<p>This thesis is based on six papers, Papers I-VI, focusing on the interplay between the stabilizing elements of nucleic acids self-assembly; hydrogen bonding, stacking and solvent effects. In Paper I we investigate how the substitution of the O4' for CH₂ in the sugar moiety of adenosine (2'-deoxyaristeromycin) at the A⁶ position of the Dickerson-Drew dodecamer makes the two modified bases exist in a dynamic equilibrium between Hoogsteen and Watson-Crick base pairing in the NMR time scale. Paper II is a structural study of the incorporation of 1-(1',3'-<i>O</i>-anhydro-<i>β</i>-D-psicofuranosyl)thymine in the T⁷ position of the Dickerson-Drew dodecamer. NMR constrained molecular dynamics and hydration studies show the base-base distortions caused by the introduction of a North-type locked sugar in an otherwise B-type DNA•DNA duplex. Paper III shows that the stacking distortion caused by the 1-(1',3'-<i>O</i>-anhydro-<i>β</i>-D-psicofuranosyl)thymine building block perturbs the charge transfer similar to a DNA mismatch. Paper IV highlights how the sequence context affects the physico-chemical properties, monitored by the p<i>K</i><i>a</i> of guanine itself as well as how the charge perturbation is experienced by the neighboring bases, in ssDNA and ssRNA. Paper V focuses on the differences between the structural equilibria of single-stranded ssDNA and ssRNA. Directional differences in single-stranded stacking between ssDNA and ssRNA are identified and provide a basis to explain directional differences in p<i>K</i><i>a</i> modulation and dangling-end stabilization. In Paper VI the thermodynamic gains of dangling ends on DNA and RNA core duplexes are found to correlate with the X-ray geometries of dangling nucleobases relative to the hydrogen bonds of the closing base pairs.</p>

Crystallographic and spectroscopic studies have been performed of structures, coordination and chemical bonding for series of trivalent metal ions solvated by two oxygen-coordinating solvents, water and dimethyl sulfoxide (DMSO). The hydrated scandium(III) and lanthanoid(III) ions, La to Lu, are surrounded by tricapped trigonal prisms of aqua ligands in the isomorphous series of trifluoromethanesulfonates, [M(H2O)n](CF3SO3)3. For the smallest ions, M = Er, Tm, Yb, Lu, Sc, the hydration numbers decrease, n = 8.96(5), 8.8(1), 8.7(1), 8.5(1), 8.0(1), respectively, with decreasing size of the ion. The crystal structures at ambient temperature indicate randomly distributed vacancies of the capping oxygen atoms, and 2H solid-state NMR of the diamagnetic [M(H2O)n](CF3SO3)3, M = Sc, Lu, Y and La compounds revealed increasing mobility of the water ligands in the coordination sphere with increasing temperature, also for the fully nonahydrated LaIII and YIII ions. The stretching force constants of the Ln-O bonds, evaluated from vibrational spectroscopy, increased from 0.81 to 1.16 N cm-1 for the Ln-6O trigonal prism in a smooth correlation with the bond distances from La to Lu. For the capping Ln-3O bonds the increase from 0.49 to 0.65 N cm-1 reflects the increased ligand-ligand repulsion with decreasing ion size. This is also the reason for the water deficiency of the Er, Tm, Yb, Lu and Sc salts, and for [Sc(H2O)8.0](CF3SO3)3 the repulsion induced a phase transition at about 185 K that, by low temperature crystallography, was found to distort the coordination of water molecules toward a monocapped trigonal prism around the scandium(III) ion. All crystal structures of the octakis(dimethyl sulfoxide)lanthanoid(III) iodides comprise discrete [Ln(dmso)8]3+ complexes surrounded by iodide ions. The lanthanum(III) and praseodymium(III) compounds crystallize in the orthorhombic space group Pbca with more efficient packing than for the heavier and smaller ions in the lanthanoid series, which crystallize in the monoclinic space group P21/n. The group 13 metal ions, aluminium(III), gallium(III), indium(III), thallium(III), and also scandium(III) of group 3, form crystalline hexakis(dimethyl sulfoxide) solvates in the space group R 3, with octahedral MO6 coordination entities, which are increasingly compressed along one threefold axis for increasing ionic size. EXAFS measurements on the solvated ions display similar M-O bond distances in dimethyl sulfoxide solution as in the solid solvates. For all the solid dimethyl sulfoxide solvates the strength and nature of the metal-oxygen bond has been evaluated by normal coordinate analysis of vibrational spectra, and correlated with the S-O stretching vibrational mode. Distortions from regular octahedral six coordination are discussed for the hydrated isoelectronic soft mercury(II) and thallium(III) ions in the solid bisaquamercury(II) and trisaquatallium(III) trifluoromethanesulfonates, in terms of pseudo Jahn-Teller effects (PJTE). Mercury(II), generally more strongly influenced by PJTE distortions, displays a 2 + 4 Hg-O coordination forming chains that are held together in sheets by hydrogen bonds and in layers by van der Waals interactions, which explain the fragile structure of the crystals.

This thesis is based on six papers, Papers I-VI, focusing on the interplay between the stabilizing elements of nucleic acids self-assembly; hydrogen bonding, stacking and solvent effects. In Paper I we investigate how the substitution of the O4' for CH2 in the sugar moiety of adenosine (2'-deoxyaristeromycin) at the A6 position of the Dickerson-Drew dodecamer makes the two modified bases exist in a dynamic equilibrium between Hoogsteen and Watson-Crick base pairing in the NMR time scale. Paper II is a structural study of the incorporation of 1-(1',3'-O-anhydro-β-D-psicofuranosyl)thymine in the T7 position of the Dickerson-Drew dodecamer. NMR constrained molecular dynamics and hydration studies show the base-base distortions caused by the introduction of a North-type locked sugar in an otherwise B-type DNA•DNA duplex. Paper III shows that the stacking distortion caused by the 1-(1',3'-O-anhydro-β-D-psicofuranosyl)thymine building block perturbs the charge transfer similar to a DNA mismatch. Paper IV highlights how the sequence context affects the physico-chemical properties, monitored by the pKa of guanine itself as well as how the charge perturbation is experienced by the neighboring bases, in ssDNA and ssRNA. Paper V focuses on the differences between the structural equilibria of single-stranded ssDNA and ssRNA. Directional differences in single-stranded stacking between ssDNA and ssRNA are identified and provide a basis to explain directional differences in pKa modulation and dangling-end stabilization. In Paper VI the thermodynamic gains of dangling ends on DNA and RNA core duplexes are found to correlate with the X-ray geometries of dangling nucleobases relative to the hydrogen bonds of the closing base pairs.

Hydrophobic interactions guide important molecular self-assembly processes such as protein folding. On the macroscale, hydrophobic interactions consist of the aggregation of "oil-like" objects in water by minimizing the interfacial energy. However, the hydration mechanism of small hydrophobic molecules on the nanoscale (~1 nm) differs fundamentally from its macroscopic counterpart. Theoretical studies over the last two decades have pointed to an intricate dependence of molecular hydration mechanisms on the length scale. The microscopic-to-macroscopic cross-over length scale is critically important to hydrophobic interactions in polymers, proteins and other macromolecules. Accurate experimental determination of hydration mechanisms and their interaction strengths are needed to understand protein folding. This thesis reports the development of experimental and analytical techniques that allow for direct measurements of hydrophobic interactions in a single molecule. Using single molecule force spectroscopy, the mechanical unfolding of a single hydrophobic homopolymer was identified and modeled. Two experiments examined how hydrophobicity at the molecular scale differ from the macroscopic scale. The first experiment identifies macroscopic interfacial tension as a critical parameter governing the molecular hydrophobic hydration strength. This experiment shows that the solvent conditions affect the microscopic and macroscopic hydrophobic strengths in similar ways, consistent with theoretical predictions. The second experiment probes the hydrophobic size effect by studying how the size of a non-polar side-chain affects the thermal signatures of hydration. Our experimental results reveal a cross-over length scale of approximately 1 nm that bridges the transition from entropically driven microscopic hydration mechanism to enthalpically driven macroscopic hydration mechanism. These results indicate that hydrophobic interactions at the molecular scale differ from macroscopic scale, pointing to potential ways to improve our understanding and predictions of molecular interactions. The system established in this thesis forms the foundation for further investigation of polymer hydrophobicity.

Gegenstand der Arbeit ist die Untersuchung der kollektiven Diffusion von Wasser und Ionen in wässrigen Elektrolytlösungen. Dabei wird insbesondere die Dynamik der Wassermoleküle innerhalb der Hydratationshüllen der Ionen und der Einfluss poröser Materialien untersucht. Nach einer Einführung zur Dynamik der Hydratationshülle folgen Grundlagen der NMR-Diffusometrie, welche genutzt wurde um die Selbstdiffusionskoefifizienten der Wassermoleküle und der Ionen der Lösungen zu messen. Daraus wurden die dynamischen Hydratationszahlen der Ionen bestimmt, welche die Anzahl an Wassermolekülen angeben, die durch die Diffusion des Ions in ihrer translatorischen Bewegung beeinflusst sind. Der Einfluss poröser Materialien auf die Dynamik wird am Beispiel nanoporöser Glasmonolithe und mikroporöser Li-LSX Kristalle untersucht.

The complex interaction between cement and chemical/mineral admixtures in concrete mixtures sometimes leads to unpredictable concrete performance in the field which is generally defined as concrete incompatibilities. Cement paste rheology measurements instead of traditional workability tests (i.e., slump cone test) can have great potential in detecting those incompatibilities in concrete before the concrete is placed, which can, in turn, avoid related workability problems and setting time as well as heat evolution abnormalities. The objectives of the present study were to examine the applicability of the dynamic shear rheometer (DSR) to measure cement paste rheology, and to identify cement and mineral/chemical admixture incompatibilities, based on the determined rheological parameters. The DSR was modified and optimized for cement paste rheology measurements. Two different modes of operations (i.e., static and dynamic methods) with the modified DSR were investigated to measure representative rheological parameters as well as to identify cement and chemical/mineral admixture incompatibility. The conventional plastic viscosity and yield stress are measured in static mode and storage modulus curve, as a function of time, is measured in dynamic mode. The rate of change of plastic viscosity (RPV) as another static rheological parameter and the modeled magnitude parameter ?, from the dynamic rheological method, showed great potentialities as acceptance criteria to identify incompatible mixtures. The heat of hydration data from isothermal conduction calorimeter tests and setting time results for the studied mixtures have strongly supported the rheology based observations as supporting tools. Based on the main tests results, the acceptance criteria were set up using the rheological parameters in accordance with heat of hydration data. This will ultimately help material suppliers, concrete producers, and other users to detect problematic combinations of concrete ingredients before a given concrete mixture is placed.

The determination and following up the development of properties during the fresh state and early ages of concrete are important in order to schedule the work and to obtain the desired properties in the hardened concrete. As the traditional methods such as Vicat and Penetrometer mostly depend on the experience of the operator and do not provide a continuous picture of the development of properties, reliable and objective non-destructive test methods are needed for the quality control of fresh concrete. The purpose of this thesis is to observe the development of properties of fresh pastes and mortars continuously by longitudinal ultrasonic waves. For this purpose, cement pastes and mortars with three different w/c ratios were prepared with ordinary portland cement. The ultrasonic pulse velocities were determined continuously during hydration. The setting times were also determined by standard test methods. The flexural and compressive strength were determined at 1, 2, 3, 7 and 28 days by standard test method and the volume of permeable pores were also obtained at the same ages. Lastly, the heat of hydration of cement pastes of similar w/c ratios were determined by isothermal calorimetry. UPV (Ultrasonic Pulse Velocity) development was compared with the results of standard tests applied on the samples. The results revealed that the UPV is a useful method in monitoring the hydration process of cementitious materials.

<p>Zr-based materials have found their main application in the nuclear field having high corrosion resistance and low neutron absorption cross-section. The oxide layer that is formed on the surface of these alloys is meant to be the barrier between the metal and the corrosive environment. The deterioration of this protective layer limits the lifetime of these alloys. A better understanding of the transport phenomena, which take place in the oxide layer during oxidation, could be beneficial for the development of more resistant alloys.</p><p>In the present study, oxygen and hydrogen transport through the zirconia layer during oxidation of Zr-based materials at temperatures around 400C have been investigated using the isotope-monitoring techniques Gas Phase Analysis and Secondary Ion Mass Spectrometry. The processes, which take place at oxide/gas and oxide/metal interface, in the bulk oxide and metal, have to be considered in the investigation of the mechanism of hydration and oxidation. Inward transport of oxygen and hydrogen species can be influenced by modification of the surface properties. We found that CO molecules adsorbed on Zr surface can block the surface reaction centers for H₂ dissociation, and as a result, hydrogen uptake in Zr is reduced. On the other hand, coating the Zr surface with Pt, resulted in increased oxygen dissociation rate at the oxide/gas interface. This generated enhanced oxygen transport towards the oxide/metal interface and formation of thicker oxides. Our results show that at temperatures relevant for the nuclear industry, oxygen dissociation efficiency decreases in the order: Pt > Zr₂Fe > Zr₂Ni > ZrCr₂ ≥ Zircaloy-2.</p><p>Porosity development in the oxide scales generates easy diffusion pathways for molecules across the oxide layer during oxidation. A novel method for evaluation of the gas diffusion, gas concentration and effective pore size of oxide scales is presented in this study. Effective pore sizes in the nanometer range were found for pretransition oxides on Zircaloy-2.</p><p>A mechanism for densification of oxide scales by obtaining a better balance between inward oxygen and outward metal transport is suggested. Outward Zr transport can be influenced by the presence of hydrogen in the oxide/metal substrate. Inward oxygen transport can be promoted by oxygen dissociating elements such as Fe-containing second phase particles. The results suggest furthermore that a proper choice of the second-phase particle composition and size distribution can lead to the formation of dense oxides, which are characterized by low oxygen and hydrogen uptake rates during oxidation.</p>

Includes vita. / Title from PDF of title page. / Document formatted into pages; contains 187 pages. / Thesis (Ph.D.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: This dissertation investigates the importance of diffusional and convective fluxes for salts in reverse osmosis (RO) and nanofiltration (NF) membranes. Moreover, the physical and thermodynamic factors controlling the salt permeability are analyzed. The study utilizes direct osmosis (DO) experiments and RO experiments, the later using both flat sheet and spiral wound membrane configurations. The salts considered are chlorides and acetates of alkali metals and alkaline earth metals. The equation governing the salt transport in DO experiments is derived and a phenomenon inverse to concentration polarization in RO is observed. The salt permeability in DO is equal to the salt permeability calculated for the valid cases of the used RO models. DO is suggested as an alternative method in characterizing the salt transport in membranes. The method can be more advantageous than RO due to the lower costs and simplicity of the apparatus. / ABSTRACT: The models used to calculate the salt transport parameters in RO experiments are Spiegler-Kedem model, which considers both diffusion and convection of salt, and Kimura-Sourirajan model, which considers only diffusion of salt. It is found that diffusion is the dominant mechanism of transport in both RO and NF membranes. The percentage of the salt diffusional flux of the total flux is highest for seawater membranes and it is approximately equal for brackish water and nanofiltration membranes. The salt diffusive flux contribute more to the total flux for the 1:2 salts than for 1:1 salts. The two RO models are found equivalent in determining the salt permeability for only the seawater membranes. The Kimura-Sourirajan model overestimates the salt permeability coefficient for salts with rejection coefficient lower than 86%. / ABSTRACT: The permeation rates for studied salts follow the lyotropic series regardless the membrane type (RO or NF), the membrane configuration (flat sheet or spiral wound), the process (DO or RO), or the models used for the calculations. This order of salt permeability is explained by the hydration of the cations, which is quantified by the enthalpy and entropy of hydration. The relative free energy theory can also be used to predict the salt permeability in a membrane based on preliminary data. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Abstract This thesis has shown that the development of the instrumentation necessary to provide in-situ thermal imaging for the determination of homogeneity of concrete is theoretically sound. Drilled shafts are large diameter underground cast-in-place columns that necessarily rely on sound integrity to properly withstand imposed loadings. As a by-product of the most common construction techniques, the entire process is often completely blind whereby the excavation and concreting processes are conducted beneath the surface of the water table (or slurry level). This results in an inability to inspect the final product and in many cases allows anomalous inclusions (soil cave-ins, slurry pockets, etc) to go undetected especially when they are formed outside the steel reinforcing cage. In an effort to gain verification of the as-built, below ground structure, numerous non-destructive test methods have been devised. Each of these methods have merits and drawbacks with regards to the full extent of the tested concrete volume. To further this cause, a new methodology was developed that uses the energy from hydrating concrete to assess the presence or absence of an intact concrete. Therein, the temperature generated by the curing concrete can be measured and correlated to the probable dimensions of the drilled shaft. This thesis outlines the development of the instrumentation capable of making in-situ temperature measurement of drilled shafts to assure the homogeneity of concrete is acceptable. To that end, several configurations of instrumentation approach were tested on varying scales from small lab specimens to full-size field constructed drilled shafts. The bulk of this work was conducted several years before the completion of the thesis and has the benefit of noting later developments. For instance, this study was used to seed future research and led to subsequent FDOT and WSDOT (Washington State DOT) funded research for the express purpose of identifying capabilities of thermal testing in those states. Likewise, present day practice and use of the approach has also been documented.