation. The purpose of this study is to evaluate the extraction efficiency of the various SPE columns with different sorbent materials for two designer drugs, cathinone and mephedrone in …

Cancer Cell Spheroids Are A Better Screen For The Photodynamic Efficiency Of Glycosylated Photosensitizers, Patrícia M. R. Pereira, Naxhije Berisha, N.V.S. Dinesh K. Bhupathiraju, Rosa Fernandes, João P.C. Tomé, Charles Michael Drain

Publications and Research

Environmental remediation requires ion-selective polymers that operate under a wide range of solution conditions. In one example, removal of trivalent and divalent metal ions from waste streams resulting from mining operations before they enter the environment requires treatment at acidic pH. The monoethyl ester phosphate ligands developed in this report operate from acidic solutions. They have been prepared on polystyrene-bound ethylene glycol, glycerol, and pentaerythritol, and it is found that intraligand hydrogen bonding affects their metal ion affinities. The affinity for a set of trivalent (Fe(III), Al(III), La(III), and Lu(III)) and divalent (Pb(II), Cd(II), Cu(II), and Zn(II)) ions is greater …

29si Nmr And Saxs Investigation Of The Hybrid Organic-Inorganic Glasses Obtained By Consolidation Of The Melting Gels, Andrei Jitianu, Sylvian Cadars, Fan Zhang, Gabriela Rodriguez, Quentin Picard, Mario Aparicio, Jadra Mosa, Lisa C. Klein

Publications and Research

This study is focused on structural characterization of hybrid glasses obtained by consolidation of melting gels. The melting gels were prepared in molar ratios of methyltriethoxysilane (MTES) and dimethyldiethoxysilane (DMDES) of 75%MTES-25%DMDES and 65%MTES-35%DMDES. Following consolidation, the hybrid glasses were characterized using Raman, ²⁹Si and ¹³C Nuclear Magnetic Resonance (NMR) spectroscopies, synchrotron Small Angle X-Ray Scattering (SAXS) and scanning electron microscopy (SEM). Raman spectroscopy revealed the presence of Si–C bonds in the hybrid glasses and 8-membered ring structures in the Si–O–Si network. Qualitative NMR spectroscopy identified the main molecular species, while quantitative NMR data showed that the ratio …

Thickness-Properties Synergy In Organic–Inorganic Consolidated Melting-Gel Coatings For Protection Of 304 Stainless Steel In Nacl Solutions, Mario Amapricio, Andrei Jitianu, Gabriela Rodriguez, Kutaiba Al-Marzoki, Mihaela Jitianu, Jadra Mosa, Lisa C. Klein

Publications and Research

Homogeneous and crack-free methyl-substituted organic–inorganic hybrid glass coatings (thickness up to 10 μm) were deposited on AISI 304 stainless steel. Different hybrid glasses obtained fromconsolidation of the diluted melting gels with various methyltriethoxysilane (MTES)/dimethyldiethoxysilane (DMDES) ratios were evaluated considering chemical structure, coating adhesion and corrosion protection. The 70MTES/30DMDES (molar%) melting-gel coating provided improved corrosion protection for this steel due to the synergy of different properties: a highly cross-linked inorganic structure, a coating plasticity based on the hybrid network, and a good adhesion to the substrate through hydroxyl groups. Electrochemical results showa good barrier film with a passive range of 500 …

A Computational Study Of Lithium Carbamate Synthetic Intermediate Structures And Aggregation, Lawrence M. Pratt

Publications and Research

Computational quantum chemistry was used to investigate the structures of lithium carbamates in the gas phase and in ethereal solvents. These compounds act as nucleophiles with either inversion or retention of configuration at the chiral center and knowledge of the aggregation state is the first step in understanding the reactivity. The sterically hindered lithium phenyl carbamate is calculated to exist largely as the ether or THF solvated monomer in solution. Higher aggregates are possible in the gas phase, which is often taken as an approximation for solutions in non-polar solvents.

Glass Polymorphism In Glycerol–Water Mixtures: I. A Computer Simulation Study, David A. Jahn, Jessina Wong, Johannes Bachler, Thomas Loerting, Nicolas Giovambattista

Publications and Research

We perform out-of-equilibrium molecular dynamics (MD) simulations of water–glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA–HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/ decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration wg = 0–13% and find that, for the …

Tuning The Polarity Of Charge Carriers Using Electron Deficient Thiophenes, Jonathan Z. Low, Brian Capozzi, Jing Cui, Sujun Wei, Latha Venkataraman, Luis M. Campos

Publications and Research

Thiophene-1,1-dioxide (TDO) oligomers have fascinating electronic properties. We previously used thermopower measurements to show that a change in charge carrier from hole to electron occurs with increasing length of TDO oligomers when single-molecule junctions are formed between gold electrodes. In this article, we show for the first time that the dominant conducting orbitals for thiophene/ TDO oligomers of fixed length can be tuned by altering the strength of the electron acceptors incorporated into the backbone. We use the scanning tunneling microscope break-junction (STM-BJ) technique and apply a recently developed method to determine the dominant transport channel in single-molecule junctions formed …

Design Of Collagen-Mimetic Peptides, Parminder Jeet Kaur

Dissertations, Theses, and Capstone Projects

Collagen is the major component of the extracellular matrix and is involved in a wide range of cellular functions during tissue development and action. At the core of the diverse functions of this versatile protein is its remarkable ability to form supramolecular structures through self-assembly and/or through interactions with other biomolecules. One typical example of such supramolecular structure is the fibrils of collagen types I, II and III of the connective tissues. These fibrils have staggered arrangement of the laterally associated collagen triple helices – the structural unit of collagen – to form long, smooth fibrils with a characteristic 67 …

Synthesis Of Complex/Multifunctional Metal (Hydr)Oxide/Graphite Oxide/Aunps Or Agnps Adsorbents And Analysis Of Their Interactions With Chemical Warfare Agents, Dimitrios A. Giannakoudakis

Dissertations, Theses, and Capstone Projects

One of the most widely used chemical warfare agent (CWA) is mustard gas, which is a highly toxic blistering agent. In this study we investigated the interactions of mustard gas surrogates’ vapors on zinc and zirconium hydroxides and their composites with graphite oxide (GO) and/or Au or Ag nanoparticles. Even though a small quantity of reports about the detoxification of CWAs on metal oxides is reported in the literature, almost all of these studies are performed in the liquid phase. Both herein reported Zn(OH)₂ and Zr(OH)₄ showed a good adsorption performance, with the former being photoactive under visible …

Evolution Of Complex Target Selex To Identify Aptamers Against Mammalian Cell-Surface Antigens, Prabodhika R. Mallikaratchy

Publications and Research

The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This …

Circular Dichroistic Impacts Of 1‑(3-Dimethylaminopropyl)-3- Ethylurea: Secondary Structure Artifacts Arising From Bioconjugation Using 1‑Ethyl-3-[3-Dimethylaminopropyl]Carbodiimide, Matthew B. Kubilius, Raymond S. Tu

Publications and Research

1-Ethyl-3-[3-dimethylaminopropyl]carbodiimide (EDC) is a commonly used reagent for bioconjugation and peptide synthesis. Both EDC and the corresponding urea derivative, 1-(3-dimethylaminopropyl)-3-ethylurea (EDU), are achiral. As the reagent is active in aqueous solutions, it is a common choice for the study of evolving secondary structural changes via circular dichroism. This work highlights the effect of EDU on spectropolarimetric measurements, namely, the problematic absorption profile at low wavelengths (190−220 nm). We demonstrate that EDU is capable of erroneously indicating structural changes, particularly loss of α-helical character, through masking of the characteristic minimum at 208 nm. However, if the concentrations of the EDU in …

Evolution From The Plasmon To Exciton State In Ligand-Protected Atomically Precise Gold Nanoparticles, Meng Zhou, Chenjie Zeng, Yuxiang Chen, Shuo Zhao, Matthew Y. Sfeir, Manzhou Zhu, Rongchao Jin

Publications and Research

The evolution from the metallic (or plasmonic) to molecular state in metal nanoparticles constitutes a central question in nanoscience research because of its importance in revealing the origin of metallic bonding and offering fundamental insights into the birth of surface plasmon resonance. Previous research has not been able to probe the transition due to the unavailability of atomically precise nanoparticles in the 1-3 nm size regime. Herein, we investigate the transition by performing ultrafast spectroscopic studies on atomically precise thiolate-protected Au₂₅, Au₃₈, Au₁₄₄, Au₃₃₃, Au_∼520 and Au_∼940 nanoparticles. Our results …

Electrochemical Nanoprobes For Electron Transfer Kinetics And Electrocatalysis Study, Yun Yu

Dissertations, Theses, and Capstone Projects

The studies of electrochemical processes on the nanoscale have led to a significant progress in understanding of electrochemical mechanisms and characterization of nanomaterials in the fields of energy, catalysis, and biological research. Electrochemical experiments at nanoscale require the fabrication and characterization of nanometer-sized electrochemical probes. The main advantages of the nanoprobes include very fast mass-transfer rate, high signal-to-noise ratio and extremely fine spatial resolution of electrochemical imaging. In the course of my Ph.D. research, different types of electrochemical probes were developed for measuring electron-transfer kinetics, probing single catalytic nanoparticles and sampling ultra-small volume of liquids.

We developed methodologies to fabricate …

Development Of New Radiolabeling Methods And Insights On Ionizing Radiation Interactions With Nanoparticles, Travis Shaffer

Dissertations, Theses, and Capstone Projects

Nanoparticles are often combined with radionuclides for various applications, ranging from waste remediation to imaging and therapy in the medical field. The overarching aim of this body of work is two-fold. The first aim is development of new radiolabeling methods for various nanoparticles that allow stable attachment of a variety of imaging and therapeutic radionuclides. The second portion more fully describes mechanisms of interaction between ionizing radiation and nanoparticles.

The following advancements will be presented in this dissertation: i) a new radiolabeling method for silica and silica-based nanoparticles that does not require the use of specific chelators, with both radiochemical …

Sustainable Molecular Gelators: Beta-D-Glucoside Derived Structuring Agents And Their Material Application, Julian R. Silverman

Dissertations, Theses, and Capstone Projects

Though molecular gelators may by synthesized and formulated into gels following a variety of methods, it should serve that the most valued methods may utilize renewable and waste resources and follow sustainable procedures. Molecular gelators are systems capable of structuring liquids into solid-like materials and they represent a class of surfactant and amphiphilic materials which posses the capability to be not only useful in their ability to form gels, but multifunctional in the ability to respond smartly to a variety of stimuli. Thus there is an interest in the development of sustainable molecular gelators capable of being applied to applications, …

I. Synthesis Of Diverse Structures From Quinone Monoketal And Quinone Imine Ketal With Efficiency And Control Ii. Synthetic Study Of Phalarine, Zhiwei Yin

Dissertations, Theses, and Capstone Projects

Quinonoids are quinone derivatives that have carbonyl or carbonyl equivalent and even number of double bonds embedded in six member rings. As a result of the intrinsic α,β-unsaturated ketone or imine structures, quinonoids, such as quinone monoketals, quinols, quinol ethers and quinone imine ketals, can accommodate a wide range of reactions including 1,2-additon, 1,4-addtion, SN2’ reaction (allylic substitution) to the α-carbon of the carbonyl or imine and cycloaddition reactions (e.g. Diels-Alder reaction). Quinonoids are effective building blocks for synthesizing heterocycles, which are ubiquitous in pharmaceutically useful agents. Developing new quinonoid based methodologies is essential to expanding the boundary of synthetic …

Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed

Dissertations, Theses, and Capstone Projects

Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and …

Metabolic Profiling Of Genetically Modified Potato Periderm Tissues, Liqing Jin

Dissertations, Theses, and Capstone Projects

Potato tubers are protected from dehydration and pathogens by a covering peel (periderm) impregnated with suberin, a complex cross-linked biopolymer that contains both polyaliphatic and lignin-like aromatic domains. Current models describing the macromolecular structure of suberin assume that ferulic acid cross-links both domains as it may form carboxyl ester bonds with aliphatic monomers and non-ester radical-coupled bonds with phenolics. Ferulic acid also links by ester bonds to glycans and acts in cross-linking polysaccharides and lignin. Fatty alcohol/ω-hydroxyacid hydroxycinnamoyl transferase (FHT) is a BADH acyltransferase responsible for the synthesis of akyl-ferulates that is necessary for suberin biosynthesis. Periderm from FHT-RNAi …

Metabolic Profiling And Polymer Formation Of Gene Silenced Potato Periderms, Qing Cai

Dissertations, Theses, and Capstone Projects

Suberin is a biopolyester constituent of specialized plant periderm tissues formed within the phellem cell walls. Suberin and waxes of the periderm layer act to prevent water diffusion, mechanical breakdown and pathogenic invasion in plants. Ferulic esters, ω-hydroxyacids and α,ω-fatty diacids are considered to be the most important linkage between aliphatic and aromatic suberin domains and also linked with cell-wall polysaccharides. The potato gene FHT (fatty ω- hydroxyacid/fatty alcohol hydroxycinnamoyl transferase) esterifies ferulic acid to suberin. Diminished levels of feruloyl transferase activity have been associated with lowered amounts of feruloyl esters of fatty acids in both suberin-associated waxes and suberin …

Nmr Studies Of Electrochemical Energy Storage Materials, Jing Peng

Dissertations, Theses, and Capstone Projects

Electrochemical energy storage materials constitute essential elements in the development of sustainable energy technologies. They are crucial for improving the efficiency of energy storage devices to facilitate the use of renewable resources. The increasing human demands for energy and limitation of fossil fuel stimulates the continued development of energy storage materials. Better understanding of their working mechanisms and electrochemical properties from a view of chemistry is quite necessary for improving the energy storage technology. In this work, Nuclear Magnetic Resonance (NMR) has been used as a powerful tool to characterize the solvation behavior and diffusion ability of some commonly used …

Photodynamic Killing Of Human Cancer Cells With Smart Photosensitizer Materials And An Endoscopic Implement For Singlet Oxygen Delivery, Mihaela N. Minnis

Dissertations, Theses, and Capstone Projects

The thesis describes progress on probe tips for a microoptic device for the precise delivery of the components necessary for photodynamic therapy (PDT) in a highly localized and controllable fashion. The thesis also summarizes results of a photosensitized oxidation study. The work focused on i) developing a photoactive fluoropolymer surface that will release sensitizer drug molecule for use in PDT, ii) designing new probe tips surfaces for use as sensitizer support for a microoptic PDT device, iii) exploring strategies for covalent attachment of sensitizers and model compounds to Teflon/PVA surfaces with the aim of being coupled with our microoptic device, …

Probing The Structure And Photophysics Of Porphyrinoid Systems For Functional Materials, Christopher D. Farley

Dissertations, Theses, and Capstone Projects

Porphyrins (Pors) and their many cousins, including phthalocyanines (Pcs), corroles (Cors), subphthalocyanines (SubPcs), porphyrazines (Pzs), and naphthalocyanines (NPcs), play amazingly diverse roles in biological and non-biological systems because of their unique and tunable physical and chemical properties. These compounds, collectively known as porphyrinoids, can be employed in any number of functional devices that have the potential to address the challenges of modern society. Their incorporation into such devices, however, depends on many structural factors that must be well understood and carefully controlled in order to achieve the desired behavior. Self-assembly and self-organization are key processes for developing these new technologies, …

Free Energy-Based Virtual Screening And Optimization Of Rnase H Inhibitors Of Hiv‑1 Reverse Transcriptase, Baofeng Zhang, Michael P. D'Erasmo, Ryan P. Murelli, Emilio Gallicchio

Publications and Research

We report the results of a binding free energy-based virtual screening campaign of a library of 77 α-hydroxytropolone derivatives against the challenging RNase H active site of the reverse transcriptase (RT) enzyme of human immunodeficiency virus-1. Multiple protonation states, rotamer states, and binding modalities of each compound were individually evaluated. The work involved more than 300 individual absolute alchemical binding free energy parallel molecular dynamics calculations and over 1 million CPU hours on national computing clusters and a local campus computational grid. The thermodynamic and structural measures obtained in this work rationalize a series of characteristics of this system useful …

Electrochemical Properties Of Melting Gel Coatings, Lisa C. Klein, Ahmad Dengah, Kutaiba Al-Marzoki, Gabriela Rodriguez, Andrei Jitianu, Jadra Mosa, Mario Amapricio

Publications and Research

Organic-inorganic melting gel coatings were applied to titanium alloy substrates to decrease their corrosion and extend their lifetime in an electrochemical application. Melting gels containing phenyl substitutions were coated onto the substrates. The ratio of diphenyl dimethoxysilane (DPhDMS) to methanol was varied to change the thickness of the coatings. The coatings were inspected visually to see that there is good adhesion between the coating and the substrate. Nanoindenter tests were performed to determine hardness

Ionophoric Polyphenols Selectively Bind Cu2+, Display Potent Antioxidant And Anti-Amyloidogenic Properties, And Are Non-Toxic Toward Tetrahymena Thermophila, Alberto Martinez, Ralph Alcendor, Tanzeen Rahman, Magdalena Podgorny, Ismaila Sanogo, Rebecca Mccurdy

Publications and Research

Alzheimer’s disease (AD) is the most common form of dementia affecting more than 28 million people in the world. Only symptomatic treatments are currently available. Anticipated tri-fold increase of AD incidence in the next 50 years has established the need to explore new possible treatments. Accumulation of extracellular amyloid-b (Ab) plaques, intracellular tangles in the brain, and formation of reactive oxygen species (ROS) are the major hallmarks of the disease. The active role of some metal ions, especially Cu²⁺, in promoting both Ab aggregation and reactive oxygen species formation has rendered ionophoric drugs as a promising treatment strategy. …

Atomistic Corrective Scheme For Supercell Density Functional Theory Calculations Of Charged Defects, Tengfei Cao, Angelo Bongiorno

Publications and Research

A new method to correct formation energies of charged defects obtained by supercell densityfunctional calculations is presented and applied to bulk, surface, and low-dimensional systems. The method relies on atomistic models and a polarizable force field to describe a material system and its dielectric properties. The polarizable force field is based on a minimal set of fitting parameters, it accounts for the dielectric screening arising from ions and electrons separately, and it can be easily implemented in any software for atomistic molecular dynamics simulations. This work illustrates both technical aspects and applications of the new corrective scheme. The method is …

Photooxidation Chemistry And Photodynamic Therapy: Pointsource Delivery Of Singlet Oxygen, Sensitizer And Nitrosamine Drugs, Ashwini Anil Ghogare

Dissertations, Theses, and Capstone Projects

Eradication of residual tumor cells that are directly adjacent to vital tissue is a daunting challenge to surgeons. Because the field needs advances in intraoperative settings and a means for high-precision delivery of singlet oxygen for photodynamic therapy (PDT) of cancers, this dissertation outlines the development and application of a “pointsource” fiber optic device. The device offers highly localized and simultaneous delivery of sensitizer drug, light, and oxygen (components necessary for PDT) for cancer cell eradication in-vitro and in-vivo. The following chapters describe (a) the photokilling activity and precision of pointsource PDT in monolayer ovarian and brain cancer cells …

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is …

Light-Activated Photocurrent Degradation And Self-Healing In Perovskite Solar Cells, Wanyi Nie, Jean-Christophe Blancon, Amanda J. Neukirch, Kannatassen Appavoo, Hsinhan Tsai, Manish Chhowalla, Muhammad A. Alam, Matthew Y. Sfeir, Claudine Katan, Jacky Even, Sergei Tretiak, Jared J. Crochet, Gautam Gupta, Aditya D. Mohite

Publications and Research

Solution-processed organometallic perovskite solar cells have emerged as one of the most promising thin-film photovoltaic technology. However, a key challenge is their lack of stability over prolonged solar irradiation. Few studies have investigated the effect of light soaking on hybrid perovskites and have attributed the degradation in the optoelectronic properties to photochemical or field-assisted ion migration. Here we show that the slow photocurrent degradation in thin-film photovoltaic devices is due to the formation of light-activated meta-stable deep-level trap states. However, the devices can self-heal completely by resting them in the dark for <1 min or the degradation can be completely prevented by operating the devices at 0°C. We investigate several physical mechanisms to explain the microscopic origin for the formation of these trap states, among which the creation of small polaronic states involving localized cooperative lattice strain and molecular orientations emerges as a credible microscopic mechanism requiring further detailed studies.

A Direct Mechanism Of Ultrafast Intramolecular Singlet Fission In Pentacene Dimers, Eric G. Fuemmeler, Samuel N. Sanders, Andrew B. Pun, Elango Kumarasamy, Tao Zeng, Kiyoshi Miyata, Michael L. Steigerwald, X.-Y. Zhu, Matthew Y. Sfeir, Luis M. Campos, Nandini Ananth

Publications and Research

Interest in materials that undergo singlet fission (SF) has been catalyzed by the potential to exceed the Shockley–Queisser limit of solar power conversion efficiency. In conventional materials, the mechanism of SF is an intermolecular process (xSF), which is mediated by charge transfer (CT) states and depends sensitively on crystal packing or molecular collisions. In contrast, recently reported covalently coupled pentacenes yield ∼2 triplets per photon absorbed in individual molecules: the hallmark of intramolecular singlet fission (iSF). However, the mechanism of iSF is unclear. Here, using multireference electronic structure calculations and transient absorption spectroscopy, we establish that iSF can occur via …