Student Number : 0002483R - MSc dissertation - School of Molecular and Cell Biology - Faculty of Science / Isothermal titration calorimetry was used to investigate the forces that drive ligand binding to the active site of rGST M1-1. In an attempt to gain insight into the recognition of non-substrate ligands by GSTs, this study also investigates interactions between rGST M1-1 and ANS, a non-substrate ligand. At 25 °C, complex formation between rGST M1-1 and GSH, GSO3 -, and S-hexylglutathione is characterised by a monophasic binding isotherm with Kd values of 38.5 mM, 2.1 mM and 0.2 mM, respectively. One molecule of each ligand is bound per monomer of rGST M1-1. Binding of these ligands is enthalpically favourable and entropically unfavourable with a resultant favourable Gibbs free energy, overall. The effects of temperature and buffer ionisation on the energetics of binding were studied. The enthalpic and entropic contributions for all three ligands exhibited temperature dependence over the temperature range investigated (5-30 °C). The Gibbs free energy showed negligible changes with increasing temperature due to enthalpy-entropy compensation. The temperature dependence of the binding enthalpy yielded heat capacity changes of – 2.69 kJ/mol/K and –3.68 kJ/mol/K at 25 °C for GSH and S-hexylglutathione binding and –1.86 kJ/mol/K overall for GSO3 -. The linear dependence of DH on temperature for GSO3 - binding to rGST M1-1 suggests the formation of a more constrained complex which limits the fluctuations in conformations of the mu-loop at the active site. The non-linear dependence of DH on temperature for GSH and Shexylglutathione binding to the enzyme suggests the formation of a complex that samples different bound conformations due to the mobility of the mu-loop even after ligand is bound. Calorimetric binding experiments in various buffer systems with different ionisation enthalpies suggest that the binding of GSH to rGST M1-1 is coupled to the deprotonation of the thiol of GSH while GSO3 - binding to rGST M1-1 is independent of the buffer ionisation. At 25 °C, the rGST M1-1#1;ANS association is represented by a monophasic binding isotherm with one molecule of ANS bound per monomer of rGST M1-1. The interaction is both enthalpically and entropically driven with a Kd value of 27.2 mM representing moderate affinity. The effect of temperature on the interaction was investigated over the temperature range of 5-30 °C. The linear dependence of the binding enthalpy on temperature indicates that no significant structural changes occur upon binding of ANS to the enzyme (DCp = -0.34 kJ/mol/K). The change in heat capacity associated with the interaction can be attributed to the burial of the polar sulphonate group of ANS and the exposure of the anilino and naphthyl rings to solvent as well as the possibility of weak electrostatic interactions between ANS and residues at the active site. The effect of ethacrynic acid, GSH, GSO3 - and S-hexylglutathione on the fluorescence of ANS was investigated in order to obtain some idea as to the location of the ANS binding site on rGST M1-1. ANS was displaced by GSO3 -, S-hexylglutathione and ethacrynic acid, while no displacement occurred upon binding of GSH to the active site of rGST M1-1. Displacement studies and molecular docking simulations indicate that ANS binds to the H-site of rGST M1-1 and the possibility of a second binding site for the molecule cannot be ruled out.

The spatial stability of hypersonic conical boundary layers is investigated utilizing different numerical techniques. First, the development and verification of a Linearized Compressible Navier-Stokes solver (LinCS) is presented, followed by an investigation of different effects that affect the stability of the flow in free-flight/ground tests, such as: high-enthalpy effects, wall-temperature ratio, and three-dimensionality (i.e. angle-of-attack). A temporally/spatially high-order of accuracy parallelized Linearized Compressible Navier-Stokes solver in disturbance formulation was developed, verified and employed in stability investigations. Herein, the solver was applied and verified against LST, PSE and DNS, for different hypersonic boundary-layer flows over several geometries (e.g. flat plate - M=5.35 & 10; straight cone - M=5.32, 6 & 7.95; flared cone - M=6; straight cone at AoA = 6 deg - M=6). The stability of a high-enthalpy flow was investigated utilizing LST, LinCS and DNS of the experiments performed for a 5 deg sharp cone in the T5 tunnel at Caltech. The results from axisymmetric and 3D wave-packet investigations in the linear, weakly, and strongly nonlinear regimes using DNS are presented. High-order spectral analysis was employed in order to elucidate the presence of nonlinear couplings, and the fundamental breakdown of second mode waves was investigated using parametric studies. The three-dimensionality of the flow over the Purdue 7 deg sharp cone at M=6 and AoA =6 deg was also investigated. The development of the crossflow instability was investigated utilizing suction/blowing at the wall in the LinCS/DNS framework. Results show good agreement with previous computational investigations, and that the proper basic flow computation/formation of the vortices is very sensitive to grid resolution.

The pyrolysis mechanics of Phenolic Impregnated Carbon Ablators (PICA) makes it a valued material for use in thermal protection systems for spacecraft atmospheric re-entry. The present study of the interaction of pyrolysis gases and char with plasma gases in the boundary layer over PICA and its substrate, FiberForm, extends previous work on this topic that has been done in the UVM 30 kW Inductively Coupled Plasma (ICP) Torch Facility. Exposure of these material samples separately to argon, nitrogen, oxygen, air, and carbon dioxide plasmas, and combinations of said test gases provides insight into the evolution of the pyrolysis gases as they react with the different environments. Measurements done to date include time-resolved absolute emission spectroscopy, location-based temperature response, flow characterization of temperature, enthalpy, and enthalpy flux, and more recently, spatially resolved and high-resolution emission spectroscopy, all of which provide measure of the characteristics of the pyrolysis chemistry and material response. Flow characterization tests construct an general knowledge of the test condition temperature, composition, and enthalpy. Tests with relatively inert argon plasmas established a baseline for the pyrolysis gases that leave the material. Key pyrolysis species such as CN Violet bands, NH, OH and Hydrogen Alpha (Hα) lines were seen with relative repeatability in temporal, spectral, and intensity values. Tests with incremental addition, and static mixtures, of reactive plasmas provided a preliminary image of how the gases interacted with atmospheric flows and other pyrolysis gases. Evidence of a temporal relationship between NH and Hα relating to nitrogen addition is seen, as well as a similar relationship between OH and Hα in oxygen based environments. Temperature analysis highlighted the reaction of the material to various flow conditions and displayed the in depth material response to argon and air/argon plasmas. The development of spatial emission analysis has been started with the hope of better resolving the previously seen pyrolysis behavior in time and space.

A sustentabilidade das regiões de produção intensiva de suínos depende de destinos alternativos para os resíduos nelas gerados. A calcinação da cama sobreposta gera sílica vítrea que pode ser utilizada na substituição parcial de aglomerantes comerciais. A utilização de cinzas de casca de arroz como material pozolânico para a confecção de argamassas e concretos tem merecido atenção considerável, nos últimos anos, não apenas por melhorar as propriedades mecânicas de materiais cimentícios, mas, sobretudo pelos benefícios ambientais gerados, com a redução do consumo de clínquer. A falta de sustentabilidade ambiental pode limitar o crescimento econômico da suinocultura, dada a tendência do setor de crescimento concentrado em grandes empreendimentos, e, por conseqüência, do aumento da poluição provocada pelos dejetos. Com a busca de alternativas que solucionem ou minimizem tal problema, o objetivo geral deste trabalho foi o aproveitamento de resíduos agropecuários (cama sobreposta de suínos e fibra curta de sisal) para a fabricação de placas à base de compósitos cimentícios para escamoteadores com diferentes tipos de aquecimento (lâmpada incandescente e resistência elétrica). As cinzas de cama sobreposta de suínos substituíram 30% do cimento Portland. A matriz cimentícia resultante foi reforçada com fibra curta de sisal. Os resultados obtidos com a utilização da cinza da cama sobreposta de suínos valida seu uso como material de substituição parcial do cimento Portland. A temperatura ideal de calcinação é de 600 ºC, com rampa de 5 ºC/min durante 3 h. O material selecionado foi o passante na peneira ABNT No 200 (# 0,074 mm). A cinza da cama sobreposta de suínos aumentou a condutividade térmica e a fibra de sisal incorporou o ar na placa e, assim, reduziu a conducao do calor para a parte inferior. O melhor tratamento foi a utilização da placa em duas camadas com cinza de cama sobreposta e fibra de sisal, associada ao uso da lâmpada de 200 W. / The sustainability of intensive areas of swine production depends on alternative destinations for the generated residues. The calcination of swine deep bedding generates vitreous silica for partial replacement of commercial binders. The use of rice husk ashes as pozzolanic material for mortars and concretes has deserved considerable attention in the last years, not just for improving their mechanical properties, but also for the environmental benefits linked to the reduction of clinker consumption. The lack of environmental sustainability can limit the economical growth of swine production, due to the tendency for concentration in sites with intensive activity, and, as a consequence, the increase of the contamination by wastes. Aiming alternatives that can minimize or decrease such problem, the objective of this work is to test the use of agricultural waste (swine deep bedding ashes and sisal fiber) for the manufacture of piggy`s house plates with different types of heating (filament lamps and electric resistance) on based cement composite materials. The swine deep bedding ashes replaced 30% of Portland cement. The resulting cementations matrix was reinforced with sisal fiber. The results obtained with the use of swine deep bedding ashes validates the use of this material for partial replacement of Portland cement. The optimal calcination temperature is 600 °C with rate of 5 ºC/min for over 3 hours. The material selected should be as pass in ABNT sieve No 200 (# 0.074 mm). The swine deep bedding ashes increased the thermal conductivity and sisal fiber entrapped air in the plate and due to the pores incorporated there was a reduction in the heat conduction to the bottom. The best treatment was the plate with two layers of swine deep bedding ashes and sisal fiber, associated with 200 W lamp.

O modelo F–SAC (Functional–Segment Activity Coefficient), recentemente introduzido, combina a ideia de contribuição de grupos com a teoria de superfícies de contato COSMO–RS. Este modelo tem uma dependência reduzida dos parâmetros de interação binária quando comparado com as variantes do modelo UNIFAC e precisão melhorada quando comparada com modelos baseados em COSMO. No presente trabalho uma modificação na formulação do modelo F–SAC é proposta para a inclusão de interações dispersivas. Para testar esta modificação, foram considerados os dados experimentais de alcanos, ciclo–alcanos, alcenos, aromáticos e perfluorocarbonetos. O modelo proposto foi capaz de correlacionar entalpias de vaporização de substâncias puras, não consideradas em versões anteriores do modelo. Uma vez que a capacidade calorífica de líquidos está intimamente relacionada com a entalpia de vaporização, o modelo também pode prever a capacidade calorífica de substâncias puras. Em relação ao coeficiente de atividade em diluição infinita e dados de equilíbrio líquido–vapor, o modelo modificado manteve o bom desempenho do modelo original, também semelhante a outros modelos similares, como variantes do modelo UNIFAC. Além disso, o modelo modificado pode agora calcular valores consistentes para a entalpia e entropia de excesso para sistemas onde as interações são principalmente dispersivas. Para estes sistemas, a maioria dos modelos de coeficiente de atividade prevê entalpia de excesso zero, contrabalançando valores de energia de Gibbs de excesso confiáveis com entropias de excesso distorcidas. / The recently introduced F–SAC (Functional–Segment Activity Coefficient) model combines the group contribution idea with a COSMO–RS surface contacting theory. This model has a reduced dependency on binary interaction parameters when compared to classical UNIFAC type models and improved accuracy when compared with COSMO based models. In the present work a modified F–SAC formulation is proposed for including dispersive interactions. For testing the modification, experimental data of alkanes, cycloalkanes, alkenes aromatics and perfluorocarbons were considered. The proposed model was able to correlate pure compound enthalpies of vaporization, not considered in previous versions of the model. Since the heat capacity of liquids is closely related to the enthalpies of vaporization, the model also can predict pure compound heat capacity of liquids. Regarding mixture infinite dilution activity coefficient and vapor–liquid equilibrium data, the modified model maintained the good performance of the original model, also similar to other competing models such as UNIFAC variants. Additionally, the modified model now can compute consistent values for the excess enthalpy and entropy for systems where the interactions are mainly dispersive. For these systems, most activity coefficient models predict zero excess enthalpies, counterbalancing that with distorted excess entropies.

A presença de sais no petróleo ocasiona grandes problemas operacionais relacionados à corrosão, uma vez que estes acabam formando ácido clorídrico no processo de separação do óleo bruto. Com o intuito de amenizar os efeitos de corrosão ácida, aminas podem ser adicionadas no topo das colunas para agir como neutralizantes. Porém, dependendo das condições operacionais e da quantidade de amina adicionada, pode ocorrer a deposição de cloridratos de aminas, promovendo a corrosão sob depósito. Assim, o conhecimento da pressão de sublimação desses sólidos é de extrema importância para especificar as condições de operação e o melhor desempenho destes aditivos no processo. Dentro desse contexto, o objetivo deste trabalho é determinar as pressões e entalpias de sublimação de cloridratos de aminas com a técnica termogravimétrica. Devido às dificuldades encontradas para obtenção de dados precisos de pressão em baixas temperaturas, uma extensão ao método termogravimétrico foi proposta, tornando possível medir pressões na ordem de 1 0,5 Pa. As substâncias estudadas foram: brometo de amônio, cloreto de amônio, cloridrato de etanolamina, cloridrato de metilamina, cloridrato de piridina, cloridrato de trimetilamina e dicloridrato de n-(1- naftil)etilenodiamina. Resultados de pressão e entalpia de sublimação alcançados com ácido benzoico, brometo de amônio e cloreto de amônio foram validados com dados da literatura Para os demais sólidos estudados, não há muitos dados disponíveis na literatura. No entanto, como a reação de sublimação do cloreto de amônio é análoga à dos demais cloridratos de amina, as entalpias de sublimação puderam ser comparadas e os resultados encontrados foram satisfatórios. Por fim, para uma melhor aplicabilidade dos resultados obtidos, uma equação de Clausius-Clapeyron modificada foi utilizada para correlacionar os dados medidos. Uma ótima correlação foi possível para todos os sais estudados, com coeficiente de correlação sempre superior a 0,97. / The presence of salts in petroleum causes operational problems related to corrosion, due to the fact that they end up forming hydrochloric acid in the crude oil separation process. In order to mitigate the effects of acid corrosion, amines can be added at the top of the columns to act as neutralizers. However, depending on the operational conditions and the amount of amine added, a deposition of amine hydrochlorides may occur, promoting under-deposit corrosion. Thus, the knowledge of the sublimation pressure of these salts has an extreme importance in trying to predict and to optimize the performance of the additives in the process. Within this context, the purpose of this study is to determine pressure and enthalpy of sublimation of amine hydrochlorides with the thermogravimetric technique. Due to the difficulties encountered to obtain precise pressure data at low temperatures, an extension of the thermogravimetric method was proposed, enabling to measure sublimation pressures in the order of 1 0,5 Pa. The substances studied were: ammonium bromide, ammonium chloride, ethanolamine hydrochloride, methylamine hydrochloride, pyridine hydrochloride, trimethylamine hydrochloride and n-(1-naphthyl)ethylenediamine dihydrochloride. Results of pressure and enthalpy of sublimation obtained with benzoic acid, ammonium bromide and ammonium chloride were validated using literature data. For other solids investigated in this study, experimental data is scarce in the literature. However, as the sublimation reaction of ammonium chloride is analogous to the others amine hydrochlorides, enthalpies of sublimation could be compared with the results found. Since similar values were observed, the results were considered satisfactory. Finally, the measured data were correlated using a modified Clausius-Clapeyron equation. A good correlation was possible for all salts studied, with correlation coefficient always higher than 0.97.

The enthalpies of solution, HS, of carbon dioxide in aqueous methyldiethanolamine were measured with an isothermal flow calorimeter over wide ranges of temperature, pressure, weight percent MDEA, and loading (gmole CO2/gmole MDEA). The values of HS (kJ/gmole CO2) were found to be constant up to the saturation concentration of CO2 in the aqueous solution. In addition, experimental data showed that HS was independent of the total pressure over the solution, but linearly dependent upon both temperature and weight percent MDEA as was given by a correlation. A computer program based upon basic thermodynamic quantities was developed to model HS of CO2 in MDEA solutions. The values of K and ΔH for each of the chemical reactions (except the MDEA protonation reaction) were fitted values from the literature. Activity coefficient correlations used in the program were also obtained from the literature. Using these data, the program was first used to find the values of K and ΔH for the MDEA protonation reaction which gave the minimum error between the model and the experimental data. Finally, the values of HS predicted by the program were compared to the experimental data and the differences were discussed.

Cross flow heat exchangers are a fairly common apparatus employed throughout many industrial processes. For these types of systems, correlations have been extensively developed. However, there have been no correlations done for very high enthalpy flows as produced by Arnold Engineering Development Center’s (AEDC) H2 facility. The H2 facility uses a direct current electric arc to heat air which is then expanded through a converging-diverging nozzle to impart a supersonic velocity to the air. This high enthalpy, high temperature air must be cooled downstream by the use of a cross flow heat exchanger. It is of interest to evaluate the actual performance of the air cooler to determine the effectiveness of possible facility upgrades. In order to characterize cooler effectiveness, a numerical model is built to calculate per-tube-row energy balances using real (temperature and pressure dependent) air and water properties and cross-flow Nusselt number calculations.

Biocatalysis has become a popular technique in organic synthesis due to high activity and selectivity of enzyme catalyzed reactions. Enantioselectivity is a particularly attractive enzyme property, which is utilized for the production of enantiopure substances. Determination of the temperature dependence of enzyme enantioselectivity allows for thermodynamic analyses that reveal the contribution of differential activation enthalpy, ΔR-SΔH‡, and entropy, ΔR-SΔS‡. In the present investigation the influence of substrate structure, variations on enzyme structure and of reaction media on the enantioselectivity of Candida Antarctica lipase B has been studied. The contribution of enthalpy, ΔR-SΔH‡, and entropy, TΔR-SΔS‡, to the differential free energy, ΔR-SΔG‡, of kinetic resolutions of sec-alcohols were of similar magnitude. Generally the two terms were counteracting, meaning that the enantiomer favored by enthalpy was disfavored by entropy. 3-Hexanol was an exception where the preferred enantiomer was favored both by enthalpy and by entropy. Resolution of 1-bromo-2-butanol revealed non-steric interactions to influence both ΔR-SΔH‡ and ΔR-SΔS‡. Molecular modeling of the spatial freedom of the enzyme-substrate transition state indicated correlation tothe transition state entropy. The acyl chain length was shown to affect enantioselectivity in transesterifications of a sec-alcohol. Point mutations in the active site were found to decrease or increase enantioselectivity. The changes were caused by partly compensatory changes in both ΔR-SΔH‡ and ΔR-SΔS‡. Studies on single and double mutation variants showed that the observed changes were not additive. Enantioselectivity was strongly affected by the reaction media. Transesterifications of a sec-alcohol catalyzed by Candida Antarctica lipase B was studied in eight liquidorganic solvents and supercritical carbon dioxide. A correlation of enantioselectivity and the molecular volume of the solvent was found. Differential activation enthalpy, ΔR-SΔH‡, and entropy, ΔR-SΔS‡, display a compensatory nature. However this compensation is not perfect, which allows for modifications of enantioselectivity. The components of the thermodynamic parameters are highly complex and interdependent but if their roles are elucidated rational design of enantioselective enzymatic processes may be possible. / QC 20100616

A set of algorithms were designed, implemented and evaluated in order to, first, identifyclusters of conserved waters in binding pockets, i.e. hydration sites. Then, their contributionto the free energy of binding in a ligand-protein association was quantified by calculatingtheir enthalpy and entropy. The information obtained by using these algorithms couldcontribute to the development of new drugs by generating new ligands that target specifichigh-energy, unfavorable waters. Evaluation tests show that our algorithms can indeedprovide relevant data about how hydration sites influence ligand-protein binding.