Dissertation (Ph.D.)--Auburn University,2008. / Abstract. Vita. Includes bibliographic references (p.141-157).

Thesis (M.S.)--University of Missouri-Columbia, 2003. / Typescript. Includes bibliographical references (leaves 109-112). Also available on the Internet.

Thesis (M.S.)--University of Missouri-Columbia, 2003. / Typescript. Includes bibliographical references (leaves 109-112). Also available on the Internet.

Chemical reactions can be understood as transitions from basin to basin on a high dimensional potential energy landscape. Varying temperature only changes the average kinetic energy of the system. While applying voltages or external pressures directly tilts the landscape and drives the reactions in desired directions. In solids at relatively low temperature, where the entropy term is approximately invariant, the reaction spontaneity is determined by the energy difference between the reactant and product basins and the reaction rate can be calculated from the barriers in between. To achieve sufficient accuracy to explain experimental observations we are interested in, density functional theory (DFT) is usually employed to calculate energies. There are two types of reactions I have studied: the first type of reaction only involves a few number of individual atoms, corresponding to traveling in a small volume in the high dimensional configuration space; the other type involves a large amount of atoms moving in a concerted pattern, and the distance traveled in the configuration space is significantly longer. The scopes of these two in the energy landscapes are in different scales and thus proper metrics for distance measurements are required. In the first case, I have mainly studied Li/Na behaviors in the cathode materials of secondary batteries. Here resolving the energy landscape step by step with detailed information is possible and useful. By analyzing the energy landscapes with DFT plus the Hubbard U correction, I have explained several phenomena related to the degradation of lithium-rich layered oxides, rate performance of surface modified LiFePO₄, and capacity of vanadium-based fluorophosphates. Predictions on both thermodynamic and kinetic properties of materials are also made based on the calculation results and some are confirmed by experiments. In the second case, my focus is on solid-solid phase transitions. With a tremendous long reaction pathway, examining every possible atomic step is too expensive. By adopting periodic boundary conditions, a small supercell can represent the main feature of the energy landscape in a coarse grained way, where the connection between phases is easier to explore. After the big picture of a phase transition mechanism learned from this simplified model, details along the reaction pathway, like new phase nucleation and growth, could be resolved by using a larger supercell. In the above treatment, two types of variables, the cell vectors and atomic positions, span a generalized configuration space. Special consideration is required to balance these two to keep consistency under different supercells and avoid biases. A solid-state NEB (SSNEB) and a solid-state dimer (SSD) method are then developed to locate saddle points in the generalized configuration space. With the methodology well justified, we are able to efficiently find possible nucleation mechanisms, for examples the CdSe rock salt to wurtzite and Mo A15 to BCC phase transitions. SSNEB is also applied in studying phases transitions under pressures, including the graphite to diamond, and CaIrO₃ perovskite to post-perovskite transitions. Combined with the adaptive kinetic Monte Carlo (AKMC) algorithm, SSD shows the ability to find new polymorphs of CdSe and the connecting barriers between them. / text

A method for the synthesis of a symmetrical fluorous tagged benzodithiol support has been developed through a seven-step synthetic pathway. The Wittig olefination and catalytic hydrogenation reactions were employed to attach two perfluoroalkyl chains in the o-positions of phthalaldehyde. These fluorous tags were used as soluble supports which facilitated the purification of the crude reaction mixtures using fluorous solid phase extraction (FSPE). A selective and high yielding dibromination reaction was developed to synthesize a fluorous tagged 1,2-dibromo aryl compound. A thorough study was carried out to demonstrate the ease of an aryl-sulfur bond formation with the 1,2-dibromo compound varying palladium catalysts and ligands. A new palladium catalyzed dithiolation reaction is reported to synthesize a surrogated dithiol, which was exploited as a precursor for the synthesis of hitherto inaccessible symmetrical fluorous tagged benzodithiol support. The utility of the benzodithiol was explored by the synthesis of benzodithianes with two aldehydes. The lithiated dithiane generated was further used to form a C-C bond employing the umpolung reaction. The ring-closing metathesis reaction using Grubbs II catalyst was performed to construct 5-membered and 6-membered spiro-ring systems. Several approaches were made to form a C-C bond with lithiated dithianes using various nitrogen containing electrophiles leading to N-heterocycles.

The cold fiber solid phase microextraction (SPME) system was improved by minimizing the coating temperature fluctuation range, and the performance of the system was evaluated by investigating the extraction of PAHs from spiked sand samples. The coating temperature can be made relatively constant and the relative standard division (RSD) for most compounds was smaller than 2%. A simplified cold fiber system without the solenoid valve was modified to connect CO2 delivery tubing directly to the liquid CO2 tank. The robustness of this system was evaluated with different sizes of CO2 delivery tubings. The system is stable, low cost and can be easily controlled, which provides a supplementary extraction strategy to the traditional cold fiber system. The extraction amount of the analyte in a specific system was calculated theoretically in advance. The extraction amount for the experiment agreed with that of the calculated result. By using theoretical calculations as a guide, desorption efficiency for aged spiked samples was investigated. In order to achieve better extraction efficiency for PAHs, a programmed coating temperature method was developed and optimized, which led to higher extraction efficiency for most studied analytes compared to the traditional methods. In real sample analysis, certified reference soils were analyzed using cold fiber SPME and the addition of diethylamine successfully realized the exhaustive extraction for volatile compounds and enhanced the recoveries for semi-volatile compounds. Satisfactory extraction amounts for all compounds were achieved by the proposed method after method optimization.

A method for the synthesis of a symmetrical fluorous tagged benzodithiol support has been developed through a seven-step synthetic pathway. The Wittig olefination and catalytic hydrogenation reactions were employed to attach two perfluoroalkyl chains in the o-positions of phthalaldehyde. These fluorous tags were used as soluble supports which facilitated the purification of the crude reaction mixtures using fluorous solid phase extraction (FSPE). A selective and high yielding dibromination reaction was developed to synthesize a fluorous tagged 1,2-dibromo aryl compound. A thorough study was carried out to demonstrate the ease of an aryl-sulfur bond formation with the 1,2-dibromo compound varying palladium catalysts and ligands. A new palladium catalyzed dithiolation reaction is reported to synthesize a surrogated dithiol, which was exploited as a precursor for the synthesis of hitherto inaccessible symmetrical fluorous tagged benzodithiol support. The utility of the benzodithiol was explored by the synthesis of benzodithianes with two aldehydes. The lithiated dithiane generated was further used to form a C-C bond employing the umpolung reaction. The ring-closing metathesis reaction using Grubbs II catalyst was performed to construct 5-membered and 6-membered spiro-ring systems. Several approaches were made to form a C-C bond with lithiated dithianes using various nitrogen containing electrophiles leading to N-heterocycles.

Accurate characterization of risk of adverse ecological effects related to contaminated sediment presents a particularly difficult challenge. A series of studies has been conducted to investigate the utility of various tools for assessment of sediment toxicity. The goal of this research was to provide information which could help increase the accuracy with which predictions of toxicity could be made at hazardous sites. A calibration study was conducted using model PAHs, PCBs, a binary PAH mixture and a coal-tar mixture. This study was a collaborative effort among five university-based Superfund Research Programs (SRPs). Each program, with the help of funding through the NIEHS Superfund Research Program, has developed a chemical-class specific assay to estimate toxicity of contaminants in sediment. This suite of bioassays expands the range of data typically obtained through the use of standard aquatic toxicity assays. A series of caged in situ exposure studies has been conducted using juvenile Chinook salmon and Pacific staghorn sculpin in the Lower Duwamish Waterway. The study aimed to investigate the utility of selected biomarkers in evaluating the relationship between contaminants present in environmental samples and response in receptors following an in situ caged exposure. Results found that DNA adducts detected in exposed fish were significantly higher than controls in 2004 and 2006, and DNA adducts appear to be a reliable indicator of exposure, although no dose-response relationship was present. Western blot analysis of CYP1A1 was not indicative of exposure levels. The final study conducted was concerned with evaluating the utility of using solid phase microextraction (SPME) fibers in situ to evaluate contaminated sediment. Levels of PAHs and PCBs in sediment often exceeded sediment quality guidelines; however, results from aquatic toxicity bioassays using Hyalella azteca were mostly negative, thus levels of contaminants detected on SPME fibers could not be associated with adverse effects in Hyalella. However, regression analysis of total PAHs present in sediment and levels of PAHs detected in porewater SPME fiber samplers, which were placed 5 cm into the sediment for 30 days, revealed a strongly correlated linear relationship (R2 = .779). Normalization of the sediment data to total organic carbon was performed to determine if the trend would remain present, and the linear relationship was again confirmed (R2 =.709).

Until recently, multiple SPME fibres could not be automatically evaluated in a single sequence without manual intervention. This drawback had been a critical issue until recently, particularly during the analysis of numerous on-site samples. Recently, GERSTEL® has developed and commercialized a Multi-Fibre Exchanger (MFX) system designed to overcome this drawback. In this research, a critical evaluation of the MFX performance in terms of storage stability and long term operation is presented. It was established in the course of our research that the MFX can operate continuously and precisely for over 200 extraction/injection cycles. However, when the effect of residence time of commercial fibres on the MFX tray was evaluated, the results have shown that amongst the evaluated fibre coatings, carboxen/polydimethylsiloxane (CAR/PDMS) was the only coating capable of efficient storage on the MFX tray for up to 24 hours after field sampling without suffering significant loss of analytes. Additionally, the MFX system capability for high-throughput analysis was demonstrated by the unattended desorption of multiple fibres after on-site sampling of two different systems, indoor air and biogenic emissions. Subsequently, a protocol based on a new, fast, reproducible, reusable and completely automated method that enables quick assessment of SPME coatings was developed. The protocol consists of an innovative in-vial standard generator containing vacuum pump oil doped with McReynolds probes and subsequently mixed with a polystyrene-divinylbenzene resin. According to our results, the protocol has proven to be a useful tool for the quick assessment of inter-fibre reproducibility prior to their application in on-site analysis. The implications of such protocols include, but are not limited to: time-saving, assurance of reliable and reproducible data, and a dependable guide for novice users of the technique. Finally, an innovative, reusable and readily deployable pen-like diffusive sampler for needle traps (PDS-NT) is proposed. Results have shown that the new PDS-NT is effective for air analysis of benzene, toluene, and o-xylene (BTX). In addition, no statistically significant effects of pen geometry on the uptake of analytes were found.

Synthetic cannabinoids were first created in a pharmaceutical setting where scientists were studying marijuana. Researchers were trying to develop medically beneficial marijuana analogs. The compounds, however, were found to give physiological effects that were more potent than marijuana. Presently, synthetic cannabinoids have become a psychoactive drug of abuse, sold in head shops and over the Internet. New compounds are constantly being synthesized, which makes analysis of the drugs difficult. Solid phase extraction (SPE) is a well-studied method used in toxicological analysis to extract drugs and their metabolites from biological fluids. This sample preparation method is necessary to isolate the desired components of a sample for analysis by gas chromatography and mass spectrometry (GC/MS). This study sought to compare four brands of commercially available SPE cartridges using a procedure from United Chemical Technologies (UCT) for the simultaneous extraction of the three synthetic cannabinoid metabolites, JWH-018 N-(4-hydroxypentyl), JWH-122 N-(5-hydroxypentyl), and JWH-250 N-(5-hydroxypentyl), from urine. The cartridges from UCT, Thermo Scientific, Agilent Technologies, and SiliCycle were evaluated to determine how they performed throughout the SPE procedure. A recovery efficiency study was conducted to measure the amount of extracted metabolites from the urine. The responses of the quantification ion of the metabolites from an extracted urine sample were compared to a neat sample and the percent recovery was calculated. A within-run precision study was also utilized to measure the reproducibility of the cartridges, which was determined by the coefficient of variation (CV) of the different brands. The outcome of this research led to a development of a GC/MS method for detection of the three metabolites, creation of calibration curves for quantification, use of SPE for the extraction of the metabolites from urine, and the quantification of the extracted compounds to determine the efficacy and consistency of four brands of SPE cartridges. Method optimization was able to minimize the interday variations seen in the results of aliquots of the same samples. Optimal parameters include initial validation of the GC/MS method, a clean liner for the analysis of synthetic cannabinoid metabolites, using a GC column with a high temperature limit, and derivatization of the extracts before injection into the GC. While this study shows it is possible to use GC/MS for the analysis of these metabolites, LC/MS does not have the same restrictions because a liner, temperature elution, and derivatization of the analytes are not utilized. It was determined from the results of these studies that SiliCycle had the most reproducible and efficient cartridges. SiliCycle cartridges had a consistent and fast flow rate with a percent recovery efficiency within ±20% of the actual value. The results from SiliCycle were followed by cartridges from UCT, Thermo Scientific, and Agilent brands, respectively.