In this thesis, fundamental questions about the nature of the solvent/counter-ion region of x-ray crystal structures are raised. The ambiguity in the identity and occupancy of the molecular and atomic species in this region is explored experimentally. Anomalous scattering is proposed as a possible method for resolving this ambiguity. To this effect, the properties of rubidium I and thallium I are compared and contrasted to each other and to other group I metals. Finally, the structures of two modified B-DNA dodecamers are determined to explore the effect of monovalent cations on B-DNA structure. The modifications in these structures harbor tethered cations that are covalently linked to the DNA in the major groove. In one structure, the tethered cation causes axial bending of the DNA molecule, while in the second structure the molecule remains linear. We posit that the discrepancy between the two structures is due to lattice packing forces. In addition, we show evidence for the displacement of thallium I cations from the major groove of the bent structure.

The main theme of this thesis is to develop a fluorescent probe for imaging the subcellular distribution of kinetically labile copper pools that might play a critical role in copper homeostasis. Various copper-selective sensors were designed by combining 1,3,5-triaryl-2-pyrazoline fluorophores with polythioethers as receptor moieties. A series of donor-substituted 1,3,5-triaryl-2-pyrazoline fluorophores were synthesized and characterized in terms of their photophysical and electrochemical properties. Interestingly, the aryl substituents attached to the 1- and 3-position of the pyrazoline ring influence the photophysical properties of the fluorophore in distinctly different ways. The excited-state equilibrium energy is primarily influenced by changes of the substituent in the 1-position, whereas the reduction potential of the fluorophore is determined by the 3-aryl group. Results from computational analyses agree well with the experimental data. A pyrazoline fluorophore library was synthesized, and their photophysical and electrochemical properties were studied. The compounds cover a broad range of excited state energies and reduction potentials, and allow for selective and differential tuning of these two parameters. A series of thiazacrownethers and tripodal aniline copper(I) receptors were synthesized and their copper binding stoichiometries, stability constants, and copper-self-exchange kinetics were investigated. The measured self-exchange activation parameters revealed for all studied ligands a negative activation entropy, suggesting a predominant associative exchange mechanism. With detailed knowledge of the fluorophore platform and copper receptors, sensor CTAP-1 was designed, synthesized and characterized. The probe shows a 4.6-fold emission enhancement and reaches a quantum yield of 14% upon saturation with Cu(I). The sensor exhibits excellent selectivity towards Cu(I) and is insensitive towards millimolar concentrations of Mg(II) or Ca(II). Mouse fibroblast cells (3T3) incubated with the sensor produced a copper-dependent perinuclear staining pattern, which colocalizes with the subcellular location of the mitochondria and the Golgi apparatus. The subcellular topography of copper was further determined by synchrotron-based x-ray fluorescence (SXRF) microscopy. Furthermore, microprobe x-ray absorption measurements at various subcellular locations showed a near-edge feature that is characteristic for low-coordinate monovalent copper. The data provide a coherent picture with evidence for a kinetically labile copper pool, which is predominantly localized in the mitochondria and the Golgi apparatus.

To better understand the optical and electronic properties of thiophene- and pyrrole-based organic compounds on a molecular level, several aromatic compounds and their corresponding monocations were analyzed by a variety of solution-based spectroscopic techniques. The derivatives were initially synthesized using palladium-catalyzed amination reactions, condensation reactions, Horner-Emmons reactions, and Stille coupling reactions. Once isolated, the neutral compounds were analyzed by UV-visible-NIR absorption spectroscopy, fluorescence spectroscopy, cyclic voltammetry, and / or differential pulse voltammetry. Monocations were generated by chemical oxidation and were analyzed by visible-NIR absorption spectroscopy and electron paramagnetic resonance spectroscopy. By quantifying the extent of the electron-donor abilities of some chromophores and the electron delocalization of positive charge in the monocations, a more thorough understanding of the optical and electronic properties of the compounds was obtained.

Typescript (Photocopy) / Includes bibliographies / x, 157, A.xxxi : ill ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Summary: Studies the complexation of various monovalent metal ions by the diaza-crown ether C21 and the cryptands, C211 and C22C5 to form cryptates in various solvents, and investigates the kinetics for the interaction of the pendant arm ligand 1,4,8,11-tetrakis (2-hydroxyethyl)-1,4,8,11-tetraazacyclotetradecane (THEC) with the divalent metal ions Cd2+, Hg2+ and Pb2 / Thesis (Ph.D.)--Dept. of Physical and Inorganic Chemistry, University of Adelaide, 1993

In this work, the evolutionary biophysics approach is applied to the two of the largest protein superfamilies present in human genomes, namely P-loop fold nucleoside triphosphatases (P-loop NTPases) and G-protein coupled receptors (GPCRs). This approach combines comparative analysis of protein structures and sequences with molecular modeling techniques in order to reveal not only the conservation of particular residues among proteins within each superfamily but also their role in the fundamental mechanisms underlying common functions. The study of the hydrolysis activation mechanism in P-loop NTPases started with the molecular dynamics simulations of Mg-NTP complexes (Mg-ATP and Mg-GTP) in the presence of K+, NH4+, and Na+ ions. These simulations showed that in the presence of large cations (K+ and NH4+), the conformation of the phosphate chain of ATP and GTP is extended, with large distances between alpha- and gamma-phosphates. This conformation is similar to the shape of ATP and GTP molecules (or their analogs) in the crystal structures of various P-loop NTPases. To clarify the role of monovalent cations in P-loop NTPases, MD simulations were conducted for two cation-dependent GTPases: tRNA modification GTPase MnmE and translation factor EF-Tu. MD simulations of Mg-GTP/EF-Tu complex bound to the tRNA and ribosome fragment in the presence of K+ ions have shown consistent binding of a potassium ion from the solution between alpha- and gamma-phosphates (AG site), similar to the cation binding in MnmE and other cation-dependent P-loop GTPases. In both proteins, binding of K+ ion in the AG site led to the rotation of gamma-phosphate, making this group more eclipsed with alpha-phosphate. The new rotated position of gamma-phosphate was stabilized by a novel H-bond with the backbone nitrogen of the K-3 residue (relative to the ubiquitously conserved Lys) of the P-loop motif. The activation mechanism observed in MD simulations of MnmE and EF-Tu could be envisioned as basic for P-loop NTPases, as these cation-dependent proteins are among the most ancient members of the P-loop superfamily. This mechanism was used as a basis for extensive comparative analysis of representative proteins from all major classes of P-loop NTPases. Based on the established conservation and presence of the key features in active sites of P-loop NTPases, the chain of events where rotation of gamma-phosphate triggers the nucleophilic attack and gamma-phosphate cleavage has been proposed as the basic universal activation mechanism of NTP hydrolysis in P-loop NTPases. The second part of this work explores the activation of GPCRs as sodium-translocating receptors. Crystal structures of the novel Na-pumping microbial rhodopsin along with the recent avalanche of GPCR structures provided the basis for comparative structure analysis, focused on investigating the similarities in the Na-binding sites of the two superfamilies. Structure superposition of GPCRs and microbial rhodopsins (MRs) based on comparison of their Na-binding sites was used to produce structure-guided sequence alignments of the two superfamilies. The only residue universally conserved between the two superfamilies was Trp in the helix 6/F (Trp6.48 in GPCRs). In both families, the signaling mechanism directly involves this residue, which is likely to be an ancient feature inherited from the common ancestor of MRs and GPCRs – the Na-pumping light-activated rhodopsin. The similarity of GPCRs with light-activated sodium pumps endorses the suggestion that GPCRs may also function as Na+ ion translocators. A model of GPCR activation accompanied by translocation of Na+ was constructed to demonstrate how this mechanism can explain the voltage sensitivity of certain Class A GPCRs. Two modes of activation were modeled – one where Na+ ion is transported into the cytoplasm and the one where Na+ ion is expelled to the intracellular space. The two modes quantitatively describe the behavior of voltage-activated and voltage-suppressed GPCRs, respectively. Finally, further structure scrutiny and rotamer analysis provided a plausible pathway of Na+ transmembrane translocation through the helical bundle of GPCRs.

Osmoregulation is an essential process to maintain water and ionic balance and when euryhaline fish move between freshwater and seawater environments as part of their life cycle this presents additional osmoregulatory challenges. Migrating fish can be exposed in both environments to pollutants such as endocrine disrupting chemicals (EDCs) that include natural hormones (e.g. 17β-estradiol; E2), synthetic hormones (e.g. 17α-ethinylestradiol; EE2), and industrial chemicals (e.g. nonylphenol). The focus of this thesis was to study the effects of different categories of EDCs on the osmoregulatory functions of euryhaline fish such as three-spined sticklebacks (Gasterosteus aculeatus) and rainbow trout (Oncorhynchus mykiss). Osmoregulatory variables (such as osmolality, water and ionic content) were compared in plasma and tissues (white muscle and carcass) of rainbow trout. This validated the use of specific tissue parameters as a surrogate of plasma responses to various osmoregulatory challenges. Waterborne exposure to 17α-ethinylestradiol revealed differential sensitivity of vitellogenesis in the three-spined sticklebacks (no induction) and rainbow trout, but had a significant effect on calcium homeostasis in both species. Intraperitoneal implants of 17β-estradiol reduced CaCO3 production and apparent water absorption in the intestine and increased in tissue calcium stores of seawater-acclimated trout, but fish were able to compensate and showed no overall osmoregulatory disturbance. Waterborne exposure to nonylphenol in freshwater trout was also investigated, but no effects on osmoregulation were found up to 2 ng/l. Overall, estrogens can affect osmoregulation differentially in euryhaline fish species, and sometimes at EDC levels lower than the threshold for reproductive effects (i.e. vitellogenin induction).

L’étude de l’adsorption et de la mobilité des ions dans les argiles est importante pour mieux appréhender de nombreux processus géochimiques et environnementaux, de même que pour prédire le comportement des radionucléides dans les conditions du stockage géologique. A cause de leurs tailles très petites (< 2μm), il n’est pas toujours évident d’étudier les argiles à l’aide des méthodes et techniques expérimentales existantes. L’une des alternatives à ce problème consiste alors à utiliser la modélisation moléculaire pour les étudier. En plus de leurs tailles fines, les argiles présentent également des structures complexes, qui peuvent survenir en raison de la multiplicité de possibilités de distributions et d’arrangements des substitutions isomorphiques dans leurs couches. Il a été clairement démontré qu’il existe une corrélation entre la distribution des substitutions dans les couches des argiles et les propriétés de ces dernières. En revanche, ceci reste à démontrer en ce qui concerne l’arrangement de ces substitutions dans les couches de l’argile. Dans ce travail, la modélisation moléculaire est utilisée pour déterminer et comparer les propriétés d’hydratation, ainsi que la structure et la mobilité des ions (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺, Ni²⁺, UO₂²⁺) et de l’eau dans l’espace interfoliaire de trois modèles de montmorillonite, différents entre eux par l’arrangement des substitutions isomorphiques dans les couches de l’argile.L’adsorption et la diffusion des cations cités plus haut et de l’eau sont également étudiées à la surface de la montmorillonite et les résultats sont comparés à ceux obtenus dans l’espace interfoliaire à 298 K et à 363 K. Les résultats obtenus dans ce travail s’accordent bien avec les observations expérimentales, et font ressortir une corrélation plus ou moins importante entre le modèle d’argile utilisé et le type de propriété calculée. Cette corrélation dépend également de la nature du cation présent dans la structure de la montmorillonite et de sa teneur en eau. / The study of adsorption and ion mobility in clay minerals is important for a better understanding of many geochemical and environmental processes, as well as to predict the behavior of radionuclides in geological storage conditions. Because of their very small size (<2μm), it is not always easy to study clays by using the existing experimental methods and techniques. One alternative to this issue is to use computational molecular modeling to carry out clay studies. In addition to their tiny size, clays minerals also have complex structures, which can appear due to various possibilities in the distribution and arrangement of isomorphic substitutions in their layers. It has been clearly demonstrated that there is a strong correlation between the distribution of substitutions in the clay layers and their properties. However, this remains to be shown regarding the arrangement of the substitutions in the layers of the clay. In this work, computational molecular modeling techniques are used to determine and compare the hydration properties, as well as the structure and mobility of ions (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺, Ni²⁺,UO₂²⁺) and water in the interlayer space of the three models of montmorillonite, that differ from each other by the arrangement of isomorphic substitutions in the clay layers.The adsorption and diffusion of the previously listed cations and water are also studied on the surface of montmorillonite clay and the results are compared to those obtained in the interlayer space both at 298 K and at 363 K. The data generated in this work agree well with experimental observations, and show a more or less significant correlation between the clay model used and the type of property calculated.

This dissertation describes our study on different physical properties of passivated and chemically modified hybrid metal halide perovskite materials and development of highly efficient charge transport layers for perovskite solar cells. We first developed an efficient electron transport layer via modification of titanium dioxide nanostructure followed by a unique chemical treatment in order to have clean interface with fast electron injection form the absorber layer in the perovskite solar cells. We then explored monovalent cation doping of lead halide perovskites using sodium, copper and silver with similar ionic radii to lead to enhance structural and optoelectronic properties leading to higher photovoltaic performance of the resulting perovskite solar cells. We also performed thorough experimental characterizations together with modeling to further understand the chemical distribution and local structure of perovskite films upon monovalent cation doping. Then, we demonstrate a novel passivation approach in alloyed perovskite films to inhibit the ion segregation and parasitic non-radiative losses, which are key barriers against the continuous bandgap tunability and potential for high-performance of metal halide perovskites in device applications, by decorating the surfaces and grain boundaries with potassium halides. This leads to luminescence quantum yields approaching unity while maintaining high charge mobilities along with the inhibition of transient photo-induced ion migration processes even in mixed halide perovskites that otherwise show bandgap instabilities. We demonstrate a wide range of bandgaps stabilized against photo-induced ion migration, leading to solar cell power conversion efficiencies of 21.6% for a 1.56 eV absorber and 18.3% for a 1.78 eV absorber ideally suited for tandem solar cells. We then systematically compare the optoelectronic properties and moisture stability of the two developed passivation routes for alloyed perovskites with rubidium and potassium where the latter passivation route showed higher stability and loading capacity leading to achieve substantially higher photoluminescence quantum yield. Finally, we explored the possibility of singlet exciton fission between low bandgap perovskites and tetracene as the triplet sensitizer finding no significant energy transfer between the two. We then used tetracene as an efficient dopant-free hole transport layer providing clean interfaces with perovskite layer leading to high photoluminescence yield (e.g. ~18%). To enhance the poor ohmic contact between tetracene and the metal electrode, we added capping layer of a second hole transport layer which is extrinsically doped leading to 21.5% power conversion efficiency for the subsequent solar cells and stabilised power output over 550 hours continuous illumination.

De nouveaux composés fluorés à chaines magnétiques appartenant aux types weberite et pyrochlore ont été isolés. Les corrélations entre propriétés structurales et magnétiques ont été étudiées. Plusieurs familles a base de palladium(II) ont été caractérisées. Des structures cristallines ont été déterminées (soit sur monocristal, soit sur des échantillons polycristallins par la méthode de Rietveld). Divers types structuraux ont été identifies (types CsPd2F5, LiSbF6 ou dérivant de Na2CuF4): le palladium y est localisé en site octaédrique ou plan carré mais peut posséder simultanément ces deux coordinences. Des structures magnétiques ont été établies par diffraction de neutrons. Dans un certain nombre de ces matériaux des transitions de phases ont été mises en évidence par micro-ATD et analyse radiocristallographique. Leur caractérisation magnétique a été réalisée. Des phases inédites à base de cuivre et d'éléments lanthanidiques apparentées au type KBrF4 ont été synthétisées. La luminescence de l'argent monovalent a été étudiée dans des composés fluorés de la structure elpasolite ou dérivée. Les propriétés ont été analysées en fonction de la coordinence de Ag+.

Les propriétés spectroscopiques du cuivre monovalent ont été étudiées dans deux familles de matériaux oxygénés.<br />Deux types de verres borate et phosphate, de composition nominales LaMgB5O10:Cu+ et LiLaP4O12:Cu+ ont été caractérisés, essentiellement par spectroscopie UV-visible et par EXAFS. Des tests d'émission laser ont été effectués sur un échantillon de verre borate.<br />Trois matériaux-modèle fortement concentrés en cuivre, dans lesquels cet élément adopte une coordinence linéaire par rapport à l'oxygène, ont fait l'objet de tentatives de modélisation visant à corréler structure et propriétés de spectroscopie optique. Il s'agit des delafossites CuLaO2 et CuYO2 ainsi que du phosphate CuTh2(PO4)3. Des calculs de structures de bandes ont été effectués pour les composés CuLaO2 et CuYO2 par les méthodes ASW et HÜCKEL ETENDUE. L'étude spectroscopique de CuTh2(PO4)3 a été étendue à la solution solide Na1-xCuxTh2(PO4)3 (0 < x < 0,25).