Chemistry Commons^™

Synthesis And Study Of The Electrochemical And Optoelectronic Properties Of Π-Conjugated Poly-P-Phenylene-Based Molecular Wires, Anitha Boddeda

Dissertations (1934 -)

Organic photovoltaics will play an important role in supplementing the energy needs of the twenty first century in a most cost-effective way to convert the solar energy into usable forms of energy. One of the bottlenecks in promoting widespread use of photovoltaic devices for solar energy storage is the inefficiency of the devices, which in part arises due to the inefficient charge separation and long-range charge transport. Design and synthesis of efficient charge-transfer materials would require one to first identify and establish the structural features necessary in a given molecular wire, which may promote effective charge transfer to long distances. …

Computational Modeling Of S-Thiolation Reaction: Toward Discovering The Enzymatic Mechanisms Of Endogenous Hno Formation, Elena Ivanova

Dissertations (1934 -)

S-nitrosothiols (RSNOs) have long been proposed as potential sources of the elusive endogenous nitroxyl (HNO) via S-thiolation reaction with thiols. It is however not clear how S-thiolation can compete with the trans-S-nitrosation pathway commonly observed in vitro. Based on the insights into the highly unusual, antagonistic chemical nature of RSNO molecules, we hypothesize that, while difficult in vitro, S-thiolation could easily lend itself to enzymatic catalysis. To explore this possibility, we adopted a bottom-up computational approach that aims to identify possible catalytic mechanisms able to steer the RSNO + thiol reaction toward HNO production. Inspired by recent discovery of small …

Alicyclic And Aromatic Carboxylic Acids In Soil Organic Matter: An Investigation Of Potential Origin And Association With Plutonium Using Advanced Analytical Techniques, Nicole Didonato

Chemistry & Biochemistry Theses & Dissertations

Carboxylic acids are a defining component of soil organic matter, responsible for many of the physical and chemical properties, including metal-organic matter interactions, which govern its role as an important constituent of soils. However, there is a shortage of detailed molecular level information regarding orientation and structural arrangement of carboxylic acids within soil organic matter. This dissertation utilizes electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) as well as solid-state and multi-dimensional nuclear magnetic resonance (NMR) to investigate the molecular formula composition within several organic matter sources and the primary structures that feature carboxylic acids. Soil organic matter …

Oxygen Activation By Mononuclear Mn, Co, And Ni Centers In Biology And Synthetic Complexes, Adam T. Fiedler, Anne A. Fischer

Chemistry Faculty Research and Publications

The active sites of metalloenzymes that catalyze O₂-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O₂ at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O₂ reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or …

Nmr Line Shape Analysis Of A Multi-State Ligand Binding Mechanism In Chitosanase, Shoko Shinya, Mariana G. Ghinet, Ryszard Brzezinski, Kyoko Furuita, Chojiro Kojima, Sneha Shah, Evgenii L. Kovrigin, Tamo Fukamizo

Chemistry Faculty Research and Publications

Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomerization of the bound-state into the final conformation. Mapping of the chemical shift perturbations in two sequential steps of the mechanism highlighted involvement of the substrate-binding subsites and the hinge region in the binding reaction. Equilibrium parameters of the three-state model agreed with the overall thermodynamic dissociation constant determined by ITC. This study presented the first …

Investigation Of Ai-2 Binding To The Quorum Sensing Receptor Lsrb, Meghann R. Kasal , '17

Senior Theses, Projects, and Awards

Bacterial cell-cell communication, known as quorum sensing, is a density-dependent phenomenon that regulates multicellular behaviors such as bioluminescence and virulence. Interspecies quorum sensing is mediated by a signal known as autoinducer-2 (AI-2), which belongs to a family of molecules derived from 4,5-Dihydroxy-2,3 pentanedione (DPD), a key metabolic product of the enzyme LuxS. AI-2 is recognized by many bacteria that belong to several phyla, including Enterobacteriaceae, Rhizobiaceae, and Bacillaceae, as a non-borated cyclic derivative of DPD known as (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (R-THMF). Building on previous research, we have recently identified several novel LsrB orthologs through sequence alignments and fold-prediction software. …

Diastereoselective Transformations And Intramolecular Cyclizations Of Enantiomerically Pure Planar Chiral N-Oxazolidinoyl Diene Lron(O) Tricarbonyl Complexes, Sooyun Choi , '17

Senior Theses, Projects, and Awards

Organoiron complexes have established their utility in organic synthesis as stereodirecting groups as well as diene protecting groups. Since its first discovery in 1930, the diene tricarbonyl iron(O) complex underwent an impressive development that allows us to use its rich chemistry to accomplish complex molecule synthesis and to explore various synthetic methods that would broaden the scope of this field. The Paley laboratory utilizes the planar chirality of N-oxazolidinoyl diene tricarbonyl iron complexes to expand the boundaries of diastereoselective synthesis of novel compounds. The findings reported here reflect our attempts not only to reiterate the successful chemistry previously done …

Sdsl-Epr Of Residues 60-70 Of Influenza M2 Protein Reveals Structural Properties Of A Region Involved In Viral Budding, Grace Kim , '17

Senior Theses, Projects, and Awards

The M2 protein is a 97-residue multifunctional transmembrane homotetrameric protein. It is found in the viral coat of the Influenza A virus, which is responsible for approximately 250,000 to 500,000 deaths annually worldwide.¹ Extensive research has elucidated M2's role as an ion channel, which plays a critical role in the uncoating of the viron once it has entered the host cell. The C-terminal tail of M2 has also been shown to play a crucial role in generating curvature in the cell membrane to mediate viral budding.²³ Deletions in the C-terminal tail of the M2 protein lead to impaired viral infectivity.⁴ …

Biosorption Of Pharmaceuticals And Noble Metals Nanoparticles By Algal Turf Communities, Haider Abid Faraj

Dissertations

Pharmaceuticals and nanoparticles are increasingly released into the aquatic ecosystem, while removing these contaminants from waters can be challenging. This study explores the use of periphytic algal turf communities to remove these contaminants. Initially algal turfs from different locations and aquatic systems were analyzed for pharmaceuticals commonly observed in wastewater outflows. Lab-grown turfs were exposed to a mixture of six representative pharmaceuticals of different functionality (acid, base, neutral and steroidal). Analysis of water column and the algal biomass showed pharmaceutical removal rates varied, specific to each pharmaceutical. Caffeine and estradiol had the highest removal rates while carbamazepine was not removed. …

Topological And Thermodynamic Factors That Influence The Evolution Of Small Networks Of Catalytic Rna Species, Jessica Anne Mellor Yeates, Philippe Nghe, Niles Lehman

Chemistry Faculty Publications and Presentations

An RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks could have been an important feature of the RNA world during the nascent evolution of life on the Earth. However, the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self-assemble via genotype-selfish and genotype-cooperative …

Reactivity Of Ketyl And Acetyl Radicals From Direct Solar Actinic Photolysis Of Aqueous Pyruvic Acid, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

The variable composition of secondary organic aerosols (SOA) contributes to the large uncertainty for predicting radiative forcing. A better understanding of the reaction mechanisms leading to aerosol formation such as for the photochemical reaction of aqueous pyruvic acid (PA) at λ ≥ 305 nm can contribute to constrain these uncertainties. Herein, the photochemistry of aqueous PA (5-300 mM) continuously sparged with air is re-examined in the laboratory under comparable irradiance at 38° N at noon on a summer day. Several analytical methods are employed to monitor the time series of the reaction, including (1) the derivatization of carbonyl (C═O) functional …

Collective Quadrupole Behavior In 106Pd, Francisco M. Prados-Estévez, Erin E. Peters, A. Chakraborty, M. G. Mynk, D. Bandyopadhyay, N. Boukharouba, S. N. Choudry, Benjamin P. Crider, P. E. Garrett, S. F. Hicks, A. Kumar, S. R. Lesher, C. J. Mckay, Marcus T. Mcellistrem, Sharmistha Mukhopadhyay, J. N. Orce, M. Scheck, J. R. Vanhoy, J. L. Wood, Steven W. Yates

Chemistry Faculty Publications

Excited states in ¹⁰⁶Pd were studied with the (n,n′γ) reaction, and comprehensive information for excitations with spin ≤6ℏ was obtained. The data include level lifetimes in the femtosecond regime, spins and parities, transition multipolarities, and multipole mixing ratios, which allow the determination of reduced transition probabilities. The E2 decay strength to the low-lying states is mapped up to ≈2.4 MeV in excitation energy. The structures associated with quadrupole collectivity are elucidated and organized into bands.

Comparative Analysis Of Antihistamines And Nonsteroidal Anti-Inflammatory Drugs (Nsaids): Properties, Structure And Prediction Of New Potential Drugs, Ronald Bartzatt

Chemistry Faculty Publications

Aims: To determine the molecular properties of common antihistamines and non-steroidal antiinflammatory agents (NSAIDs). To identify interrelationships among these two groups of drugs utilizing pattern recognition methods and statistical analysis.

Study Design: After determination of molecular properties, values thereof are examined using pattern recognition methods and other numerical analysis for underlying relationships and similarities.

Place and Duration of Study: Durham Science Center, University of Nebraska, Omaha, Nebraska from September 2016 to January 2017.

Methodology: Thirty compounds were identified as antihistamines and 27 compounds identified as NSAIDs. Properties such as Log P, molecular weight, polar surface area, etc. are determined. Molecular …

Synthesis, Structural Characterization And Catalytic Activity Of Indenyl Complexes Of Ruthenium Bearing Fluorinated Phosphine Ligands, Matthew J. Stark, Michael J. Shaw, Arghavan Fadamin, Nigam P. Rath, Eike B. Bauer

SIUE Faculty Research, Scholarship, and Creative Activity

The synthesis, characterization and catalytic activity of new ruthenium complexes of fluorinated triarylphosphines is described. The new ruthenium complexes [RuCl(ind)(PPh₃){P(p-C₆H₄CF₃)₃}] and [RuCl(ind)(PPh₃){P(3,5-C₆H₃(CF₃)₂)₃}] were synthesized in 57% and 24% isolated yield, respectively, by thermal ligand exchange of [RuCl(ind)(PPh₃)₂], where ind = indenyl ligand η⁵-C₉H₇⁻. The electronic and steric properties of the new complexes were studied through analysis of the X-ray structures and through cyclic voltammetry. The …

Stable Isotope Chemistry In Titan Haze Aerosol, Allison Wold, Thomas Gautier, Jennifer Stern, Joshua Sebree, Melissa Trainer

Research in the Capitol

Titan, a moon of Saturn, has a thick atmosphere made up of nitrogen and a few percent methane, with a surface pressure of 1.5x that of Earth. Titan’s atmosphere is believed to be that similar to that of early Earth before the rise of O2. One significant source of information on the history and evolution of the atmosphere is the measurement of stable isotopes of elements in the molecules of major gases such as nitrogen, methane, and higher order hydrocarbons. The fractionation associated with the formation of Titan aerosol analogs are explored in the laboratory as a function of environmental …

The Use Of Ammonia As A Qualitative Test For Determining When Solid Copper Has Completely Precipitated From Aqueous Solutions Containing Copper(Ii) Ions, M. Olivia Byrd, Carl J. Ohrenberg

Georgia Journal of Science

In this study, two methods were compared to efficiently determine the absence of copper ions from a copper(II) chloride dihydrate (37.274% copper by mass) solution after precipitation using solid magnesium. In one method, a solution color change from pale blue to colorless was used as indication of a completed precipitation of copper. In the alternative method, ammonia was added to aliquots of solution which indicated remaining copper ions with a royal blue complex. For both methods, magnesium turnings were added to a blue copper(II) chloride solution until it was determined, as indicated above, that all copper had precipitated from solution. …

Dye Rejection Membranes Prepared From Oxidized Graphite Particles, Anastasia Colomba, Mark C. Biesinger, Ranjith Divigalpitiya, Frank A. Brandys, Joe Gilroy

Chemistry Publications

This article reports the comparison of different chemical methods to produce graphite-based particles with varying degrees of oxidation as well as graphene oxide (GO) and pristine graphite (PG). Detailed physico-chemical characterization of the resulting materials was carried out, highlighting structural differences and variable oxygen content. The particles were then used to produce supported membranes, which were tested for the rejection of three different organic dyes (Rhodamine B, Methyl Blue and Congo Red), and their performance was rationalized in terms of a combination of properties of the membranes and dyes. In particular, membranes produced using edge-oxidized graphite (EOG) showed comparable performance …

Plp And Gaba Trigger Gabr-Mediated Transcription Regulation In Bacillus Subtilis Via External Aldimine Formation, Rui Wu, Ruslan Sanishvili, Boris R. Belitsky, Jose I. Juncosa, Hoang V. Le, Helaina J. S. Lehrer, Michael Farley, Richard B. Silverman, Gregory A. Petsko, Dagmar Ringe, Dali Liu

Chemistry: Faculty Publications and Other Works

The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of γ-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5′-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the “active site” in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic γ-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, ( …

Photochemical Properties And Structure-Activity Relationships Of RuIi Complexes With Pyridylbenzazole Ligands As Promising Anticancer Agents, Dmytro Havrylyuk, David K. Heidary, Leona Nease, Sean Parkin, Edith C. Glazer

Chemistry Faculty Publications

Ruthenium complexes capable of light‐triggered cytotoxicity are appealing potential prodrugs for photodynamic therapy (PDT) and photoactivated chemotherapy (PACT). Two groups of (polypyridyl)Ru^II complexes with 2‐(2‐pyridyl)benzazole ligands were synthesized and investigated for their photochemical properties and anticancer activity to compare strained and unstrained systems that are likely to have different biological mechanisms of action. The structure–activity relationship was focused on the benzazole‐core bioisosterism and replacement of coligands in Ru^II complexes. Strained compounds rapidly ejected the 2‐(2‐pyridyl)benzazole ligand after light irradiation, and possessed strong toxicity in the HL‐60 cell line both under dark and light conditions. In contrast, unstrained Ru …

Angiotensin Receptor Blocker Drugs And Inhibition Of Adrenal Beta-Arrestin-1-Dependent Aldosterone Production: Implications For Heart Failure Therapy, Anastasios Lymperopoulos, Beatrix Aukszi

Chemistry and Physics Faculty Articles

Aldosterone mediates many of the physiological and pathophysiological/cardio-toxic effects of angiotensin II (AngII). Its synthesis and secretion from the zona glomerulosa cells of the adrenal cortex, elevated in chronic heart failure (HF), is induced by AngII type 1 receptors (AT1Rs). The AT1R is a G protein-coupled receptor, mainly coupling to Gq/11 proteins. However, it can also signal through β-arrestin-1 (βarr1) or -2 (βarr2), both of which mediate G protein-independent signaling. Over the past decade, a second, Gq/11 protein-independent but βarr1-dependent signaling pathway emanating from the adrenocortical AT1R and leading to aldosterone production has become appreciated. Thus, it became apparent that …

One-Pot Dialkylation Of Cycloalkanones And Their Ring-Closing Metathesis To Make Bridged Bicyclic Compounds, Dylan Sacenti, Ashley Yoon, Nathan Behrens

Seaver College Research And Scholarly Achievement Symposium

No abstract provided.

Hydrogen Peroxide Inhibition And Inactivation Of Bicupin Oxalate Oxidase, John M. Goodwin Vii

Master of Science in Chemical Sciences Theses

Oxalate oxidase is a manganese containing enzyme that catalyzes the oxygen dependent oxidation of oxalate to carbon dioxide and hydrogen peroxide. Oxalate oxidase from Ceriporiopsis subvermispora (CsOxOx) is the first characterized bicupin oxalate oxidase. Potential applications of oxalate oxidase in cancer treatment, paper pulping, and biofuel cells highlight the need to study the effects of hydrogen peroxide on the CsOxOx catalyzed oxidation of oxalate. Membrane inlet mass spectrometry (MIMS) was used to directly measure initial rates of carbon dioxide formation and oxygen consumption in varying initial concentrations of hydrogen peroxide. This work demonstrates that hydrogen peroxide is both a reversible …

Hierarchical Corannulene-Based Materials: Energy Transfer And Solid-State Photophysics, Allison M. Rice, W. Brett Fellows, Ekaterina A. Dolgopolova, Andrew B. Greytak, Aaron K. Vannucci, Mark D. Smith, Stavros G. Karakalos, Jeanette A. Krause, Stanislav M. Avdoshenko, Alexey A. Popov, Natalia B. Shustova Prof. Dr.

Faculty Publications

We report the first example of a donor–acceptor corannulene-containing hybrid material with rapid ligand-to-ligand energy transfer (ET). Additionally, we provide the first time-resolved photoluminescence (PL) data for any corannulene-based compounds in the solid state. Comprehensive analysis of PL data in combination with theoretical calculations of donor–acceptor exciton coupling was employed to estimate ET rate and efficiency in the prepared material. The ligand-to-ligand ET rate calculated using two models is comparable with that observed in fullerene-containing materials, which are generally considered for molecular electronics development. Thus, the presented studies not only demonstrate the possibility of merging the intrinsic properties of π-bowls, …

Fatty Acid Biomarker Detection For Breast Cancer Using Differential Mobility Spectrometry With Non-Radioactive Ion Source, James Joseph Alberti

USF Tampa Graduate Theses and Dissertations

Differential Mobility Spectrometry (DMS) using a non-radioactive ion source (NRIS) is investigated as a possible medical diagnostic instrument for near real-time detection of breast cancer biomarkers. In previous clinical studies, concentrations of Linoleic, Palmitic and Stearic fatty acids have been observed at different levels in women with carcinoma breast cancer versus women with benign tumors or healthy women showing no signs of breast cancer. Present diagnostic methods require a biopsy of the suspect tissue and a microscopic lab analysis performed to determine its disease state. This process can take hours or days before the patient and doctor are informed of …

Uv-Vis And Fluorescence Studies Of Zinc Enzyme Active Site Mimics And Their Binding Of Inhibitor Compounds, Aeshah Hussain Niyazi

College of Science and Health Theses and Dissertations

This research aimed to synthesize and characterize Zn2+-ligand complexes that have the same zinc coordination environment as in histone deacetylase (HDAC) and other important zincdependent enzymes. Mimicking the structural and the functional properties of Zn2+-enzymes will allow us to understand the binding reactivity between Zn2+ and small molecule enzyme inhibitors. The new understanding will help to develop new approaches to target disease states such as cancer. A variety of Zn2+ binary complexes have been synthesized and their interactions with inhibitors such as suberanilohydroxamic acid (SAHA) and 8-Hydroxyquinoline (8HQ) have been studied using 1H NMR, UV-Vis, and fluorescence spectroscopies. Attempts were …

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.

Metal-Containing Polymers Bearing Pendant Nickel(Ii) Complexes Of Goedken's Macrocycle, Joseph A. Paquette, Amir Rabiee Kenaree, Joe Gilroy

Chemistry Publications

The design, synthesis, and polymerization of a norbornene-based monomer bearing a nickel(II) complex of Goedken's macrocycle (endo-13) and the characterization of the resulting polymer are described. Detailed studies of the ring-opening metathesis polymerization of endo-13 using the 3-bromopyridine adduct of Grubbs' 3^rd generation catalyst revealed that the polymerization shares many characteristics associated with a living polymer, but deviated from ideal behavior when high degrees of polymerization were targeted. The installation of a 3-hexylphenyl substituent at the macrocyclic backbone allowed for the realization of soluble polymers (14) and shut down an oxidative dimerization pathway …

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 …

Calmodulin Lobes Facilitate Dimerization And Activation Of Estrogen Receptor-Alpha, Zhigang Li, Yonghong Zhang, Andrew C. Hedman, James B. Ames, David B. Sacks

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Estrogen receptor α (ER-α) is a nuclear hormone receptor that controls selected genes, thereby regulating proliferation and differentiation of target tissues, such as breast. Gene expression controlled by ER-α is modulated by Ca²⁺ via calmodulin (CaM). Here we present the NMR structure of Ca²⁺-CaM bound to two molecules of ER-α (residues 287–305). The two lobes of CaM bind to the same site on two separate ER-α molecules (residues 292, 296, 299, 302, and 303), which explains why CaM binds two molecules of ER-α in a 1:2 complex and stabilizes ER-α dimerization. Exposed glutamate residues in CaM (Glu-11, …

Calmodulin Lobes Facilitate Dimerization And Activation Of Estrogen Receptor-Α, Zhigang Li, Yonghong Zhang, Andrew C. Hedman, James B. Ames, David B. Sacks

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Estrogen receptor α (ER-α) is a nuclear hormone receptor that controls selected genes, thereby regulating proliferation and differentiation of target tissues, such as breast. Gene expression controlled by ER-α is modulated by Ca2+ via calmodulin (CaM). Here we present the NMR structure of Ca2+-CaM bound to two molecules of ER-α (residues 287–305). The two lobes of CaM bind to the same site on two separate ER-α molecules (residues 292, 296, 299, 302, and 303), which explains why CaM binds two molecules of ER-α in a 1:2 complex and stabilizes ER-α dimerization. Exposed glutamate residues in CaM (Glu-11, Glu-14, Glu-84, …