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Organic Chemistry With A Biological Emphasis Volume Ii, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

Organic Chemistry With A Biological Emphasis Volume I, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

The Development Of An Integrated Simulation Model On Understandings On The Interaction Between Electromagnetic Waves And Nanoparticles, Xiaojin Wang

Masters Theses & Specialist Projects

To investigate the interaction between nanoparticles and electromagnetic waves, a numerical simulation model based on FEM was built in this thesis. Numerical simulation is an important auxiliary research method besides experiments. The optical properties of nanoparticles consist of scattering, absorption, and extinction, and in the case of nanoparticle suspension, the transmission is also involved. This thesis addressed two typical applications based on the established model, one was regarding the nanofluids for solar energy harvesting, and the other was regarding the optical properties of atmospheric soot. In the case of the nanofluids solar energy harvesting, the established model provided a convenient …

Characterization Of Metal Binding Sites Within The Protein Only Rnase P, Ganga Nilmini Kumari Wijesinghe Mudiyanselage

Master's Theses (2009 -)

Transfer RNA (tRNA) maturation is an essential step that occurs after transcription and prior to the translation. In all domains of life, an RNA-based ribonuclease (RNase) P catalyzes the cleavage of the phosphodiester bond at the 5′ end of precursor tRNA. However, not all organelles utilize the RNA-based version of RNase P. A recent discovery altering the paradigm of RNase P has revealed that chloroplast organelles, parasitic trypanosomes, and the compact human mitochondrial (mt) genome rely solely on a protein-only 5′ tRNA processing enzyme. Structural and biochemical studies of the RNA-based and protein-based plant RNase P systems suggest that these …

Lipid Biomarkers Of Bering And Chukchi Sea Euphausiids And Their Application To Diet History, Rachel L. Pleuthner

OES Theses and Dissertations

In the eastern Bering Sea, Thysanoessa raschii are the most abundant krill species and a keystone trophic member that serve as both an important grazer and link to upper level consumers. In this system krill experience large annual variation in food resources, especially during ice advance and retreat; multiple lipid classes are used to temper the effects of those fluctuations, as well as to fuel reproduction and growth. Two shipboard feeding experiments that occurred during late spring and early summer of 2010, respectively, monitored the lipid retention in adult T. raschii and examined the fluctuation of specific lipid biomarkers under …

The Alpha-Activator Complex, Cellular Maturation, And Catalytic Mechanism Of Iron-Type Nitrile Hydratase, Wasantha Lankathilaka Karunagala Pathiranage

Dissertations (1934 -)

In industry, chemicals are typically synthesized through catalytically accelerated chemical processes. The use of biocatalysts is an increasingly important trend in achieving environmentally friendly chemical production processes. Nitrile Hydratases (NHases) are well-known biocatalysts that are used by several manufacturers such as Mitsubishi Rayon Corporation and Lonza for the conversion of acrylonitrile to acrylamide and 3-cyanopyridine to nicotinamide, respectively. Amides, in general, are used in polymer preparation, adhesive manufacturing, and the paper industry. Refrigeration is needed in the enzymatic hydration process on the industrial scale to maintain a low reaction temperature to stabilize the NHase enzyme. The use of whole cells …

Structure And Mechanisms Of Metalloenzymes For Incorporation Of Water Across Cn And C-Cl Bonds, Xinhang Yang

Dissertations (1934 -)

Metalloenzymes are widely involved in water incorporation across CN and C-Cl bonds.1 In this research, the structure and mechanisms of two novel metalloenzymes that incorporate water across CN and C-Cl bonds were examined by biophysical approaches, computational modeling, and crystallographic methods.In the research of water incorporation across CN bonds, a novel eukaryotic nitrile hydratase (NHase, EC 4.2.1.84) from Monosiga brevicollis (MbNHase) was characterized, and the functional role of a (His)17 section and an insert region in the MbNHase, were examined by gene modifications. Each of these MbNHase enzymes provided an 22 heterotetramer, identical to that observed for prokaryotic NHases …

Investigation Of The Active Site Maturation And Catalytic Mechanism Of Nitrile Hydratases (Nhase, E.C.4.2.1.84), Irene Anyango Ogutu

Dissertations (1934 -)

Nitrile hydratase (NHase, E.C.4.2.1.84) is a metalloenzyme that catalyzes the hydration of nitriles into their corresponding amide under ambient conditions. NHase enzymes contain either a non-heme Fe3+ ion or a non-corrin Co3+ ion in their active site. NHase enzymes have industrial applications as biocatalysts in the large-scale production of acrylamide and nicotinamide, though it’s catalytic and biochemical properties are not fully understood. This research project provides insight into the active site maturation process and catalytic mechanism of NHase using peptide model complexes, site-directed mutagenesis and synthesis of deuterated proteins.Insight into the sequential maturation of the NHase active site has been …

Disinfection By-Products: Method Optimization For Quantification, Unknown Analysis, And Calculated Toxicity, Amy A. Cuthbertson

Theses and Dissertations

Disinfected drinking water contains hundreds of disinfection by-products (DBPs) that are formed by the reaction of disinfectants with natural and anthropogenic organic matter, bromide, and iodide. Understanding what these DBPs are is important because millions of people worldwide consume drinking water every day, and human epidemiologic studies have reported cancer, miscarriage, and birth defects from consuming such waters. While more than 700 DBPs are reported in the literature, very few studies quantify complete classes of chlorinated, brominated, and iodinated DBPs. The following document contains five chapters in the format designated for specific scientific journals on this subject. Chapter 1 describes …

Metastable-State Photoacid: A Comprehensive Theoretical Study Of The Photoreaction, Reverse Reaction, Thermal Isomerization, And Td-Dft Absorption In Solvent, Arwa Wasel Hamed Alharbi

Theses and Dissertations

The main objective of the research is to investigate the fundamentals of novel metastable-state photoacids. These photoacids can reversibly produce a large concentration of protons while undergoing photo-irradiation. This change in proton concentration can induce and catalyze chemical reactions, biological functions, and material properties that do not occur in the dark. (IMAGE) Scheme 1. Energy diagram of the photoreaction. (The red route is the forward photoreaction; the blue route is the reverse reaction; and the process that involves the proton dissociation of the photoacid in the dark is the green route; "t-" means trans- and "c-" means cis-). Scheme 1 …

Metastable-State Photoacids And Polymers With High Photoacidity, Thaaer Khalil

Theses and Dissertations

In recent years, metastable-state photoacids (mPAH) have been utilized to control various chemical processes using visible light and have found many applications in materials, energy, and biomedical areas. An introduction of metastable state photoacid is given in Chapter 1. In chapter 2, to clearly understand the relationship between the structures and the physicochemical properties of mPAHs, a series of mPAHs were designed and synthesized. The reversibility, stability, reverse reaction rate, and photoreaction of the mPAHs were studied in detail using UV/VIS spectroscopy. The results demonstrated that the electron-withdrawing groups on the electron-accepting moiety enhance the overall photoreaction and stability of …

Analysis Of N-Alkanes And N-Alkenes In Chukchi Sea Sediments, Salomey Asantewaa Sasu

Theses and Dissertations

This study determined the concentrations, distribution and sources of n-alkanes in core sediments from four locations: Stations H24, H30, H32 and BarC5 in the Chukchi Sea, which is in the Arctic Ocean. n-Alkanes are valuable tracers of aquatic, terrigenous and petroleum inputs and may give evidence to the extent of climate change. The study of climate change in the Arctic is important since the Arctic is warming faster than any other part of Earth. The increase in temperature is causing enhanced evaporation leading to a higher precipitation rate and hence enhanced erosion. The n-alkanes C12-C35 were analysed and characterized using …

Ph Dependent Reversible Formation Of A Binuclear Ni2 Metal-Center Within A Peptide Scaffold, Breena C. Keegan, Daniel Ocampo, Jason M. Shearer

Chemistry Faculty Research

A disulfide-bridged peptide containing two Ni²⁺ binding sites based on the nickel superoxide dismutase protein, {Ni₂(SOD^mds)} has been prepared. At physiological pH (7.4), it was found that the metal sites are mononuclear with a square planar NOS₂ coordination environment with the two sulfur-based ligands derived from cysteinate residues, the nitrogen ligand derived from the amide backbone, and a water ligand. Furthermore, S K-edge X-ray absorption spectroscopy indicated that the two cysteinate sulfur atoms ligated to nickel are each protonated. Elevation of the pH to 9.6 results in the deprotonation of the cysteinate sulfur atoms, …

Mechanistic Studies Of Atypical Reactions And Uncommon Substrates Native To Bacterial Cytochrome P450 Enzymes OletJe And Nikq, Courtney Elizabeth Wise

Theses and Dissertations

Cytochrome P450 (CYP) enzymes typically perform hydroxylation chemistry on small molecule substrates using atmospheric oxygen and electrons from redox partner proteins. This reactivity is dependent on a thiolate-ligated heme cofactor that also allows for spectroscopic detection of ligation, oxidation, and environmental changes to the iron metal. The onset of the genomics era has resulted in the discovery of CYPs that deviate from this paradigm in terms of reaction performed, cosubstrate requirements, and substrate-scope. This work focuses on two of these unusual P450s – OleT and NikQ. OleT performs an unconventional H2O2-dependent decarboxylation reaction on a standard small molecule fatty acid …

Probing The Relationship Of Cyanobacterial Toxins And Reactive Oxygen Species Within The Natural World, Meagan Lachelle Smith

Theses and Dissertations

The occurrence of harmful algal blooms (HABs) and their impacts on human health and the economy are only expected to worsen in the coming years, mainly due to climate change related factors. In Lake Wateree, SC, a HAB of the species Lyngbya wollei, has been persistent for more than 10 years and is estimated to occupy 60 - 90 km of shoreline. This natural laboratory provided and continues to provide a unique window into the chemistry and microbial ecology of HABs. Work in this dissertation was directed at answering a critical question: are biomass-to-toxin ratios constant in HABs? Initial …

Investigation Of Energy-Related Wastewater Impacts On Disinfection By-Product Formation In Drinking Water, Hannah K. Liberatore

Theses and Dissertations

Elevated bromide and iodide in drinking water sources contribute to the formation of toxic brominated and iodinated disinfection by-products (DBPs) during drinking water treatment. Energy extraction and utilization processes, including hydraulic fracturing (HF) and coal-fired power plants (CFPPs), produce wastewaters with bromide/iodide levels on the order of tens to thousands of mg/L. These wastes have the potential to impact drinking water sources through both intentional (e.g., direct discharge) and accidental (e.g., basin overflow, spill) release pathways. This research focuses on a combination of quantitative and non-targeted approaches to assess DBP formation impacts from HF and CFPP wastewaters, with complementary toxicity …

Research Progresses In Structural Modulation And Electrochemiluminescence Of Supertetrahedral Chalcogenide Clusters, Gang Lei, Yang Liu

Journal of Electrochemistry

Electrochemiluminescence (ECL) exhibits a broad application prospect in the field of biological analysis due to its unique performance features, and the exploitation of high efficient ECL reagents offers an important tool for the development of sensors with excellent performance and practical clinical applications. Open-framework supertetrahedral chalcogenide clusters both possess the porous structure of molecular sieve and the excellent optical properties of the semiconductor, so it has attracted more and more attention in ECL analysis. Different from the traditional semiconductor quantum dots, the structure and composition of supertetrahedral chalcogenide clusters can be accurately controlled at the atomic level, and supertetrahedral chalcogenide …

Single Particle Impact Electrochemistry: Analyses Of Nanoparticles And Biomolecules, Jian-Hua Zhang, Yi-Ge Zhou

Journal of Electrochemistry

Single particle impact electrochemistry (SPIEC) has grown rapidly in recent years and shown great promise in the analysis of nanoparticle properties as well as the detection of biomolecules including DNA, RNA, protein, enzyme, bacteria, virus, vesicles and others. This minireview summarizes recent advances in electroanalytical applications of SPIEC according to different analytical methods, i.e., direct electrolysis of nanoparticles or labeled nanoparticles, direct electrolysis of soft particles encapsulated redox molecule, indirect electrochemistry of particles, area and diffusion blocking, and changes in current magnitude and collision frequency.

Cysteine And Cystamine Co-Self-Assembled Monolayers For In Vivo Detection Of Ascorbic Acid, Yue Zhang, Tao-Tao Feng, Wen-Liang Ji, Mei-Ning Zhang

Journal of Electrochemistry

Self-assembled monolayers (SAMs), which form highly ordered monolayers on the electrode surface through the gold-suffer bond, have attracted much attention in recent years. This stable layer not only can regulate the wettable properties of surface, but also can act as a promoter towards redox-active molecules. Here, we developed a simple and effective method to construct cysteine and cystamine co-self-assembled monolayer on gold microelectrode for  in vivo detection of ascorbic acid (AA). The molar ratio at 1:1 of mixed monolayer has been found the optimum to enhance the electron-transfer kinetics of AA oxidation at low potential (ca. 0.10 V), meanwhile, it …

Nitrogen Heterocycles Form Peptide Nucleic Acid Precursors In Complex Prebiotic Mixtures, Laura E. Rodriguez, Christopher H. House, Karen E. Smith, Melissa R. Roberts, Michael P. Callahan

Chemistry and Biochemistry Faculty Publications and Presentations

The ability to store information is believed to have been crucial for the origin and evolution of life; however, little is known about the genetic polymers relevant to abiogenesis. Nitrogen heterocycles (N-heterocycles) are plausible components of such polymers as they may have been readily available on early Earth and are the means by which the extant genetic macromolecules RNA and DNA store information. Here, we report the reactivity of numerous N-heterocycles in highly complex mixtures, which were generated using a Miller-Urey spark discharge apparatus with either a reducing or neutral atmosphere, to investigate how N-heterocycles are modified under plausible prebiotic …

Synthesis, Discovery And Delivery Of Therapeutic Natural Products And Analogs, Zachary P. Shultz

USF Tampa Graduate Theses and Dissertations

Small molecule drug discovery relies heavily on synthetic organic chemistry to develop novel chemical entities that elicit desirable therapeutic effects. The development of targeted chemical syntheses is of paramount importance to access molecules for biological evaluation and is usually considered the bottleneck in most drug discovery campaigns. Targets for chemical syntheses commonly draw inspiration from molecules of natural origin. Nature harbors a wealth of chemical diversity that has established itself over millions of years through chemical and biological evolution. Organisms have an inherent ability to protect themselves from predators and harmful environments. In doing so, many of them evolve to …

Correlating Lipid Membrane Permeabilities Of Imidazolium Ionic Liquids With Their Cytotoxicities On Yeast, Bacterial, And Mammalian Cells, Kendall Cook, Katharine Tarnawsky, Alana J. Swinton, Daniel D. Yang, Alexandria S. Senetra, Gregory A. Caputo, Benjamin Carone, Timothy Vaden

College of Science & Mathematics Departmental Research

Alkyl-imidazolium chloride ionic liquids (ILs) have been broadly studied for biochemical and biomedical technologies. They can permeabilize lipid bilayer membranes and have cytotoxic effects, which makes them targets for drug delivery biomaterials. We assessed the lipid-membrane permeabilities of ILs with increasing alkyl chain lengths from ethyl to octyl groups on large unilamellar vesicles using a trapped-fluorophore fluorescence lifetime-based leakage experiment. Only the most hydrophobic IL, with the octyl chain, permeabilizes vesicles, and the concentration required for permeabilization corresponds to its critical micelle concentration. To correlate the model vesicle studies with biological cells, we quantified the IL permeabilities and cytotoxicities on …

Organometallic Compounds As Carriers Of Extraterrestrial Cyanide In Primitive Meteorites, Karen E. Smith, Christopher H. House, Ricardo D. Arevalo Jr., Jason P. Dworkin, Michael P. Callahan

Chemistry and Biochemistry Faculty Publications and Presentations

Extraterrestrial delivery of cyanide may have been crucial for the origin of life on Earth since cyanide is involved in the abiotic synthesis of numerous organic compounds found in extant life; however, little is known about the abundance and species of cyanide present in meteorites. Here, we report cyanide abundance in a set of CM chondrites ranging from 50 ± 1 to 2472 ± 38 nmol·g⁻¹, which relates to the degree of aqueous alteration of the meteorite and indicates that parent body processing influenced cyanide abundance. Analysis of the Lewis Cliff 85311 meteorite shows that its releasable cyanide …

Nepal Ambient Monitoring And Source Testing Experiment (Namaste): Emissions Of Particulate Matter And Sulfur Dioxide From Vehicles And Brick Kilns And Their Impacts On Air Quality In The Kathmandu Valley, Nepal, Min Zhong, Eri Saikawa, Alexander Avramov, Chen Chen, Boya Sun, Wenlu Ye, William C. Keene, Robert J. Yokelson, Thilina Jayarathne, Elizabeth A. Stone, Maheswar Rupakheti, Arnico K. Panday

Chemistry and Biochemistry Faculty Publications

Air pollution is one of the most pressing environmental issues in the Kathmandu Valley, where the capital city of Nepal is located. We estimated emissions from two of the major source types in the valley (vehicles and brick kilns) and analyzed the corresponding impacts on regional air quality. First, we estimated the on-road vehicle emissions in the valley using the International Vehicle Emissions (IVE) model with local emissions factors and the latest available data for vehicle registration. We also identified the locations of the brick kilns in the Kathmandu Valley and developed an emissions inventory for these kilns using emissions …

Comparison Between Hydrogen And Halogen Bonds In Complexes Of 6-Ox-Fulvene With Pnicogen And Chalcogen Electron Donors, Mingchang Hou, Qing-Zhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum chemical calculations are applied to complexes of 6‐OX‐fulvene (X=H, Cl, Br, I) with ZH3/H2Y (Z=N, P, As, Sb; Y=O, S, Se, Te) to study the competition between the hydrogen bond and the halogen bond. The H‐bond weakens as the base atom grows in size and the associated negative electrostatic potential on the Lewis base atom diminishes. The pattern for the halogen bonds is more complicated. In most cases, the halogen bond is stronger for the heavier halogen atom, and pnicogen electron donors are more strongly bound than chalcogen. Halogen bonds to chalcogen atoms strengthen in the order O

Triplet Population Dynamics And Excited State Relaxation In Chalcogenophene Polymers, Benjamin D. Datko

Chemistry and Chemical Biology ETDs

The conventional understanding of intersystem crossing in multichromophoric conju- gated polymers is usually depicted via a pure electronic model, neglecting contributions of vibrations or conformational order. Obtaining accurate structure-function correlations on spin-conversion processes involving photogenerated singlet excitons to triplet excitons and the excited state dynamics requires sensitivity to the subtle conformational ordering within conjugated polymers. This dissertation seeks to understand the kinetics of multi-exciton singlet-triplet interactions and the excited state relaxation of chalcogen containing (S, Se) conjugated polymers. Utilizing single molecule modulation spectroscopy allows determi- nation of triplet formation of individual conjugated polymer chains and aggregates. This technique resolves triplet-induced …

Assay Of Vitamin B6 (Pyridoxine Hydrochloride) Utilizing Isocratic Reversed Phase High Performance Liquid Chromatography, Ronald Bartzatt, Purnima Gajmer, Mai Han Cassandra Nguyen, Alexndra My-Hanh Tran

Chemistry Faculty Publications

Aims: To demonstrate an analysis for vitamin B6 from commercial aqueous nutritional drinks and solid tablets, utilizing isocratic conditions with high performance liquid chromatography (HPLC) and UV detection at 290 nm. Study Design: Vitamin B6 in the form of pyridoxine hydrochloride is assayed by HPLC from various samples. Place and Duration of Study: Department of Chemistry, Durham Science Center, University of Nebraska, Omaha Nebraska from May to August 2016. Methodology: Utilizing a reversed-phase C-18 column with eluent solvent (19% ethanol, 77% water, 4% acetic acid), the samples were prepared in sample solvent (19% ethanol, 81% distilled water). Detection of vitamin …

In Vitro Evaluation Of Ovarian Cancer Tumorigenesis As A Function Of Quinone Oxidoreducatse-1 And Cell Phenotype, Milcah S. Jackson

LSU Doctoral Dissertations

In vitro multicellular spheroids are attractive model systems for assessing genetic and epigenetic changes that occur in diseased tissues. Understanding how such alterations in gene and subsequent protein expression affect disease progression and metastasis, drug resistance, and recurrence is of great interest in cancer research. In this regard, examining expression and activity of proteins, such as those with cytoprotective ability that are overexpressed in cancer cells, in addition to cell phenotype (i.e., stem-like, epithelial, mesenchymal, or mixed), are two ways to evaluate genetic and epigenetic changes. Moreover, determining the impact that cytoprotective proteins and cell phenotype have on tumor formation …

Investigating Color Additive Molecules For Pharmaceutical And Cosmetic Applications: A Comparison Of Theoretical And Experimental Uv-Visible Absorbance Spectra In Tunable Solvents, Jacqueline Casey Mohen

Theses and Dissertations

Color additive molecules have widespread applications ranging from ingestible foods and pharmaceutics to non-ingestible cosmetics and other naturally or synthetically developed consumer products available worldwide. Certification for approved use of color additives varies globally; therefore, a feasible method to analyze existing color additives or to design novel color additive molecules with enhanced or otherwise desired physicochemical properties (such as hue) is in high demand for universal adoption. The studies herein provide sufficient proof that density functional theory and time-dependent density functional theory serve as effective predictive modeling techniques for generating theoretical maximum absorbance spectral peak responsivity for a single color …

Chemosensors Based On Higher Energy Gap Control Of Fluorescence In Conjugated Polymers, Chun-Han Wang

LSU Doctoral Dissertations

Conjugated polymers (CPs) have been widely investigated for their remarkably high sensitivity towards various chemical detection applications. CPs can exhibit effective transduction of certain analyte binding events through changes in fluorescence. These changes include amplified fluorescence quenching ("turn-offmechanism") or an appearance of a fluorescent emission ("turn-onmechanism"). Whereas turn-offsensors can be readily designed and are widely used, amplifying turn-onsensors, from a practical standpoint, are more convenient to use but are more challenging to design.

This dissertation primarily focuses on the development and study of conjugated polymer based amplifying turn-onfluorescence chemosensors utilizing the novel “higher …