Chemistry Commons^™

Toward The Probing Of Dhqs Activity By Protein Engineering Through The Introduction Of Unnatural Amino Acids And The Selection Of Trna/Trna Synthetase Pairs, Shaina E. Ives

Department of Chemistry: Dissertations, Theses, and Student Research

Protein engineering is a valuable tool that allows scientist to explore how an enzyme works by mutation of key residues. This method has been used to improve function or stability of enzymes, thus allowing their use in both the lab and in industry to be expanded. Genetic incorporation of unnatural amino acids (unAA) can be used with protein engineering to exceed the current limitations, due to the limited number of functional groups of the 20 common amino acids.

The majority of this thesis will discuss the progress on incorporating the various unAA into the active site of the enzyme, Dehydroquinate …

Hybrid Aryl-Ether-Ketone And Hyperbranched Epoxy Networks, John Misasi

Dissertations

In this dissertation, relationships between chemical structures, cure kinetics and network architectures are correlated to bulk mechanical properties for novel, hybrid epoxy-amine networks. The work is split into two primary sections: the first is the synthesis and characterization of multifunctional glassy networks based on aryl-ether-ketone diamine curatives, while the second is based on the synthesis and characterization of hyperbranched epoxy polymers and their resulting networks.

Three aryl-ether-ketone (AEK) diamines of increasing molecular weights were synthesized and used to cure 4,4’-tetraglycidylether of diaminodiphenylmethane (TGDDM); the resulting networks were compared to 4,4’-diaminodiphenyl sulfone cured TGDDM. Architectural differences were created by varying cure …

Development Of Dual-Cure Hybrid Polybenzoxazine Thermosets, Jananee Narayanan Sivakami

Dissertations

Polybenzoxazines are potential high performance thermoset replacements for traditional phenolic resins that can undergo an autocatalytic, thermally initiated ring - opening polymerization, and possess superior processing advantages including excellent shelf-life stability, zero volatile loss and limited volumetric shrinkage. The simplistic monomer synthesis and availability of a wide variety of inexpensive starting materials allows enormous molecular design flexibility for accessing a wide range of tailorable material properties for targeted applications. Despite the fact, once fully cured, benzoxazines are difficult to handle due to their inherent brittleness, leaving a very little scope for any modifications. The motivation of this dissertation is directed …

Asymmetric Synthesis Of Cα-Methyl-Γ- And Δ-Amino Acids From A Common Synthon And Evaluation Of Thionyl Chloride Assisted Peptide Esterifications, Emily Rose Vogel

Dissertations

C^α-methyl-γ- and δ-unnatural amino acids (UAAs) are important class of biomolecules used extensively as structural scaffolds, peptidomimetics, and in the development of pharmaceuticals. Due to steric congestion surrounding the quaternary center, asymmetric preparation of α,α-disubstituted UAAs are synthetically challenging. Herein, two methods for the synthesis of chiral synthons to prepare C^α-methyl-γ- and -δ-UAAs are reported. A crucial step in both strategies includes an enzymatic hydrolysis of prochiral malonic esters with pig liver esterase (PLE). The first method utilizes the Meyer Schuster rearrangement to prepare α,β-unsaturated diesters synthons, but the preparation of the precursor propargyl alcohol decomposes …

Hydrogen Bond-Mediated Structural Order In Hydroxylated Bis-Mpa Dendritic Polymers: Experimental And Molecular Dynamics Simulation Study, Maliha N. Syed

Dissertations

Dendritic architectures are echoed throughout nature. While the significance of these pervasive patterns is not entirely clear, connections between their structures and physical properties are fascinating to contemplate. Particular interest has been paid to a family of synthetically manufactured and commercially available dendritic polymers based on 2,2-bis(hydroxymethyl) propionic acid (bis-MPA) as a monomer. Composed of two hydroxyls and a carboxyl group, bis-MPA based structures hydrogen bond (H-bond) profusely. Given the high concentration and unique spatial orientation of end-groups, as well as the multitude of carbonyl, ester, and ether interior H-bond acceptors, a set of distinct H-bond organizations may be observed …

Validation Of The Global Distribution Of Co2 Volume Mixing Ratio In The Mesosphere And Lower Thermosphere From Saber, L. Rezac, Y. Jian, J. Yue, J. M. Russell Iii, A. Kutepov, R. Garcia, K. Walker, P. Bernath

Chemistry & Biochemistry Faculty Publications

The Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on board the Thermosphere Ionosphere Mesosphere Energetics and Dynamics satellite has been measuring the limb radiance in 10 broadband infrared channels over the altitude range from ~ 400 km to the Earth's surface since 2002. The kinetic temperatures and CO₂ volume mixing ratios (VMRs) in the mesosphere and lower thermosphere have been simultaneously retrieved using SABER limb radiances at 15 and 4.3 μm under nonlocal thermodynamic equilibrium (non-LTE) conditions. This paper presents results of a validation study of the SABER CO₂ VMRs obtained with a two-channel, self-consistent …

Data In Support Of Ubsrd: The Ubiquitin Structural Relational Database, Joseph S. Harrison, Tim M. Jacobs, Kevin Houlihan, Koenraad Van Doorslaer, Brian Kuhlman

College of the Pacific Faculty Articles

This article provides information to support the database article titled "UbSRD: The Ubiquitin Structural Relational Database" (Harrison et al., 2015) [1] . The ubiquitin-like homology fold (UBL) represents a large family that encompasses both post-translational modifications, like ubiquitin (UBQ) and SUMO, and functional domains on many biologically important proteins like Parkin, UHRF1 (ubiquitin-like with PDB and RING finger domains-1), and Usp7 (ubiquitin-specific protease-7) (Zhang et al., 2015; Rothbart et al., 2013; Burroughs et al., 2012; Wauer et al., 2015) [2], [3], [4], [5]. The UBL domain can participate in several unique protein-protein interactions (PPI) since protein adducts can be attached …

Facile Sol-Gel Molten Salt Synthesis Of Double Perovskite La 2nimno6 As An Electrocatalyst For Oxygen Evolution Reactions, Padmini Kukkapalli

Theses and Dissertations

Double perovskites have attracted a great attention recently for its high intrinsic activity in oxygen evolution reaction (OER) in electrochemical energy storage and conversion systems in alkaline media. In this study, we are the first to report the new approach of La2NiMnO6 double perovskite which was synthesized via Sol-gel molten-Salt synthesis method. However their stability and specific activity remain challenging that need to be addressed to meet the reqiurement for OER activities. Here in this study we synthesized three different samples with varying concentrations by taking molten salts NaNO 3 and KNO3 in (1:1) ratio such as 30:30, 60:60, 90:90. …

Advanced Data Analysis Tools And Multi-Instrument Material Characterization, Bhupinder Singh

Theses and Dissertations

My dissertation focuses on (i) the development of new analysis tools and methodologies for analyzing X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) data, and (ii) the comprehensive characterization of materials (nanodiamonds) using a multi-instrument approach. Chapter 1 contains (i) a discussion of the two techniques I focused on most in my work: XPS and ToF-SIMS, (ii) a discussion of the common chemometrics techniques used to analyze data from these methods, and (iii) the advantages/rationale behind the multi-instrument characterization of materials. Chapter 2 describes various good practices for obtaining reasonable peak fits in XPS, which can also …

Electrochemical Formation Of One-Dimensional Metal Nanostructures Across Microgaps Electrodes For Resistive Switching And Optical Sensing Applications., Nidhi Shah

Electronic Theses and Dissertations

This dissertation focuses on the electrochemical formation of one-dimensional (1D) Ag nanostructures (in particular nanowires and nanochains) directly on electrode surfaces or gap of two electrodes. Ag nanowires (NWs) and nanorods (NRs) grow directly on glass/indium tin oxide (ITO) surfaces from electrode-attached Au nanoparticle seeds in the presence of cetyltrimethylammonium bromide (CTAB) at appropriate potentials with a 5-15 % yield and the average length ranging from 100 nm to 3 µm for growth times of 30 to 120 min. This method failed when trying to grow Ag NRs/NWs across 5 µm Au electrode gaps. Interestingly, applying voltage in air leads …

Molecular Modeling And Mutational Mapping Of The Gpr119 Binding Site, Shane M. Askar

Theses and Dissertations

GPR119 receptor’s biological role in regulating glucose homeostasis has been studied extensively. Results in the scientific literature indicate that, when activated, GPR119 releases insulin in a glucose dependent manner. Currently the 3D structure of GPR119 has not been resolved.

The goal of this research is to use a combination of homology modeling and ligand docking studies to predict the binding mode of GPR119 ligands. Amino acids implicated to have direct interactions with docked ligands will further be assessed experimentally for their roll in binding and activation of GPR119. Our results indicate that residues W2656.48 and R813.28 are likely to be …

The Unique Electrochemical Reactivity Of Small Metal Nanoparticles., Rafael A. Masitas

Electronic Theses and Dissertations

This dissertation describes the factors controlling metal nanoparticle (NP) oxidation, using Au oxidation in Br- and Ag oxidation in acid as model systems. We found that the oxidation potential depends on size, surface charge, and electrode material. Size has a dramatic effect, shifting about 200 mV from > 200 nm diameter down to 4 nm diameter. The shift is more dramatic below 4 nm. 2.3 nm average diameter Au NPs oxidized in the 300-500 mV range and 1.5 nm average diameter Au NPs displayed several sharp peaks from 200 mV to as low as -200 mV. These smallest Au NPs show …

Chemical And Electronic Structure Of Surfaces And Interfaces In Cadmium Telluride Based Photovoltaic Devices, Douglas Arthur Duncan

UNLV Theses, Dissertations, Professional Papers, and Capstones

The surface and interface properties are of the upmost importance in the understanding, optimization, and application for photovoltaic devices. Often the chemical, electronic, and morphological properties of the films are empirically optimized, however when progress slows, a fundamental understanding of these properties can lead to breakthroughs. In this work, surfaces and interfaces of solar cell-relevant films are probed with a repertoire of X-ray analytical and microanalysis techniques including X-ray photoelectron (XPS), X-ray excited Auger electron (XAES), X-ray emission (XES) spectroscopies, and atomic force (AFM) and scanning electron (SEM) microscopies.

Silicon-based devices currently dominate the solar market, which is rather inflexible …

Crystal Structure Of (E)-13-(Pyrimidin-5-Yl)Parthenolide, Shobanbabu Bommagani, Narsimha Reddy Penthala, Sean Parkin, Peter A. Crooks

Chemistry Faculty Publications

The title compound, C₁₉H₂₂N₂O₃, {systematic name (1aR,4E,7aS,8E,10aS,10bR)-1a,5-dimethyl-8-[(pyrimidin-5-yl)­methylid­ene]-2,3,6,7,7a,8,10a,10b-octa­hydro­oxireno[2′,3′:9,10]cyclo­deca­[1,2-b]furan-9(1aH)-one} was obtained from the reaction of parthenolide [systematic name (1aR,7aS,10aS,10bR,E)-1a,5-dimethyl-8-methyl­ene-2,3,6,7,7a,8,10a,10b-octa­hydro­oxireno[2′,3′:9,10]cyclodeca­[1,2-b]furan-9(1aH)-one] with 5-bromo­pyrimidine under Heck reaction conditions, and was identified as an E isomer. The mol­ecule possesses ten-, five- (lactone) and three-membered (epoxide) rings with a pyrimidine group as a substituent. The ten-membered ring displays an approximate chair–chair conformation, while the lactone ring shows a flattened …

Assessment And Comparison Of The Electronic Properties Of Group 10 Bimetallic Nanoparticles Relative To Their Monometallic Counterparts, Ali Bolandi

Dissertations

Group 10 transition metals with nanoscale dimensions offer significant advantages over their bulk counterparts. Significant work has been devoted toward studying the benefits of their catalytic efficiencies, however, less has been dedicated toward understanding their electronic properties and how such changes influence charge storage and sensor efficiency. The dissertation work focuses on designing metallic and bimetallic nanoparticles consisting of nanoscale Group 10 transition metals with welldefined structures, prepared using a facile synthetic procedure. The nanoparticles were characterized by electron microscopy, spectroscopic and x-ray techniques. The efficiency of monometallic and bimetallic nanoparticles toward electron storage was investigated electrochemically and by optical …

Design And Synthesis Of New Non-Steroidal Anti-Inflammatory Drugs With Anti-Cancer Activity On Colon Rectal Cancer Cell Lines Hct-116 And Caco-2, Wanda Ivette Rodríguez Rivera

Dissertations

Colon rectal cancer is one of the most common types of cancer and is the third leading cause of cancer related deaths among western countries. Current chemotherapy treatments are highly toxic and mostly result in only a low percentage of tumor reduction; therefore an effective treatment with low toxicity is needed.

In this study, different innovative new COX-2 inhibitors were synthesized using the frame of biologically active chalcones to which active COX-2 pharmacophores SO₂CH₃, SO₂NH₂, SO₂NHCOCH₃ were added. Additionally, the effect of different alkyl chain lengths and the effect …

Tracking Anisotropic Optical Tracers To Study Biophysical Processes And Cytotoxicity, Khanh Van Nguyen

All Dissertations

We use anisotropic optical tracers (also called magnetically modulated optical nanoprobes – MagMOONs or MOONs for non-magnetic nanoprobes in this dissertation) to study biophysical processes such as enzyme-catalyzed cleavage through tissue, intracellular transport of these tracers and cytotoxicity based on this transport. The anisotropic optical properties cause these tracers to blink when rotating. This blinking is distinguishable from the background and can be tracked on a single-particle level in the absence of tissue, or for an ensemble average of tracers blinking through tissue. An alginate gel containing these tracers in the form of a thin film can be used as …

Bombardment Simulations And Intercalation Studies Of Carbon Materials, Charles Lowe

All Dissertations

Molecular bombardment experiments have led to the possibility of altering materials with properties not normally associated with those materials. Molecular bombardment leads to defect formation in the material, potentially creating a pore, depending on the material and bombarding molecule. Carbon allotropes, specifically graphite and graphene, make excellent candidates for molecular bombardment experimentation. Depending on the bombarding molecule and the kinetic energy associated with that molecule, the defects induced will be sufficient to create a pore in the graphene. The AIREBO potential is used to simulate a graphene bilayer being bombarded with a single Ar atom, or a fullerene molecule, to …

Production And Characterization Of Cut Resistant Acrylic/Copolyaramid Fibers Via Bicomponent Wet Spinning, Stephen Hipp

All Dissertations

A composite fiber system consisting of a sheath core bicomponent polymer fiber loaded with hard ceramic particles was developed and characterized for use in cut protective clothing. The core component was comprised of a copolyaramid in order to provide high base cut resistance. An acrylic-copolyaramid polymer blend was used for the sheath component to improve processability and provide potential benefits such as dyeability. Lastly, aluminum oxide particles were incorporated into the fiber core to deflect and deform the cutting edge, further improving cut resistance. A series of designed experiments was used to explore the effects of the wet spinning and …

High Temperature Synthesis And Characterization Of Reduced Polyoxometalate Salt-Inclusion Solids, Dino Sulejmanovic

All Dissertations

Herein, several new salt-inclusion solids (SISs) featuring electronically reduced Keggin polyoxometalate (POM) clusters were isolated for the first time using molten-salt high temperature (> 500 oC) synthetic method. These POM-based SISs are novel all-inorganic materials featuring an integrated lattice of ionic halide salt and covalent metal oxide clusters. Due to the weak interactions at the interface between these two chemically dissimilar lattices, these POM SISs are soluble in aqueous and polar solvents. While POM compounds are well-studied and are routinely synthesized in solution, the synthetic method presented in this dissertation yielded several POM solids with interesting structures and infrequently observed, …

Towards A Greater Understanding Of Hydrothermally Grown Garnets And Sesquioxide Crystals For Laser Applications, Cheryl Moore

All Dissertations

ABSTRACT The hydrothermal method of crystal growth offers many benefits over traditional melt-based techniques such as lower temperature requirements relieving detrimental high temperature effects such as stress fracturing and a closed-environment, which limits impurities. The continued study of this type of growth including hydrothermal epitaxy is crucial in our world of constant miniaturization. Presented in this thesis is the hydrothermal growth of crystals of LuAG and Lu2O3 doped with a variety of dopants. Their room-temperature and cryogenic absorption spectra are also presented. Much like Nature uses heat, pressure, water and a nutrient-rich feedstock we have used this hydrothermal technique to …

Understanding How Synthetic Organic Chemistry Graduate Students Navigate Scifinder, Lindsey Whitfield Cain

All Dissertations

Students pursuing a Ph.D. degree are expected to contribute research to their field, for which the success depends, in part, on their ability to find, interpret, and use scholarly information from the primary literature. However, studies from the information sciences show that graduate students from a variety of fields, including the sciences, frequently struggle to comprehensively search their respective dissertation topics because of insufficient prior content knowledge and lack of guidance from their disciplinary community. This body of literature is consistent with the results of my previous research of chemistry graduate students’ laboratory decision-making processes. Specifically, that study showed their …

Influence Of Shelling Temperature And Time On The Optical And Structural Properties Of Cuins2/Zns Quantum Dots, Colette Robinson

Graduate Theses and Dissertations

CIS/ZnS core/shell QDs are an important class of nanomaterials for optoelectronic, photovoltaic and photoluminescence applications. They consist of lower toxicity materials than the prototypical II-VI Cd-based QDs and show long fluorescence lifetimes, which generates prospective in biological imaging applications. It is vital to develop reproducible synthetic methods for this new class of nanomaterials in order to maintain small sizes with high QYs. CIS core QDs have been shelled with ZnS at various temperatures from 90-210°C for reaction times ranging from 20-140 minutes to examine the role of thermodynamics and kinetics on the shell growth. Using HR-TEM and ICP-MS, it was …

Photochemistry Of A Series Of Weakly Coupled Dinuclear Ruthenium(Ii) Complexes, Latisha Michelle Puckett

Graduate Theses and Dissertations

An improved synthetic method was developed for symmetric ruthenium(II) polypyridine complexes with the form L2Ru(diphen)RuL2. The scope of the reaction was investigated in regards to the ligands, bridging ligands, and starting materials. Several ligands were successful in the synthesis, including 2,2’-bipyridine (bpy), 4,4’-dimethyl-2,2’-dipyridyl (dmb), 1,10-phenanthroline (phen), 4,7-diphenyl-1,10-phenanthroline (dpphen), and 3,4,7,8-tetramethyl-1,10-phenanthroline (tmphen). Ligands that did not react to form symmetric dimeric complexes were 2,2’-bipyrazine, bpz, and 2,2’-bipyrimidine, bpm.

Dpp, 2,3-bis(2-pyridyl)-pyrazine, effectively replaced diphen as the bridging ligand to produce (phen)2Ru(dpp)Ru(phen)24+. However, replacing the [Ru(CO)2Cl2]n with Ru(DMSO)4Cl2 did not prove successful. The newly developed synthesis was also applied to the synthesis of …

Syneresis And Rheology Mechanisms Of A Latex-Heur Associative Thickener System, Travis Bruno Smith

Master's Theses

Rheology modifiers are used in paints and coatings to ease their application to a surface, prevent sagging once applied, and allow the leveling of brushstrokes, among other benefits. The early rheology modifiers were hydroxyethyl celluloses (HECs), a type of non-associative thickener that is relatively inexpensive and synthesized from cellulose, which is abundant. However, coatings that are modified with HECs tend to suffer from poor leveling and syneresis (phase separation). HECs have since been replaced with associative thickeners (ATs). These thickeners, when properly formulated, produce stable dispersions that have improved rheological properties, yet, unlike HECs, are sensitive to changes to the …

A Circle Has No End: Role Of Cyclic Topology And Accompanying Structural Reorganization On The Hole Distribution In Cyclic And Linear Poly‑P‑Phenylene Molecular Wires, Marat R. Talipov, Ramesh Jasti, Rajendra Rathore

Chemistry Faculty Research and Publications

π-Conjugated organic oligomers/polymers hold great promise as long-range charge-transfer materials for modern photovoltaic applications. However, a set of criteria for the rational design of functional materials is not yet available, in part because of a lack of understanding of charge distribution in extended π-conjugated systems of different topologies, and concomitant effects on redox and optical properties. Herein we demonstrate the role of cyclic versus linear topology in controlling the redox/optical properties and hole distribution in poly-p-phenylenes (PPs) with the aid of experiment, computation, and our recently developed multistate parabolic model (MPM). It is unequivocally shown that the hole …

Direct Observation Of Photoinduced Charge Separation In Ruthenium Complex/Ni(Oh)2 Nanoparticle Hybrid, Yu Tang, Brian Pattengale, John Ludwig, Abderrahman Atifi, Alexander V. Zinovev, Bin Dong, Qingyu Kong, Xiaobing Zuo, Xiaoyi Zhang, Jier Huang

Chemistry Faculty Research and Publications

Ni(OH)₂ have emerged as important functional materials for solar fuel conversion because of their potential as cost-effective bifunctional catalysts for both hydrogen and oxygen evolution reactions. However, their roles as photocatalysts in the photoinduced charge separation (CS) reactions remain unexplored. In this paper, we investigate the CS dynamics of a newly designed hybrid catalyst by integrating a Ru complex with Ni(OH)₂ nanoparticles (NPs). Using time resolved X-ray absorption spectroscopy (XTA), we directly observed the formation of the reduced Ni metal site (~60 ps), unambiguously demonstrating CS process in the hybrid through ultrafast electron transfer from Ru complex to …

Unveiling The Crucial Intermediates In Androgen Production, Piotr J. Mak, Michael C. Gregory, Ilia G. Denisov, Stephen G. Sligar, James R. Kincaid

Chemistry Faculty Research and Publications

Significance: The human enzyme cytochrome P450 17A1 (CYP17A1) catalyzes the critical step in the biosynthesis of the male sex hormones, and, as such, it is a key target for the inhibition of testosterone production that is necessary for the progression of certain cancers. CYP17A1 catalyzes two distinct types of chemical transformations. The first is the hydroxylation of the steroid precursors pregnenolone and progesterone. The second is a different reaction involving carbon–carbon (C-C) bond cleavage, the mechanism of which has been actively debated in the literature. Using a combination of chemical and biophysical methods, we have been able to trap and …

Hand-Portable Capillary Liquid Chromatography Instrumentation, Sonika Sharma

Theses and Dissertations

This dissertation focuses on the development of hand-portable capillary liquid chromatography (LC) instrumentation. In this work, battery-operable nano-flow pumping systems (isocratic and gradient) were developed and integrated with portable UV-absorption detectors for capillary LC. The systems were reduced in size to acceptable weights and power usage for field operation. A major advantage of the pumps is that they do not employ a splitter, since they were specifically designed for capillary column use, thereby greatly reducing solvent consumption and waste generation. UV-absorption detectors were specifically designed and optimized for on-column detection to minimize extra-column band broadening. Initially, an isocratic nano-flow pumping …

High Flow Air Sampler For Rapid Analysis Of Volatile And Semi-Volatile Organic Compounds, Xiaofeng Xie

Theses and Dissertations

Volatile and semi-volatile organic compounds are ubiquitous, and some of them are hazardous. The ability to rapidly detect and identify trace levels of them in air has become increasingly important. The conventional device used today for sampling and concentrating them in air is thermal desorption tubes filled with specific sorbents, which can only collect air samples at flow rates of 100-200 mL/min. In order to detect low concentration (ppt level) VOC compounds, long sampling time (>2 h) and sensitive detection are required. At the same time, portable instrumentation for on-site analysis has been developing rapidly. The somewhat lower performance …