Physical Chemistry Commons^™

Using An Extended Broken Symmetry Approximation To Characterize Structure And Spectroscopic Properties Of 2fe-2s Clusters, Ashlyn M. Koval

Electronic Theses and Dissertations

Iron-sulfur proteins perform a wide variety of biological functions that assist in mediating protein function via electron transfer reactions. The Rieske and mitoNEET iron-sulfur clusters have been shown to undergo proton coupled electron transfer facilitated by a histidine ligand. The protonation state of the histidine residue is key to understanding the mechanism of proton coupled electron transfer. This work reports a study of the 2Fe-2S ferredoxin, Rieske, and mitoNEET clusters using the extended broken symmetry approximation. Calculations were performed on the ferredoxin cluster to establish appropriate methodologies. Calculations were then performed for Rieske and mitoNEET clusters to suggest experiments capable …

Aerobic Photolysis Mecbl: Structure And Electronic Properties Of Cbl-O-O-Ch3 Intermediate., Aida Bazarganpour

Electronic Theses and Dissertations

The photolysis of methylcobalamin (coenzyme B₁₂) results in homolytic cleavage of the Co-C bond, forming cob(II)alamin and the Co(II)/CH₃ radical pair (RP) which further react with O₂ to form the intermediate (R-O-O-Cbl) that involves in the aerobic photolysis. It has been suggested that the key intermediate (R-O-O-Cbl) involves in aerobic photolysis is the insertion of O₂ between the Co-C bond. Clearly, the exposure of light is needed to induce the activation Co-C bond for generating the Co(II)/CH₃ radical pair (RP). The intermediate (R-O-O-Cbl) undergoes further decomposition to aldehyde as the final product of aerobic …

Nontraditional Hydrogen Bonding In Asymmetric Lewis Acid Catalysis, Brandon Vernier

Electronic Theses and Dissertations

In the field of asymmetric induction, there is a shift from the synthesis of reaction

specific chiral auxiliaries towards a broader mechanistic approach. Our approach is to

develop a theory of asymmetric catalyst design from first principles. The Diels-Alder

reaction of 2-methacrolein and 1,3-cyclopentadiene in the presence of 15 mole % lmenthoxy

aluminum dichloride, reported by Koga, achieved the (S)-exo-Diels-Alder

cycloadduct with 72% ee (0% ee Endo for acrolein). The dramatic change from 72% to 0%

ee is a significant fact that has been overlooked in practical organic synthesis.

In the first phase of this work, the conformational landscape of …

Characterization Of Hydrogen Bonding, Halogen Bonding And Argyrophilic Interactions Using Computational Modeling, Sarah Nicole Arradondo

Electronic Theses and Dissertations

Non-covalent interactions govern multiple important chemical processes throughout nature from those within the human body to the complex environment of the atmosphere. Quantum mechanical electronic structure modeling of these relatively weak interactions can provide molecular level insight that can further our understanding of specific macroscopic properties. In the present work different non-covalent interactions are computationally evaluated within four systems. A small prototypical hydrogen bonded system and the various structural motifs that promoted proton transfer within concentrated acid and water clusters are characterized with sophisticated wavefunction based methods and large robust basis sets in order to accurately predict the structures energies …

Computational Quantum Chemistry Studies Of The Interactions Of Amino Acids Side Chains With The Guanine Radical Cation., Edward Acheampong

Electronic Theses and Dissertations

Guanine is generally accepted as the most easily oxidized DNA base when cells are subjected to ionizing radiation, photoionization or photosensitization. At pH 7, the midpoint reduction potential is on the order of 0.2 – 0.3 V higher than those of the radicals of e.g. tyrosine, tryptophan cysteine and histidine, so that the radical “repair” (or at least, a thermodynamically favorable reaction) involving these amino acids is feasible. Computational quantum studies have been done on tyrosine, tryptophan, cysteine and histidine side chains as they appear in histones. Density functional theory was employed using B3LYP/6-31G+ (d, p) basis set to study …

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This …

Novel Relative Spontaneous Ignition Temperature Determination Using Carbon Dioxide Onset With Sta/Ir, Antonio David Trevino

Electronic Theses and Dissertations

Simultaneous thermal analysis, coupled with infrared spectroscopy (STA/IR), was utilized to monitor the evolution of gaseous products during the thermal degradation of samples from Triadica sebifera (Chinese tallow), Ligustrum sinense (Chinese privet), and Ilex vomitoria (yaupon) plants. Identification of carbon dioxide was successful with a spectral match of 90.2 percent and further used in the determination of relative spontaneous ignition temperature, or RSIT. The RSIT value during the growing season for Chinese tallow, Chinese tallow stem, Chinese privet, and Yaupon were 208.4°C, 250.3°C, 210.1°C, and 232.3°C respectively. During the dormant seasons, the values for Chinese tallow stem, Chinese privet, and …

Steric Effects Of Alkyl Ammonium Salts On The Combustion Of Exchanged Smectite Clays, Celeste A. Keith

Electronic Theses and Dissertations

Bomb calorimetry was explored as a new method for determining the cation exchange capacity (CEC) of clays. Smectite clays were modified with several alkyl ammonium salts varying in number of carbons and the spatial orientation of the carbons about the central nitrogen atom. The clays used, standards purchased from the Source Clay Repository, have CECs of 44, 80, 88, and 120 meq/100 g. Theoretically, the combustion energy of the organo-clays should be approximately the same for each salt. Any differences in energy would be due to the different structures of the salts and how they are oriented in the interlamellar …

Computational Modeling Of Electronically Excited States In Cobalamin-Dependent Reactions., Brady D. Garabato

Electronic Theses and Dissertations

The current understanding of the photolytic properties of Vitamin B12 derivatives or cobalamins are summarized from a computational point of view. The focus is on two non-alkylcobalamins, cyanocobalamin (CNCbl) and hydroxocobalamin (HOCbl), two alkylcobalamins, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), as well as the stable cob(II)alamin radical. Photolysis of alkylcobalamins involves low-lying singlet excited states where photo-dissociation of the Co-C bond forms singlet-born alkyl/cob(II)alamin radical pairs (RPs). Potential energy surfaces (PESs) of low-lying excited states as functions of both axial bonds provide the most reliable tool for analysis of photochemical and photophysical properties. Due to the size limitations associated with the …

Artificial Olfactory System For Multi-Component Analysis Of Gas Mixtures., Alexander Aleksandrovich Larin

Electronic Theses and Dissertations

Gas analysis is an important part of our world and gas sensing technology is becoming more essential for various aspects of our life. A novel approach for gas mixture analysis by using portable gas chromatography in combination with an array of highly integrated and selective metal oxide (MOX) sensors has been studied. We developed a system with small size (7 x 13 x 16 inches), low power consumption (~10 W) and absence of special carrier gases designed for portable field analysis (assuming apriori calibration). Low ppb and even sub-ppb level of detection for some VOCs was achieved during the analysis …

Study Of 2,5-Diaminoimidazolone, A Mutagenic Product Of Oxidation Of Guanine In Dna, Hannah Catherine J. Pollard

Electronic Theses and Dissertations

2,5-diaminoimidazolone (Iz) is an important product of a 4-electron oxidation of guanine. The present research focuses on the mechanisms of formation of Iz via pathways initiated by guanine oxidation by one-electron oxidants (OEOs) generated by X-ray radiolysis in aqueous solutions. The kinetics of formation and yields of Iz in reactions of native highly polymerized DNA with different OEOs have been compared using an HPLC-based quantitative analysis of low-molecular products generated from the reaction of DNA-bound Iz with primary amines. Mechanisms of Iz formation in DNA have been investigated including oxygen and superoxide dependence as well as the hypothesis that 8-oxo-G, …

Transient Absorption Studies Of Cdse Nanocluster Passivated With Phenyldithiocarbamate Ligands., Yizhou Xie

Electronic Theses and Dissertations

Semiconductor nanocluster (SCNC) research is a rapidly growing field driven by the promising fact that properties of such materials can be tailored by modifying their size, shape, and structure. Combination of nanocluster and organic ligands provides even wider possibilities of design and development of effective and task-specific nanostructures. Understanding of and, eventually, control of energetics, interfacial interaction, and photoinduced processes in such highly heterogeneous structures is critical to invention of novel materials including those in photovoltaic devices. In the newly established Ultrafast Laser Facility (ULF), transient absorption pump-probe spectroscopy (TAPPS) has been employed to investigate the electron transfer (ET) and …

Controlled Electrochemical Synthesis Of Single One-Dimensional Metal Nanochains Across Microgap Electrodes., Amareshwari Konutham

Electronic Theses and Dissertations

This study mainly focuses on the fabrication of single one dimensional (1D) NP chains across the 5-micron gap of Au two electrode devices (TED). This has been achieved by electrochemical deposition of Ag onto the two electrodes, soaking the TED in 0.1 M Cetyltrimethyl ammonium bromide for 2-3 hours, and then close monitoring of the current as a function of time while a voltage across the two Ag coated Au electrodes in air. One dimensional Ag nanoparticle chain formation occurred by oxidation of Ag to Ag⁺ at the positive electrode followed by movement of Ag⁺ ions to the …

Homogeneous Ligand-Centered Hydrogen Evolution And Hydrogen Oxidation : Exploiting Redox Non-Innocence To Drive Catalysis., Andrew Z. Haddad

Electronic Theses and Dissertations

Hydrogen is a promising carbon-free fuel / energy carrier and is an essential building block for many industrial and agricultural processes. Rising energy demands have ignited interest in the development of carbon-free and carbon neutral energy sources. In this context, hydrogen is an attractive candidate—being energy-dense, carbon-free—and easily accessible through a two-electron reduction of water. Accordingly, many electrochemical homogeneous catalyst systems have been studied, with a focus on understanding the mechanism of hydrogen evolution proceeding through metal-hydride intermediates. However, there has been a renaissance in hydrogen evolution reaction (HER) catalyst design, with many groups implicating ligand redox non-innocence as a …

Ab Initio And Semi-Empirical Calculations Of Cyanoligated Rhodium Dimer Complexs, Yazeed Asiri

Electronic Theses and Dissertations

Molecular modeling, using both ab initio and semi-empirical methods has been undertaken for a series of dirhodium complexes in order to improve the understanding of the nature of the chemical bonding in this class of homogeneous catalysts. These complexes, with carboxylamidate and carboxylate ligands, are extremely functional metal catalysts used in the synthesis of pharmaceuticals and agrochemicals. The X-ray crystallography shows anomalies in the bond angles that have potential impact on understanding the catalysis. To resolve these issues, minimum energy structures of several examples (e.g. Rh₂(NHCOCH₃)₄, Rh₂(NHCOCH₃)₄NC, Rh …

Rationalizing The Band Gap Tunability Of Semiconductors Via Electronic Structure Calculations, Matthew N. Srnec

Electronic Theses and Dissertations

The polymorphs of titanium dioxide and various diamond-like semiconductor materials are promising candidates in photovoltaic solar cell applications. Several of these polymorphs have been studied with experimental and computational methods, which often aim at tuning the electronic structure, particularly the band gap value of the crystalline solid. Prior studies report that the addition of a substituent into the structure of titanium dioxide decreases its band gap value, but the reasons for this are unknown. Possible explanations for the change in band gap involve the substituent atom's crystal radius, electronegativity, and ionization energy. Understanding the cause of these changes will provide …

Computational Quantum Chemistry Studies Of The Stabilities Of Radical Intermediates Formed During The Oxidation Of Melatonin, Constance E. Warden

Electronic Theses and Dissertations

Melatonin, a nontoxic natural antioxidant, is of interest as a possible spin trap for use in spectroscopic methods to observe and identify short-lived free radicals, which have been linked to oxidative stress that may result in serious health problems. However, the reaction mechanisms for the oxidation of melatonin to form the product N¹-acetyl-N²-formyl-5-methoxykynuramine are still not well understood. Computational quantum chemistry studies have been done on four proposed reaction mechanisms, involving the following major intermediate structures: a dioxetane, an epoxide, a melatonin radical cation, and a spin radical adduct. Molecular geometries were optimized at the …

Computational Studies Of Spin Trapping Of Biologically Relevant Radicals By New Heteroaryl Nitrones, Eyram Asempa

Electronic Theses and Dissertations

Heteroaryl nitrone spin traps have been suggested to act as free radical scavengers. The geometry optimizations and the single-point energies of the spin trapping reactions of the heteroaryl nitrones, 5,5-dimethylpyrroline-N-oxide (DMPO) and α-phenyl-N-t-butylnitrone (PBN) have been computationally studied using ab initio (Hartree-Fock (HF) and second-order Møller-Plesset (MP2)) methods and Density Functional Theory (DFT) methods. The effects of new heteroaryl substituents on a parent nitrone spin trap have been examined at the HF and MP2 levels with the 6-31G*, and cc-pVnZ (n=D, T, Q) basis sets. The thermodynamics of the spin trapping at the C-site and O-site with •H, …

Characterization Of Charge Accommodation In Biologically Important Hydrogen-Bonded Clusters, John Thomas Kelly

Electronic Theses and Dissertations

The underlying motivation of chemical physics and physical chemistry is to understand naturally occurring chemical and physical processes from the nanoscopic molecular level to the macroscopic condensed phase. Over the past half-century, experimentalists have developed a number of laser-based analytical techniques to bridge the gap between the bulk phase and the single molecule. Here, we look at bulk phase and gas phase clusters to compare the local hydrogen-bonded network. To better understand the role noncovalent interactions have on biologically relevant building blocks in a natural environment, we compare the microhydration of gas phase cluster ions to condensed phase spectra. The …

Rapid Scan Electron Paramagnetic Resonance (Epr) And Digital Epr Development, Zhelin Yu

Electronic Theses and Dissertations

Rapid scan electron paramagnetic resonance (EPR) was developed in the Eaton laboratory at the University of Denver. Applications of rapid scan to wider spectra, such as for immobilized nitroxides, spin-labeled proteins, irradiated tooth and fingernail samples were demonstrated in this dissertation. The scan width has been increased from 55 G to 160 G. The signal to noise (S/N) improvement for slowly tumbling spin-labeled protein samples that is provided by rapid scan EPR will be highly advantageous for biophysical studies. With substantial improvement in S/N by rapid scan, the dose estimation for irradiated tooth enamels became more reliable than …

New Methods For Measuring Transient Interactions Between Proteins And Curved Membranes, Philip P. Cheney

Electronic Theses and Dissertations

Variations in the physical deformation of the plasma membrane play a significant role in the sorting and behavior of the proteins that occupy it. Determining the interplay between membrane curvature and protein behavior required the development and thorough characterization of a model plasma membrane with well defined and localized regions of curvature. This model system consists of a fluid lipid bilayer that is supported by a dye-loaded polystyrene nanoparticle patterned glass substrate. As the physical deformation of the supported lipid bilayer is essential to our understanding of the behavior of the protein occupying the bilayer, extensive characterization of the structure …

The Spectroscopic Characterization Of Newly Developed Emissive Materials And The Effects Of Environment On Their Photophysical Properties, Louis Edward Mcnamara

Electronic Theses and Dissertations

The development of new materials capable of efficient charge transfer and energy storage has become increasingly important in many areas of modern chemical research. This is especially true for the development of emissive optoelectronic devices and in the field of solar to electric energy conversion. The characterization of the photophysical properties of new molecular systems for these applications has become critical in the design and development of these materials. Many molecular building blocks have been developed and understanding the properties of these molecules at a fundamental level is essential for their successful implementation and future engineering. This dissertation focuses on …

Oxidative Damage To Dna 2´-Deoxyribose By Carbonate Radicals: Reaction Mechanisms And Products, Terence J. Moore

Electronic Theses and Dissertations

The carbonate radical anion (CO₃^•-, CR) is an important reactive oxygen species produced in vivo by one-electron oxidation of CO₂ or bicarbonate, constituents of the major physiological buffer. It was demonstrated for the first time by using an HPLC-based analysis of low-molecular products of DNA damage that CRs react with DNA 2΄-deoxyribose by the hydrogen abstraction mechanism. CRs exhibit a ~ 800-fold preference for one-electron oxidation of guanine over hydrogen abstraction from DNA sugar, in sharp contrast with •OH. CRs also have, as compared to •OH, an increased preference for the H1΄ abstraction, which is the …

Nitroxide Radicals For Low Frequency Electron Paramagnetic Resonance Imaging (Epri), Joshua R. Biller

Electronic Theses and Dissertations

Optimization of nitroxides as probes for EPR imaging requires detailed understanding of spectral properties such as spin lattice relaxation times, spin packet linewidths, and nuclear hyperfine splitting. Initial measurements of relaxation times for six low molecular weight nitroxides at X-band stimulated further measurement at frequencies between 250 MHz and 34 GHz. The impact of tumbling was studied with perdeuterated 2,2,6,6-tetramethyl-4-piperidinyl-1-oxyl (PDT) in five solvents with viscosities resulting in tumbling correlation times, τ_R, between 4 and 50 ps. A set of three ¹⁴N/¹⁵N pairs of nitroxides in water was selected such that τ_R varied between …

Probing Structure For Photophysical Properties Through Synthesis Of Novel Nucleosides, Brittney Jean Rodgers

Electronic Theses and Dissertations

A brief history of nucleosides and their photophysics provides the background information for the discussion of synthesis, photophysics and incorporation of fluorescent nucleotide analogs during enzymatic DNA synthesis. Through the use of nucleoside starting material, it is possible to synthesize a number of modified nucleotides for use as fluorescent probes in biochemical research. Synthetic endeavors into the synthesis of these and related molecules from nucleobase starting materials are also presented. The synthesis of these molecules involved re-development of the synthetic routes to broaden substrate scope by overcoming the changed reactivity resulting from the presence of additional functionality.

While many highly …

Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide, Kristina Andrea Cuellar

Electronic Theses and Dissertations

This thesis research focuses on the effects of the formation of hydrogen-bonded networks with the important osmolyte trimethylamine N-oxide (TMAO). Vibrational spectroscopy, in this case Raman spectroscopy, is used to interpret the effects of noncovalent interactions by solvation with select hydrogen bond donors such as water, methanol, ethanol and ethylene glycol in the form of slight changes in vibrational frequencies. Spectral shifts in the experimental Raman spectra of interacting molecules are compared to the results of electronic structure calculations on explicit hydrogen bonded molecular clusters. The similarities in the Raman spectra of microsolvated TMAO using a variety of hydrogen bond …

X-Band Rapid-Scan Epr, Deborah Gale Mitchell

Electronic Theses and Dissertations

The advantages of rapid-scan EPR relative to CW and pulse techniques for samples with long longitudinal relaxation time T₁ (N_s⁰ defects in diamond, N@C₆₀, and amorphous hydrogenated silicon), heterogeneous samples (crystalline 1:1 α,γ-bisdiphenylene-β-phenylallyl (BDPA):benzene), lossy samples (aqueous nitroxyl radicals), and transient radicals (5-tert-butoxycarbonyl-5-methyl-1-pyrroline-N-oxide (BMPO)-superoxide adduct) were studied.

For samples with long relaxation times, CW (continuous wave) EPR is challenging due to power saturation and distortions from passage effects. In rapid-scan EPR, the field is swept through resonance in a time that is short relative to T₂. In rapid-scan EPR, the magnetic field is …

On The Nature Of Weak Intermolecular Forces: A First Principles Approach To Hydrogen Bonding And Pi-Type Interactions, Kari Lorene Copeland

Electronic Theses and Dissertations

Computational quantum chemistry is a branch of chemistry that is based on quantum mechanics. In this field, chemical phenomena is represented in mathematical form and computers are used to provide numerical solutions to rigorous mathematical equations. Through this medium, the properties of atoms and molecules are calculated with high accuracy. Chapter 1 opens with a general discussion of science, the development of atomic theory and computational chemistry. Electronic structure theory is more extensively reviein Chapter 2. Hydrogen bonding and dispersion forces are defined in Chapter 3, and the procedures used to computationally study these type interactions are considered. Chapter 4 …

Investigations Of Noncovalent Interactions Using Raman Spectroscopy And Electronic Structure Computations, Ashley Wright

Electronic Theses and Dissertations

This dissertation research focuses on the effects of noncovalent interactions on vibrational energy levels. Vibrational spectroscopy is a powerful tool for the study of the effects of weak intermolecular interactions such as hydrogen bonding and interactions with the environment, including solvation effects. Changes in the vibrational spectra of interacting molecules allow us to ascertain exactly which atoms and bonds are affected and to what extent they are affected. Quantum mechanical methods, ab initio theory and density functional theory, are employed to model molecular geometries, properties, and subtle interactions between molecules. Much of this research centers on the comparison of these …

Multi-Configurational Investigation Of Thermolytic Pathways Of Highly Strained Ring Systems, Jeffrey Dwayne Veals

Electronic Theses and Dissertations

The isomerization pathways of model high energy structures are of interest because of their relation to high energy density fuels. Electron resonance has been found to greatly affect the relative activation barriers for several isomerization pathways, and the major goal of this research is to accurately describe its role in determining the relative barriers for strain energy release pathways. This research is centered around the potential energy surfaces (PES's) for ? bond breaking and ? bond rotation in these highly strained structures. Of particular interest was how would resonance and or electronegativity affect the allowed/disallonature of the activation barriers in …