Physical Chemistry Commons^™

Investigating Dna Damage Caused By Reactive Oxygen And Nitrogen Species Via Guided-Ion-Beam Scattering And Computational Techniques, Jonathan Benny

Dissertations, Theses, and Capstone Projects

Among DNA nucleobases, guanine (G) is the primary target for one-electron ionization and oxidation, generating G●+ through various processes, including photooxidation, electrocatalytic oxidation, DNA-binding transition metals, ionizing radiation, and photolysis. This is due to the low adiabatic ionization potential and oxidation potential of guanine. Electron holes from other nucleobases can move to guanine, proving that G●+ production traps oxidative DNA damage. G●+ formation can exacerbate DNA damages and cause secondary reactions from reactive oxygen species (ROS) and reactive nitrogen species (RNS) during pathological processes. The following three projects were conducted using a customized electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer, …

Studies On The Synthesis, Function, And Properties Of Troponoids, John-Charles A. Baucom

Dissertations, Theses, and Capstone Projects

Troponoids are a unique class of non-benzenoid aromatic compounds with a wide range of demonstrated applications in pharmaceuticals and molecular sensing. The cycloheptatrienone scaffold possesses a noteworthy degree of tunability as a function of ring oxygenation. This manuscript describes our efforts toward a better understanding of the physical consequences of the scaffold to better utilize the motif. Chapter the first discusses our efforts at elucidating the mechanism of troponoid inhibition of the Hepatitis B virus reverse transcriptase RNAse H enzymatic domain. Using homology modeling in conjunction with traditional in vitro assays we were able to establish the likely mechanism of …

The Role Of Confined Hydration And Water Reorganization In Molecular Binding, Joe Z. Wu

Dissertations, Theses, and Capstone Projects

An important factor in guiding the development of drug discovery efforts is the comprehensive assessment of a ligand or drug’s ability to bind its receptor. The metric used to measure this interaction strength is by calculating the binding free energy (BFE). To achieve this accurately, we combine two concepts: (1) Grid Inhomogeneous Solvation Theory (GIST) returns the local water thermodynamic and structural contributions to free energy; and the (2) Alchemical Transfer Method (ATM) obtains the absolute (ABFE) and relative binding free energy (RBFE) estimates between ligand pairs. In this work, we employ Alchemical Water-Transfer to tether bridging water(s) during the …

Dft Study Of The Mechanism Of Selective Hydrogenation Of Acetylene By Rhodium Single-Atom Catalyst Supported On Hy Zeolite, Melisa Su Yordanlı, Roberto Escobar, Jessica Meza, Deniz Akgül, Yuxin Zhao, Alper Uzun, Fatma Ahu Akin, Viktorya Aviyente, Abdurrahman Cagri Atesin, Tülay A. Ateşin

School of Earth, Environmental, & Marine Sciences Faculty Publications

The selectivity of acetylene hydrogenation by the Rh single-atom catalyst (SAC) supported on HY zeolite was investigated using density functional theory (DFT) and a 5/83T quantum mechanics/molecular mechanics (QM/MM) embedded cluster model. The calculated activation barrier (ΔG‡) for the oxidative addition of dihydrogen to the Rh metal center (15.9 kcal/mol) is lower in energy than that for the σ-bond metathesis of dihydrogen to the Rh—C bond (22.7 kcal/mol) and the Rh—O bond (28.4 kcal/mol). The activation barriers of the oxidative addition of subsequent dihydrogen molecules are significantly higher than that of the oxidative addition of the first dihydrogen molecule. These …

Introduction To Epr, Gareth R. Eaton

TeachEPR Submissions

A very brief introduction to the scope of EPR at the beginning of a workshop in 2019.

Anisotropy Of Nitroxide Radicals, Gareth R. Eaton

TeachEPR Submissions

The special utility of nitroxide radicals for probing orientation and motion depends on the anisotropy of g-values and hyperfine values, especially the ¹⁴N hyperfine.

Copper Line Shapes, Gareth R. Eaton

TeachEPR Submissions

The spectrum of Cu²⁺ has 4 lines, since I = 3/2. Cu has two major isotopes, ⁶³Cu (69.2%) and ⁶⁵Cu (30.8%). The magnetic moment of ⁶⁵Cu is 7% larger than that for ⁶³Cu, so the hyperfine coupling is 7% larger. If the lines are narrow enough, one can observe superposition of spectra due to complexes of the two isotopes.

Concentration Effects On Nitroxides, Gareth R. Eaton

TeachEPR Submissions

We need to distinguish line broadening due to restricted motion from line broadening due to concentration of the same or other paramagnetic species. For example, if you increase the concentration of nitroxyl to get better S/N, the lines will broaden due to collisions with other nitroxyl molecules.

Workshop On Rapid Scan Epr, Gareth R. Eaton, Arthur H. Heiss, Deborah Gale Mitchell, Joshua R. Biller, Richard W. Quine, George A. Rinard, Mark Tseitlin, Sandra S. Eaton

TeachEPR Submissions

An introduction to the method of rapid scan EPR is given with emphasis on the design of rapid scan coils, selection of scan parameters, and the reasons that the method improves signal to noise per unit time.

Workshop On Selecting An Epr Resonator, Gareth R. Eaton

TeachEPR Submissions

Guidance is presented to help select a resonator to optimize a measurement. Different resonator types are described with information about resonator Q and microwave power efficiency.

Workshop presented at the 28th International EPR Symposium on July 31, 2005.

New Insights Into Controlling The Functional Properties Of Tin Oxide-Based Materials, Alexandra Kuriganova, Nina Smirnova

Journal of Electrochemistry

Development of methodologies for fabrications of nanostructured materials that provide control over their microstructural features and compositions represents a fundamental step in the advancement of technologies for productions of materials with well-defined functional properties. Pulse electrolysis, a top-down electrochemical approach, has been demonstrated to be a viable method for producing nanostructured materials with a particular efficacy in the synthesis of tin oxides. This method allows for significant control over the composition and shape of the resulting tin oxides particles by modifying the anionic composition of the aqueous electrolyte, obviating the need for additional capping agents in the synthesis process and …

A Cnt Intercalated Co Porphyrin-Based Metal Organic Framework Catalyst For Oxygen Reduction Reaction, Pei-Pei He, Jin-Hua Shi, Xiao-Yu Li, Ming-Jie Liu, Zhou Fang, Jing He, Zhong-Jian Li, Xin-Sheng Peng, Qing-Gang He

Journal of Electrochemistry

The poor electronic conductivity of metal-organic framework (MOF) materials hinders their direct application in the field of electrocatalysis in fuel cells. Herein, we proposed a strategy of embedding carbon nanotubes (CNTs) during the growth process of MOF crystals, synthesizing a metalloporphyrin-based MOF catalyst TCPPCo-MOF-CNT with a unique CNT-intercalated MOF structure. Physical characterization revealed that the CNTs enhance the overall conductivity while retaining the original characteristics of the MOF and metalloporphyrin. Simultaneously, the insertion of CNTs generated adequate mesopores and created a hierarchical porous structure that enhances mass transfer efficiency. X-ray photoelectron spectroscopic analysis confirmed that the C atom in CNT …

Nanostructured Graphitic Carbon Nitride For Photocatalytic And Electrochemical Applications, Muhammad Abdul Qadeer, Iqra Fareed, Asif Hussaine, Muhammad Asim Farid, Sadia Nazir, Faheem K. Butt, Ji-Jun Zou, Muhammad Tahir, Shang-Feng Du

Journal of Electrochemistry

Graphitic carbon nitride (g-C₃N₄) exhibits great mechanical as well as thermal characteristics, making it a valuable material for use in photoelectric conversion devices, an accelerator for synthesis of organic compounds, an electrolyte for fuel cell applications or power sources, and a hydrogen storage substance and a fluorescence detector. It is fabricated using different methods, and there is a variety of morphologies and nanostructures such as zero to three dimensions that have been designed for different purposes. There are many reports about g-C₃N₄ in recent years, but a comprehensive review which covers nanostructure dimensions …

A Sensitivity Analysis Of The Modeling Of Polycyclic Aromatic Hydrocarbon Emission In Galaxies, A. Maragkoudakis, C. Boersma, P. Temi, J. D. Bregman, L. J. Allamandola, Vincent J. Esposito, A. Ricca, E. Peeters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We have conducted a sensitivity analysis on the mid-infrared spectral decomposition of galaxies and the modeling of the polycyclic aromatic hydrocarbon (PAH) emission spectrum with the NASA Ames PAH Infrared Spectroscopic Database (PAHdb) to assess the variance on the average galaxy PAH population properties under a grid of different modeling parameters. We find that the short-low and short-low+long-low Spitzer-IRS decomposition with PAHFIT provides consistent modeling and recovery of the 5–15 μm PAH emission spectrum. For PAHdb modeling, application of a redshift to the calculated spectra to account for anharmonic effects introduces a 15%–20% variance on the derived parameters, while its …

Photolysis And Sublimation Chemistry Of Ammonium Cyanide With Relevance To Cometary Environments, O. H. Wilkins, K. M. Yocum, Vincent J. Esposito, E. Harel, S. N. Milam, P. A. Gerakines

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bulk nitrogen is depleted in solar system objects, including the terrestrial planets, chondritic meteorites, and comets. Recently, it was suggested that cometary nitrogen may be locked up in ammonium salts—ionic solids comprising ammonia (NH₃) and an acid such as hydrogen cyanide (HCN)—based on Rosetta/ROSINA data from comet 67P/Churyumov–Gerasimanko. Among the proposed salts to have been found in 67P were ammonium cyanide (NH₄CN) and ammonium cyanate (NH₄OCN), which were inferred from identifying HCN, cyanamide (NH₂CN), and isocyanic acid (HNCO) in the mass spectrometry data collected in the coma of 67P. However, the relationship …

Synthesis And Characterization Of Bimetallic Plasmonic Nanoparticles Using Linear And Nonlinear Spectroscopy, Daniel Babayode

LSU Doctoral Dissertations

Recent exploration in the field of nanomaterials has led to the investigation of noble metal nanoparticles for various nanomedical applications. The spectroscopy of these nanoparticles is studied using both linear and nonlinear optical processes such as second harmonic generation (SHG), two-photon fluorescence (TPF), and extinction spectroscopy. Details pertaining to the growth dynamics of silver-gold core-shell (Ag@Au CS) nanoparticles (NPs) and gold-silver-gold core-shell-shell (Au@Ag@Au CSS) nanoparticles (NPs) are currently being investigated in order to obtain better control and optimization of the nanoparticle size and surface morphology. Transmission electron microscopy (TEM) images show that the nanoparticles have tunable core and shell sizes …

Investigation Of The Binding Mechanisms Between Naphthenic Acids And Humic Acid Using Raman Spectroscopy And Computational Modeling, Jaelyn N. Palmer

Theses and Dissertations

The oil sand regions in Alberta, Canada have proven to be costly to the environment despite its economic benefits. The toxins produced during oil processing are sent to tailing ponds to be recycled, though often leaking into nearby waterways and soil. Naphthenic acids, NAs, are one of the most common toxins produced and have shown to be toxic to aquatic life, animals, and humans. As there is dissolved organic matter in tailing ponds and surrounding environments, tailing ponds often lead to NAs coming in contact with organic material. Humic acid, HA, is a major soil component that has been suspected …

Complexometric Titration Of Terbium(Iii) Compounds: An Analytical Blast From The Past Gives Purity Assurance When Modern Instruments Fail Us., Jake E. Timbes, Cameron Bateman, Justin Stace

Science University Research Symposium (SURS)

Lanthanide ions have attracted attention for applications in microwave electronics, memory devices, lighting applications, and chemical sensors. Terbium(III)-centered homoleptic complexes show promise as potential fluorescence-based chemical sensing agents. Tb(phen)2(NO3)3 (phen = 1,10-phenothroline) exhibits striking visible emission when excited by short-wave ultraviolet light; this emission is completely quenched by exposure to water or strong acid. However, the luminescence returns under relatively benign conditions. Unfortunately, our array of terbium(III) complexes are notoriously insoluble; rendering standard analytical techniques useless to assess purity, notably, 1H and 13C-NMR. Titration is a useful technique to give us, an assurance of purity—in conjunction with the ad-hoc purity …

Kinetic Analysis Of A Carbon-Rich Sico Model System, Takhya Holley

Chemistry & Biochemistry Theses - Archive

Kinetic Analysis of a Silicon Oxycarbide (polymethylhydrosiloxane/divinylbenzene) material was done for meaning of kinetic analysis methodology development. The material was synthesized using the standard procedure from, Blum 2005. A series of TGA’s was done using non-isothermal experiments. The analysis involved an initial isoconversional analysis using Friedman method, then decomposition of processes into individual processes using the Fraser-Suzuki function. The validation agreed within 1%, which is permissible by the ICTAC recommendations. The activation energies of the individual processes were determined using the Friedman method.The pre-dominant process #2 was found to have an activation energy of 220 +- 20 kj/mol and first-order …

Investigating The Photophysical Dynamics Of Anthracene And Acridine Derivatives Using Time-Resolved Spectroscopy, Sophia Tiano

Open Access Dissertations

Anthracenes and acridines are among the simplest visible light absorbing heterocyclic and polycyclic aromatic hydrocarbons and as such are extensively used in a variety of applications including photosensitizers and fluorescent sensors. Although the photophysics of some derivatives have been studied in the past, there is still a lot of unknown fundamental information that is vital in order to optimize these molecules for particular applications. Transient absorption spectroscopy was used to study the photophysics of the 9-substituted methyl, hydroxymethyl and formyl derivatives of acridine and anthracene. The growth and decay of the triplet-triplet absorption peak were quantified for each dye in …