Chemistry Commons^™

Monitoring Crystal Structure Refinements Using Solid-State Nmr Chemical Shift Tensors, Keyton Kalakewich

Electronic Theses and Dissertations

Inclusion of lattice-fields in density functional theory (DFT) methods has enabled the accurate calculation of solid-state nuclear magnetic resonance (SSNMR) chemical shift tensors. Calculated 13C and 15N tensors (i.e. 3 principle values per nucleus) can be used to monitor crystal structure refinements and to select the correct structure from a large population of computationally generated candidates. In this dissertation, chapter 2 describes a methodology to improve established crystal structures from three different diffraction techniques involving geometric refinement monitored using SSNMR tensor values. The calculated 13C tensors for three relatively simple organic compounds (i.e. acetaminophen, naphthalene, and adenosine) are shown to …

Do Elevated Levels Of Glutathione Decrease The Toxicity Of Plasticizers In Mouse Liver Cells?, Khatoon Albahrani

All Master's Theses

Phthalates are esters of phthalic acid that play a crucial role in the manufacturing industries for enhancing the properties of plastic materials. Di-(2-ethylhexyl) phthalate (DEHP) is one of the most common phthalates used in a variety of products including food packaging and medical equipment. Their use has caused public health concerns because of their toxic effects on reproductive and developmental processes. This study aims to investigate the response of two mouse hepatoma cell lines to the effects of DEHP and its bioactive metabolite mono (2-ethylhexyl) phthalate (MEHP). Cells were exposed to four concentrations (10, 50, 100, and 300 µM) of …

The T6a Modification Acts As A Positive Determinant For The Anticodon Nuclease Prrc, And Is Distinctively Nonessential In Streptococcus Mutans, Jo Marie Bacusmo, Silvia S. Orsini, Jennifer Hu, Michael Demott, Patrick C. Thiaville, Ameer Elfarash, Mellie June Paulines, Diego Rojas-Benítez, Birthe Meineke, Christopher Deutsch, Dirk Iwata-Reuyl, Patrick A. Limbach, Peter C. Dedon, Kelly C. Rice, Stewart Shuman, Valérie De Crécy-Lagard

Chemistry Faculty Publications and Presentations

Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNALys UUU in the anticodon loop. In vitro studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t⁶A) is required for PrrC activity but this prediction had never been validated in vivo. Here, by using t⁶A-deficient yeast derivatives, it is shown that t⁶A is a positive determinant for PrrC proteins from various bacterial species. Streptococcus mutans is one of the few bacteria where the t …

Tropospheric Ozone Assessment Report: Database And Metrics Data Of Global Surface Ozone Observations, Martin G. Schultz, Sabine Schroder, Oleg Lyapina, Owen Cooper, Ian Galbally, Irina Petropavlovskikh, Lynn Mazzoleni, Et Al.

Department of Chemistry Publications

In support of the first Tropospheric Ozone Assessment Report (TOAR) a relational database of global surface ozone observations has been developed and populated with hourly measurement data and enhanced metadata. A comprehensive suite of ozone data products including standard statistics, health and vegetation impact metrics, and trend information, are made available through a common data portal and a web interface. These data form the basis of the TOAR analyses focusing on human health, vegetation, and climate relevant ozone issues, which are part of this special feature.

Cooperation among many data centers and individual researchers worldwide made it possible to build …

Energetic Effects Of Hole Transporting Materials On The Performance Of Organometal Halide Perovskite Photovoltaic Cells, So Min Park

Theses and Dissertations--Chemistry

Efficient, inexpensive, lightweight and flexible solar cells are desired to help meet the world’s growing energy needs. Organometal halide perovskite (OMHP) photovoltaic (PV) cells have shown dramatic increases in solar cell efficiencies increase over the last 5 years. OMHP PV cells have attracted significant attention due to their broad absorption spectra, high electron and hole mobility, and low production cost. The interface between hole transporting layer (HTL) and perovskite thin films have a significant influence on charge transfer and overall solar cell performance. 2,2’,7,7’-tetrakis(N,N-di-p-methoxyphenylamine)9,9’-spirobifluorene (Spiro-OMeTAD) is a small molecule largely used as HTL in perovskite solar cells. However, this material …

Biomimetic Devices To Drive A Thermodynamically Uphill Reaction Using Light And To Degrade Industrial Waste Stream Components, Madison Joanne Sloan

Theses and Dissertations--Chemistry

Given the amount of industrial waste produced each year, as well as the accruing amount of greenhouse gases in our atmosphere produced by the burning of fossil fuels, it is imperative that humanity develop environmentally-sustainable sources of energy and methods of remediation. Nature achieves both of these by use of enzymes as catalysts, inspiring interest in designing biomimetic systems capable of harnessing clean energy and remediating industrial waste. This study examined the ability of enzymes in electrochemical and convective flow systems to achieve these tasks. The first portion studied the incorporation of enzymes into an electrochemical system to drive the …

Oxidative Stress And Proteomic Studies Of Mammalian Models Of Age-Related Metabolic Dysfunction In Neurodegenerative Disorders, Aaron M. Swomley

Theses and Dissertations--Chemistry

Expression proteomics is the field of science wherein proteins that make up the cellular proteome are identified both by name and by fold-change. Depending on the application of proteomics, this change in level could be due to internal cellular stressors or introduction of xenobiotics. Global oxidative stress measures use immunohistochemistry to determine the relative level of oxidative stress of macromolecules within the cell. In this dissertation, both global oxidative stress measures and expression proteomics were used in a variety of mammalian models in order to determine the effects of protein upregulation, intranasal insulin administration, and resveratrol supplementation on the cellular …

Mechanisms Of Heterogeneous Oxidations At Model Aerosol Interfaces By Ozone And Hydroxyl Radicals, Elizabeth A. Pillar-Little

Theses and Dissertations--Chemistry

Atmospheric aerosols play an important role in climate by scattering and absorbing radiation and by serving as cloud condensation nuclei. An aerosol’s optical or nucleation properties are driven by its chemical composition. Chemical aging of aerosols by atmospheric oxidants, such as ozone, alters the physiochemical properties of aerosol to become more hygroscopic, light absorbing, and viscous during transport. However the mechanism of these transformations is poorly understood. While ozone is a protective and beneficial atmospheric gas in the stratosphere, it is a potent greenhouse gas in the troposphere that traps heat near the Earth’s surface. It also impacts human heath …

Heterogeneous Base Metal Catalyzed Oxidative Depolymerization Of Lignin And Lignin Model Compounds, John Adam Jennings

Theses and Dissertations--Chemistry

With the dwindling availability of petroleum, focus has shifted to renewable energy sources such as lignocellulosic biomass. Lignocellulosic biomass is composed of three main constituents, lignin, cellulose and hemicellulose. Due to the low value of cellulosic ethanol, utilization of the lignin component is necessary for the realization of an economically sustainable biorefinery model. Once depolymerized, lignin has the potential to replace petroleum-derived molecules used as bulk and specialty aromatic chemicals. Numerous lignin depolymerization strategies focus on cleavage of β-aryl ether linkages, usually at high temperatures and under reductive conditions.

Alternatively, selective benzylic oxidation strategies have recently been explored for …

Semiconductor Photocatalysis: Mechanisms, Photocatalytic Performances And Lifetime Of Redox Carriers, Ruixin Zhou

Theses and Dissertations--Chemistry

Photocatalytic reactions mediated by semiconductors such as ZnS, TiO₂, ZnO, etc. can harvest solar energy into chemical bonds, a process with important prebiotic and environmental chemistry applications. The recycling of CO₂ into organic molecules (e.g., formate, methane, and methanol) facilitated by irradiated semiconductors such as colloidal ZnS nanoparticles has been demonstrated. ZnS can also drive prebiotic reactions from the reductive tricarboxylic acid (rTCA) cycle such as the reduction of fumarate to succinate. However, the mechanism of photoreduction by ZnS of the previous reaction has not been understood. Thus, this thesis reports the mechanisms for heterogeneous photocatalytic reductions …

Characterization And Application Of Hybrid Nanostructures For Enhanced Biological Imaging Using Fluorescence Microscopy Techniques, William E. Martin

Theses and Dissertations--Chemistry

Fluorescence microscopy is a powerful tool for interpreting the structure and function of biomolecules, and their interactions with one another. Understanding fundamental biological mechanisms is important to the development of improved treatments for a variety of diseases. Fluorescent tags are used to track the motion and longevity of such events, with the ability to monitor several biomolecules at once. Currently, many of these studies are conducted using bulk measurements, or several biological events at the same time, because the added light from several emitters can more easily overcome the high fluorescence background inherent to biological systems. Although important in their …

Interactions Of Compounds Containing Group 12 And 16 Elements, Daniel Burriss

Theses and Dissertations--Chemistry

The focus of this dissertation is on the interactions of compounds containing group 12 and 16 elements. This work is presented in three major parts. First, the interaction of the synthetic dithiol N,N’-bis(2-mercaptoethyl)isophthalamide), abbreviated BDTH₂, with selenite. Second, the interaction of cysteine with Cd(II) and the biologically relevant Cd-Cysteine crystal structure. Third, the green synthesis of CdSe quantum dots (QDs).

The interaction of BDTH₂ with selenite is different from the interactions with other metals and metalloids previously studied. Under ambient conditions, BDTH₂ is oxidized to the disulfide, BDT(S-S), while selenite is reduced to elemental selenium. However, …

Epigenetic Modifications To Cytosine And Alzheimer’S Disease: A Quantitative Analysis Of Post-Mortem Tissue, Elizabeth M. Ellison

Theses and Dissertations--Chemistry

Alzheimer’s disease (AD) is the most common form of dementia and the sixth leading cause of death in the United States, with no therapeutic option to slow or halt disease progression. Development of two characteristic pathologic lesions, amyloid beta plaques and neurofibrillary tangles, in the brain are associated with synaptic dysfunction and neuron loss leading to memory impairment and cognitive decline. Although mutations in genes involved in amyloid beta processing are linked to increased plaque formation in the inherited familial form of AD, the more common idiopathic form, termed sporadic AD, develops in the absence of gene mutations. In contrast, …

Charge Transport In Electronic-Ionic Composites, Long Zhang

Theses and Dissertations--Chemical and Materials Engineering

The goal of this thesis is to generate fundamental understandings of charge transport behaviors of composites consisting of garnet structured Al substituted Li₇La₃Zr₂O₁₂ (LLZO) electrolyte and LiCoO₂ electrode. In order to take full advantage of all-solid-state batteries, bulk type composite electrodes should be introduced to increase energy and power density. However, the charge utilization of bulk type composite electrodes is quite low. Understanding ionic conduction behavior is, therefore, important for improving the performance of all-solid-state batteries, because ion conduction within solids depends on effective pathways. Electronic conductivity can be easily compensated by …

Formation Of The Ether Bridge In The Loline Alkaloid Biosynthetic Pathway, Minakshi Bhardwaj

Theses and Dissertations--Chemistry

Lolines are specialized metabolites produced by endophytic fungi, such as Neotyphodium and Epichloë species, that are in symbiotic relationships with cool-season grasses. Lolines are vital for the survival of the grasses because their insecticidal and antifeedant properties protect the plant from insect herbivory. Although lolines have various bioactivities, they do not have any concomitant antimammalian activities.

Lolines have complex structures that are unique among naturally occurring pyrrolizidine alkaloids. Lolines have four contiguous stereocenters, and they contain an ether bridge connecting C(2) and C(7) of the pyrrolizidine ring. An ether bridge connecting bridgehead C atoms is unusual in natural products and …

Photoluminescence Mechanism And Applications Of Graphene Quantum Dots, Yiyang Liu

Theses and Dissertations--Chemistry

Graphene quantum dots (GQDs) are small pieces of graphene oxide whose physical dimensions are so confined (a few to a few tens nm) that they have a finite bandgap due to a quantum confinement effect. The finite bandgap of GQDs grants them pronounced absorption bands and a substantial photoluminescence. These optical properties are rarely observed in traditional carbon materials, since most of carbon materials are metallic with a near-zero bandgap and thus have broad absorption spectra with no photoluminescence. The unique optical properties of GQDs, along with GQDs’ inherited advantages from carbon material family (cheap, abundant, non-toxic), make GQDs an …

Arsenic Removal With A Dithiol Ligand Supported On Magnetic Nanoparticles, John Hamilton Walrod Ii

Theses and Dissertations--Chemistry

Exposure to arsenic (As) in water, the ubiquitous toxin that poses adverse health risks to tens of millions, is the result of both anthropogenic and geochemical mobilization. Despite recent publicity and an increased public awareness, the dangers associated with arsenic exposure rank among the top priorities of public health agencies globally. Existing sequestration applications mainly include reductions and adsorption with zero-valent metals and their oxides. The performance of adsorption media is known to preferentially favor aqueous As(V) over As(III) due to the charge of the dissolved oxyanion. Magnetic nanoparticles (MNP) have been the focus of multidisciplinary research efforts for the …

Synthesis And Characterization Of Cu(Ii)-Cu(I) Mixed Valence Complexes, Hansani T. Lekam Wasam Liyanage

Masters Theses

Our study was focused on synthesis and characterization of new family of metal complexes that mimic the active site of copper containing enzymes. Our approach focused on preparing a series of metalloligands which vary systematically in structure and use them in combination with additional metallic centers to synthesize our desired complexes.

We synthesized a main ligand, which is named as HL^Q 2Pz, which contain a quinoline body, one amide bond and two pyrazolyl rings. We synthesized a copper complex by deprotonating HL^Q 2Pz using KOH. The ligand coordinated to the copper(II) center through its quinoline nitrogen, two of …

Exploring The Structure And Properties Of Nanomaterials Using Advanced Electron Microscopy Techniques, Yao-Jen Chang

Theses and Dissertations--Chemistry

Nowadays people are relying on all kinds of electronic devices in their daily life. All these devices are getting smaller and lighter with longer battery life due to the improvement of nanotechnology and materials sciences. Electron microscopy (EM) plays a vital role in the evolution of materials characterization which shapes the technology in today’s life. In electron microscopy, electron beam is used as the illumination source instead of visible light used in traditional optical microscopy, the wavelength of an electron is about 10⁵ times shorter than visible light. By taking this advantage, the resolving power and magnification are greatly …

Application Of High-Resolution Accurate Mass (Hram) Mass Spectrometry For Analysis Of Lignin Model Compounds And The Post-Pretreatment Products, Fan Huang

Theses and Dissertations--Chemistry

Lignin, one of main components in the woody cell walls, is a complex heterogeneous biopolymer, which provides structural support and transportation of water in plants. It is highly recalcitrant to degradation (both chemically and environmentally) and protects cellulose from being degraded/hydrolyzed. Due to the structural complexity of native lignin, complete characterization and elucidation of lignin’s structure remains very challenging. The overarching goal of this work is to develop mass spectrometry based analytical methods to contribute to a better understanding of lignin structures.

This dissertation will focus on the development and application of High-Resolution Accurate-Mass (HRAM) Mass Spectrometry (MS) as main …

Acenes, Heteroacenes And Analogous Molecules For Organic Photovoltaic And Field Effect Transistor Applications, Devin B. Granger

Theses and Dissertations--Chemistry

Polycyclic aromatic hydrocarbons composed of benzenoid rings fused in a linear fashion comprise the class of compounds known as acenes. The structures containing three to six ring fusions are brightly colored and possess band gaps and charge transport efficiencies sufficient for semiconductor applications. These molecules have been investigated throughout the past several decades to assess their optoelectronic properties. The absorption, emission and charge transport properties of this series of molecules has been studied extensively to elucidate structure-property relationships. A wide variety of analogous molecules, incorporating heterocycles in place of benzenoid rings, demonstrate similar properties to the parent compounds and have …

Towards The Total Synthesis Of 7-Epi-Clusianone, Shubhankar Dutta

Theses and Dissertations--Chemistry

Polycyclic polyprenylated acylphloroglucinols (PPAPs) are plant- (Guttiferae) derived natural products. They have fascinating bicyclo[3.3.1]nonane-2,4,9-trione or [3.2.1]nonane-2,4,8-trione cores decorated with prenyl or geranyl groups. More than 200 PPAPs have been isolated, but only a few of them have been synthesized, although most of the synthesized PPAPs are of type A and have an exo substituent at C (7). Here, we are trying to make a type B 7-endo PPAP, 7-epi-clusianone. The synthetic plan involves an alkynylation–aldol strategy to construct the bicyclic core. Having established the bicyclic core, the synthesis presents a new challenge: the oxidation of a very hindered …

Deconvolving The Steps To Control Morphology, Composition, And Structure, In The Synthesis Of High-Aspect-Ratio Metal Oxide Nanomaterials, Lei Yu

Theses and Dissertations--Chemistry

Metal oxides are of interest not only because of their huge abundance but also for their many applications such as for electrocatalysts, gas sensors, diodes, solar cells and lithium ion batteries (LIBs). Nano-sized metal oxides are especially desirable since they have larger surface-to-volume ratios advantageous for catalytic properties, and can display size and shape confinement properties such as magnetism. Thus, it is very important to explore the synthetic methods for these materials. It is essential, therefore, to understand the reaction mechanisms to create these materials, both on the nanoscale, and in real-time, to have design control of materials with desired …

Synthesis And Development Of Zwitterionic Pei (Zpei) For Optimized Delivery Of Nucleic Acids, Joseph Raleigh Duke Iii

Theses and Dissertations--Chemistry

Gene therapy holds promise for the treatment a wide range of diseases ranging from cystic fibrosis to cardiovascular disease to cancer. The need for safe and efficient gene delivery methods remains the primary barrier to human gene therapy. Non-viral vector materials, including polymers, can be designed to be biocompatible and non-immunogenic, but lack the efficiency to be clinically relevant. Gene therapy awaits the development of new materials that are both safe and efficient. Here, we have synthesized a series of modified zwitterionic polymers based on the common transfecting agent polyethylenimine (PEI). Using a variety of biochemical and biophysical methods we …

Extraction And Quantification Of Sinapinic Acid From Irish Rapeseed Meal And Assessment Of Angiotensin-I Converting Enzyme (Ace-I) Inhibitory Activity, Leah Quinn, Steven Gray, Steve Meaney, Stephen Finn, Padraig Mcloughlin, Maria Hayes

Articles

Phenolic compounds, including phenolic acids, are known to play a protective role against the development of cardiovascular disease. The aim of this work was to generate a phenolic acid extract from Irish rapeseed meal, to determine the quantity of sinapinic acid (SA) in this fraction and to assess the ability of this fraction to inhibit the enzyme angiotensin-I converting enzyme (ACE-I; EC 3.4.15.1). A crude phenolic extract (fraction 1), free phenolic acid containing extract (fraction 2), and an extract containing phenolic acids liberated from esters (fraction 3) were generated from Irish rapeseed meal using a methanol:acetone:water solvent mixture (7:7:6). The …

Feasibility Of Laser-Induced Breakdown Spectroscopy (Libs) As An At-Line Validation Tool For Calcium Determination In Infant Formula, Xavier Cama-Moncunill, Maria Markiewicz-Keszycka, Yash Dixit, Raquel Cama-Moncunill, Maria Piedad Casado-Gavalda, Patrick J. Cullen, Carl Sullivan

Articles

In this study, a 150 mJ laser-induced breakdown spectroscopy (LIBS) system was assessed to determine calcium content in infant formula (IF) samples. LIBS is a promising emission spectroscopic technique for elemental analysis, which offers advantages over conventional methods such as real-time analyses, little to no sample preparation and ease of use. The aim of this work was to evaluate the feasibility of LIBS as an at-line tool for IF manufacturing. To this end, IF mixtures with varying content of calcium were prepared over a range (approx. 1.5–7 mg/g of calcium) selected to be in conformity with the guidelines provided by …

Fragment-Based Excitonic Coupled-Cluster Theory For Large Chemical Systems, Yuhong Liu

University of the Pacific Theses and Dissertations

Accurate energetic modeling of large molecular systems is always desired by chemists. For example, ligand-protein binding simulations and enzymatic catalysis studies all involve with a small energy difference. The energetic accuracy depends largely on a proper handling of electronic correlations. Molecular mechanics (MM) methods deliver a parameterized Newtonian treatment to these problems. They show great capability in handling large calculations but give only qualitatively good results. Quantum mechanics (QM) methods solve Schrödinger equations and exhibit much better energy accuracy, though the computational cost can be prohibitive if directly applied to very large systems.

Fragment-based methods have been developed to decompose …

Investigating Secondary Structure Features Of Yap1 Protein Fragments Using Molecular Dynamics (Md) And Steered Molecular Dynamics (Smd) Simulations, Ferdiemar Cardenas Guinto Jr.

University of the Pacific Theses and Dissertations

Molecular dynamics (MD) is a powerful tool that can be applied to protein folding and protein structure. MD allows for the calculation of movement, and final position, of atoms in a biomolecule. These movements can be used to investigate the pathways that allow proteins to fold into energetically favorable structures. While MD is very useful, it still has its limitations. Most notable, computing power and time are of constant concern.

Protein structure is inherently important due to the direct link between the structure of a protein and its function. One of the four levels of protein structure, the secondary structure, …

The Rational Investigation Of Anti-Cancer Peptide Specificity Using The Knob-Socket Model, Shivarni Patel

University of the Pacific Theses and Dissertations

Cancer has been a pervasive and deadly problem for many years. No treatments have been developed that effectively destroy cancer cells while also keeping healthy cells safe. In this work, the knob-socket construct is used to analyze two systems involved in cancer pathways, the PDZ domain and the Bcl-BH3 complex. Application of the knob-socket model in mapping the packing surface topology (PST) allows a direct analysis of the residue groups important for peptide specificity and affinity in both of these systems. PDZ domains are regulatory proteins that bind the C-terminus of peptides involved in the signaling pathway of cancer progression. …

Solubility Enhancement Of Model Compounds, Lavanya Pitani

University of the Pacific Theses and Dissertations

Solubility is the amount of solute in the solvent system at phase equilibrium with certain temperature and pressure. Many of the new chemical entities are lipophilic molecules that require techniques to enhance solubility. Solubility enhancement can be achieved by either physical and/or chemical modification of the drug. Various techniques are available for solubility enhancement of poorly soluble drugs include particle size reduction, salt formation, solid dispersions, use of surfactants, prodrug, crystal modification, etc.

In this study, the three model drugs belong to BCS class II and IV having low solubility with a certain range of physicochemical properties were studies in …