A near-IR absorbing phthalocyanine containing alkylthio and alyklamino substituents along the periphery was determined to have optical properties that vary depending on surrounding solvent environment. Solvatochromic behavior of this novel chromophore has been characterized through UV-Vis absorbance and fluorescence spectroscopy. Conformational analysis using the B3LYP/6-31G* model indicates the lowest energy conformer with hydrogen bond like interactions between the sulfur lone pair and the hydrogen on the alkylamino substituent. TD-DFT analysis of the solvatochromic phthalocyanine and its parent molecule confirms the derivative exhibits tunable optical properties based on various solvent parameters. Chapter 1 reviews the energy crisis and the potential biological implications of near-IR absorbing phthalocyanines. In addition, a brief introduction of TD-DFT is given to further describe the computational analysis utilized herein. Chapter 2 describes the synthesis, spectroscopic studies, and computational analysis of a near-IR absorbing solvatochromic phthalocyanine derivative. Chapter 3 provides a summary of the work described in this thesis and provides future directions based on the completed research.

Im Wasser-oxidierenden Cluster („oxygen-evolving complex“, OEC) des Photosystem II findet sich die primäre Quelle der Sauerstoffproduktion der Erde. Der OEC katalysiert in grünen Pflanzen unter Absorption von Sonnenlicht die Vierelektronen-Oxidation von Wasser zu Sauerstoff in einer zyklischen Sequenz von Oxidationszuständen (Kok-Zyklus). In dieser Arbeit wurden Strukturen, Spindichteverteilungen sowie EPR-Parameter ein-, zwei- und vierkerniger Mangankomplexe, die in Bezug auf den OEC modelliert wurden, mit Hilfe der Dichtefunktionaltheorie (DFT) berechnet. Hauptziel war das Verständnis der molekularen und elektronischen Struktur des vierkernigen Manganclusters des OEC durch direkten Vergleich mit experimentellen EPR-Daten. / Photosynthesis is the most fundamental process of life on earth. The biological production of oxygen in plant photosynthesis occurs in photosystem II (PSII). Here two water molecules are coupled in a four-electron oxidation to one O2 molecule, catalyzed by a tetranuclear manganese complex, known as the oxygen-evolving complex (OEC). In this thesis, density-functional theory (DFT) methods were validated and subsequently employed to study structures, spin-density distributions and EPR parameters of mono-, di-, and tetranuclear complexes with regard to the OEC. The goal was to draw conclusions on the molecular and electronic structure of the OEC.

<p>Catalysis has a responsibility to provide solutions to the growing grand challenge of sustainability in the fuels and chemical industry to help combat climate change. These changes; however, cannot be realized without a more fundamental understanding of the active sites that catalyze chemical reactions, and how they can be tuned to control rates and selectivities. Four specific examples of active site modification will be considered in this work: the speciation of isolated metals in zeolite frameworks, solvent thermodynamics and structure at defects in zeolite frameworks, the electronic modification of platinum through alloying in well-defined intermetallic nanoparticles, and the mobility and shape of gold nanoparticles in zeolite channels. Each will highlight how quantum chemistry calculations can provide a fundamental understanding of how these active site modifications influence the kinetics of chemical reactions, and how they can be controlled to pursue solutions to the reduction of carbon through sustainable utilization of shale gas as well as renewable chemicals production through biomass upgrading.</p> <p>Zeolites exchanged with metal heteroatoms can behave as solid Lewis or Br<a>ø</a>nsted acids depending on heteroatom identity. Lewis acid heteroatoms can adsorb water and hydrolyze to speciate into “open sites” which have been shown to differ in their ability to catalyze reactions such as glucose isomerization as compared to “closed sites” which are fully coordinated to the zeolite framework. The structure and catalytic properties of these sites are interrogated by a gas phase reaction, ethanol dehydration, in Sn-Beta by a combined Density Functional Theory (DFT) and experimental study. DFT is used to map the possible reaction mechanisms for ethanol dehydration, including the speciation of Sn sites into hydrolyzed configurations from water or ethanol. A microkinetic model for ethanol dehydration including unselective and inhibitory intermediates is constructed. This microkinetic model predicts the population of reactants and products on the catalyst surface as well as the sensitivity of individual elementary steps to the total rates. Powerful anharmonic entropy methods using <i>ab-initio </i>molecular dynamics (AIMD) is used to capture the entropy of confined reactive intermediates, which is shown to be necessary to compare with experiment. Results on closed and hydrolyzed open zeolite sites can then be compared with ethanol dehydration on “defect open” sites which were shown experimentally to occur at material stacking faults. A grain boundary model is constructed of zeolite Beta, where unique sites have similar ligand identity as hydrolyzed open sites. These defect open sites are found to not contribute to the observed reaction rate as they cannot stabilize the same transition state structures that were observed in internal Beta sites. </p> <p>Intuition about the ethanol dehydration reaction in Sn-Beta was then used to map a more expansive and diverse chemical network, the synthesis of butadiene from acetaldehyde and ethanol. For elementary reactions in this mechanism, which included aldol condensation, MPV reduction, and crotyl alcohol dehydration in addition to ethanol dehydration, the hydrolyzed open sites were found to be crucial reactive intermediates. Hydrolyzed sites were necessary to stabilize favorable transition states, which requires reconstruction of the local framework environment. Methods to preferentially stabilize hydrolyzed sites were then explored, using a screening algorithm developed to consider all possible sites in each zeolite framework. It was found that the stability of these hydrolyzed sites could be correlated to the local strain exerted by the surrounding silica matrix. This provides a new descriptor that stabilizes intermediates relevant to the synthesis of butadiene and ethanol dehydration.</p> <p>Next, the structure and thermodynamic stability of water networks around Sn-Beta defects and heteroatom active sites was considered using AIMD. As many biomass reactions occur in the presence of water, the interactions of water with hydrophobic and hydrophilic functionalized defects dictate how the stability of reactive intermediates and transition states is affected by a solvating environment. Locally stable and strongly nucleated clusters of water were observed to form at Sn defects, with less densely packed water structures stable at hydrophilic defects. This is in comparison to defect-free siliceous Beta, where significantly less water uptake is observed. These local clusters are in equilibrium with the less dense liquid-like phase that extends between defects. These results motivate localized cluster models around active sites in Lewis acids, as well as advance the fundamental understanding of hydrophobic/hydrophilic interactions in microporous materials. The local cluster models are then applied to the ethanol dehydration reaction in protonated aluminum Beta zeolites where experimentally observed non-unity coefficient ratios are rationalized by quantifying a different degree of solvation for the ethanol reactant state as opposed to the transition state, validated by a thermodynamic phase diagram.</p> <p>Changes in the electronic energy levels of <i>d</i> electrons upon alloying was studied in conjunction with a new spectroscopic technique being performed at Argonne National Laboratory to develop new descriptors to predict the degree of coking for different alloys. Resonant Inelastic X-ray Scattering (RIXS) simultaneously probes the occupied and unoccupied valence states of platinum in nanoparticles at ambient conditions. The specific excitation process of this spectroscopy is particularly amendable to DFT modeling, which was used to provide richer chemical insight into how changes in observed RIXS signature related to the electronic structure changes of platinum upon alloying. From a suite of multiple 3d alloy promoter catalysts synthesized, a quantitative comparison with DFT modeled spectroscopy was developed. The stability of DFT calculated coke precursors, relevant to dehydrogenation catalysts to convert light alkanes into olefins, was then correlated to DFT modeled RIXS spectra, which is a better descriptor for adsorption of unsaturated chemical intermediates that used previously, as well as being a descriptor accessible to direct experimental usage.</p> <p>Finally, the diffusion of gold nanoparticles in the TS-1 catalyst was studied using AIMD to help understand what structural motifs of gold are present under reaction conditions and how the shape and binding sites of gold is strongly influenced by deformation by the zeolite framework. This is used to help predict new zeolites for use in direct propylene epoxidation using molecular oxygen and hydrogen. The optimization of this catalyst is environmentally relevant to reduce the usage of inorganics and reduce the cost associated with production of hydrogen peroxide. Following these discussions, the role of computation in the prediction of active site structures and kinetics in conjunction with experiment was included. The broader impact of these findings will also be considered, which span beyond these specific reactions and materials.</p>

The aim of this thesis is to use computer simulation methods to consider adsorption of both water and carbon dioxide onto oxide surfaces. The materials chosen have direct relevance to current environmental concerns, alkaline earth metal oxides for carbon sequestration and uranium dioxide for the storage and stability of nuclear materials. Chapter one outlines both previous experimental and computational work relevant to these research areas. The computational methodologies used in this thesis are described in chapters two and three. Chapter two outlines how the forces between atoms in the simulation are modelled using both potential-based and electronic structure models. Chapter three details how these are then used to find lowest energy configurations. The main results of the alkaline earth metal oxides are discussed in chapters four and five. Chapter four uses multiconfigurational static lattice simulations of water and CO2 surface adsorptions to identify the most probable adsorption sites and to generate surface phase diagrams as a function of surface composition. Whereas the focus of chapter five is to model interactions in liquid water with both surface and nanoparticles. Chapters six and seven describe the results of simulations on uranium dioxide. Chapter six uses electronic structure methods to model defects and nonstoichiometry in bulk and thin film structures. Chapter seven then describes the calculations of the interactions of water with uranium dioxide surfaces, in terms of both gas phase adsorption and the mineral – water interface with results showing the favourability of surface hydroxylation on the {100} and {110} surfaces. Finally, a summary of the main findings and achievements of this thesis are given in chapter nine, along with a discussion of possible future work.

The aim of this thesis is to provide insight into the structures and properties of the uranium oxides. As UO2 is easily oxidised during the nuclear fuel cycle it is important to have a detailed understanding of the structures and properties of the oxidation products. Experimental work over the years has revealed many stable oxides including UO2, U4O9, U3O7, U2O5, U3O8 and UO3, all with a number of different polymorphs. The oxides are broadly split into two categories, fluorite-based structures with stoichiometries in the range of UO2 to U2O5 and less dense layered-type structures with stoichiometries in the range of U2O5 to UO3. While UO2 is well characterised, both experimentally and computationally, there is a paucity of data concerning higher stoichiometry oxides in the literature. Experiments and simulations are emerging that deal with individual phases, however a comprehensive study that assesses the properties of all polymorphs and provides comparison over the full range of stoichiometries has been lacking from the literature First the nuclear fuel cycle is introduced, as well as UO2 as a nuclear fuel (Chapter 1), before the quantum mechanical methodology used throughout is explained (Chapter 2). Applying a number of different density functionals (including GGAs, meta-GGAs and hybrids) to UO2 in Chapter 3 it emerges that the PBE + U formalism reproduces the experimentally observed properties to a good degree of accuracy, and so is selected for the rest of the simulations. Following this Chapter 4 examines defect clusters in UO2, finding split interstitials to dominate at low stoichiometry (UO2 – UO2.0625), chains of 2:2:2 Willis clusters at higher stoichiometry (UO2.125 – UO2.25 (U4O9)) and split quad interstitials at higher stoichiometry (UO2.33 (U3O7)). Chapter 5 is an investigation of layered U2O5, where it emerges that the Np2O5 structure is more stable than δ-U2O5 and all uranium ions are in the U5+ oxidation state. Next Chapter 6 considers layered U3O8, which is structurally oxygen rich U2O5, where it is found that U5+ and U6+ ions exist in pentagonal bipyramidal and octahedral coordination respectively. The final set of results in Chapter 7 concern the polymorphs of UO3, where it is found that U6+ adopts a range of coordination environments and the predicted relative stability of each modification matches well with experiment. Finally the conclusions are presented in Chapter 8 along with plans for future work.

N-Nitrosodimethylamine (NDMA), which is a carcinogenic and toxic N-nitrosamine, can be found in water resources associated with a multitude of processes in various industrial facilities or merely as a by-product of water or wastewater treatment. Therefore, the removal of NDMA from drinking water represents an important human safety and public health concern. The present paper presents a density functional theory study of NDMA adsorption in all-silica MFI, Na-ZSM-5 and H-ZSM-5 zeolites. The stability of NDMA inside the zeolite pores was investigated by calculating the amount of energy released during adsorption. Various configurations of adsorbed NDMA to the zeolites were investigated, predominantly at the intersection of straight and sinusoidal channels. The strength of the adsorption energies followed the order H-ZSM5 > Na-ZSM-5 > all-silica MFI. NDMA has a dipole moment and the strongest binding of NDMA occurred through the interactions of the negatively charged O atom of the molecule to positive atoms of the zeolite. Similar calculations were performed for water adsorption in these three zeolites. The adsorption energy of water to these three structures followed the order Na-ZSM5 > H-ZSM-5 > all-silica MFI. We also incorporated van der Waals corrections in the simulations, which had the effect of stabilizing NDMA within the zeolite channels, but did not significantly change the relative stability of the different adsorption geometries. It was concluded that H-ZSM-5 is the best choice to remove NDMA because it is strong enough to adsorb NDMA and it is not too strong in adsorption of water molecules.

Low-dimensional systems are an important and intensely studied area of condensed matter physics. When a material is forced to adopt a low-dimensional structure, its behaviour is often dramatically different to that of the bulk phase. It is vital to predict the structures of low-dimensional systems in order to reliably predict their properties. To this end, the ab initio random structure searching (AIRSS) method, which has previously been used to identify the structures of bulk materials, has been extended to deal with the case of nanowires encapsulated inside carbon nanotubes. Such systems are a rapidly developing area of research with important nanotechnological applications, including information storage, energy storage and chemical sensing. The extended AIRSS method for encapsulated nanowires (ENWs) was implemented and used to identify the structures formed by germanium telluride, silver chloride, and molybdenum diselenide ENWs. In each of these cases, a number of novel nanowire structures were identified, and a phase diagram predicting the ground state nanowire structure as a function of the radius of the encapsulating nanotube was calculated. In the case of germanium telluride, which is a technologically important phase-change material, the potential use of GeTe ENWs as switchable nanoscale memory devices was investigated. The vibrational properties of silver chloride ENWs were also considered, and a novel scheme was developed to predict the Raman spectra of systems which can be decomposed into multiple weakly interacting subsystems. This scheme was used to obtain a close approximation to the Raman spectra of AgCl ENWs at a fraction of the computational cost that would otherwise be necessary. The encapsulation of AgCl was shown to produce substantial shifts in the Raman spectra of nanotubes, providing an important link with experiment. A method was developed to predict the stress-strain response of an ENW based on a polygonal representation of its surface, and was used to investigate the elastic response of molybdenum diselenide ENWs. This was used to predict stress-radius phase diagrams for MoSe_2 ENWs, and hence to investigate stress-induced phase change within such systems. The X-ray diffraction of ENWs was also considered. A program was written to simulate X-ray diffraction in low-dimensional systems, and was used to predict the diffraction patterns of some of the encapsulated GeTe nanowire structures predicted by AIRSS. By modelling the interactions within a bundle of nanotubes, diffraction patterns for bundles of ENWs were obtained.

Les travaux effectués durant cette thèse ont eu pour objectif le développement de chromophores fonctionnels à base de sels de styrylpyrylium et styrylpyridinium. Les divers composés synthétisés ont montré une très grande flexibilité concernant leurs propriétés optiques, avec notamment des longueurs d’onde d’absorption et d’émission couvrant la quasi-totalité du spectre visible. Associée à la variabilité structurelle inhérente à ce type de chromophore, il est possible d’obtenir des composés aux propriétés modulables, et intégrables dans une large gamme d’applications.Ce manuscrit est constitué de trois parties principales. La première décrit la synthèse et les propriétés photophysiques de divers chromophores obtenus durant cette thèse. La seconde décrit l’approche théorique, utilisée pour faciliter la conception et l’analyse des composés étudiés. Finalement, la troisième partie décrit les applications pour lesquelles certaines variations de sels de styrylpyrylium et styrylpyridinium ont étés spécialement développés. / The work done during this thesis aimed to develop functional chromophores based on styrylpyrylium and styrylpyrylium salts. The compounds synthesized have shown a great flexibility regarding their optical properties, including maximum wavelength of absorption and emission covering almost the entire visible spectrum. Combined to their structural adaptability, it was possible to design various compounds compatible with a wide range of applications.This manuscript is composed of three main parts. The first part describes the synthesis and the photophysical properties of some chromophores obtained during this thesis. The second describes the theoretical approach, used to assist the design and the analysis of the studied compounds. Finally, the third part describes various applications for which some styrylpyrylium and styrylpyridinium salts have been specially designed.

Lithium ion batteries are ubiquitous in modern life, from powering hand-held electronic devices to electric vehicles. And with the necessary drive toward renewable energy sources like solar and wind, electricity storage for the grid promises to drive up the demand for higher performing, less expensive, safer, and more environmentally friendly secondary batteries. Recent research has theorized that replacing halogens in batteries’ electrolytes with non-halogens can yield desirable performance characteristics while eliminating the most dangerous and problematic chemicals. This thesis explores the possibility that a similar approach can be taken with the cathodes of lithium ion batteries. The active material in a cathode is a salt composed of an alkali cation – the positive lithium ion, and a negative ion – usually a metal oxide. Replacing the negative ion with a superhalogen, which is more electronegative than the most electronegative element, may yield comparable electronic properties to current cathode materials while also opening up opportunities to research materials previously not considered for lithium ion battery cathodes.

L'élaboration d'auto-assemblages constitués par des molécules conjuguées, sur des surfaces semi-conductrices et stables à température ambiante, est l'un des défis majeurs qui doit être résolu pour permettre l'avènement de l'électronique moléculaire. Au cours de ma thèse, j'ai développé de nouveaux concepts permettant d'aboutir à ce type d'assemblage en évitant une trop forte interaction molécule/silicium. Pour cela, j'ai adopté trois stratégies distinctes en fonction de la dimensionnalité des édifices supramoléculaires recherchés : 1) minimiser l'interaction molécule/silicium en utilisant une surface de silicium très dopée en atomes de bore, 2) utiliser l'effet « template » d'une reconstruction 1D semi-métallique de l'interface SmSi pour créer et auto-aligner des molécules, 3) et protéger le squelette conjugué des molécules organiques et guider un assemblage bidimensionnel en utilisant des molécules zwitterioniques. Les images STM à très haute résolution sous ultravide et à température ambiante ont été obtenues. Tous les résultats expérimentaux sont confortés par des calculs de type « théorie de la fonctionnelle densité ».