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  Partner: UNT Libraries
 Department: Department of Chemistry
 Decade: 2010-2019
 Collection: UNT Theses and Dissertations
Ab Initio and Density Functional Investigation of the Conformer Manifold of Melatonin and a Proposal for a Simple Dft-based Diagnostic for Nondynamical Correlation

Ab Initio and Density Functional Investigation of the Conformer Manifold of Melatonin and a Proposal for a Simple Dft-based Diagnostic for Nondynamical Correlation

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Date: August 2013
Creator: Fogueri, Uma
Description: In this work we address two problems in computational chemistry relevant to biomolecular modeling. In the first project, we consider the conformer space of melatonin as a a representative example of “real-life” flexible biomolecules. Geometries for all 52 unique conformers are optimized using spin-component scaled MP2, and then relative energies are obtained at the CCSD (T) level near the complete basis set limit. These are then used to validate a variety of DFT methods with and without empirical dispersion corrections, as well as some lower-level ab initio methods. Basis set convergence is found to be relatively slow due to internal C-H…O and C-H…N contacts. Absent dispersion corrections, many DFT functionals will transpose the two lowest conformers. Dispersion corrections resolve the problem for most functionals. Double hybrids yield particularly good performance, as does MP2.5. In the second project, we propose a simple DFT-based diagnostic for nondynamical correlation effects. Aλ= (1-TAE [ΧλC]/TAE[XC])/λ where TAE is the total atomization energy, XC the “pure” DFT exchange-correlation functional, and ΧλC the corresponding hybrid with 100λ% HF-type exchange. The diagnostic is a good predictor for sensitivity of energetics to the level of theory, unlike most of the wavefunction-based diagnostics. For GGA functionals, Aλ values approaching unity ...
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Acceptor-sensitizers for Nanostructured Oxide Semiconductor in Excitonic Solar Cells

Acceptor-sensitizers for Nanostructured Oxide Semiconductor in Excitonic Solar Cells

Date: August 2014
Creator: Berhe, Seare Ahferom
Description: Organic dyes are examined in photoelectrochemical systems wherein they engage in thermal (rather than photoexcited) electron donation into metal oxide semiconductors. These studies are intended to elucidate fundamental parameters of electron transfer in photoelectrochemical cells. Development of novel methods for the structure/property tuning of electroactive dyes and the preparation of nanostructured semiconductors have also been discovered in the course of the presented work. Acceptor sensitized polymer oxide solar cell devices were assembled and the impact of the acceptor dyes were studied. The optoelectronic tuning of boron-chelated azadipyrromethene dyes has been explored by the substitution of carbon substituents in place of fluoride atoms at boron. Stability of singlet exited state and level of reduction potential of these series of aza-BODIPY coumpounds were studied in order to employ them as electron-accepting sensitizers in solid state dye sensitized solar cells.
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Accuracy and Efficiency in Computational Chemistry: The Correlation Consistent Composite Approach

Accuracy and Efficiency in Computational Chemistry: The Correlation Consistent Composite Approach

Date: August 2011
Creator: Wilson, Brent R.
Description: One of the central concerns of computational chemistry is that of efficiency (i.e. the development of methodologies which will yield increased accuracy of prediction without requiring additional computational resources – RAM, disk space, computing time). Though the equations of quantum mechanics are known, the solutions to these equations often require a great deal of computing power. This dissertation primarily concerns the theme of improved computational efficiency (i.e. the achievement of greater accuracy with reduced computational cost). Improvements in the efficiency of computational chemistry are explored first in terms of the correlation consistent composite approach (ccCA). The ccCA methodology was modified and this enhanced ccCA methodology was tested against the diverse G3/05 set of 454 energetic properties. As computational efficiency improves, molecules of increasing size may be studied and this dissertation explored the issues (differential correlation and size extensivity effects) associated with obtaining chemically accurate (within 1 kcal mol-1) enthalpies of formation for hydrocarbon molecules of escalating size. Two applied projects are also described; these projects concerned the theoretical prediction of a novel rare gas compound, FKrOH, and the mechanism of human glutathione synthetase’s (hGS) negative cooperativity. The final work examined the prospect for the parameterization of the modified embedded atom ...
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Accurate and Reliable Prediction of Energetic and Spectroscopic Properties Via Electronic Structure Methods

Accurate and Reliable Prediction of Energetic and Spectroscopic Properties Via Electronic Structure Methods

Date: August 2013
Creator: Laury, Marie L.
Description: Computational chemistry has led to the greater understanding of the molecular world, from the interaction of molecules, to the composition of molecular species and materials. Of the families of computational chemistry approaches available, the main families of electronic structure methods that are capable of accurate and/or reliable predictions of energetic, structural, and spectroscopic properties are ab initio methods and density functional theory (DFT). The focus of this dissertation is to improve the accuracy of predictions and computational efficiency (with respect to memory, disk space, and computer processing time) of some computational chemistry methods, which, in turn, can extend the size of molecule that can be addressed, and, for other methods, DFT, in particular, gain greater insight into which DFT methods are more reliable than others. Much, though not all, of the focus of this dissertation is upon transition metal species – species for which much less method development has been targeted or insight about method performance has been well established. The ab initio approach that has been targeted in this work is the correlation consistent composite approach (ccCA), which has proven to be a robust, ab initio computational method for main group and first row transition metal-containing molecules yielding, on ...
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Accurate Energetics Across the Periodic Table Via Quantum Chemistry

Accurate Energetics Across the Periodic Table Via Quantum Chemistry

Date: December 2015
Creator: Peterson, Charles Campbell
Description: Greater understanding and accurate predictions of structural, thermochemical, and spectroscopic properties of chemical compounds is critical for the advancements of not only basic science, but also in applications needed for the growth and health of the U.S. economy. This dissertation includes new ab initio composite approaches to predict accurate energetics of lanthanide-containing compounds including relativistic effects, and optimization of parameters for semi-empirical methods for transition metals. Studies of properties and energetics of chemical compounds through various computational methods are also the focus of this research, including the C-O bond cleavage of dimethyl ether by transition metal ions, the study of thermochemical and structural properties of small silicon containing compounds with the Multi-Reference correlation consistent Composite Approach, the development of a composite method for heavy element systems, spectroscopic of compounds containing noble gases and metals (ArxZn and ArxAg+ where x = 1, 2), and the effects due to Basis Set Superposition Error (BSSE) on these van der Waals complexes.
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Advancements in Instrumentation for Fourier Transform Microwave Spectroscopy

Advancements in Instrumentation for Fourier Transform Microwave Spectroscopy

Date: August 2011
Creator: Dewberry, Christopher Thomas
Description: The efforts of my research have led to the successful construction of several instruments that have helped expand the field of microwave spectroscopy. The classic Balle-Flygare spectrometer has been modified to include two different sets of antenna to operate in the frequency ranges 6-18 GHz and 18-26 GHz, allowing it to function for a large range without having to break vacuum. This modified FTMW instrument houses two low noise amplifiers in the vacuum chamber to allow for the LNAs to be as close to the antenna as physically possible, improving sensitivity. A new innovative Balle-Flygare type spectrometer, the efficient low frequency FTMW, was conceived and built to operate at frequencies as low as 500 MHz through the use of highly curved mirrors. This is new for FTMW techniques that normally operate at 4 GHz or higher with only a few exceptions around 2 GHz. The chirped pulse FTMW spectrometer uses horn antennas to observe spectra that span 2 GHz versus the standard 1 MHz of a cavity technique. This instrument decreases the amount of time to obtain a large spectral region of relative correct intensity molecular transitions. A Nd:YAG laser ablation apparatus was attached to the classic Balle-Flygare and chirped ...
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Affordances of Instrumentation in General Chemistry Laboratories

Affordances of Instrumentation in General Chemistry Laboratories

Date: August 2010
Creator: Sherman, Kristin Mary Daniels
Description: The purpose of this study is to find out what students in the first chemistry course at the undergraduate level (general chemistry for science majors) know about the affordances of instrumentation used in the general chemistry laboratory and how their knowledge develops over time. Overall, students see the PASCO™ system as a useful and accurate measuring tool for general chemistry labs. They see the probeware as easy to use, portable, and able to interact with computers. Students find that the PASCO™ probeware system is useful in their general chemistry labs, more advanced chemistry labs, and in other science classes, and can be used in a variety of labs done in general chemistry. Students learn the affordances of the probeware through the lab manual, the laboratory teaching assistant, by trial and error, and from each other. The use of probeware systems provides lab instructors the opportunity to focus on the concepts illustrated by experiments and the opportunity to spend time discussing the results. In order to teach effectively, the instructor must know the correct name of the components involved, how to assemble and disassemble it correctly, how to troubleshoot the software, and must be able to replace broken or missing components ...
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Application of the Correlation Consistent Composite Approach to Biological Systems and Noncovalent Interactions

Application of the Correlation Consistent Composite Approach to Biological Systems and Noncovalent Interactions

Date: May 2015
Creator: Riojas, Amanda G
Description: Advances in computing capabilities have facilitated the application of quantum mechanical methods to increasingly larger and more complex chemical systems, including weakly interacting and biologically relevant species. One such ab initio-based composite methodology, the correlation consistent composite approach (ccCA), has been shown to be reliable for the prediction of enthalpies of formation and reaction energies of main group species in the gas phase to within 1 kcal mol-1, on average, of well-established experiment, without dependence on experimental parameterization or empirical corrections. In this collection of work, ccCA has been utilized to determine the proton affinities of deoxyribonucleosides within an ONIOM framework (ONIOM-ccCA) and to predict accurate enthalpies of formation for organophosphorus compounds. Despite the complexity of these systems, ccCA is shown to result in enthalpies of formation to within ~2 kcal mol-1 of experiment and predict reliable reaction energies for systems with little to no experimental data. New applications for the ccCA method have also been introduced, expanding the utility of ccCA to solvated systems and complexes with significant noncovalent interactions. By incorporating the SMD solvation model into the ccCA formulation, the Solv-ccCA method is able to predict the pKa values of nitrogen systems to within 0.7 pKa unit (less ...
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Applications of Single Reference Methods to Multi-Reference Problems

Applications of Single Reference Methods to Multi-Reference Problems

Date: May 2015
Creator: Jeffrey, Chris C.
Description: Density functional theory is an efficient and useful method of solving single-reference computational chemistry problems, however it struggles with multi-reference systems. Modifications have been developed in order to improve the capabilities of density functional theory. In this work, density functional theory has been successfully applied to solve multi-reference systems with large amounts of non-dynamical correlation by use of modifications. It has also been successfully applied for geometry optimizations for lanthanide trifluorides.
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Biological Applications of a Strongly Luminescent Platinum (Ii) Complex in Reactive Oxygen Species Scavenging and Hypoxia Imaging in Caenorhabditis Elegans

Biological Applications of a Strongly Luminescent Platinum (Ii) Complex in Reactive Oxygen Species Scavenging and Hypoxia Imaging in Caenorhabditis Elegans

Date: December 2015
Creator: Kinyanjui, Sophia Nduta
Description: Phosphorescent transition metal complexes make up an important group of compounds that continues to attract intense research owing to their intrinsic bioimaging applications that arise from bright emissions, relatively long excited state lifetimes, and large stokes shifts. Now for biomaging assay a model organism is required which must meet certain criteria for practical applications. The organism needs to be small, with a high turn-over of progeny (high fecundity), a short lifecycle, and low maintenance and assay costs. Our model organism C. elegans met all the criteria. The ideal phosphor has low toxicity in the model organism. In this work the strongly phosphorescent platinum (II) pyrophosphito-complex was tested for biological applications as a potential in vivo hypoxia sensor. The suitability of the phosphor was derived from its water solubility, bright phosphorescence at room temperature, and long excited state lifetime (~ 10 µs). The applications branched off to include testing of C. elegans survival when treated with the phosphor, which included lifespan and fecundity assays, toxicity assays including the determination of the LC50, and recovery after paraquat poisoning. Quenching experiments were performed using some well knows oxygen derivatives, and the quenching mechanisms were derived from Stern-Volmer plots. Reaction stoichiometries were derived from ...
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