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

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 indicate severe non-dynamical correlation. The diagnostic is only weakly sensitive to the basis set (beyond polarized double zeta) and can be applied to problems beyond practical reach of wavefunction ab-initio methods required for other diagnostics.
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Date: August 2013
Creator: Fogueri, Uma

Acceptor-sensitizers for Nanostructured Oxide Semiconductor in Excitonic Solar Cells

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.
Date: August 2014
Creator: Berhe, Seare Ahferom

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

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 method (MEAM) potential using first principles calculations of dimer and trimer energies of nickel and carbon systems. This method of parameterization holds promise for increasing the accuracy of simulations for bulk properties within the field of materials science.
Date: August 2011
Creator: Wilson, Brent R.

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

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 average, accurate thermodynamic properties, i.e., within 1 kcal/mol of experiment for main group species and within 3 kcal/mol of experiment for first row transition metal molecules. In order to make ccCA applicable to systems containing any element from the periodic table, development of the method for second row transition metals and heavier elements, including lower p-block (5p and 6p) elements was pursued. The resulting method, the relativistic pseudopotential variant of ccCA (rp-ccCA), and its application are detailed for second row transition metals and lower p-block elements. Because of the computational cost of ab initio methods, DFT is a popular choice ...
Date: August 2013
Creator: Laury, Marie L.

Accurate Energetics Across the Periodic Table Via Quantum Chemistry

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.
Date: December 2015
Creator: Peterson, Charles Campbell

Adherence/Diffusion Barrier Layers for Copper Metallization: Amorphous Carbon:Silicon Polymerized Films

Description: Semiconductor circuitry feature miniaturization continues in response to Moore 's Law pushing the limits of aluminum and forcing the transition to Cu due to its lower resistivity and electromigration. Copper diffuses into silicon dioxide under thermal and electrical stresses, requiring the use of barriers to inhibit diffusion, adding to the insulator thickness and delay time, or replacement of SiO2 with new insulator materials that can inhibit diffusion while enabling Cu wetting. This study proposes modified amorphous silicon carbon hydrogen (a-Si:C:H) films as possible diffusion barriers and replacements for SiO2 between metal levels, interlevel dielectric (ILD), or between metal lines (IMD), based upon the diffusion inhibition of previous a-Si:C:H species expected lower dielectric constants, acceptable thermal conductivity. Vinyltrimethylsilane (VTMS) precursor was condensed on a titanium substrate at 90 K and bombarded with electron beams to induce crosslinking and form polymerized a-Si:C:H films. Modifications of the films with hydroxyl and nitrogen was accomplished by dosing the condensed VTMS with water or ammonia before electron bombardment producing a-Si:C:H/OH and a-Si:C:H/N and a-Si:C:H/OH/N polymerized films in expectation of developing films that would inhibit copper diffusion and promote Cu adherence, wetting, on the film surface. X-ray Photoelectron Spectroscopy was used to characterize Cu metallization of these a-Si:C:H films. XPS revealed substantial Cu wetting of a-Si:C:H/OH and a-Si:C:H/OH/N films and some wetting of a-Si:C:H/N films, and similar Cu diffusion inhibition to 800 K by all of the a-:S:C:H films. These findings suggest the possible use of a-Si:C:H films as ILD and IMD materials, with the possibility of further tailoring a-Si:C:H films to meet future device requirements.
Date: May 2004
Creator: Pritchett, Merry

Adhesion/Diffusion Barrier Layers for Copper Integration: Carbon-Silicon Polymer Films and Tantalum Substrates

Description: The Semiconductor Industry Association (SIA) has identified the integration of copper (Cu) with low-dielectric-constant (low-k) materials as a critical goal for future interconnect architectures. A fundamental understanding of the chemical interaction of Cu with various substrates, including diffusion barriers and adhesion promoters, is essential to achieve this goal. The objective of this research is to develop novel organic polymers as Cu/low-k interfacial layers and to investigate popular barrier candidates, such as clean and modified tantalum (Ta) substrates. Carbon-silicon (C-Si) polymeric films have been formed by electron beam bombardment or ultraviolet (UV) radiation of molecularly adsorbed vinyl silane precursors on metal substrates under ultra-high vacuum (UHV) conditions. Temperature programmed desorption (TPD) studies show that polymerization is via the vinyl groups, while Auger electron spectroscopy (AES) results show that the polymerized films have compositions similar to the precursors. Films derived from vinyltrimethyl silane (VTMS) are adherent and stable on Ta substrates until 1100 K. Diffusion of deposited Cu overlayers is not observed below 800 K, with dewetting occurred only above 400 K. Hexafluorobenzene moieties can also be incorporated into the growing film with good thermal stability. Studies on the Ta substrates demonstrate that even sub-monolayer coverages of oxygen or carbide on polycrystalline Ta significantly degrade the strength of Cu/Ta chemical interactions, and affect the kinetics of Cu diffusion into bulk Ta. On clean Ta, monolayer coverages of Cu will de-wet only above 600 K. A partial monolayer of adsorbed oxygen (3L O2 at 300 K) results in a lowering of the de-wetting temperature to 500 K, while saturation oxygen coverage (10 L O2, 300 K) results in de-wetting at 300 K. Carbide formation also lowers the de-wetting temperature to 300 K. Diffusion of Cu into the Ta substrate at 1100 K occurs only after a 5-minute induction period. This induction period increases ...
Date: December 1999
Creator: Chen, Li

The Adsorption of Radioactive Isotopes on Precipitates

Description: This thesis concerns the investigation of radioisotopes as indicators for precipitation reactions. As a precipitate forms in the presence of a radioisotope, adsorption may take place on its surface. If this adsorption changes markedly at the stoichiometric point it will be possible to use this variation as an indicator for the reaction.
Date: January 1954
Creator: Bulloch, Newman Payne

Advancements in Instrumentation for Fourier Transform Microwave Spectroscopy

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 pulse FTMW spectrometers. This allowed the study of heavy metal containing compounds. The instruments I constructed and the techniques I used have allowed the discovery of further insights into molecular chemistry. I have seen the effects of fluorinating an alkyl halide by determining the geometry of the carbon backbone of trans-1-iodoperfluoropropane and observing a ΔJ = 3 forbidden transition caused by a strong quadrupole coupling constant on this heavy molecule. The quadrupole coupling tensors of butyronitrile, a molecule observed in space, have been improved. The nuclear quadrupole coupling tensor of difluoroiodomethane was added to a list of variably fluorinated methyl ...
Date: August 2011
Creator: Dewberry, Christopher Thomas

Affordances of Instrumentation in General Chemistry Laboratories

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 quickly. The use of podcasts or Web-based videos should increase student understanding of affordances of the probeware.
Date: August 2010
Creator: Sherman, Kristin Mary Daniels

Analysis of Acid Gas Emissions in the Combustion of the Binder Enhanced d-RDF by Ion Chromatography

Description: Waste-to-energy has become an attractive alternative to landfills. One concern in this development is the release of pollutants in the combustion process. The binder enhanced d-RDF pellets satisfy the requirements of environmental acceptance, chemical/biological stability, and being storeable. The acid gas emissions of combusting d-RDF pellets with sulfur-rich coal were analyzed by ion chromatography and decreased when d-RDF pellets were utilized. The results imply the possibility of using d-RDF pellets to substitute for sulfur-rich coal as fuel, and also substantiate the effectiveness of a binder, calcium hydroxide, in decreasing emissions of SOx. In order to perform the analysis of the combustion sample, sampling and sample pretreatment methods prior to the IC analysis and the first derivative detection mode in IC are investigated as well. At least two trapping reagents are necessary for collecting acid gases: one for hydrogen halides, and the other for NOx and SOx. Factors affecting the absorption of acid gases are studied, and the strength of an oxidizing agent is the main factor affecting the collection of NOx and SOx. The absorption preference series of acid gases are determined and the absorption models of acid gases in trapping reagents are derived from the analytical results. To prevent the back-flushing of trapping reagents between impingers when leak-checking, a design for the sampling train is suggested, which can be adopted in sample collections. Several reducing agents are studied for pretreating the sample collected in alkali-permanganate media. Besides the recommendation of the hydrogen peroxide solution in EPA method, methanol and formic acid are worth considering as alternate reducing agents in the pretreatment of alkaline-permanganate media prior to IC analysis. The first derivative conductivity detection mode is developed and used in IC system. It is efficient for the detection and quantification of overlapping peaks as well as being applicable for non-overlapping ...
Date: August 1988
Creator: Jen, Jen-Fon

The Analysis of Fire Debris Using Nuclear Magnetic Resonance Spectroscopy

Description: This paper describes a new technique for analyzing fire debris using nuclear magnetic resonance (NMR) spectroscopy. Petroleum distillates, which are commonly used accelerants, were weathered, burned, and steamdistilled. These, as well as virgin samples of the accelerants, were analyzed by gas chromatography and nuclear magnetic resonance spectroscopy. In addition, solvent studies and detectibility limit studies were conducted. The use of NMR is described as a valuable adjunct to the existing methods of analysis.
Date: August 1981
Creator: Bryce, Kenneth L.

Analysis of PAH and PCB Emissions from the Combustion of dRDF and the Nondestructive Analysis of Stamp Adhesives

Description: This work includes two unrelated areas of research. The first portion of this work involved combusting densified refuse derived fuel (dRDF) with coal and studying the effect that Ca(0H)2 binder had on reducing polycyclic aromatic hydrocarbon (PAH) and polychlorinated biphenyl (PCB) emissions. The second area of work was directed at developing nondestructive infrared techniques in order to aid in the analysis of postage stamp adhesives. With Americans generating 150-200 million tons a year of Municipal Solid Waste (MSW) and disposing of nearly ninety percent of it in landfills, it is easy to understand why American landfills are approaching capacity. One alternative to landfilling is to process the MSW into RDF. There are technical and environmental problems associated with RDF. This work provides some answers concerning the amount of PAH and PCB emissions generated via the combustion of RDF with coal. It was found that the Ca(OH)2 binder greatly reduced both the PAH and the PCB emissions. In fact, PAH emissions at the ten-percent level were reduced more by using the binder than by the pollution control equipment. If the Ca(0H)2 binder can reduce not only PAH and PCB emissions, but also other noxious emissions, such as acid gases or dioxin, RDF technology could soon be the answer to the current landfill problems. The second portion of this work focused on developing a method to analyze stamp adhesives nondestructively. Using this method, it was fairly easy to differentiate among the three different types of adhesives that have been used by the United States Postal Service: gum arabic, dextrin, and polyvinyl alcohol. Differences caused by changes in chemicals added to the adhesives were also detected. Also, forgeries were detected with as much success, if not more, than by conventional methods. This work also led to the construction of equipment that allows large ...
Date: May 1989
Creator: Poslusny, Matthew