It is well known that folded proteins in water are destabilized by the addition of urea. When a protein loses its ability to perform its biological activity due to a change in its structure, it is said to denaturate. The mechanism by which urea denatures proteins has been thoroughly studied in the past but no proposed mechanism has yet been widely accepted. The topic of this thesis is the study of the mechanism of urea-induced protein denaturation, by means of Molecular Dynamics (MD) computer simulations and Nuclear Magnetic Resonance (NMR) spectroscopy. Paper I takes a thermodynamic approach to the analysis of protein – urea solution MD simulations. It is shown that the protein – solvent interaction energies decrease significantly upon the addition of urea. This is the result of a decrease in the Lennard-Jones energies, which is the MD simulation equivalent to van der Waals interactions. This effect will favor the unfolded protein state due to its higher number of protein - solvent contacts. In Paper II, we show that a combination of NMR spin relaxation experiments and MD simulations can successfully be used to study urea in the protein solvation shell. The urea molecule was found to be dynamic, which indicates that no specific binding sites exist. In contrast to the thermodynamic approach in Paper I, in Paper III we utilize MD simulations to analyze the affect of urea on the kinetics of local processes in proteins. Urea is found to passively unfold proteins by decreasing the refolding rate of local parts of the protein that have unfolded by thermal fluctuations. Based upon the results of Paper I – III and previous studies in the field, I propose a mechanism in which urea denatures proteins mainly by an enthalpic driving force due to attractive van der Waals interactions. Urea interacts favorably with all the different parts of the protein. The greater solvent accessibility of the unfolded protein is ultimately the factor that causes unfolded protein structures to be favored in concentrated urea solutions.

This thesis is concerned with the thermodynamic analyses of ion and proton-conducting solid oxide fuel cells (SOFC) fed with ammonia and urea as fuels. A multi-level approach was used to determine the feasibility and the performance of the fuel cells. First, the cell-level thermodynamics were examined to capture the effect of various operating parameters on the cell voltage under open-circuit conditions. Second, electrochemical studies were conducted to characterize the cell-level performance under closed-circuit conditions. Third, the fuel cells were individually integrated in a combined-cycle power generation system and parametric studies were performed to assess the overall performance as well as the thermal and exergy efficiencies. The findings of this study showed that the overall performance and efficiency of the ammonia fed SOFC is superior in comparison to that of the urea fed counterpart. In particular, the ammonia fed system combined with proton-conducting SOFC achieved a thermal efficiency as high as 85% and exergy efficiency as high as 75%. The respective efficiencies of the ammonia fed system combined with ion-conducting SOFC were lower by 5-10%. However, the urea fed system combined with ion or proton-conducting SOFC demonstrated much lower performance and efficiencies due to higher thermodynamic irreversibilities. / UOIT

Urea is an important nitrogen fertilizer for plant nutrition, but is very susceptible to moisture sorption and caking even at low moisture contents, e.g. 0.25% w/w. When urea particles adsorb moisture followed by drying, crystal bridges form between urea particles. For particles in a bed, this process is called caking. Cakes in stored urea cause a degradation of its quality and value. Investigations of the moisture absorption in beds of manufactured urea particles and adsorption on the external and internal surfaces of urea particles are a necessary step if engineers are to recommend procedures to reduce caking and control inventories. Research on moisture adsorption and cake strength of urea fertilizer has not been sufficiently explored. Only recently have researchers started to devise tests to investigate the crystal bonding between two urea particles. Prior to this research, investigations of the moisture interactions in beds of urea were nearly non-existent. This thesis presents experimental, theoretical and numerical methods to investigate the coupled heat and moisture transfer processes in a bed of urea particles while the bed is exposed to ambient air with changing temperature and humidity.<p> Urea particles are nearly spherical with uniform particle size distribution. The particle size, its internal pore structure and rough crystalline external surface depend on the manufacturing process. In this thesis, two types of urea products are investigated, i.e. prill Georgia urea and granular Terico urea. The rough external surface and internal pore structure of each particle makes the total surface area exposed to water much larger than similar smooth and solid spherical particles. Although Georgia urea has higher external surface area than Terico urea, the latter type has larger total surface area and internal pore volume. For both Terico urea and Georgia, the internal surface area dominates the water sorption process but the external moisture sorption of Georgia urea is more important than that of Terico urea.<p> All the water vapor interaction experiments were carried out with air flow through a test bed because it shortens the duration of each experiment to a few hours in most cases. A series of experiments with step changes in inlet air temperature and humidity for air flow through a urea bed indicated that the measured outlet air temperature and humidity responses, each at a specific air flow rate, reveals a typical exponential or transient time change that can be characterized by a time constant. After formulating the theoretical problem for step changes in the inlet properties, the analytical solutions showed that the time constants of outlet response to whether a temperature step change or a humidity step change are functions of the convection coefficient and air velocity. The predicted outlet air temperature is determined by only one time constant for a temperature step change while it is determined by these two time constants for a humidity step change.<p> A new test cell with sampling test ports was developed to measure the transient moisture uptake of a urea particle bed and its distribution at any time without any interruption of the experiment. A novel particle sampling device, modified from a syringe and pistons, was designed to minimize the particle exposure to ambient air during the moisture content determination using a Karl Fischer titrator. Data from two continuous cyclic step changes in the inlet flow with relative humidities between 4% and 70% at room temperature showed a hysteresis in the isothermal moisture content for only the first cycle. After the second sorption- desorption cycle, the hysteresis disappeared. This implies that the internal pore and particle surface geometry changes are very slow after the first cycle.<p> A new theoretical porous media model was developed for a coupled heat and moisture transport process when humid air flowed uniformly through a large test bed in two coupled computational domains: internal domain (i.e., the particle phase) and the external domain (i.e., the interstitial air space). The moisture migration in two computational domains included: water vapor diffusion inside each particle, and water vapor convection and diffusion in the interstitial air space in the urea particle bed. For energy transport, the temperature was assumed to be uniform inside each particle, but heat convection and conduction between the urea particles and the interstitial air outside particles occurred throughout the bed. Both heat transfer and mass transfer in internal domain and external domain were coupled by the heat and mass convection at the gas-particle interface. The numerical simulation was compared with the data of moisture uptake and showed good agreement implying that the internal moisture diffusion that dominates the moisture uptake process is a very slow process.<p> These above experimental, theoretical and numerical research studies provide a set of information on how urea particles adsorb or desorb moisture from or to ambient air on the external and internal pore surface, which offers a useful suggestion for urea caking prevention and is also a first and necessary step to the study of further caking formation and strength.

Urea is an important nitrogen fertilizer for plant nutrition, but is very susceptible to moisture sorption and caking even at low moisture contents, e.g. 0.25% w/w. When urea particles adsorb moisture followed by drying, crystal bridges form between urea particles. For particles in a bed, this process is called caking. Cakes in stored urea cause a degradation of its quality and value. Investigations of the moisture absorption in beds of manufactured urea particles and adsorption on the external and internal surfaces of urea particles are a necessary step if engineers are to recommend procedures to reduce caking and control inventories. Research on moisture adsorption and cake strength of urea fertilizer has not been sufficiently explored. Only recently have researchers started to devise tests to investigate the crystal bonding between two urea particles. Prior to this research, investigations of the moisture interactions in beds of urea were nearly non-existent. This thesis presents experimental, theoretical and numerical methods to investigate the coupled heat and moisture transfer processes in a bed of urea particles while the bed is exposed to ambient air with changing temperature and humidity.<p> Urea particles are nearly spherical with uniform particle size distribution. The particle size, its internal pore structure and rough crystalline external surface depend on the manufacturing process. In this thesis, two types of urea products are investigated, i.e. prill Georgia urea and granular Terico urea. The rough external surface and internal pore structure of each particle makes the total surface area exposed to water much larger than similar smooth and solid spherical particles. Although Georgia urea has higher external surface area than Terico urea, the latter type has larger total surface area and internal pore volume. For both Terico urea and Georgia, the internal surface area dominates the water sorption process but the external moisture sorption of Georgia urea is more important than that of Terico urea.<p> All the water vapor interaction experiments were carried out with air flow through a test bed because it shortens the duration of each experiment to a few hours in most cases. A series of experiments with step changes in inlet air temperature and humidity for air flow through a urea bed indicated that the measured outlet air temperature and humidity responses, each at a specific air flow rate, reveals a typical exponential or transient time change that can be characterized by a time constant. After formulating the theoretical problem for step changes in the inlet properties, the analytical solutions showed that the time constants of outlet response to whether a temperature step change or a humidity step change are functions of the convection coefficient and air velocity. The predicted outlet air temperature is determined by only one time constant for a temperature step change while it is determined by these two time constants for a humidity step change.<p> A new test cell with sampling test ports was developed to measure the transient moisture uptake of a urea particle bed and its distribution at any time without any interruption of the experiment. A novel particle sampling device, modified from a syringe and pistons, was designed to minimize the particle exposure to ambient air during the moisture content determination using a Karl Fischer titrator. Data from two continuous cyclic step changes in the inlet flow with relative humidities between 4% and 70% at room temperature showed a hysteresis in the isothermal moisture content for only the first cycle. After the second sorption- desorption cycle, the hysteresis disappeared. This implies that the internal pore and particle surface geometry changes are very slow after the first cycle.<p> A new theoretical porous media model was developed for a coupled heat and moisture transport process when humid air flowed uniformly through a large test bed in two coupled computational domains: internal domain (i.e., the particle phase) and the external domain (i.e., the interstitial air space). The moisture migration in two computational domains included: water vapor diffusion inside each particle, and water vapor convection and diffusion in the interstitial air space in the urea particle bed. For energy transport, the temperature was assumed to be uniform inside each particle, but heat convection and conduction between the urea particles and the interstitial air outside particles occurred throughout the bed. Both heat transfer and mass transfer in internal domain and external domain were coupled by the heat and mass convection at the gas-particle interface. The numerical simulation was compared with the data of moisture uptake and showed good agreement implying that the internal moisture diffusion that dominates the moisture uptake process is a very slow process.<p> These above experimental, theoretical and numerical research studies provide a set of information on how urea particles adsorb or desorb moisture from or to ambient air on the external and internal pore surface, which offers a useful suggestion for urea caking prevention and is also a first and necessary step to the study of further caking formation and strength.

The thiourea derivatives have become a main focus of research in asymmetric synthesis as an organocatalyst in recent years. In the first part, the thiourea catalysts are synthesized starting from easily available L-tartaric acid and application of the catalysts to some addition reactions showed no significant asymmetric induction. A number of HDAC inhibitors have been developed as anti-cancer agent at the present time.In the second part, some aryl butenoic acid derivatives are synthesized as HDAC inhibitors starting from substituted benzaldehyde and pyruvic acid. The HDAC activity studies showed comparable results with known molecules. In the last part, some acyl phosphonates are synthesized and addition of ethylcyanoformate to acyl phosphonates furnished the products in good yields.

Two flow reactor studies, using an electrically heated laminar flow reactor over Vanadia based (V2O5-WO3/TiO2) honeycomb catalyst, were performed at 1 atm pressure and various temperatures. The experiments were conducted using simulated exhaust gas compositions for different exhaust gases. A quartz tube was used in order to establish inert conditions inside the reactor. The experiments utilized a Fourier transform infrared (FTIR) spectrometer in order to perform both qualitative and quantitative analysis of the reaction products. Urea-water solution decomposition was investigated over V2O5-WO3/TiO2 catalyst over the entire SCR temperature range using the temperature controlled flow reactor. The solution was preheated and then injected into pure nitrogen (N2) stream. The decomposition experiments were conducted with a number of oxygen (O2) compositions (0, 1, 10, and 15%) over the temperature range of 227oC to 477oC. The study showed ammonia (NH3), carbon-dioxide (CO2) and nitric oxide (NO) as the major products of decomposition along with other products such as nitrous oxide (N2O) and nitrogen dioxide (NO2). The selective catalytic reduction (SCR) of nitric oxide (NO) with urea-water solution over V2O5-WO3/TiO2 catalyst using a laboratory laminar-flow reactor was investigated. Urea-water solution was injected at a temperature higher than the vaporization temperature of water and the flow reactor temperature was varied from 127oC to 477oC. A FTIR spectrometer was used to determine the concentrations of the product species. The major products of SCR reduction were NH3, NO and CO2 along with the presence of other minor products NO2 and N2O. NO removal of up to 87% was observed. The aim of the urea-water decomposition experiments was to study the decomposition process as close to the SCR configuration as possible. The aim of the SCR experiments was to delineate the effect of various parameters including reaction temperature and O2 concentration on the reduction process. The SCR investigation showed that changing parameter values significantly affected the NO removal, the residual NH3 concentration, the temperature of the maximum NO reduction, and the temperature of complete NH3 conversion. In the presence of O2, the reaction temperature for maximum NO reduction was 377?C for ratio of 1.0.

Thesis (Ph. D.)--Swedish University of Agricultural Sciences, 2000. / Errata tipped in. Includes bibliographical references.

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 112-114). Also available on the World Wide Web.

HIV-1 protease binds to its peptide/protein substrates in extended conformations. Therefore protease inhibitors that are constrained to form extended conformations are likely to produce very active protease inhibitors. This is because they are pre-organized to form favorable interactions with the enzyme environment immediately surrounding the active site. With this hypothesis in mind, we designed a family of structurally related molecules, which contain dipeptide analogs constrained to adopt the extended conformation. Core structural intermediates that are required for the total synthesis of the novel class of HIV-1 protease inhibitors are outlined in Chapter One. Chapter Two discusses the enantioselective synthesis of 2-alkyl-3-nitropropionates (NPA's) that is the part A of the cyclic urea molecule 8, and can also be used as the building block for the synthesis of unnatural beta-amino acids. In conclusion on this project, we were able to successfully achieve the novel enantioselective route for the synthesis of NPA's and also obtain the absolute stereochemistry of one of the NPA's by solving the crystal structure. Various routes were explored for the synthesis of the substituted orthogonally protected geminal diamino acids (OPGDA's) and these were discussed in Chapter Three. Chapter Three also discusses the synthesis of a versatile N-Boc transfer reagent and the applications of it in the synthesis of alpha-helix mimics. The outcomes of this project were the efficient synthesis of oxaziridine (104) and the methods that show how we cannot make the "substituted OPGDA's" which can serve as the guidance for future research on them. The proteasome is cellular machinery that is responsible for the breakdown of the complex proteins that are not required by a living cell. The inhibition of its activity in cancerous cells can promote apoptosis. Chapter Four discusses the synthesis of a new class of 20S proteasome inhibitors, their biological testing and lead optimization by molecular modeling, library synthesis and biological evaluation. In short this project achieves our goal for the synthesis of a novel class of 20S proteasome inhibitors that have a potential to act as drug molecules in the future.

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