Dissertations / Theses on the topic 'Bondi solutions'

The aims of this thesis are to develop and validate a robust and efficient algorithm for the numerical solution of the equations of General Relativistic Hydrodynamics, to implement the algorithm in a computationally efficient manner, and to apply the resulting computer code to the problem of perturbed Bondi-Hoyle-Lyttleton accretion onto a Kerr black hole. The algorithm will also be designed to evolve the space-time metric, and standardised tests will be applied to this aspect of the algorithm. The algorithm will use up-to-date High-Resolution Shock-Capturing numerical schemes that have been developed for the stable and accurate solution of complex systems of equations. It will be built around the Adaptive Mesh Refinement and overlapping, curvilinear grid methodologies in order to extend these schemes to the efficient solution of two and three-dimensional problems. When implementing the algorithm, we will use previously written code libraries, where appropriate, to avoid excessive software development. We will validate the algorithm against standard test-cases for Special and General Relativistic Hydrodynamics, and for Einstein's equations for the evolution of the space-time metric. The methodologies we use will be tested to ensure that they lead to the stable and accurate numerical solution of these problems. Finally, the implemented algorithm will be applied to the problem of Bondi-Hoyle-Lyttleton flow onto a Kerr black hole in three dimensions. It will be validated against existing exact and numerical solutions of the problem, and then be used to perform an extensive parametric study of the problem, varying the spin of the black hole and the incident wind direction, and allowing for the perturbation of the fluid density upstream of the black hole. We will then analyze the results of the study, and present the complete set of results on a DVD accompanying this thesis.

Excess thermodynamic properties have been determined for several binary liquid mixtures with the aim of testing various thermodynamic theories and postulates. Excess molar enthalpies, HEm, have been determined using an LKB flow microcalorimeter and excess molar volumes, VEm, have been determined using an Anton Paar vibrating tube densitometer. The activity coefficients at infinite dilution ƴ∞₁₃, have been determined using an atmospheric pressure gas-liquid chromatograph. The excess molar enthalpies and the excess molar volumes have been measured at 298.15 K for systems involving the bicyclic compounds decahydronaphthalene (decalin), 1,2,3,4-tetrahydronaphthalene (tetralin), bicyclohexyl, or cyclohexylbenzene mixed with 1- hexene, 1-hexyne, 1-heptene, 1-heptyne, cyclohexene, 1,3-cyclohexadiene, 1,4- cyclohexadiene, or benzene. These excess properties have also been measured for systems where the bicyclic compound has been replaced with benzene, cyclohexane or n-hexane. The results show defmite trends related to the size, shape, and the degree of unsaturation of the component molecules. The Flory theory has been used to predict excess molar enthalpies and excess molar volumes for {(a bicyclic compound or benzene or cyclohexane or n-hexane) +(an n-alkane or a 1-alkene or a 1-alkyne or a cycloalkane or cyclohexene or a cycloalkadiene or benzene)}. The one parameter equations offer reasonably good correlations between the predicted and the experimental results. More insight into the origins of the contnbutions to the excess thermodynamic properties for these systems has been gained by considering the approximate equations of Patterson and co-workers, which separate the interactional and the free volume contributions to the excess molar enthalpy and the excess molar volume. The one parameter equations have adequately rationalized a good deal of the observed behaviour for HEm and VEm. The theory of Liebermann and co-workers, which does not employ any adjustable parameters, has not been as successful at predicting the excess thermodynamic properties for the above systems. The activity coefficients at infinite dilution have been measured at 278.15 K, 288.15 K and 298.15 K for n-bexane, 1-bexene, 1-hexyne, n-heptane, 1-heptene, 1-heptyne, cyclohexane, cyclohexene, 1,3-cyclohexadiene, 1,4-cyclohexadiene, and benzene, in decalin, tetralin, bicyclohexyl, and cyclohexylbenzene. Solvent losses from the column have been accounted for by an extrapolation procedure. The activity coefficient results together with the HEm and VEm values have been used to calculate the partial molar excess thermodynamic properties of mixing at infinite dilution. The partial molar excess properties at infinite dilution for decalin mixtures are similar to those for bicyclohexyl mixtures. There is also a similarity between the properties of the tetralin mixtures and the cyclohexylbenzene mixtures. The cycloalkadienes, benzene and the 1-alkynes exhibit a strong dissociation effect on being mixed with the saturated solvents, decalin and bicyclohexyl, but associate strongly with tetralin and with cyclohexylbenzene. The Flory theory bas been used to predict activity coefficients at infinite dilution from the experimentally determined HEm results for { (n-bexane or 1-hexene or 1-hexyne or naheptane or 1-heptene or 1-beptyne) + (a bicyclic compound)}. The theory is much better at predicting values for mixtures where both components are either saturated molecules or are unsaturated molecules than for {saturated + unsaturated} mixtures.

Non-covalent interactions taking place in solution are essential in chemical and biological systems. The solvent environment plays an important role in determining the geometry and stability of interactions. This thesis examines aromatic stacking interactions, alkyl-alkyl interactions, edge-to-face aromatic interactions, halogen bonds and hydrogen…hydrogen interactions in solution. Chapter 1 briefly introduces the different classes of non-covalent interactions, in addition to the state-of-the-art models and methods for investigating these weak interactions. The chapter finishes with a focus on dispersion interaction in alkanes and arenes. Chapter 2 investigates dispersion interactions between stacked aromatics in solution using a new class of complexes and thermodynamic double mutant cycles (DMCs). In extended aromatics, dispersion was detected as providing a small but significant contribution to the overall stacking free energies. Chapter 3 concerns the experimental measurement of alkyl-alkyl dispersion interactions in a wide range of solvents using Wilcox torsion balances. The contribution of dispersion interactions to alkyl-alkyl association was shown to be very small, with DMC, QSPR method and Hunter's solvation model. Chapter 4 studies edge-to-face aromatic interactions in series of solvents. In the open system, edge-to-face aromatic interactions were found to be sensitive to the solvent environment. The solvent effects were complicated and cannot be rationalised by a single parameter. Further analysis is needed. Chapter 5 describes a preliminary approach to investigate organic halogen…π interactions in solution using supramolecular complexes and torsion balances. Chapter 6 is a preliminary investigation of the ability of hydrogen atoms to act as H bond acceptors in silane compounds. Computations and 1H NMR demonstrated a weak interaction between silane and perfluoro-tert-butanol.

Water is one of the most common compounds on earth and is essential for all biological activities. Water has, however, been a mystery for many years due to the large number of unusual chemical and physical properties, e.g. decreased volume during melting and maximum density at 4 °C. The origin of the anomalies behavior is the nature of the hydrogen bond. This thesis will presented an x-ray absorption spectroscopy (XAS) study to reveal the hydrogen bond structure in liquid water.

The x-ray absorption process is faster than a femtosecond and thereby reflects the molecular orbital structure in a frozen geometry locally around the probed water molecules. The results indicate that the electronic structure of liquid water is significantly different from that of the solid and gaseous forms. The molecular arrangement in the first coordination shell of liquid water is actually very similar as the two-hydrogen-bonded configurations at the surface of ice. This discovery suggests that most molecules in liquid water have two-hydrogen-bonded configurations with one donor and one acceptor hydrogen bond compared to the four-hydrogen-bonded tetrahedral structure in ice. This result is controversial since the general picture is that the structure of liquid water is very similar to the structure of ice. The results are, however, consistent with x-ray and neutron diffraction data but reveals serious discrepancies with structures based on current molecular dynamics simulations. The two-hydrogen-bond configuration in liquid water is rigid and heating from 25 °C to 90 °C introduce a minor change in the hydrogen-bonded configurations. Furthermore, XAS studies of water in aqueous solutions show that ion hydration does not affect the hydrogen bond configuration of the bulk. Only water molecules in the close vicinity to the ions show changes in the hydrogen bond formation. XAS data obtained with fluorescence yield are sensitive enough to resolved electronic structure of water molecules in the first hydration sphere and to distinguish between different protonated species. Hence, XAS is a useful tool to provide insight into the local electronic structure of a hydrogen-bonded liquid and it is applied for the first time on water revealing unique information of high importance.

Cette thèse s'inscrit dans la problématique relative à la modélisation des systèmes linéaires incertains pour l'étude de la sensibilité et de la robustesse des modèles aux incertitudes paramétriques. La détermination de la fonction de sensibilité paramétrique y est abordée sous deux aspects : le premier porte sur l'application de la règle de Mason directement sur les modèles bond graphs pour la détermination sous forme formelle de la fonction de sensibilité paramétrique, le second propose une nouvelle modélisation des composants bond graphs en vue de simulations directement avec les logiciels bond graphs existants. La détermination de la forme d'état canonique est traitée en considérant les incertitudes paramétriques comme étant des composants avec un sens physique, et des procédures graphiques pour sa détermination sont données. La forme standard d'interconnexion utilisée dans le cadre de la [mu]-analyse et de la [mu]-synthèse, est déterminée à l'aide de procédures graphiques mises en œuvres après une nouvelle modélisation des composants bond graphs. Enfin, les méthodes développées sont appliquées sur un exemple automobile.

Herein we describe a straight-forward and reproducible method for the preparation of homogeneous, multicomponent cocrystals and supramolecular solid solutions. We prepared these multicomponent materials based on small organic molecules that employ a two-point supramolecular hydrogen bond synthon. We report the creation and characterization of two, three, four, five, and seven component crystals containing a variety of 2-aminopyridines and monosubstituted benzoic acids. These systems exhibit the ability to accommodate multiple components in varying proportions while coordinating into an identical packing structure. The flexibility of the system to incorporate multiple components also gives rise to gradual modulation of physical properties.

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics
This study examines whether ‘climate bonds’ are achieving the desired investment scale to tackle climate change and whether those bonds are being issued with features that are attractive to institutional investors. Several cases of climate bond issuances, especially by companies were analyzed. While investor’s interest in climate bonds exists, this market is still small and investors are not being offered with an attractive investment scale. As the results indicate, both credit enhancements and aggregation vehicles to enable scale investments are possible solutions to boost the climate bond market.

Thesis (MSc)--University of Stellenbosch, 2006.
ENGLISH ABSTRACT: static density and magnetic structure functions of a melt of flexible polymers whose monomers possess bond-directed dipoles which interact with each other. In order to observe the effect of screening of the dipolar interaction on the structure functions we obtain results for cases with and without steric interactions and also for cases with and without Debye-H¨uckel screening of the dipole moments.
AFRIKAANSE OPSOMMING: Approximation” RPA) om die statiese digtheids- en magnetiese struktuurfunksies te bereken vir ’n smelt van hoogsbuigsame polimere, waarvan die monomere dipole langs die verbindings besit wat met mekaar in wisselwerking tree. Om die effek van afskerming op die dipolare wisselwerking en die struktuurfunksies te kan waarneem, bepaal ons resultate vir die gevalle met en sonder steriese wisselwerkings en ook vir gevalle met en sonder die Debye-H¨uckel afskerming van die dipoolmomente.

Thesis (M.S.)--University of North Carolina at Chapel Hill, 2009.
Title from electronic title page (viewed Sep. 3, 2009). "... in partial fulfillment of the requirements for the degree of Master of Science in the Department of Operative Dentistry, School of Dentistry." Discipline: Operative Dentistry; Department/School: Dentistry.

Abstract The correct three dimensional structures of proteins are essential for their ability to function properly. Proteins start to fold as soon as they are synthesized in the ribosomes from activated amino acids. Many secreted, cell-surface, secretory pathway and endoplasmic reticulum (ER) lumenal proteins have in their amino acid sequence cysteine residues which form intra- and intermolecular disulfide bridges that stabilize the overall fold of the proteins and protein complexes. The formation of correct disulfide bonds is a complex process which takes place within the ER. Protein disulfide isomerase (PDI) is the key enzyme in the formation and rearrangement of correct disulfide bonds in the ER. It is an archetypal and the best studied member of the PDI family, i.e. a group of ER proteins that resemble thioredoxin (TRX), a protein reductase, in their structure. PDI has a four domain a-b-b'-a' structure the a and a' domains having the catalytic activity and amino acid sequence similarity to TRX. In addition to its function as a thiol-disulfide oxidoreductase, PDI acts as the β subunit in two protein complexes: collagen prolyl 4-hydroxylase (C-P4H) and microsomal triglyceride transfer protein (MTP). The closest homologue of PDI is the multifunctional enzyme and chaperone ERp57 that functions in concert with two lectins, calnexin (CNX) and calreticulin (CRT) specifically in the folding of proteins that have sugar moieties linked to them. ERp57 is 56% similar to PDI in its amino acid sequence and has also the four-domain architecture. Despite the high similarity in their structures ERp57 cannot substitute for PDI as the β subunit of C-P4H. The minimum requirement for the C-P4H tetramer assembly is fulfilled by domains b' and a' of PDI, while domains a and b enhance this function and can be substituted in part by those of ERp57. Until very recently the structural information of any of the PDI family members, which contains the TRX active site was limited to solution structures of human PDI domains a and b. In this research the domain boundaries of the full length ERp57 were defined and the individual domains characterized. Furthermore the solution structures of the catalytically active domains a and a' of ERp57 were studied by nuclear magnetic resonance (NMR).

Ce rapport de thèse présente une étude de la dynamique transitoire de molécules de taille réduite en solution induite par photoexcitation. Celle-ci est réalisée au travers d'une expérience de mesure de diffusion de rayons X aux grands angles (TR-WAXS). La partie principale de ce rapport s'articule autour de la dertermination des structures transitoires avec l'utilisation de plusieurs schémas structurelles d'optimisation. Certains résultats obtenus par TR-WAXS sont complétés avec ceux obtenus par spectroscopie optique résolue dans le temps (TOAS) ainsi que par spectroscopie d'émission de rayons X de ces molécules (TR-XES) permettant une plus complète description de ces systèmes.Ce travail est composé de 4 differents projets lesquelles peuvent être regroupé en 2 groupes selon le type de réaction declenchées par photoexcitation: dissociation et transfert d'électron. Le premier groupe comprends la molécule triatomique de mercure, halogénure métallique et le triiodide où nous étudions la dynamique de recombinaison des photofragments libres. Cette partie démontre la possibilité de développer de nouvelles connaissances concernant la dynamique de ces modèles, comme par exemple, la découverte de la recombinaison par canaux ou bien par l'apparition de réactions intermédiaires en moins de 100 ps, correspondant à la longueur de l'impulsion de rayons X générée par le synchrotron, mise en évidence en utilisant la technique de découpage temporelle. Le deuxième groupe de systèmes est composé de complexes de métaux de transition, très pertinents pour les applications liées à la récolte de lumière, [Fe(NHC)2]2+ et Ru=Co, où le spin et les structures dynamiques sont étudiées. Ces projets prolongent de précedents travaux à une famille de systèmes plus complexes avec un numéro atomique bas (première colonne de transition metallique) et fait la lumière sur de nouveaux composés en photochimie
This thesis investigates photoinduced transient dynamics of small molecules in solution with the use of time-resolved wide angle x-ray scattering (TR-WAXS). The core of the thesis is the precise determination of transient structures with the use of various structural optimization schemes. Some of the TR-WAXS results are supplemented with transient absorption optical spectroscopy (TOAS) and time-resolved x-ray emission spectroscopy (TR-XES) measurements allowing for a more complete description of the systems.par The work includes four different projects which can be grouped into two classes according to the type of reaction appearing upon photoexcitation: dissociation and electron transfer. The first class includes the simple triatomic molecules mercury halides and triiodide where we study the recombination dynamics of the free photofragments. This part of the thesis demonstrates the possibility to gain new knowledge about the dynamics of these model systems such as new recombination channels and reaction intermediates appearing in less than 100 ps, the xray pulse length from the synchrotron, by the use of time-slicing technique. The second class of systems includes transition metal complexes that are highly relevant for light harvesting applications, [Fe(NHC)2]2+ and Ru=Co, where the spin and structural dynamics are investigated. These projects extend previous work to a family of more complex systems constituted of relatively low-Z atoms (first row transition metals) and bring new insights into the photochemistry of the compounds

This thesis details ultrafast absorption spectroscopy studies of photo-induced processes in solution phase aromatic molecules. Application of this technique to the systems detailed below, using both a broadband infrared (IR) and/or ultraviolet (UV)/visible probe, has allowed the key species created directly by photo-excitation and subsequent processes to be identified as well as their transient behaviour to be followed. Kinetic and mechanistic information on the process or reaction is obtained, adding to both the understanding of the underlying photo-physics that drive the process in addition to the transient behaviour of the process itself. The systems investigated are; the UV photodissociation of phenol, the photo-Claisen and photo-Fries rearrangement of allyl phenyl ether and phenyl acetate respectively all in cyclohexane solvent, and three Paterno-Bilchi reactions between c),clohexene, furan or 2,3- dihydrofuran. The photodissociation of phenol in cyclohexane was studied by transient vibrational absorption spectroscopy. The spectra obtained supp0l1ed the results of a previous study of the photodissociation of phenol in solution using transient electronic absorption which found that the mechanism of photodissociation of phenol in a weakly interacting solvent remained the same as observed in the gas phase. Additionally, solution phase specific processes were observed following dissociation, such as recombination. Study of the photo-Claisen and photo-Fries rearrangements in solution using both transient absorption techniques allowed kinetic and mechanistic information on these processes to be obtained including rate coefficients for individual processes and quantum yields for the competing processes that determine the fate of the produced radical pair; solvent cage escape, recombination to form a cyclohexadienone of the original So product. The Paterno-Bilchi reactions between benzaldehyde and three solvents were also investigated. The first studied was the reaction with cyclohexene. This study proved that the biradical intermediates in this reaction along with other key species could be identified using these techniques. The subsequent study of the Paterno-Bilchi reaction with furan and 2,3- dihydrofuran investigated more detailed facets of this reaction.

This thesis reports on the research outcome of corrosion mechanism and corrosion rate of mild steel in different environments (saline, alkaline solutions and concrete media) using potentiodynamic polarization technique. The study also included the effect of corrosion on bond strength between reinforcing steel and concrete using pull-out test. Corrosion of mild steel and 316L stainless steel with different surface conditions in 1, 3 and 5% saline (NaCl + Distilled water) was investigated. Specimens ground with 200 and 600 grit silicon carbide grinding paper as well as 1μm surface finish (polished with 1μm diamond paste) were tested. In case of mild steel specimens, reduction in surface roughness caused increase in corrosion rate, while in 316L stainless steel corrosion rate decreased as the surface roughness improved. Metallographic examination of corroded specimens confirmed breakdown of passive region due to pitting corrosion. Corrosion of mild steel was also investigated in alkaline solution (saturated calcium hydroxide, pH =12.5) contaminated with 1, 3 and 5% saline. A series of corrosion experiments were also conducted to examine the efficiency of various concentrations of calcium nitrite (CN) on corrosion behaviour of both as-received and polished mild steel in alkaline solution containing 3% saline after 1 hour and 28 days of exposure. Corrosion rate was higher for the as-received than polished mild steel surface under the same testing conditions in NaCl alkaline solution with and without nitrites due to the effect of surface roughness. Morphology investigation of mild steel specimens in alkaline solution ii containing chlorides and nitrites showed localized pits even at nitrite concentration equal to chloride concentration. Corrosion of steel bars embedded in concrete having compressive strengths of 20, 30 and 46MPa was also investigated. The effect of 2 and 4% CN by weight of cement on corrosion behaviour of steel bar in low and high concrete strengths specimens were also studied. All reinforced concrete specimens were immersed in 3% saline solution for three different periods of 1, 7 and 15 days. In order to accelerate the chemical reactions, an external current of 0.4A was applied. Corrosion rate was measured by retrieving electrochemical information from polarization tests. Pull-out tests of reinforced concrete specimens were then conducted to assess the corroded steel/concrete bond characteristics. Experimental results showed that corrosion rate of steel bars and bond strength were dependent on concrete strength, amount of CN and acceleration corrosion period. As concrete strength increased from 20 to 46MPa, corrosion rate of embedded steel decreased. First day of corrosion acceleration showed a slight increase in steel/concrete bond strength, whereas severe corrosion due to 7 and 15 days corrosion acceleration significantly reduced steel/concrete bond strength. Addition of only 2% CN did not give corrosion protection for steel reinforcement in concrete with 20MPa strength at long time of exposure. However, the combination of good quality concrete and addition of CN appear to be a desirable approach to reduce the effect of chloride induced corrosion of steel reinforcement. At less time of exposure, specimens without CN showed higher bond strength in both concrete mixes than those with CN. After 7 days of corrosion acceleration, the higher concentration of CN gave higher bond strength in both concrete mixes. The same trend was observed at 15 days of corrosion acceleration except for the specimen with 20MPa compressive strength and 2% CN which recorded the highest deterioration in bond strength.

This thesis covers detailed analysis of bond pricing function. It focuses on connections between mathematical definitions and financial practice and it points out advantages and drawbacks of currently used function. Well known properties of this function are extended to negative internal rate of return values. This topic is further discussed with internal rate of return polynomial equations solving. Taylor series approximation is also shown regarding duration and convexity of bonds.

Denna uppsats behandlar hur fastighetsbolagens finansiering har utvecklats efter finanskrisen, hur finanskrisen specifikt har påverkat fastighetsbolagens finansieringsverksamhet samt i vilken utsträckning fastighetsbolagen har börjat använda alternativa finansieringssätt i sin verksamhet. Detta ämne är intressant då finanskrisen har haft en stor inverkan på det ekonomiska klimatet världen över vilket också inkluderar de svenska fastighetsbolagen och de svenska bankerna. Uppsatsen kombinerar en kvantitativ undersökning av alla svenska börsnoterade fastighetsbolagskapitalstrukturer med en kvalitativ undersökning bestående av ett antal intervjuer medrepresentanter från flera fasighetsbolag och banker. Den kvantitativa undersökningen visar att det skett stora förändringar i fastighetsbolagensfinansiering. Användningen av alternativa finansieringssätt, såsom preferensaktier, obligationer,MTN- och Certifikatsprogram har blivit vanligare i fastighetsbolagen. En stor anledning till detta är att bankerna i många fall har velat begränsa sin utlåning till fastighetsbolagen samtidigt som kreditmarginalerna har ökat på grund av bland annat högre kapitaltäckningskrav för bankerna. Utvecklingen av fastighetsbolagens finansiering kommer fortsätta framöver och alternativa finansieringssätt kommer i större utsträckning användas som komplement till banklån och stamaktiekapital.
This paper deals with how the financing in real estate companies has developed after the recentfinancial crisis, how the financial crisis specifically has affected the financing in real estatecompanies and to what extent real estate companies have started to use alternative ways to finance their operations. This subject is of high interest because the financial crisis has had a huge impact on the global economic climate, which also affects Swedish real estate companies andbanks. The paper combines a quantitative survey of the capital structure in all Swedish publicly listed realestate companies with a qualitative survey consisting of a number of interviews withrepresentatives from a number of real estate companies and banks. The quantitative survey shows that big changes have occurred in the financing of real estatecompanies. The use of alternative ways to finance them, such as preference shares, bonds, MTN and certificate programs have become much more common in real estate companies. A big reason to this is that banks in many cases have wanted to restrict their lending to real estate companies whilst the credit margins have increased due to, among other things, higher capitalrequirement rates for the banks. The fast development of financing in real estate companies will continue for years to come andalternative ways to finance real estate companies will continue to get stronger as a complement to bank loans and common stock equity.

L'astate (At, Z = 85) est un élément halogène rare, tous ses isotopes étant radioactifs. En raison des quantités disponibles limitées, aucun outil spectroscopique n'est applicable pour identifier la nature moléculaire des espèces d'At. En conséquence, la chimie de l'At reste méconnue. L'un de ses isotopes, ²¹¹At, est un candidat potentiel pour le traitement de cancers par thérapie alpha ciblée. Cependant, la connaissance limitée de ses propriétés chimiques a entravé les tentatives de marquage de ²¹¹At avec des molécules porteuses ciblant la maladie. Cela a conduit au développement d’un programme de recherches sur la chimie de base de At. Cette thèse s’intéresse plus particulièrement au diagramme de Pourbaix de l’astate et à la caractérisation de liaisons halogènes avec l’espèce AtI, au moyen de divers outils expérimentaux (chromatographie ionique, méthode de compétition et électromobilité). Dans une première partie, des études de spéciation de At en milieu alcalin confirment la présence de l'espèce At⁻ en conditions réductrices. Lorsque le potentiel augmente, l’espèce AtO(OH)₂⁻ se forme. Le changement de spéciation entre ces deux espèces est décrit pour la première fois. Dans une deuxième partie, la formation de liaisons halogènes entre l'espèce AtI et divers composés organiques a été étudiée. La réactivité se résume par une échelle de basicité nouvellement établie dont la force entre le donneur (AtI) et l’atome accepteur varie suivant l’ordre C ≤ O ≤ S (≈ Se)
Astatine (At, Z = 85) is a scarce halogen element, all of its isotopes being radioactive. Due to the limited available quantities, no spectroscopic tool is applicable to identify the molecular nature of At species. Consequently, the chemistry of At remains poorly known. One of its isotopes, ²¹¹At, is a potential candidate for the treatment of cancers by targeted alpha therapy. However, the limited knowledge of its chemical properties has hindered attempts to label ²¹¹At with disease targeting carrier molecules. This led to the development of a research program on the basic chemistry of At. This thesis focuses more particularly on the Pourbaix diagram of astatine and the characterization of halogen bonds with the AtI species, by means of various experimental tools (ion chromatography, competition method and electromobility). In the first part, speciation studies of At in alkaline medium confirm the presence of the At⁻ species under reducing conditions. As the potential increases, the AtO(OH)₂⁻ species is formed. The speciation change between these two species is described for the first time. In a second part, the formation of halogen bonds between the AtI species and various organic compounds was studied. The reactivity is summarized by a newly established basicity scale, with the strength between the donor (AtI) and the acceptor atom following the order of C≤ O ≤ S (≈ Se)

L’agencement relatif de systèmes cristallins moléculaires, par une méthode d’organisation avancée est une stratégie de premier plan. Le développement de tels systèmes permet la conception de dispositifs innovants dans le domaine des matériaux poreux, magnétiques ou optiques.Les travaux menés dans le cadre de cette étude ont pour objectif l’élaboration d’architectures macroscopiques hiérarchisées concernant l’état cristallin, de type « réseaux de cristaux ». Dans un premier temps, le développement et la caractérisation de réseaux iso-structuraux ont été réalisés. Ces séries, formées par liaisons hydrogènes, servent à l’étude de la croissance cristalline épitaxiale, développée par la suite. À partir de ces résultats, la préparation d’architectures monocristallines de type cristal cœur-coquille ainsi que la soudure cristalline sont entreprises.Enfin, la généralisation de cette mise en forme de l’état cristallin à des systèmes formés par liaisons de coordination est présentée
The relative disposition of applicative molecular systems by an advanced organization method is a well-defined strategy (core-shell type crystals). It is aimed at developing innovative materials.The presented study deals with the elaboration of a new organization method concerning the crystalline matter to obtain “network of crystals”. This strategy of materials processing occurs at a macroscopic scale and in a hierarchical way.Firstly, series of isostructural crystalline molecular networks have been designed with a molecular tectonics approach. These series, formed by hydrogen bonds, are then used for the study of the epitaxial growth of crystal. The preparation of a single crystalline architecture with a defined sequenced area of different compositions is demonstrated: core-shell crystals and welded crystals.Finally, the developed strategy is applied to coordination networks exhibiting luminescent properties in order to generalize the described process

Die Struktur von DNS Molekülen und ihre Wechselwirkung mit Wasser werden seit langer Zeit heiß diskutiert. In der vorliegenden Arbeit wird nichtlineare Spektroskopie zur Untersuchung dieser Systeme angewendet. Oligomere, die aus 23 alternierenden Adenin-Thymin-Basenpaaren bestehen und eine Doppelhelix bilden, wurden mit Hilfe von 2D IR Spektroskopie für verschiedene Hydratisierungsgrade untersucht. Für DNS-Filme bei 0% relativer Feuchte (r.F.) erlauben die transienten Spektren eine Unterscheidung der NH Streckschwingung von Thymin ((NH)), der symmetrischen und asymmetrischen NH2 Streckschwingung von Adenin (s(NH2) and a(NH2)) sowie die Bestimmung der jeweiligen Linienprofile. Die Spektren zeigen eine homogene Verbreiterung für die (NHT) wohingegen die s(NH2) and a(NH2) eine ausgeprägte und zeitunabhängige inhomogene Verbreiterung zeigen, welche auf Unordnungen in der DNS-Struktur hinweisen. Außerdem kann Energietransfer von der a(NH2) zur (NH) beobachtet werden. Bei Erhöhung der r.F. hat die erhöhte Anzahl von Wassermolekülen nur einen geringen Einfluss auf die Positionen und Linienprofile der NH Streckschwingungen. Dadurch wird nahegelegt, dass die spektrale Dynamik vom DNS Molekül selbst und nicht vom umgebenen Wasser bestimmt ist. Im Gegensatz dazu zeigt die OH Streckmode der Wasserhülle um die DNS spektrale Diffusion auf einer 500 fs Zeitskala. Guanosin-Cytidin(GC)-Basenpaare wurden in Chloroformlösung untersucht, um die Wechselwirkung zwischen Basenpaaren zu verstehen. Dabei wurden die NH Schwingungen in einer local mode Darstellung betrachtet, die zwei freie NH Gruppen von G und C und drei wasserstoffverbrückte NH Gruppen beeinhaltet. Die Kopplungen und Relaxationsdynamik der NH Streckanregungen wurden mit Femtosekunden-Pump-Probe und 2D IR Experimenten studiert. Die Ergebnisse zeigen eine Verringerung der Lebensdauer mit der Bildung von Wasserstoffbrücken sowie Energietransfer zwischen zwei wasserstoffverbrückten NH Streckschwingungen.
The structure of DNA molecule and the interactions with its surrounding water is a hot topic for long time. In this thesis, we employ the nonlinear spectroscopy, including femtosecond pump-probe and two-dimensional infrared (2D IR) experiment, to study the vibrational dynamics of the systems. Double-stranded DNA short oligomers containing 23 alternating adenine-thymine base pairs were studied at different hydration levels by femtosecond 2D IR spectroscopy. For a DNA film at 0% relative humidity, the transient spectra enable a separation of the NH stretching mode of thymine from the symmetric and asymmetric NH2 stretching modes of adenine and determine the individual line shapes. For the NH stretch of thymine, the spectra demonstrate an essential homogeneous broadening, whereas for the symmetric and asymmetric NH2 stretches a pronounced and time-independent inhomogeneous broadening suggests a disorder in DNA structure. An energy transfer from the asymmetric NH2 stretch of adenine to the NH stretch of thymine is also observed. When the relative humidity increases, the increased water molecules have limited influence on the positions and line shapes of NH stretching frequencies, suggesting the spectral dynamics governed by DNA rather than water fluctuations. In contrast, the OH stretching mode of water shell around hydrated DNA undergoes a spectral diffusion on a 500 fs time scale, which is slower than the neat water. The guanosine-cytidine (GC) base pairs in chloroform solution were investigated to understand the interactions within base pairs. A local mode representationof NH stretching mode is adopted, consisting two free NH groups of G and C and three hydrogen bonded NH groups. The coupling and relaxation dynamics of the NH stretching excitations are studied by femtosecond pump-probe and 2D IR experiments. The results demonstrate a lifetime shortening upon the formation of hydrogen bonds, and an energy transfer between two hydrogen-bonded NH stretches.

Gas-phase thermolysis is a long-known and well established method for the preparation of reactive species. It is, however, limited to relatively volatile substances, which are easily vaporised. In the present work, the solution-spray technique for preparative scale was developed. With this technique, it is possible to subject low-volatile substances, which hardly vaporise even under high-vacuum conditions, to gas-phase thermolysis. By utilising oil nozzles used in heating and burner systems, it was possible to integrate a stable solution-spray into the existing flash-vacuum-pyrolysis system. The influence of several variables, such as flow-rate, pressure, temperature and solvent was determined. The solution-spray technique was applied in [3,3]-sigmatropic rearrangements of certain propargyl thiocyanates to the corresponding allenyl isothiocyanates. Furthermore, the parent compound propa-1,2-dienyl isothiocyanate was reacted with various sterically demanding primary and secondary amines to form 2-amino-1,3-thiazoles in moderate to excellent yields. Based on this, a catalyst-free four-center three-component reaction was developed. 2-Amino-1,3-thiazoles with complex substituents in 5-position at the heterocyclic ring are formed. Reaction mechanisms are discussed to explain the occurance of a highly substituted 1,3-thiazine structure. The influence of reaction temperature, concentrations and solvent were determined and are also discussed. It was shown that 2-amino-5-methyl-1,3-thiazoles are the apparently first aromatic substance class, that readily undergoes Prins-type 1,3-dioxane ring-formation
Die Gasphasenthermolyse ist eine lang bekannte und etablierte Methodik zur Synthese reaktiver Spezies. Sie ist allerdings auf flüchtige Substanzen mit einer guten Verdampfbarkeit beschränkt. Für schwerflüchtige Verbindungen, welche sich selbst im Hochvakuum nur mäßig oder gar nicht in die Gasphase bringen lassen, wurde in der vorliegenden Arbeit die Solution-Spray-Technik für die Anwendung im präparativen Maßstab entwickelt. Unter Verwendung von Ölzerstäuberdüsen, wie sie in der Heizungs- und Brennertechnik Anwendung finden, wurde die Erzeugung eines stabilen Lösungs-Sprays in die vorhandene Blitzvakuumpyrolyse-Technik integriert. Der Einfluss verschiedener Variablen, wie Flussrate, Druck, Temperatur und Lösungsmittel wurde untersucht. Die Solution-Spray-Technik wurde für die [3,3]-sigmatrope Umlagerung bestimmter Propargylthiocyanate zu Allenyl-isothiocyanaten angewendet. Des Weiteren wurde Propa-1,2-dienylisothiocyanat – das einfachste Allenylisothiocyanat – mit diversen sterisch anspruchsvollen primären und sekundären Aminen in mäßigen bis exzellenten Ausbeuten zu 2-Amino-1,3-thiazolen umgesetzt. Darauf aufbauend konnte eine Vier-Zentren-drei-Komponenten-Reaktion entwickelt werden. Es entstehen in hohen Ausbeuten 2-Amino-1,3-thiazole mit komplexen Substituenten an der 5-Position des Heterocyclus. Reaktionsmechanismen werden diskutiert um die alternative Bildung einer hochsubstituierten 1,3-Thiazinstruktur zu erklären. Der Einfluss von Reaktionstemperatur, Konzentration und Lösungsmittel auf das Produktverhältnis wurde ebenfalls untersucht und wird diskutiert. Es konnte gezeigt werden, dass 2-Amino-5-methyl-1,3-thiazole als offenbar erste aromatische Substanzklasse sehr gute Substrate für die Bildung von 1,3-Dioxanen nach Prins darstellen

Determination par diffraction rx des arrangements atomiques de neuf phases cristallines hydratees. Les polyedres de coordination des cations s'organisent en trois types structuraux : chaines simples (cd); empilement en couches (cd); chaines mixtes (cd,ca). Quatre phases possedent des structures caracterisees par une pseudo-symetrie marquee. Les macles et les transformations orientees, observees sur certains cristaux, sont interpretees par l'existence de pseudo-symetrie locale et de parentes structurales entre blocs atomiques des hydrates concernes

In this thesis, we study two different aspects of accretion flows- (i) quasi-periodic oscillations (QPOs) seen in the light curves of X-ray binaries as a possible consequence of shock oscillations, (ii) global 3D ideal MHD simulations of radiatively inefficient accretion flows (RIAFs). Spherically symmetric adiabatic accretion on to a BH is described by the accretion branch of Bondi solutions (Bondi 1952), because the BH acts like a mass sink. On the other hand, stars like NSs and white dwarfs (WDs), have surface and hence the infalling matter has to slow down at the surface. Due to the presence of the surface, a standing shock forms in the accretion flow for certain boundary conditions at the inner boundary (namely steady shock boundary condition, for details see Chapter 2). The standing shock is stable in 1D, but becomes unstable under non-radial perturbations and oscillates in the vertical direction about the equatorial plane. This phenomenon is known as standing accretion shock instability (SASI). We investigate the mechanism behind SASI using axisymmetric HD and MHD simulations. By comparing different wave propagation times and vertical oscillation period of the post shock cavity, we conclude that an ‘advective acoustic’ mechanism (Foglizzo et al. 2007) is the more likely cause of SASI, instead of a ‘purely acoustic’ (Blondin & Mezzacappa 2006) one. In our MHD simulations we observe, a moderately strong (but subthermal such that thermal pressure > magnetic pressure) large-scale magnetic field adds complicated features to the shock oscillation pattern, giving rise to a low-frequency modulation in the computed light curve. We propose that this low-frequency modulation may be responsible for ∼ 100 Hz QPOs (known as hHz QPOs) (for details see Chapter 3). Finally, we study the magnetorotational instability (MRI; Balbus & Hawley 1991) in geometrically thick (H/R ∼ 0.5) RIAFs using 3D global ideal MHD simulations in spherical polar coordinates (r,θ,φ) and a pseudo-Newtonian gravity. We find that 42 grid points per scale height in the meridional direction are adequate to resolve the MRI. The condition for convergence is given by the product of quality factors ⟨⟨Qθ ⟩⟩⟨⟨Qφ ⟩⟩ ≥ 300 and magnetic tilt angle θB ∼ 13◦−14◦. Because of the huge computational costs of the global simulations, it is desirable to reduce the azimuthal domain size Φ0 to a small fraction of 2π, provided that the outcomes (in particular, the level of transport and mean/fluctuating quantities) are similar to the ones with the full extent. We find stronger mean magnetic fields for the runs with restricted azimuthal domains. This is because, for runs with smaller azimuthal extent, the large-scale turbulent fields manifest themselves as mean fields as the magnetic fields tend to be at large scales and we use periodic boundary conditions at the azimuthal boundaries. On the other hand, steady state flow profiles (for example, radial velocity, sound speed) are very similar for the runs with Φ0 ≥ π/2. We conclude that the computational domain with Φ0 ≥ π/2 is sufficient to study the structure of RIAFs. On the other hand, for the study of turbulence and dynamo in RIAFs Φ0 = 2π is necessary. We also observe the generation of large scale magnetic fields with an intermittent dynamo cycle. The irregularity is due to the sub-Keplerian nature of the angular velocity (for which the shear parameter q = 1.7). We find signatures of two kinds of dynamos– i) a direct dynamo close to the mid-plane, and ii) a Parker-type dynamo away from the mid-plane. Away from the mid-plane, back reaction of the Lorentz force plays an important role in causing the suppression of kinematic helicity (αdyn kin ) by the small scale current helicity (−αdyn mag) of a similar magnitude. The effects of dynamical quenching are shown explicitly for the first time in global simulations of accretion flows.

This thesis entitled “Design and Access to Disallowed and Unusual Conformers of Peptides in Crystals and in Solution: Structural Consequences of the Imidate and Thioimidate Isosteres for the Peptide bond” is divided into eight chapters. Imidate Modification The range of disallowed dihedral angles for residues in peptides is governed by their local steric and electrostatic clashes. Rare tolerances of violations in these angles are attributed to distortions in both local and global bond characteristics of the peptides. Discerning the origins of such disallowed angles and the consequent distortions in body of the peptides is essential, for a complete understanding of the protein fold, to improve the crystal database for validation of rare but acceptable residue conformations and for validation and improvement of theoretical models that evaluate the interactions that define the Ramachandran space. Unlike for the ordered secondary structures such as β-sheets α-helices and β-turns currently there are no models for residues constrained in disallowed folds. We reasoned that residues may be stabilized in disallowed folds in peptides if a neighbouring group and The range of disallowed dihedral angles ( , ψ) for residues in peptides is governed by their hence its local unfavorable clashes can be selectively modified to a motif that favors such space Steric clashes of the type H•••Xi±n involving the backbone amide hydrogen (H) contribute to ~60% of disallowed ,ψspace. Conversion of an amide to an imidate (A→I) will remove the corresponding H and hence the steric clashes related to it in peptides. Importantly, this will introduce an H-bond acceptor N (of imidate) in place of an H-bond donor NH (of amide), which will allow formation of unusual H-bonding interactions between the imidate N and the neighbouring Hs and hence constrain residues in otherwise inaccessible dihedral angles. The conversion of A→I is challenging owing to difficulties in selective synthesis, stability and purification of the imidate motif. We address all these concerns by the selective conversion of a backbone amide in peptides to the relatively stable cyclic 5,6-dihydro-4H-1,3-oxazine imidate isostere, by an intra¬molecular nucleophilic cyclo-O-alkylation reaction. Chapter 1:SectionB: Autocyclo-O-Alkylation of N-(3-Bromopropyl)amides into 2-Alkyl-5,6-Dihydro-4H-1,3-Oxazinehydrobromides We are describing the reactivity of N-(3-bromopropyl)amides that are precursors for 2-peptide-5,6-dihydro-4H-1,3-oxazine. The starting materials, 3-bromopropylamides, were synthesized in good yields by coupling the corresponding carboxylic acids and anhydrides with 3-bromopropylaminehydrobromide using standard mixed anhydride peptide coupling protocol. N-(3-bromopropyl)-acylamides are unstable during the isolation. Time-dependent 1H NMR of all the acetamides revealed that they underwent clean auto-cyclization to form the corresponding 2-alkyl-5,6-dihydro-4H-1,3-oxazine hydrobromides following first order rate. The salts were easily isolated in high purity by trituration of the mixtures with ether. The t1/2 of autocycliation of decreased upon increase in electron density on the R-carbon. Notably, the tert-butyl substituent cyclized significantly faster than acetamide which have enolizable hydrogens at the R-carbon. Thus, the cyclization rate is affected predominantly by the inductive effect of the R-carbon substituents. The formamide remained stable and unchanged due to the poor electron-donating ability of hydrogen. Chapter 1: Section C: Intramolecular Hydrogen Bond Assistance Improves Autocyclization in N-(3-Bromopropyl)amides The autocyclisation do not go to 100% completion. This is because the released hydrobromic acid quenches the nucleophilicity of amide carbonyl oxygen. In order to scavenge hydro bromic acid, we used 1 equivalent of DIEA base is acting only acid scavenger which conformed by unaffecting the reaction rate upon increasing equivalents of DIEA. We found that autocyclisation of N-(3-bromopropyl)amides rates in peptides involved in intramolecular backbone H-bonding interactions improve the autocyclization rates significantly than unstructured (random coil) peptides. Even with in the ordered structures the rate depends on the proximity of H-bonding distances as well as the H-bond acceptor strength. Half-life of autocyclisation in various peptide secondary structures are determined from time variant 1H NMR studies performed at 60 mM peptide concentration in CDCl3 at 32 oC. Chapter 2: Section A: Synthesis and Isolation of 5,6 Dihydro-4H-1,3-Oxazine Containing Peptidomimetics We have introduced 5,6-Dihydro-4H-1,3-oxazine as the imidate isostere at C-terminus of a number of peptides through NaH (base) mediated intramolecular cyclo-O-alkylation of N-(3-bromopropyl)amides. The amide to imidate (A→I) modification reaction is faster (1-5.5 h), Exhibiting no electronic and structural effects under these conditions. The side product NaBr can be easily separated by filtration through celite. No side products were observed and there is no need of further purification to get pure 1,3-oxazines in quantitative yields in all the peptidomimetics. Using this synthetic protocol we have synthesised a variety of 1,3-oxazine containing peptide analogues including aliphatic, branched aliphatic, polar side chains and larger peptides. We show that the retention of configuration at Cαof peptides during the base mediated cyclo-O-alkylation reaction. that the C5i.structures are more populated at Aib due to operation of The Thorpe-Ingold effect. The strength of hydrogen bonding interaction in C5i structure is similar to those of the highly buried backbone hydrogen bonding interaction found in the middle of a model 310-helical peptide as indicated by DMSO titration experiments. Chapter 3: Section A: Consequences of "Disallowed" Conformations on Constrained β-Turn Peptides Here we are describe the consequence of disallowed conformations the on a C-terminus of a type-II β-turn. We choose stereochemically constrained Type-II β-turn Pro-Aib dipeptide analogue which is the ideal model to mirror the structural effects of introducing the A→I modification at the C-terminus. The imidate containing peptidomimetic crystallised in dichloromethane and hexane mixture. Analysis of crystal structure revealed that Aib NH is involved in 3-centered H-bonding interactions with the N of oxazine and N of proline. This constrains Aib in a conformation that is natively disallowed to it. The (, ) angles of Aib residue fall in the (180,0) region which is strictly disallowed for natural peptides due to steric clashes involving the back bone amide N-H. More importantly there are two C•••O interactions which are accomidated in the crystal structures. Both oxygen‟s were place in staggered orientation of the Pro oxygen (OPro) between the two β-CH3 groups of Aib, which is again strictly disallowed in natural peptides due to strong C•••Oi-1 hard sphere clashes. However no vdW space violations are observed between these atoms. Chapter 3: Section B: Conformational Effects of “Disallowed Aib on a 310-Helical peptide In order to investigate the origins and consequences of “disallowed” conformations on a folded helical peptide body, the conformationally stable peptide sequence Boc-Leu1-Aib2-Ala3-Leu4-Aib5-Ala6-Phe7-Aib8-OMe (310-helix-OMe)was chosen which is known to adopt 310-helix in crystal structure. Analyses of the ROESY spectra, DMSO titration experiments, and CD spectra of 310-helix-OMe and its Oxa analogue reveal that their solution conformations are identical to those of the crystal structure of 310-helix-OMeSix sequential i+3→i intramolecular backbone H-bonds stabilize the 310-helical peptide fold in both peptides in solvents of varying polarity. The N-terminal and central segments of the helical molecules are quite structurally rigid and are not deformed. The presence of the disallowed Aib*8 residue in Oxa analogue has a clear conformational effect mainly on the residue Phe7. It looks like the Phe7 amide H is involved in shielding, the Aib*8 amide H through a bifurcated hydrogen bonding interactions with the nitrogen of oxazine and carbonyl oxygen of Ala6 residue. Maximum structural distortion effect on the registers closest to the putative imidate bond. Our results show that “disallowed folds need not denature order in the peptide fold”. Chapter 4: Synthetic Methods for Introducing the A → I Modification anywhere along the Peptide Chain Here we describe the incorporation of imidate isostere in the middle of any peptide sequence. In Oxa selectivity is towards 5-exo-cyclo-O-alkylation in 1 : 4. In Thi it is towards 6-exo-cyclo-S-alkylation in 3 : 1 ratio. This is because of better nucleophile of sulphur (S). We saw that Thi is stable to peptide coupling, N-and C-terminus protection, deprotection conditions and can be easily incorporated in middle of peptide. Chapter 5: Section A: Cis-trans Isomerism in the X-Pro Peptide Bond In tertiary amides like X-Pro peptides having high propensity to access cis conformations due to similar environment in both cis and trans around the Cof X. X-Pro peptide bonds, constrained in s-cis conformations are prevalently found in the turn regions of peptides with the residue „X‟ in the i+1position and Pro at the i+2position of the β¬turn. These types of turns are termed as the type VI β-turns. For better understanding of the molecular recognition at specific cis X-Pro peptide bonds in biological events, the structure and dynamics of various constrained cis X-Pro peptide bond analogues with varying steric and electronic perturbations have been studied. Many models have been developed for stabilizing cis conformer by perturbation of molecular recognition surface of proline by employing steric and electronic interaction. In biological functions proline molecular recognition surface and cis X-Pro peptide bond more important. There is need of novel method for stabilizing X-Pro peptide bond in cis conformer without modifying the pyrolidine ring in proline. Chapter 5: Section B: Biasing the cis/trans Equilibrium in X Pro Peptides using Reverse ni → ni-1 * Interactions Here we present our findings that peptidomimetics containing the 5,6-dihydro-4H-1,3¬oxazine (Oxa) and 5,6-dihydro-4H-1,3-thiazine (Thi) functional groups at the C-terminus of Pro selectively and remotely stabilize the s-cis rotamers of the preceding pyrrolyl (Xaa-Pro) 3° amide bonds, while conserving these recognition elements. The cis/trans equilibrium of Xaa-Pro peptide bonds is shifted significantly in favor of the satirically disfavored cis isomers in these peptidomimetics (upto ~90%). We also provide evidence for the influence of an unusual n→ πi-1 * interaction in the cis, and the n)(n repulsion in the trans, conformers of these molecules to beat the origin of such the origin of such cis stabilization. Chapter 6: Steric Interactions in the cis Piv-Pro Peptide Bond The inaccessibility of cis Piv-Pro rotamer in any peptide is believed to be because the steric clashes between substituents on CX and CPro are unavoidable in this conformer. Here we access the cisPiv-Pro conformer in crystal structure of Piv-Pro-Aib-OMe and that it is sufficiently flexible to undergo bond distortions and avoid all steric clashes between substituents on CPiv and CPro . It is however the unavoidable distortions in the dihedral angle of the Prothe cisPiv-Proconformer. The cisPiv -Pro conformer is indeed accessible, if such distortions are accommodated in the peptide. Chapter 7: Steric and Electronic Interactions in the cis Isomer of Piv-Pro Peptide Bond in Solution We have studied the electronic and steric interactions and the conformational equilibrium in two sets of homologous peptides, X-Pro-Aib-OMe (which contain Aib) and X-Pro-NH-Me, where X is acetyl, propionyl, isobutyryl and pivaloyl, in solvents of varying polarities consisting of carbontetrachloride, chloroform or dimethylsulfoxide, by means of their 1H and 13C-NMR, and FT-IR spectra. Formation of n * interactions between the carbonyls that flank the Aib residue, influences the alleviation of steric interactions that are believed to preclude access to the cis conformer of the Piv-Pro peptide bond. The cis Piv-Pro conformer is observable in the Aib containing peptides, at ambient conditions by FT-IR and at temperatures as low as 273 K by NMR. We estimate that the steric interactions contribute < 0.5 kcal/mol to the conformational free energy of X-Pro peptide bond isomerism, irrespective of the steric bulk on the acyl (X) group. The relative strengths of intramolecular hydrogen bonding interactions involving the X-Pro peptide motif in different conformers of these peptides influence their relative conformational stabilities. Chapter 8: Remote Effect of Oxa and Thi Functional Groups on cis-trans Isomerism at X-Pro Peptide Bonds The C5a interaction at Pro residue occurs in the transition states for the intramolecular acid catalysis of cis → trans isomerization in peptidyl prolyl isomerases (PPIs) and enables the decrease in transition energy barrier for the isomerization process. We show that the NPro….HAib interactions in C5a structures can be remotely effected in order to control in equilibrium constant values of the cis/trans isomerism (Kc/t) in X-Pro¬Aib-Oxa and Thi containing peptides. By this method we observed improvement in Kc/t values from 0.18 in esters to 0.56 in Thi and 0.66 in Oxa containing peptides. Analyses of the ROESY spectra, DMSO titration experiments, variable temperature experiments and FT-IR spectra of R-CO-Pro-Aib-Oxa (R = Me, Et, iPr) and its Thi analogues reveals that both interactions (C5a and C5i) are persistent in cis and trans conformers of this peptidomimetics. (for structural formula pl. see the abstract.)

This thesis entitled “Design and Access to Disallowed and Unusual Conformers of Peptides in Crystals and in Solution: Structural Consequences of the Imidate and Thioimidate Isosteres for the Peptide bond” is divided into eight chapters. Imidate Modification The range of disallowed dihedral angles for residues in peptides is governed by their local steric and electrostatic clashes. Rare tolerances of violations in these angles are attributed to distortions in both local and global bond characteristics of the peptides. Discerning the origins of such disallowed angles and the consequent distortions in body of the peptides is essential, for a complete understanding of the protein fold, to improve the crystal database for validation of rare but acceptable residue conformations and for validation and improvement of theoretical models that evaluate the interactions that define the Ramachandran space. Unlike for the ordered secondary structures such as β-sheets α-helices and β-turns currently there are no models for residues constrained in disallowed folds. We reasoned that residues may be stabilized in disallowed folds in peptides if a neighbouring group and The range of disallowed dihedral angles ( , ψ) for residues in peptides is governed by their hence its local unfavorable clashes can be selectively modified to a motif that favors such space Steric clashes of the type H•••Xi±n involving the backbone amide hydrogen (H) contribute to ~60% of disallowed ,ψspace. Conversion of an amide to an imidate (A→I) will remove the corresponding H and hence the steric clashes related to it in peptides. Importantly, this will introduce an H-bond acceptor N (of imidate) in place of an H-bond donor NH (of amide), which will allow formation of unusual H-bonding interactions between the imidate N and the neighbouring Hs and hence constrain residues in otherwise inaccessible dihedral angles. The conversion of A→I is challenging owing to difficulties in selective synthesis, stability and purification of the imidate motif. We address all these concerns by the selective conversion of a backbone amide in peptides to the relatively stable cyclic 5,6-dihydro-4H-1,3-oxazine imidate isostere, by an intra¬molecular nucleophilic cyclo-O-alkylation reaction. Chapter 1:SectionB: Autocyclo-O-Alkylation of N-(3-Bromopropyl)amides into 2-Alkyl-5,6-Dihydro-4H-1,3-Oxazinehydrobromides We are describing the reactivity of N-(3-bromopropyl)amides that are precursors for 2-peptide-5,6-dihydro-4H-1,3-oxazine. The starting materials, 3-bromopropylamides, were synthesized in good yields by coupling the corresponding carboxylic acids and anhydrides with 3-bromopropylaminehydrobromide using standard mixed anhydride peptide coupling protocol. N-(3-bromopropyl)-acylamides are unstable during the isolation. Time-dependent 1H NMR of all the acetamides revealed that they underwent clean auto-cyclization to form the corresponding 2-alkyl-5,6-dihydro-4H-1,3-oxazine hydrobromides following first order rate. The salts were easily isolated in high purity by trituration of the mixtures with ether. The t1/2 of autocycliation of decreased upon increase in electron density on the R-carbon. Notably, the tert-butyl substituent cyclized significantly faster than acetamide which have enolizable hydrogens at the R-carbon. Thus, the cyclization rate is affected predominantly by the inductive effect of the R-carbon substituents. The formamide remained stable and unchanged due to the poor electron-donating ability of hydrogen. Chapter 1: Section C: Intramolecular Hydrogen Bond Assistance Improves Autocyclization in N-(3-Bromopropyl)amides The autocyclisation do not go to 100% completion. This is because the released hydrobromic acid quenches the nucleophilicity of amide carbonyl oxygen. In order to scavenge hydro bromic acid, we used 1 equivalent of DIEA base is acting only acid scavenger which conformed by unaffecting the reaction rate upon increasing equivalents of DIEA. We found that autocyclisation of N-(3-bromopropyl)amides rates in peptides involved in intramolecular backbone H-bonding interactions improve the autocyclization rates significantly than unstructured (random coil) peptides. Even with in the ordered structures the rate depends on the proximity of H-bonding distances as well as the H-bond acceptor strength. Half-life of autocyclisation in various peptide secondary structures are determined from time variant 1H NMR studies performed at 60 mM peptide concentration in CDCl3 at 32 oC. Chapter 2: Section A: Synthesis and Isolation of 5,6 Dihydro-4H-1,3-Oxazine Containing Peptidomimetics We have introduced 5,6-Dihydro-4H-1,3-oxazine as the imidate isostere at C-terminus of a number of peptides through NaH (base) mediated intramolecular cyclo-O-alkylation of N-(3-bromopropyl)amides. The amide to imidate (A→I) modification reaction is faster (1-5.5 h), Exhibiting no electronic and structural effects under these conditions. The side product NaBr can be easily separated by filtration through celite. No side products were observed and there is no need of further purification to get pure 1,3-oxazines in quantitative yields in all the peptidomimetics. Using this synthetic protocol we have synthesised a variety of 1,3-oxazine containing peptide analogues including aliphatic, branched aliphatic, polar side chains and larger peptides. We show that the retention of configuration at Cαof peptides during the base mediated cyclo-O-alkylation reaction. that the C5i.structures are more populated at Aib due to operation of The Thorpe-Ingold effect. The strength of hydrogen bonding interaction in C5i structure is similar to those of the highly buried backbone hydrogen bonding interaction found in the middle of a model 310-helical peptide as indicated by DMSO titration experiments. Chapter 3: Section A: Consequences of "Disallowed" Conformations on Constrained β-Turn Peptides Here we are describe the consequence of disallowed conformations the on a C-terminus of a type-II β-turn. We choose stereochemically constrained Type-II β-turn Pro-Aib dipeptide analogue which is the ideal model to mirror the structural effects of introducing the A→I modification at the C-terminus. The imidate containing peptidomimetic crystallised in dichloromethane and hexane mixture. Analysis of crystal structure revealed that Aib NH is involved in 3-centered H-bonding interactions with the N of oxazine and N of proline. This constrains Aib in a conformation that is natively disallowed to it. The (, ) angles of Aib residue fall in the (180,0) region which is strictly disallowed for natural peptides due to steric clashes involving the back bone amide N-H. More importantly there are two C•••O interactions which are accomidated in the crystal structures. Both oxygen‟s were place in staggered orientation of the Pro oxygen (OPro) between the two β-CH3 groups of Aib, which is again strictly disallowed in natural peptides due to strong C•••Oi-1 hard sphere clashes. However no vdW space violations are observed between these atoms. Chapter 3: Section B: Conformational Effects of “Disallowed Aib on a 310-Helical peptide In order to investigate the origins and consequences of “disallowed” conformations on a folded helical peptide body, the conformationally stable peptide sequence Boc-Leu1-Aib2-Ala3-Leu4-Aib5-Ala6-Phe7-Aib8-OMe (310-helix-OMe)was chosen which is known to adopt 310-helix in crystal structure. Analyses of the ROESY spectra, DMSO titration experiments, and CD spectra of 310-helix-OMe and its Oxa analogue reveal that their solution conformations are identical to those of the crystal structure of 310-helix-OMeSix sequential i+3→i intramolecular backbone H-bonds stabilize the 310-helical peptide fold in both peptides in solvents of varying polarity. The N-terminal and central segments of the helical molecules are quite structurally rigid and are not deformed. The presence of the disallowed Aib*8 residue in Oxa analogue has a clear conformational effect mainly on the residue Phe7. It looks like the Phe7 amide H is involved in shielding, the Aib*8 amide H through a bifurcated hydrogen bonding interactions with the nitrogen of oxazine and carbonyl oxygen of Ala6 residue. Maximum structural distortion effect on the registers closest to the putative imidate bond. Our results show that “disallowed folds need not denature order in the peptide fold”. Chapter 4: Synthetic Methods for Introducing the A → I Modification anywhere along the Peptide Chain Here we describe the incorporation of imidate isostere in the middle of any peptide sequence. In Oxa selectivity is towards 5-exo-cyclo-O-alkylation in 1 : 4. In Thi it is towards 6-exo-cyclo-S-alkylation in 3 : 1 ratio. This is because of better nucleophile of sulphur (S). We saw that Thi is stable to peptide coupling, N-and C-terminus protection, deprotection conditions and can be easily incorporated in middle of peptide. Chapter 5: Section A: Cis-trans Isomerism in the X-Pro Peptide Bond In tertiary amides like X-Pro peptides having high propensity to access cis conformations due to similar environment in both cis and trans around the Cof X. X-Pro peptide bonds, constrained in s-cis conformations are prevalently found in the turn regions of peptides with the residue „X‟ in the i+1position and Pro at the i+2position of the β¬turn. These types of turns are termed as the type VI β-turns. For better understanding of the molecular recognition at specific cis X-Pro peptide bonds in biological events, the structure and dynamics of various constrained cis X-Pro peptide bond analogues with varying steric and electronic perturbations have been studied. Many models have been developed for stabilizing cis conformer by perturbation of molecular recognition surface of proline by employing steric and electronic interaction. In biological functions proline molecular recognition surface and cis X-Pro peptide bond more important. There is need of novel method for stabilizing X-Pro peptide bond in cis conformer without modifying the pyrolidine ring in proline. Chapter 5: Section B: Biasing the cis/trans Equilibrium in X Pro Peptides using Reverse ni → ni-1 * Interactions Here we present our findings that peptidomimetics containing the 5,6-dihydro-4H-1,3¬oxazine (Oxa) and 5,6-dihydro-4H-1,3-thiazine (Thi) functional groups at the C-terminus of Pro selectively and remotely stabilize the s-cis rotamers of the preceding pyrrolyl (Xaa-Pro) 3° amide bonds, while conserving these recognition elements. The cis/trans equilibrium of Xaa-Pro peptide bonds is shifted significantly in favor of the satirically disfavored cis isomers in these peptidomimetics (upto ~90%). We also provide evidence for the influence of an unusual n→ πi-1 * interaction in the cis, and the n)(n repulsion in the trans, conformers of these molecules to beat the origin of such the origin of such cis stabilization. Chapter 6: Steric Interactions in the cis Piv-Pro Peptide Bond The inaccessibility of cis Piv-Pro rotamer in any peptide is believed to be because the steric clashes between substituents on CX and CPro are unavoidable in this conformer. Here we access the cisPiv-Pro conformer in crystal structure of Piv-Pro-Aib-OMe and that it is sufficiently flexible to undergo bond distortions and avoid all steric clashes between substituents on CPiv and CPro . It is however the unavoidable distortions in the dihedral angle of the Prothe cisPiv-Proconformer. The cisPiv -Pro conformer is indeed accessible, if such distortions are accommodated in the peptide. Chapter 7: Steric and Electronic Interactions in the cis Isomer of Piv-Pro Peptide Bond in Solution We have studied the electronic and steric interactions and the conformational equilibrium in two sets of homologous peptides, X-Pro-Aib-OMe (which contain Aib) and X-Pro-NH-Me, where X is acetyl, propionyl, isobutyryl and pivaloyl, in solvents of varying polarities consisting of carbontetrachloride, chloroform or dimethylsulfoxide, by means of their 1H and 13C-NMR, and FT-IR spectra. Formation of n * interactions between the carbonyls that flank the Aib residue, influences the alleviation of steric interactions that are believed to preclude access to the cis conformer of the Piv-Pro peptide bond. The cis Piv-Pro conformer is observable in the Aib containing peptides, at ambient conditions by FT-IR and at temperatures as low as 273 K by NMR. We estimate that the steric interactions contribute < 0.5 kcal/mol to the conformational free energy of X-Pro peptide bond isomerism, irrespective of the steric bulk on the acyl (X) group. The relative strengths of intramolecular hydrogen bonding interactions involving the X-Pro peptide motif in different conformers of these peptides influence their relative conformational stabilities. Chapter 8: Remote Effect of Oxa and Thi Functional Groups on cis-trans Isomerism at X-Pro Peptide Bonds The C5a interaction at Pro residue occurs in the transition states for the intramolecular acid catalysis of cis → trans isomerization in peptidyl prolyl isomerases (PPIs) and enables the decrease in transition energy barrier for the isomerization process. We show that the NPro….HAib interactions in C5a structures can be remotely effected in order to control in equilibrium constant values of the cis/trans isomerism (Kc/t) in X-Pro¬Aib-Oxa and Thi containing peptides. By this method we observed improvement in Kc/t values from 0.18 in esters to 0.56 in Thi and 0.66 in Oxa containing peptides. Analyses of the ROESY spectra, DMSO titration experiments, variable temperature experiments and FT-IR spectra of R-CO-Pro-Aib-Oxa (R = Me, Et, iPr) and its Thi analogues reveals that both interactions (C5a and C5i) are persistent in cis and trans conformers of this peptidomimetics. (for structural formula pl. see the abstract.)

This dissertation explains the puzzling negative relationship between changes in stock volatility and credit spreads of corporate bonds. This relationship has been encountered in some empirical studies but has remained unexplained in the theoretical literature, which unanimously suggests the opposite relationship. This dissertation shows that this negative relationship can be produced by the dynamic endogenous asset composition of borrowing firms. On the one hand, higher asset volatility corresponds to lower future volatility of the firm's investments and lower credit spreads if the firm can reallocate resources optimally. On the other hand, short-term stock volatility corresponds to the current allocation of resources and thus increases with asset volatility. The combination of these two effects produces the negative relationship between changes in stock volatility and credit spreads. The empirical part of the dissertation shows that the relationship between changes in stock market volatility and credit spreads of long-term, high-quality corporate bonds (controlling for other variables) is negative, robust, and economically significant. Consistent with the predictions in this dissertation, the corresponding regression coefficient is a U-shaped function of the credit quality of the bonds. In addition, the dissertation shows that the relationship changes its sign in distressed market conditions and that a combination of normal and distressed market conditions can produce erroneous results.

No
The vitrification solutions used in the cryopreservation of biological samples aim to minimize the deleterious formation of ice by dehydrating cells and promoting the formation of the glassy state of water. They contain a mixture of different cryoprotective agents (CPAs) in water, typically polyhydroxylated alcohols and/or dimethyl sulfoxide (DMSO), which can damage cell membranes. Molecular dynamics simulations have been used to investigate the behavior of pure DPPC, pure DOPC, and mixed DOPC-β-sitosterol bilayers solvated in a vitrification solution containing glycerol, ethylene glycol, and DMSO at concentrations that approximate the widely used plant vitrification solution 2. As in the case of solutions containing a single CPA, the vitrification solution causes the bilayer to thin and become disordered, and pores form in the case of some bilayers. Importantly, the degree of thinning is, however, substantially reduced compared to solutions of DMSO containing the same total CPA concentration. The reduction in the damage done to the bilayers is a result of the ability of the polyhydroxylated species (especially glycerol) to form hydrogen bonds to the lipid and sterol molecules of the bilayer. A decrease in the amount of DMSO in the vitrification solution with a corresponding increase in the amount of glycerol or ethylene glycol diminishes further its damaging effect due to increased hydrogen bonding of the polyol species to the bilayer headgroups. These findings rationalize, to our knowledge for the first time, the synergistic effects of combining different CPAs, and form the basis for the optimization of vitrification solutions.
Australian Research Council linkage grant No. LP0884027; Alcoa Australia Ltd.; BHP Billiton Worsley Alumina Pty. Ltd.

The work presented in this thesis focusses primarily on the determination of protein structure at atomic resolution, with NMR spectroscopy as the principle investigative tool. The thesis is divided into four parts. Part I consists of Chapter 1 which provides an introduction to protein structure, folding and NMR spectroscopy. Part II, consisting of Chapters 2 and 3, describes the effects of aromatic interactions on nucleating structure in disordered regions of proteins, using variants of apo-cytochrome b5 as a model system. Part III consists of Chapter 4, which describes structural effects of introducing cross-strand disulfide bonds using variants of Thioredoxin. Part IV of this thesis consists of the Appendices A, B and C. Appendix A describes the purification and characterization of ilvM, the regulatory subunit of the E.coli enzyme AHAS II. Appendices B and C contain chemical shift information corresponding to Chapter 3 and Chapter 4 respectively. Part I : Introduction to protein structure, folding and solution structure studies Chapter 1 first gives a brief overview of protein structure followed by an introduction to protein folding, focussing on the forces involved in determining the final three-dimensional shape of the protein as well as the experimental and computational techniques involved in studying or predicting the fold of a given protein. The second section of this chapter details the methodology followed to obtain solution structures of proteins using NMR spectroscopy. Part II : Engineering aromatic interactions to nucleate folding in intrinsically disordered regions of proteins Chapter 2 describes site-specific mutagenesis, recombinant over-expression, purifica-tion and preliminary biophysical characterization of two aromatic mutants of the molten globule apo-cytochrome b5 (apocytb5) : H43F H67F cytochrome b5 (FFcytb5) and H43W H67F cytochrome b5 (WFcytb5). Analysis of the structure of wild-type apo - cytochrome b5 was done to introduce surface mutations and avoid perturbation of the interior pack-ing of the protein. The bacterial host E.coli BL21(DE3) was used for recombinant over-expression, and both mutant proteins were purified by anion-exchange chromatography followed by size-exclusion chromatography. Biophysical studies show a decrease in the hydrodynamic radii and surface hydropho-bicity of FFcytb5 and WFcytb5 compared to wt -apo cytb5. An increase in protein stability was also seen from the wt apocytb5 to WFcytb5 and FFcytb5 in the presence of the chemical denaturant Urea. Proton 1D NMR spectra exhibited sharp lines and good spectral dispersion in the amide region, indicating that both mutant proteins are well folded. In addition, conservation of two distinctive up field and downfield shifted resonances present in apocytb5 indicated that structural changes upon mutation accrued on the upon the scaffold of apocytb5. Chapter 3 describes solution structure studies to determine secondary and tertiary structure of FFcytb5 and WFcytb5. Structural studies were carried out using homonu-clear and heteronuclear NMR methods, for which isotopically enriched 15N- and 13C, 15N samples were prepared for each protein. Additionally a 2H, 13C, 15N ILV methyl labeled sample was prepared for FFcytb5 to obtain unambiguous NOE correlation data. The hydrogen bond network for WFcytb5 was determined using hydrogen/deuterium exchange data. The restraints required to define the orientations and interactions of the aromatic groups were obtained from 15N-edited NOESY HSQC, 13C -edited NOESY HSQC and 2D 1H - 1H NOE spectra. These correlations were crucial in determining the aromatic interactions present within each protein. The structure of FFcytb5 was calculated using 1163 NOE distance restraints, 179 φ and ψ dihedral angle restraints, along with 40 hydrogen bond restraints. Similarly the structure of WFcytb5 was calculated using 1282 NOE distance restraints, 177 φ and ψ dihedral angle restraints and 40 hydrogen bond restraints. The ensemble of structures obtained for FFcytb5 showed a root mean square deviation of 1.01±0.21 Å . The ensemble of structures obtained for WFcytb5 showed a root mean square deviation of 0.58±0.09 Å . In both cases, ≈ 80% of backbone dihedral angles were found to be in the allowed regions and ≈ 20% in the additionally allowed regions of the Ramachandran map. The final tertiary structure of both FFcytb5 and WFcytb5 consisted of a mixed four strand β -sheet with a four helix bundle resting on top and were seen to align well, with an RMSD of 0.6 Å. A comparison of the solution structures of apocytb5 with FFcytb5 and WFcytb5 convincingly showed the nucleation secondary and tertiary structure well beyond the site of mutation. The presence of aromatic trimers, non-canonical in context of the wt apoc-ytb5, was confirmed upon analysis of the structures of FFcytb5 and WFcytb5, with NOE correlations assigned to verify these interactions. The reduction in the hydrodynamic radii of FFcytb5 and WFcytb5 in relation to apocytb5 was also verified from tsuperscript15N-NMR relaxometry studies. The nucleation of long-range structure using aromatic interactions has been demonstrated in proteins for the first time, and can in principle be used to incorporate aromatic residues and interactions in protein design. Structural data, chemical shift data and restraints lists used for structure calculation of WFcytb5 and FFcytb5 were deposited with the PDB (accession numbers 5XE4 and 5XEE) and BMRB(accession numbers 36070, 36071) respectively1. Part III : Structural consequences of introducing disulfide bonds into β - sheets Chapter 3 describes the solution structure studies on two mutants of E.coli Thiore-doxin which were designed to incorporate a disulfide bond between two anti-parallel β-strands at the edge of the β-sheet. One mutant was designed with a disulfide bond at the hydrogen bonding position (HB, 78c90cTrx) and the other with the disulfide bond at the non-hydrogen bonding position (NHB, 77c91cTrx). Here we study the structural changes that accompany the introduction of a cross-strand disulfide and whether such structural changes could be correlated with the previously seen thermodynamic and catalytic changes. Solution structure studies were conducted using a suite of multidimensional heteronu-clear NMR experiments, for which isotopically enriched 15N and 13C, 15N labelled samples were used. The solution structure for 77c91cTrx was calculated using 1190 NOE distance restraints, 199 φ and ψ dihedral angle restraints and 48 hydrogen bond restraints. The solution structure for 78c90cTrx was calculated using 1123 NOE distance restraints, 197 φ and ψ dihedral angle restraints and 50 hydrogen bond restraints. The ensemble of structures for 77c91cTrx showed an RMSD of 0.78± 0.13 Å while the RMSD for the ensemble of structures of 78c90cTrx was seen to be 0.76±0.09 Å . In both cases, ≈ 80% of backbone dihedral angles were seen to be in the allowed regions and ≈ 20% in the additionally allowed regions of the Ramachandran map. The tertiary structures of both proteins were seen to have a 5-strand mixed β-sheet and 4 helices surrounding it. . A comparison of the solution structures of mutant and wt -Trx showed significant changes in secondary and tertiary structure. For example, an α helix was reduced from 3 turns to a single turn, and of the β-strands containing the mutation was elongated by 3 residues. A ≈ 50% loss of hydrogen bonds, primarily from the β -sheet, was seen for both mutants. The secondary and tertiary structure for both 77c91cTrx and 78c90cTrx was seen to be near identical, despite the greater strain of the disulfide bond at the hydrogen bonding position. In addition to this, the Ile75-Pro76 peptide bond is now seen to be in the trans conformation in 78c90cTrx, while in wt -Trx the Ile75-Pro76 peptide bond is in the cis conformation. This cis peptide bond is known to play a role in both folding and catalysis, and the solution structures were analyzed in the context of observed changes in folding and catalysis. The study shows that introducing disulfide bonds even at the edge of β sheets have long-range structural effects, and the structural effects cannot be directly correlated with the changes in stability. Part III: Appendix Appendix A describes the expression, purification and preliminary characterization of ilvM, the regulatory subunit of E.coliAHAS II, one of three enzyme isomers that catal-yse the first step in the synthesis of all branched chain amino acids. AHAS II is known to be insensitive to feedback regulation, but our studies showed that the presence of Ile, Leu and Val causes structural changes and increases the stability of ilvM. However we were not able to purify ilvM in sufficient quantities to proceed with solution structure studies. Appendices B and C contain chemical shift information for the structural studies carried out on FFcytb5, WFcytb5, 77c91cTrx and 78c90cTrx.

The work presented in this thesis focusses primarily on the determination of protein structure at atomic resolution, with NMR spectroscopy as the principle investigative tool. The thesis is divided into four parts. Part I consists of Chapter 1 which provides an introduction to protein structure, folding and NMR spectroscopy. Part II, consisting of Chapters 2 and 3, describes the effects of aromatic interactions on nucleating structure in disordered regions of proteins, using variants of apo-cytochrome b5 as a model system. Part III consists of Chapter 4, which describes structural effects of introducing cross-strand disulfide bonds using variants of Thioredoxin. Part IV of this thesis consists of the Appendices A, B and C. Appendix A describes the purification and characterization of ilvM, the regulatory subunit of the E.coli enzyme AHAS II. Appendices B and C contain chemical shift information corresponding to Chapter 3 and Chapter 4 respectively. Part I : Introduction to protein structure, folding and solution structure studies Chapter 1 first gives a brief overview of protein structure followed by an introduction to protein folding, focussing on the forces involved in determining the final three-dimensional shape of the protein as well as the experimental and computational techniques involved in studying or predicting the fold of a given protein. The second section of this chapter details the methodology followed to obtain solution structures of proteins using NMR spectroscopy. Part II : Engineering aromatic interactions to nucleate folding in intrinsically disordered regions of proteins Chapter 2 describes site-specific mutagenesis, recombinant over-expression, purifica-tion and preliminary biophysical characterization of two aromatic mutants of the molten globule apo-cytochrome b5 (apocytb5) : H43F H67F cytochrome b5 (FFcytb5) and H43W H67F cytochrome b5 (WFcytb5). Analysis of the structure of wild-type apo - cytochrome b5 was done to introduce surface mutations and avoid perturbation of the interior pack-ing of the protein. The bacterial host E.coli BL21(DE3) was used for recombinant over-expression, and both mutant proteins were purified by anion-exchange chromatography followed by size-exclusion chromatography. Biophysical studies show a decrease in the hydrodynamic radii and surface hydropho-bicity of FFcytb5 and WFcytb5 compared to wt -apo cytb5. An increase in protein stability was also seen from the wt apocytb5 to WFcytb5 and FFcytb5 in the presence of the chemical denaturant Urea. Proton 1D NMR spectra exhibited sharp lines and good spectral dispersion in the amide region, indicating that both mutant proteins are well folded. In addition, conservation of two distinctive up field and downfield shifted resonances present in apocytb5 indicated that structural changes upon mutation accrued on the upon the scaffold of apocytb5. Chapter 3 describes solution structure studies to determine secondary and tertiary structure of FFcytb5 and WFcytb5. Structural studies were carried out using homonu-clear and heteronuclear NMR methods, for which isotopically enriched 15N- and 13C, 15N samples were prepared for each protein. Additionally a 2H, 13C, 15N ILV methyl labeled sample was prepared for FFcytb5 to obtain unambiguous NOE correlation data. The hydrogen bond network for WFcytb5 was determined using hydrogen/deuterium exchange data. The restraints required to define the orientations and interactions of the aromatic groups were obtained from 15N-edited NOESY HSQC, 13C -edited NOESY HSQC and 2D 1H - 1H NOE spectra. These correlations were crucial in determining the aromatic interactions present within each protein. The structure of FFcytb5 was calculated using 1163 NOE distance restraints, 179 φ and ψ dihedral angle restraints, along with 40 hydrogen bond restraints. Similarly the structure of WFcytb5 was calculated using 1282 NOE distance restraints, 177 φ and ψ dihedral angle restraints and 40 hydrogen bond restraints. The ensemble of structures obtained for FFcytb5 showed a root mean square deviation of 1.01±0.21 Å . The ensemble of structures obtained for WFcytb5 showed a root mean square deviation of 0.58±0.09 Å . In both cases, ≈ 80% of backbone dihedral angles were found to be in the allowed regions and ≈ 20% in the additionally allowed regions of the Ramachandran map. The final tertiary structure of both FFcytb5 and WFcytb5 consisted of a mixed four strand β -sheet with a four helix bundle resting on top and were seen to align well, with an RMSD of 0.6 Å. A comparison of the solution structures of apocytb5 with FFcytb5 and WFcytb5 convincingly showed the nucleation secondary and tertiary structure well beyond the site of mutation. The presence of aromatic trimers, non-canonical in context of the wt apoc-ytb5, was confirmed upon analysis of the structures of FFcytb5 and WFcytb5, with NOE correlations assigned to verify these interactions. The reduction in the hydrodynamic radii of FFcytb5 and WFcytb5 in relation to apocytb5 was also verified from tsuperscript15N-NMR relaxometry studies. The nucleation of long-range structure using aromatic interactions has been demonstrated in proteins for the first time, and can in principle be used to incorporate aromatic residues and interactions in protein design. Structural data, chemical shift data and restraints lists used for structure calculation of WFcytb5 and FFcytb5 were deposited with the PDB (accession numbers 5XE4 and 5XEE) and BMRB(accession numbers 36070, 36071) respectively1. Part III : Structural consequences of introducing disulfide bonds into β - sheets Chapter 3 describes the solution structure studies on two mutants of E.coli Thiore-doxin which were designed to incorporate a disulfide bond between two anti-parallel β-strands at the edge of the β-sheet. One mutant was designed with a disulfide bond at the hydrogen bonding position (HB, 78c90cTrx) and the other with the disulfide bond at the non-hydrogen bonding position (NHB, 77c91cTrx). Here we study the structural changes that accompany the introduction of a cross-strand disulfide and whether such structural changes could be correlated with the previously seen thermodynamic and catalytic changes. Solution structure studies were conducted using a suite of multidimensional heteronu-clear NMR experiments, for which isotopically enriched 15N and 13C, 15N labelled samples were used. The solution structure for 77c91cTrx was calculated using 1190 NOE distance restraints, 199 φ and ψ dihedral angle restraints and 48 hydrogen bond restraints. The solution structure for 78c90cTrx was calculated using 1123 NOE distance restraints, 197 φ and ψ dihedral angle restraints and 50 hydrogen bond restraints. The ensemble of structures for 77c91cTrx showed an RMSD of 0.78± 0.13 Å while the RMSD for the ensemble of structures of 78c90cTrx was seen to be 0.76±0.09 Å . In both cases, ≈ 80% of backbone dihedral angles were seen to be in the allowed regions and ≈ 20% in the additionally allowed regions of the Ramachandran map. The tertiary structures of both proteins were seen to have a 5-strand mixed β-sheet and 4 helices surrounding it. . A comparison of the solution structures of mutant and wt -Trx showed significant changes in secondary and tertiary structure. For example, an α helix was reduced from 3 turns to a single turn, and of the β-strands containing the mutation was elongated by 3 residues. A ≈ 50% loss of hydrogen bonds, primarily from the β -sheet, was seen for both mutants. The secondary and tertiary structure for both 77c91cTrx and 78c90cTrx was seen to be near identical, despite the greater strain of the disulfide bond at the hydrogen bonding position. In addition to this, the Ile75-Pro76 peptide bond is now seen to be in the trans conformation in 78c90cTrx, while in wt -Trx the Ile75-Pro76 peptide bond is in the cis conformation. This cis peptide bond is known to play a role in both folding and catalysis, and the solution structures were analyzed in the context of observed changes in folding and catalysis. The study shows that introducing disulfide bonds even at the edge of β sheets have long-range structural effects, and the structural effects cannot be directly correlated with the changes in stability. Part III: Appendix Appendix A describes the expression, purification and preliminary characterization of ilvM, the regulatory subunit of E.coliAHAS II, one of three enzyme isomers that catal-yse the first step in the synthesis of all branched chain amino acids. AHAS II is known to be insensitive to feedback regulation, but our studies showed that the presence of Ile, Leu and Val causes structural changes and increases the stability of ilvM. However we were not able to purify ilvM in sufficient quantities to proceed with solution structure studies. Appendices B and C contain chemical shift information for the structural studies carried out on FFcytb5, WFcytb5, 77c91cTrx and 78c90cTrx.

Corrosion influences both of the serviceability limit state and the ultimate limit state of the reinforced concrete structures. The mass loss of reinforcement caused by corrosion not only reduces cross sectional area of the reinforcement but also the bond between the steel reinforcement and surrounding concrete. By reducing the bond between the reinforcement and surrounding concrete, at serviceability limit state, corrosion may lead to an increase crack width and deflection, while at the ultimate limit state it may lead to reinforcement debonding. Hence, knowledge of the influence of corrosion on the bond between reinforcement and concrete is required to evaluate structural behaviour and extend the life span of the reinforced concrete structures. This thesis first investigates the influence of corrosion on bond properties yielding a new bond-slip material model which has been developed from the analysis of a large data base of 377 individual test results obtained from published experimental results. From the resulting bond-slip model it is shown the debonding of reinforcement may occur at relatively low levels of corrosion and that the influence of corrosion on bond is more significant corrosion for large bar diameters. Having developed a material model illustrating how corrosion influences the bond-slip relationship, the impact of corrosion on reinforced concrete beams is considered. Firstly the performance of beams at the ultimate limit state is considered through the development of a numerical segmental analysis technique to simulate member behaviour prior to and post debonding. Importantly this model shows that although debonding of reinforcement may occur at a relatively low level of corrosion, it does not always negatively impact member strength or ductility. The impact of reinforcement corrosion at the serviceability limit state is then considered through the extension of the segmental approach to incorporate not only the influence of bond but also concrete creep and shrinkage. The resulting model couples concrete creep and shrinkage with reinforcement corrosion and predicts the influence of each on crack width and member deflection. Significantly it is shown that reinforcement corrosion can be much more easily monitored through measurement of crack widths over time rather than through consideration of member deflection and the approach proposed may be used to provide guidance on the variation in reinforcement corrosion along a span.
Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Civil, Environmental and Mining Engineering, 2016.

The aim of this dissertation is to analyze whether Social Impact Bonds are a viable instrument to finance the social project “aTTitude 3D – Educate, Teach and Integrate”. For this purpose, firstly, a literature review was carried out to obtain information regarding Social Impact Bonds, including background information, structure, and market analysis. Secondly, this information was used to conduct an analysis about the main strengths, opportunities, weaknesses, and threats (SOWT analysis) of Social Impact Bonds. The general assessment of this analysis suggested 3 major threats for the continuous development of Social Impact Bonds market: (1) Lack of existing capacity of service providers to scale up social services; (2) Government role, election cycles and change of willingness of government to support social project and/or SIB transaction; and (3) Short pool of investors due to financial risk. Finally, a Case Study was used to analyze the feasibility of a Social Impact Bond to finance a particular social project: “aTTitude 3D – Educate, Teach and Integrate” intervenes in the education area with the objective of reducing retention rates. For this purpose, a financial model was built representing the investment mechanism. The results of the model developed suggested that a Social Impact Bond is a viable instrument to fund and scale this specific project, according to the risk profile (i.e. return and impact) assumed in this thesis for the private investors. Despite this, as already noted from the SWOT analysis, the three major threats were analyzed regarding the sustainability and the practical implementation of a Social Impact Bond model for this specific Case Study.

碩士
國立高雄大學
法律學系碩士班
104
The purpose of public govermance is to provide the best welfare for the public by making use of limited resources. The purpose of government audit is to improve the impartial politics, assist the government to cleanse out political corruption, efficiently promote the government efficiency and improve welfare for the public. Audit Law was revised in 1998 last time and this version has been used for over 10 years without alteration. Whether the execution of relevant audit service meets the requirements of administration and control by current government is worth discussion. In addition, the government supervision can be divided into three parts including administration (higher authority), internal audit and audit institution, but is there functions overlapped and repeated that lower or affect the government efficiency? According to the Article 2 of Audit Law, the decision or behavior of audit institution will directly or indirectly affect the administration and policy of government. With the example of violating the recovering bid bond by Government Procurement Law, it is because when the audit institution uses the law and regulation retrieving system of Judicial Yuan to research for the cases which were related to the procurement bid bond of government recovering or confiscating, it informs the administrative agency to manage properly according to law. However, the property to audit and inform, force of law, influence on institutions and the legal nature recovering or confiscating follow-up bid bond lack of clear and specific treatment guidelines and stipulations. That made the administrative agency has ambiguity when it dealt with follow-up matters. This study focuses on discussing the nature and effect of auditing and informing laws of audit institutions, the audit system and the problem of alternate application of administrative laws and regulations. It further discusses the doubt about the audit institution informs the administrative agency to deal with the case of government procurement bid bond from the property of government procurement, hoping to provide proper advice of audit system and government procurement, improve the administrative efficiency of government and decrease the dispute of follow-up execution of administrative agency by the auditing and informing of audit institution.

碩士
國立交通大學
應用化學系所
95
Most of today’s materials require additional processing or modification steps in order to obtain the properties that make them suitable for a particular application. As an alternative to these traditional fabrication pathways, routes that use the self-assembly of polymeric building blocks are attracting increasing attention. We have synthesized poly(methyl methacrylate-b-4-vinylpyridine) (PMMA- b-P4VP) and poly(styrene-r-vinylphenol) (PS-r-PVPh) copolymers by using the anionic polymerization and the free radical polymerization, respectively. Well defined micelles through hydrogen bond have been prepared by mixing PMMA-b-P4VP diblock copolymer and PS-r-PVPh random copolymer in single solvent. The block copolymers were mixed with random copolymers, with the various B/R ratio (4/1, 2/1, 1/1, and 1/4) in which “B” and “R” represents block copolymers and random copolymers, respectively. The presence distribution of PVPh/P4VP and PVPh/PMMA hydrogen bonding depends on the feeding ratio of PVPh to P4VP. When the PVPh content lower than P4VP, hydrogen bonding occurs only between PVPh and P4VP; with excess PVPh, additional hydrogen bonding between PVPh and PMMA could occur. Furthermore, the effect of the solvent quality on the self-assembly behavior of PMMA-b-P4VP/PS-r-PVPh blends is investigated by considering THF and DMF as common solvent.

碩士
國立交通大學
應用化學系所
95
A series of poly(vinylphenol-b-styrene) (PVPh-b-PS) and poly(4-vinyl pyridine-b-methyl methacrylate) (P4VP-b-PMMA) block copolymers were prepared by anionic polymerizations of 4-tert-butoxystyrene、styrene、4-vinyl pyridine and methyl methacrylate , followed by selective removal of the 4-tert-butoxystyrene protective group by hydrolysis reaction . The dibolck copolymers were investigated by proton nuclear magnetic resonance spectrometry (1H-NMR), Fourier transfer infrared spectrophotometer (FTIR) , gel permeation chromatography (GPC) . Finally, studied by dynamic light scattering (DLS) and transmission electron microscopy (TEM) is the coaggregation of PVPh-b-PS and P4VP -b-PMMA in tetrahydrofuran (THF) and N,N-Dimethylformamide (DMF). Self-assembly of the associating diblocks by the hydrogen bonding resulted in interesting block copolymer aggregation behavior and morphologies in single solvent . Infrared spectra provide positive evidence of hydrogen bonding interaction .

Strengthening of concrete structures with a new concrete layer has been commonly used for columns, beams and slabs. This technique is economic and efficient for structural strengthening since it uses the same base materials, steel and concrete. It is usually applied on the compressed face of the concrete element due to concrete’s recognized behaviour under compression, posing several challenges to control cracking and resistance when applied on the tensile face. Strengthening of concrete structures with a new concrete layer applied on the tensile face requires controlling the debonding phenomenon of added concrete for service and ultimate limit states. Designing such strengthening solution requires the consideration for the strength of the global structure and the local interface capacity for maintaining structural integrity throughout the load history. Such requirement leads to the need for interface detailing solutions between the two concrete layers that improve the behaviour of the composite section, namely the roughening of the existing surface and stitching reinforcement. The knowledge from studying such interface was applied to the strengthening of slab specimens. This work presents the study performed on concrete unidirectional slab specimens and on columnsupported slab specimens. All specimens were strengthened with a reinforced concrete overlay on the tensile face. The former consisted on the flexural monotonic loading of the specimens until failure, and the latter consisted on specimens loaded monotonically and concentrically until failure. The calibration of numerical models based on experimental test results was also performed with the nonlinear analysis software ATENA 3D®. All results were then compared to current codes and regulations, and some guidelines were defined for the correct application of strengthening with a reinforced concrete overlay on existing structures.

Spin crossover (SCO) active metal complexes are highly versatile materials thanks to their sensitivity to tiny physical or chemical environmental changes. This property makes them very useful for a wide range of applications: employable for experimental studies as molecular switches or for theoretical studies investigating the M-L bonds. In both cases, these studies aim to develop strategies of predictably tuning them. Chapter One. An introduction to the SCO phenomenon: from gradual to cooperative SCO; various methods of monitoring the SCO transition. A summary of some literature examples of SCO-active systems is given. An overview of the published achievements in predicting the SCO phenomenon, including an introduction to the computational models deployed across the years. The EDA-NOCV model, employed in this field for the first time in this PhD thesis, is introduced. Finally, the aims of this study are presented. Chapter Two. The synthesis and characterisation of four new non-symmetrical ligands, 3-(2-(5-Z-pyridyl))-4-tolyl-5-phenyl-1,2,4-triazole (LpytZ, Z = CF3, Br, F, Me), and the corresponding [FeII(LpytZ)2(NCBH3)2] complexes are presented. All four of these new complexes are SCO-active in the solid state and in CDCl3 solution, but T1/2 tuning by the meta-Z substituents was very modest. Three literature families were also tested, successfully extending the generality of using the 15N NMR chemical shift δNA of the coordinated nitrogen atom of the free ligand as measure of the T1/2 in the resulting Fe(II) complex. Chapter Three. Theoretical study of a family of five iron(II) SCO-active [Fe(Lazine)2(NCBH3)2] (Lazine = 3-(2-azinyl)-4-tolyl-5-phenyl-1,2,4-triazole) and of the related five LS [Fe(Lazine)3(BF4)2]. The EDA-NOCV model was applied to molecular fragments to provide quantitative assessment of the σ- and π-bonding. A new corrected [Mn+ + L6] fragmentation was implemented which promises to enable a general approach suitable for any ML6 system. Finally, the σ- and π-bonding character is strongly correlated with the experimental T1/2 of the SCO-active [Fe(Lazine)2(NCBH3)2] complexes. Chapter Four. Theoretical study of the M-L bond in a family of sixteen SCO-active differently para-X substituted [Fe(bppX)2]2+ complexes (bppX is 2,6-di(pyrazol-1-yl)-4-X-pyridine). Results of the EDA-NOCV revealed the σ-strength of the bppX ligand is correlated with σp+(X), δNA(bppX), experimental T1/2([Fe(bppX)2]2+) and calculated AILFT ΔO([Fe(bppX)2]2+). Results are explained at the molecular level by investigating the orbital population of the valence orbitals of the coordinating nitrogen involved in the aromatic π-system (pπ) and in the Fe-N bond (sp2(Fe)). From the observed correlations, the unknown σp+ parameter for two substituents (X = SOMe, SO2Me) is predicted. Chapter Five. First theoretical study on [CoII(dpzca)2] SCO in the solid state, aiming to establish a computational protocol able to predict experimental T1/2 in pressure-activated SCO. The first part of the study validated a DFT protocol at p = 1 bar. The protocol was then extended and trialled up to 4300 bar. Results revealed good reproduction of the experimental results up to 2100 bar; but beyond this pressure, the theoretical and experimental findings diverge. Theoretical data suggest a possible phase change for the crystalline structure of HS [CoII(dpzca)2] at higher pressures than 2100 bar; this would explain why the implemented computational protocol lost validity.

Thesis titled, “Design, Synthesis and Conformational Analysis of Hydrogen Bond Surrogate (HBS) Stabilized Helices in Natural Sequences. Helically Constrained Peptides for Potential DNA-Binding”, describes the development of a novel covalent hydrogen bond surrogate (HBS) model and its incorporation in short (4-8 residues) unstructured peptide sequences with coded amino acids, through a facile solution phase synthetic method (SPSM), to constrain them into α- helical conformations with highest known stabilities and helicities. The synthetic protocol was developed for mass scale combinatorial synthesis of helical peptidomimetics. NMR, FT-IR, CD spectra and molecular dynamics simulations of variants of the HBS-constrained helical peptidomimetics were analyzed to determine the optimum number of sp2 atoms and the residue preferences that yield both the α-helical and the 310-helical folds with high structural integrity in the shortest sequences. The HBS-constrained helical peptidomimetics were used to derive experimental evidence that the 2-state Helix-Coil Transition occurs at each residue during helix folding and that this process is entropically driven. Further, the role of temperature on the denaturation of secondary structures was investigated using these HBS-constrained helical models. Helical peptidomimetics of the DNA-binding domain in the zinc-finger human TTK protein have been synthesized, which have proven to be promising mimics for DNA-binding and subsequent transcription regulation.
CSIR

We firstly numerically recalculate the Ricci tensor of non-stationary axisymmetric space-times (originally calculated by Chandrasekhar) and we find some discrepancies both in the linear and non-linear terms. However, these discrepancies do not affect the results concerning linear perturbations of a Schwarzschild black hole. Secondly, we use these Ricci tensors to derive the Zerilli and Regge-Wheeler equations and use the Newman-Penrose formalism to derive the Bardeen-Press equation. We show the relation between these equations because they describe the same linear perturbations of a Schwarzschild black hole. Thirdly, we illustrate heuristically (when the angular momentum (l) is 2) the relation between the linearized solution of the Einstein vacuum equations obtained from the Bondi-Sachs metric and the Zerilli equation, because they describe the same linear perturbations of a Schwarzschild black hole. Lastly, by means of a coordinate transformation, we extend Chandrasekhar's results on linear perturbations of a Schwarzschild black hole to the Bondi-Sachs framework.
Mathematical Sciences
M. Sc. (Applied Mathematics)

Celem rozprawy doktorskiej było przestawienie, co współczesna krystalografia może wnieść do badań minerałów o różnym stopniu wykształcenia, jakości kryształów. Badałem trzy rodzaje minerałów: (i) alumohydrokalcyt o słabo rozwiniętych igiełkowych kryształów (ii) minerały grupy czewkinitu, złożone roztwory stałe, często również metamiktyczne oraz (iii) fluoryt, którego kryształ był niemal doskonałej jakości.
The PhD dissertation presents what modern crystallography can deliver to the studies of minerals. Three types of minerals were studied (i) alumohydrocalcite of poorly developed tiny needle shaped crystals (ii) members of chevkinite group, complex partially metamict solid so-lutions and (iii) fluorite, of nearly prefect quality crystal.