Dissertations / Theses on the topic 'Crystal field energy'

A molecule can crystallise in more than one crystal structure, a common phenomenon in organic compounds known as polymorphism. Different polymorphic forms may have significantly different physical properties, and a reliable prediction would be beneficial to the pharmaceutical industry. However, crystal structure prediction (CSP) based on the knowledge of the chemical structure had long been considered impossible. Previous failures of some CSP attempts led to speculation that the thermodynamic calculations in CSP methodologies failed to predict the kinetically favoured structures. Similarly, regarding the stabilities of co-crystals relative to their pure components, the results from lattice energy calculations and full CSP studies were inconclusive. In this thesis, these problems are addressed using the state-of-the-art CSP methodology implemented in the GRACE software. Firstly, it is shown that the low-energy predicted structures of four organic molecules, which have previously been considered difficult for CSP, correspond to their experimental structures. The possible outcomes of crystallisation can be reliably predicted by sufficiently accurate thermodynamic calculations. Then, the polymorphism of 5- chloroaspirin is investigated theoretically. The order of polymorph stability is predicted correctly and the isostructural relationships between a number of predicted structures and the experimental structures of other aspirin derivatives are established. Regarding the stabilities of co-crystals, 99 out of 102 co-crystals and salts of nicotinamide, isonicotinamide and picolinamide reported in the Cambridge Structural Database (CSD) are found to be more stable than their corresponding co-formers. Finally, full CSP studies of two co-crystal systems are conducted to explain why the co-crystals are not easily obtained experimentally.

Studies of the radiative properties of thin films and near-field radiation transfer in layered structures are important for applications in energy, near-field imaging, coherent thermal emission, and aerospace thermal management. A comprehensive study is performed on the optical constants of dielectric tantalum pentoxide (Ta₂O₅) and hafnium oxide (HfO₂) thin films from visible to the far infrared using spectroscopic methods. These materials have broad applications in metallo-dielectric multilayers, anti-reflection coatings, and coherent emitters based on photonic crystal structures, especially at high temperatures since both materials have melting points above 2000 K. The dielectric functions of HfO₂ and Ta₂O₅ obtained from this work may facilitate future design of devices with these materials. A parametric study of near-field TPV performance using a backside reflecting mirror is also performed. Currently proposed near-field TPV devices have been shown to have increased power throughput compared to their far-field counterparts, but whose conversion efficiencies are lower than desired. This is due to their low quantum efficiency caused by recombination of minority carriers and the waste of sub-bandgap radiation. The efficiency may be improved by adding a gold mirror as well as by reducing the surface recombination velocity, as demonstrated in this thesis. The analysis of the near-field TPV and proposed methods may facilitate the development or high-efficiency energy harvesting devices. Many near-field devices may eventually utilize metallo-dielectric structures which exhibit unique properties such as negative refraction due to their hyperbolic isofrequency contour. These metamaterials are also called indefinite materials because of their ability to support propagating waves with large lateral wavevectors, which can result in enhanced near-field radiative heat transfer. The energy streamlines in such structures are studied for the first time. Energy streamlines illustrate the flow of energy through a structure when the fields are evanescent and energy propagation is not ray like. The energy streamlines through two semi-infinite uniaxially anisotropic effective medium structures, separated by a small vacuum gap, are modeled using the Green’s function. The lateral shift and penetration depth are calculated from the streamlines and shown to be relatively large compared to the vacuum gap dimension. The study of energy streamlines in hyperbolic metamaterials helps understand the near-field energy propagation on a fundamental level.

This work concerns the interrelationship between thermodynamic, kinetic and structural aspects of crystal polymorphism. It is both experimental and theoretical, and limited with respect to compounds to substituted monocyclic aromatics. Two polymorphs of the compound m-aminobenzoic acid have been experimentally isolated and characterized by ATR-FTIR spectroscopy, X-ray powder diffraction and optical microscopy. In addition, two polymorphs of the compound m-hydroxybenzoic acid have been isolated and characterized by ATR-FTIR spectroscopy, high-temperature XRPD, confocal Raman, hot-stage and scanning electron microscopy. For all polymorphs, melting properties and specific heat capacity have been determined calorimetrically, and the solubility in several pure solvents measured at different temperatures with a gravimetric method. The solid-state activity (ideal solubility), and the free energy, enthalpy and entropy of fusion have been determined as functions of temperature for all solid phases through a thermodynamic analysis of multiple experimental data. It is shown that m-aminobenzoic acid is an enantiotropic system, with a stability transition point determined to be located at approximately 156°C, and that the difference in free energy at room temperature between the polymorphs is considerable. It is further shown that m-hydroxybenzoic acid is a monotropic system, with minor differences in free energy, enthalpy and entropy. 1393 primary nucleation experiments have been carried out for both compounds in different series of repeatability experiments, differing with respect to solvent, cooling rate, saturation temperature and solution preparation and pre-treatment. It is found that in the vast majority of experiments, either the stable or the metastable polymorph is obtained in the pure form, and only for a few evaluated experimental conditions does one polymorph crystallize in all experiments. The fact that the polymorphic outcome of a crystallization is the result of the interplay between relative thermodynamic stability and nucleation kinetics, and that it is vital to perform multiple experiments under identical conditions when studying nucleation of polymorphic compounds, is strongly emphasized by the results of this work. The main experimental variable which in this work has been found to affect which polymorph will preferentially crystallize is the solvent. For m-aminobenzoic acid, it is shown how a significantly metastable polymorph can be obtained by choosing a solvent in which nucleation of the stable form is sufficiently obstructed. For m-hydroxybenzoic acid, nucleation of the stable polymorph is promoted in solvents where the solubility is high. It is shown how this partly can be rationalized by analysing solubility data with respect to temperature dependence. By crystallizing solutions differing only with respect to pre-treatment and which polymorph was dissolved, it is found that the immediate thermal and structural history of a solution can have a significant effect on nucleation, affecting the predisposition for overall nucleation as well as which polymorph will preferentially crystallize. A set of polymorphic crystal structures has been compiled from the Cambridge Structural Database. It is found that statistically, about 50% crystallize in the crystallographic space group P21/c. Furthermore, it is found that crystal structures of polymorphs tend to differ significantly with respect to either hydrogen bond network or molecular conformation. Molecular mechanics based Monte Carlo simulated annealing has been used to sample different potential crystal structures corresponding to minima in potential energy with respect to structural degrees of freedom, restricted to one space group, for each of the polymorphic compounds. It is found that all simulations result in very large numbers of predicted structures. About 15% of the predicted structures have excess relative lattice energies of <=10% compared to the most stable predicted structure; a limit verified to reflect maximum lattice energy differences between experimentally observed polymorphs of similar compounds. The number of predicted structures is found to correlate to molecular weight and to the number of rotatable covalent bonds. A close study of two compounds has shown that predicted structures tend to belong to different groups defined by unique hydrogen bond networks, located in well-defined regions in energy/packing space according to the close-packing principle. It is hypothesized that kinetic effects in combination with this structural segregation might affect the number of potential structures that can be realized experimentally. The experimentally determined crystal structures of several compounds have been geometry-optimized (relaxed) to the nearest potential energy minimum using ten different combinations of common potential energy functions (force fields) and techniques for assigning nucleus-centred point charges used in the electrostatic description of the energy. Changes in structural coordinates upon relaxation have been quantified, crystal lattice energies calculated and compared with experimentally determined enthalpies of sublimation, and the energy difference before and after relaxation computed and analysed. It is found that certain combinations of force fields and charge assignment techniques work reasonably well for modelling crystal structures of small aromatics, provided that proper attention is paid to electrostatic description and to how the force field was parameterized. A comparison of energy differences for randomly packed as well as experimentally determined crystal structures before and after relaxation suggests that the potential energy function for the solid state of a small organic molecule is highly undulating with many deep, narrow and steep minima.
QC 20110527

RésuméLes monocouches auto-assemblées d'ADN immobilisées sur électrodes d'or sont à la base de nombreux biocapteurs électrochimiques. Le contrôle du comportement interfacial de l'ADN par le biais d'un champ électrique est intéressant pour la détection de polymorphisme nucléotidique simple (PNS). La caractérisation in situ de monocouches d'ADN à l'échelle moléculaire est importante pour la fabrication de biocapteurs robustes, fiables et sensibles.La thèse porte sur la détection du PNS dans l'ADN par le biais d'hybridation/dénaturation induite par le champ électrique. La microscopie de fluorescence sous conditions électrochimiques est utilisée comme méthodologie de détection et outil de caractérisation de l'interface d'ADN. À cette fin, des séquences d'ADN marquées par des sondes fluorescentes sont immobilisées sur des électrodes d'or sous forme de monocouches auto-assemblées (SAM) thiolées.Premièrement, les SAMs sont composées de séquences cibles présentant ou non une mutation ponctuelle. La relation entre le potentiel appliqué et la dénaturation du double brin est étudiée. La dénaturation électrochimique est observée à -0,25 V vs Ag
Deoxyribonucleic acid (DNA) self-assembled monolayers (SAMs) immobilized on gold electrodes are the basis of many electrochemical biosensors. Control of the interfacial behavior of DNA by means of an electric field is of interest for sensing applications such as the detection of single nucleotide polymorphisms (SNPs). Moreover, the in situ characterization of immobilized DNA monolayers at a molecular level is important for the fabrication of robust, reliable and sensitive sensors.The thesis aims at studying the discrimination between DNA strands containing SNPs on the basis of electric-field assisted hybridization/denaturation of DNA. In situ electrochemical fluorescence microscopy is used as a detection methodology and characterization tool for DNA interfaces. For this purpose, fluorescently labeled DNA sequences are immobilized at gold electrodes as thiol SAMs.First, the SAMs under investigation were composed of perfect match or SNP-containing target sequences. The relationship between the applied potential and the denaturation of DNA duplexes was investigated. Electrochemical melting was observed at -0.25 V vs. Ag
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

Les proprietes des composes rnisb sont etudiees sous plusieurs aspects : magnetisme, transport, structure electronique. Les composes hexagonaux avec une terre rare legere sont metalliques, les phases cubiques du type semi-heusler avec les terres rares lourdes sont des semiconducteurs a faible gap. Des phenomenes de magnetoresistance geante sont observes a basse temperature, d'autant plus importants que la densite de porteurs est plus faible. Ils sont expliques par la polarisation par le moment de la couche 4f des niveaux d'impuretes situes dans le gap du semiconducteur. Le champ cristallin, ainsi que l'ordre magnetique a basse temperature, ont ete etudies par diffusion (diffraction) de neutrons. Certaines proprietes magnetiques (absence d'ordre magnetique avec le pr, structures af dans le second groupe, orientation des moments) ont pu etre expliquees au moins qualitativement. Cenisb est un compose de type kondo avec une temperature de kondo de l'ordre de 8k. Des mesures de photoemission ont permis de preciser la structure des bandes de valence de ces composes, en accord avec des calculs de structure electronique. Par photoemission resonante dans tbnisb et gdcu, differents canaux de resonance ont ete resolus en fonction de l'energie, qui dependent de la structure des multiples et de la configuration des niveaux excites.

Thesis (Ph.D.); Submitted to Iowa State Univ., Ames, IA (US); 12 Dec 2003.
Published through the Information Bridge: DOE Scientific and Technical Information. "IS-T 2048" Stavroula Foteinopoulou. 12/12/2003. Report is also available in paper and microfiche from NTIS.

In this thesis, we study mathematical models that describe the morphology of a generalized biological cell in equilibrium or under the influence of external forces. Within these models, the cell is considered as a thermodynamic system, where streaming effects in the cell bulk and the surrounding are coupled with a Helfrich-type model for the cell membrane. The governing evolution equations for the cell given in a continuum formulation are derived using an energy variation approach. Such two-phase flow problems that combine streaming effects with a free boundary problem that accounts for bending and surface tension can be described effectively by a diffuse interface approach. An advantage of the diffuse interface approach is that models for e.g. different biophysical processes can easily be combined. That makes this method suitable to describe complex phenomena such as cell motility and multi-cell dynamics. Within the first model for cell motility, we combine a biological network for GTPases with the hydrodynamic Helfrich-type model. This model allows to account for cell motility driven by membrane protrusion as a result of actin polymerization. Within the second model, we moreover extend the Helfrich-type model by an active gel theory to account for the actin filaments in the cell bulk. Caused by contractile stress within the actin-myosin solution, a spontaneous symmetry breaking event occurs that lead to cell motility. In this thesis, we further study the dynamics of multiple cells which is of wide interest since it reveals rich non-linear behavior. To apply the diffuse interface framework, we introduce several phase field variables to account for several cells that are coupled by a local interaction potential. In a first application, we study white blood cell margination, a biological phenomenon that results from the complex relation between collisions, different mechanical properties and lift forces of red blood cells and white blood cells within the vascular system. Here, it is shown that inertial effects, which can become of relevance in various parts of the cardiovascular system, lead to a decreasing tendency for margination with increasing Reynolds number. Finally, we combine the active polar gel theory and the multi-cell approach that is capable of studying collective migration of cells. This hydrodynamic approach predicts that collective migration emerges spontaneously forming coherently-moving clusters as a result of the mutual alignment of the velocity vectors during inelastic collisions. We further observe that hydrodynamics heavily influence those systems. However, a complete suppression of the onset of collective migration cannot be confirmed. Moreover, we give a brief insight how such highly coupled systems can be treated numerically using finite elements and how the numerical costs can be limited using operator splitting approaches and problem parallelization with OPENMP
Diese Dissertation beschäftigt sich mit mathematischen Modellen zur Beschreibung von Gleichgewichts- und dynamischen Zuständen von verallgemeinerten biologischen Zellen. Die Zellen werden dabei als thermodynamisches System aufgefasst, bei dem Strömungseffekte innerhalb und außerhalb der Zelle zusammen mit einem Helfrich-Modell für Zellmembranen kombiniert werden. Schließlich werden durch einen Energie-Variations-Ansatz die Evolutionsgleichungen für die Zelle hergeleitet. Es ergeben sie dabei Mehrphasen-Systeme, die Strömungseffekte mit einem freien Randwertproblem, das zusätzlich physikalischen Einflüssen wie Biegung und Oberflächenspannung unterliegt, vereinen. Um solche Probleme effizient zu lösen, wird in dieser Arbeit die Diffuse-Interface-Methode verwendet. Ein Vorteil dieser Methode ist, dass es sehr einfach möglich ist, Modelle, die verschiedenste Prozesse beschreiben, miteinander zu vereinen. Dies erlaubt es, komplexe biologische Phänomene, wie zum Beispiel Zellmotilität oder auch die kollektive Bewegung von Zellen, zu beschreiben. In den Modellen für Zellmotilität wird ein biologisches Netzwerk-Modell für GTPasen oder auch ein Active-Polar-Gel-Modell, das die Aktinfilamente im Inneren der Zellen als Flüssigkristall auffasst, mit dem Multi-Phasen-Modell kombiniert. Beide Modelle erlauben es, komplexe Vorgänge bei der selbst hervorgerufenen Bewegung von Zellen, wie das Vorantreiben der Zellmembran durch Aktinpolymerisierung oder auch die Kontraktionsbewegung des Zellkörpers durch kontraktile Spannungen innerhalb des Zytoskelets der Zelle, zu verstehen. Weiterhin ist die kollektive Bewegung von vielen Zellen von großem Interesse, da sich hier viele nichtlineare Phänomene zeigen. Um das Diffuse-Interface-Modell für eine Zelle auf die Beschreibung mehrerer Zellen zu übertragen, werden mehrere Phasenfelder eingeführt, die die Zellen jeweils kennzeichnen. Schließlich werden die Zellen durch ein lokales Abstoßungspotential gekoppelt. Das Modell wird angewendet, um White blood cell margination, das die Annäherung von Leukozyten an die Blutgefäßwand bezeichnet, zu verstehen. Dieser Prozess wird dabei bestimmt durch den komplexen Zusammenhang zwischen Kollisionen, den jeweiligen mechanischen Eigenschaften der Zellen, sowie deren Auftriebskraft innerhalb der Adern. Die Simulationen zeigen, dass diese Annäherung sich in bestimmten Gebieten des kardiovaskulären Systems stark vermindert, in denen die Blutströmung das Stokes-Regime verlässt. Schließlich wird das Active-Polar-Gel-Modell mit dem Modell für die kollektive Bewegung vom Zellen kombiniert. Dies macht es möglich, die kollektive Bewegung der Zellen und den Einfluss von Hydrodynamik auf diese Bewegung zu untersuchen. Es zeigt sich dabei, dass der Zustand der kollektiven gerichteten Bewegung sich spontan aus der Neuausrichtung der jeweiligen Zellen durch inelastische Kollisionen ergibt. Obwohl die Hydrodynamik einen großen Einfluss auf solche Systeme hat, deuten die Simulationen nicht daraufhin, dass Hydrodynamik die kollektive Bewegung vollständig unterdrückt. Weiterhin wird in dieser Arbeit gezeigt, wie die stark gekoppelten Systeme numerisch gelöst werden können mit Hilfe der Finiten-Elemente-Methode und wie die Effizienz der Methode gesteigert werden kann durch die Anwendung von Operator-Splitting-Techniken und Problemparallelisierung mittels OPENMP

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
A new approach to describe the crystal field interaction in compounds that contains trivalent lanthanide ions is presented. It is considered the electrostatic balance of the optically active site, the effective charge of the central ion and the sign of crystal field parameters (CCP) as determinant factors in the crystal field interaction. The method of the first equivalent neighbours (MENN) was reformulated, and improvements in predicting the CCP and energy levels 7FJ of Eu3+ could be realized. Moreover, it was possible to predict the lanthanide-nearest neighbour interaction of load factors (Ln-NN), the maximum coverage of the wave functions of the interacting ions and energy levels levels structure of the 7FJ of Eu3+. The physically acceptable limits are designed to load factors and the maximum overlap of the wave functions of the interacting ions. The compounds studied have high symmetry and exhibit a first neighbourhood consisting of oxygen ions, fluorine or chlorine. The use of secular determinants solutions of the energy matrices served as an excellent theoretical framework for the development of the method, which is applied based on the simple overlap model (SOM). This allowed the description of the interaction of the crystalline field by a nonparametric method and simple application. In addition, it was predicted the wave functions overlap factor of the interacting ions, the total effective bonding charge of Eu3+, and the relationships and trends of the crystal field interaction with the chemical species of the NN and the type of Ln that makes up the main host matrix. Finally, it was possible to remodulate the MENN at a more theoretical method by using theoretical data. The results served to confirm the efficiency and accuracy of MENN in describing the interaction of the crystal field on systems containing trivalent lanthanide ions.
Uma nova abordagem na descrição da interação do campo cristalino em compostos contendo íons lantanídeos trivalentes é apresentada. São considerados o equilíbrio eletrostático do sítio opticamente ativo, a carga efetiva do íon central e o sinal dos parâmetros de campo cristalino (PCC) como fatores determinantes na descrição da interação de campo cristalino. O método dos primeiros vizinhos equivalentes (MENN) foi reformulado, e assim melhorias na previsão dos PCC e dos níveis de energia 7FJ do Eu3+ puderam ser realizadas. Além disso, foi possível prever fatores de carga de interação lantanídeo-primeiro vizinho (Ln-PV), o recobrimento máximo das funções de onda dos íons interagentes e estrutura dos níveis níveis de energia 7FJ do Eu3+. Foram estabelecidos limites fisicamente aceitáveis para os fatores de carga e para o recobrimento máximo das funções de onda dos íons interagentes. Os compostos estudados possuem alta simetria e apresentam uma primeira vizinhança composta por íons de oxigênio, flúor ou cloro. A utilização das soluções dos determinantes seculares das matrizes energéticas serviram como um excelente aporte teórico para o desenvolvimento do método, o qual é aplicado tendo por base o modelo de recobrimento simples (SOM). Isto permitiu a descrição da interação do campo cristalino por um método não paramétrico e de simples aplicação. Além disso, foi realizada a previsão do fator de recobrimento das funções de onda dos íons interagentes, carga efetiva total de ligação do Eu3+, e as relações e tendências da interação do campo cristalino com a espécie química dos PV, e o tipo de Ln que compõe a matriz hospedeira principal. Por fim, foi possível tornar o MENN um método mais teórico através da utilização de dados teóricos. Os resultados obtidos serviram para confirmar a eficiência e precisão do MENN na descrição da interação do campo cristalino em sistemas contendo íons lantanídeos trivalentes.

碩士
國立清華大學
物理學系
105
The anisotropy of solid-liquid interfacial energy dominates the morphology of micro-structures in the solidification process, and material properties deeply depend on the morphology of microstructures. Therefore, the anisotropy of solid-liquid interfacial energy is an important physical parameter that controls properties of materials. On the other hand, because the phase field crystal model can describe the density wave of structure and dynamics at the atomic scale, it reasonably can describe the solid-liquid interfacial energy, elastic properties, etc. Thus, we use the phase field crystal (PFC) model to study the anisotropy of solid-liquid interfacial energy. We derive the amplitude equations and corresponding free energy functional from the PFC model under different assumptions. There are two factors that distinguish various amplitude equations, namely, the rotational invariance and the mean density difference between solid and liquid phases. We study how these two factors affect the anisotropy of solid-liquid interfacial energy. We show that the anisotropy of solid-liquid interfacial energy is weaker while the rotational invariance is present and it is stronger while the mean density difference between solid and liquid is considered. In addition, we analyse the amplitude profiles across the interface and we find that the physical origin of the anisotropy of solid-liquid interfacial energy is due to different amplitude profiles at the different orientation. Furthermore, we find that the rotational invariance gives rise to variation of the atomic spacing which genuinely captures fundamental properties across the solid-liquid interface. Finally, we show that the coupling between the amplitude profiles and the mean density is not negligible, and the mean density difference results in sharp amplitude profiles across the interface, hence a larger anisotropy of solid-liquid interfacial energy.

The properties of RNiSb compounds were studied from various points of view: Magnetism, transport, electronic structure. The compounds with a light rare earth are metallic, while the cubic phases with a heavy rare earth element have the semi-Heusler structure and are narrow gap semiconductors. A giant magnetoresistance effect was found at low temperatures, the larger as the density of charge carriers is weak. It was explained by the polarisation of the impurity levels situated within the band gap of the semiconductor under the field of the magnetic moment of the 4f shell. The crystal field, as well as the magnetic order at low temperatures, were studied by neutron scattering and diffraction. Particular magnetic properties (absence of magnetic order in the Pr compound, antiferromagnetic structure in the second group, orientation of the moments) have been explained, at least qualitatively. CeNiSb is a Kondo-type compound with a Kondo temperature of about 8 K. Photoemission measurements have allowed to analyse the electronic structure in the valence band of these compounds, in agreement with band structure calculations. By resonant photoemission of TbNiSb and GdCu, different resonance channels have been resolved, which depend on the spin configuration of the excited states.