This thesis discusses the chemistry and physics of Cu and H2O on ZnO surfaces, based primarily on results from quantum chemical calculations. The underlying context is heterogeneous catalysis, where Cu/ZnO-mixtures are used in the industrial synthesis of methanol and in the water gas shift reaction. Electron transfer between small Cu clusters and ZnO is central to this thesis, as are the design and use of models that can describe realistic and very large-scale ZnO surface structures while still retaining the electronic nature of the system. Method and model enhancements as well as tests and validations constitute a large part of this thesis. The thesis demonstrates that the charges of small Cu clusters, adsorbed on the non-polar ZnO(10-10) surface, depend on whether the Cu clusters contain an even or odd number of atoms, and whether water is present (water can induce electron transfer from Cu to ZnO). On the polar Zn-terminated ZnO(0001) surface, Cu becomes negatively charged, which causes it to attract positively charged subsurface defects and to wet the ZnO(0001) surface at elevated temperatures. When a Cu cluster on a ZnO surface becomes positively charged, this happens because it donates an electron to the ZnO conduction band. Hence, it is necessary to use a method which describes the ZnO band gap correctly, and we show that a hybrid density functional, which includes a fraction of Hartree-Fock exchange, fulfills this requirement. When the ZnO conduction band becomes populated by electrons from Cu, band-filling occurs, which affects the adsorption energy. The band-filling correction is presented as a means to extrapolate the calculated adsorption energy under periodic boundary conditions to the zero coverage (isolated adsorbate, infinite supercell) limit. A part of this thesis concerns the parameterization of the computationally very efficient SCC-DFTB method (density functional based tight binding with self-consistent charges), in a multi-scale modeling approach. Our findings suggest that the SCC-DFTB method satisfactorily describes the interaction between ZnO surfaces and water, as well as the stabilities of different surface reconstructions (such as triangularly and hexagonally shaped pits) at the polar ZnO(0001) and ZnO(000-1) surfaces.

This thesis presents a number of largely independent forays into developing an understanding of the unique chemistry of transition metal clusters. The first chapter of this thesis represents an initial foray into mapping the chemical reactivity of transition metal clusters - a monumental task that will doubtless continue for some time. The small slice undertaken in this work investigates the reactivity with CO of a series of the smallest possible metal clusters; 4d (Nb - Ag) homonuclear metal trimers. In Chapter 2, two known transition metal clusters were studied using CASSCF (MCSCF) and MRCI methods, only to find that DFT methods provided more accurate Ionisation Potentials (IPs). Thus Chapter 3 was devoted to optimising a density functional to predict IPs. As clusters get larger, the number of possible structures grows rapidly too large for human intuition to handle, thus Chapter 4 is devoted to the use of an automated stochastic algorithm, “Kick”, for structure elucidation. Chapter 5 improves on this algorithm, by permitting chemically sensible molecular fragments to be defined and used. Chapter 6 then comes full circle and uses the new Kick algorithm to investigate the reaction of CO with a series of mono-substituted niobium tetramers (i.e. Nb₃X). / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1350246 / Thesis (Ph.D.) - University of Adelaide, School of Chemistry and Physics, 2009

This thesis presents a number of largely independent forays into developing an understanding of the unique chemistry of transition metal clusters. The first chapter of this thesis represents an initial foray into mapping the chemical reactivity of transition metal clusters - a monumental task that will doubtless continue for some time. The small slice undertaken in this work investigates the reactivity with CO of a series of the smallest possible metal clusters; 4d (Nb - Ag) homonuclear metal trimers. In Chapter 2, two known transition metal clusters were studied using CASSCF (MCSCF) and MRCI methods, only to find that DFT methods provided more accurate Ionisation Potentials (IPs). Thus Chapter 3 was devoted to optimising a density functional to predict IPs. As clusters get larger, the number of possible structures grows rapidly too large for human intuition to handle, thus Chapter 4 is devoted to the use of an automated stochastic algorithm, “Kick”, for structure elucidation. Chapter 5 improves on this algorithm, by permitting chemically sensible molecular fragments to be defined and used. Chapter 6 then comes full circle and uses the new Kick algorithm to investigate the reaction of CO with a series of mono-substituted niobium tetramers (i.e. Nb₃X). / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1350246 / Thesis (Ph.D.) - University of Adelaide, School of Chemistry and Physics, 2009

We conducted a computational adsorption study of methylamine on various surface-models of gold nanoparticle which is facetted by multiple {111} and {100} planes. In addition to these flat surfaces, our models include the stepped surfaces (ridges) formed along the intersections of these planes. Binding on the flat surface was fairly weak, but substantially stronger on the ridges by an average of 4.4 kcal/mol. This finding supports the idea that ssDNA’s interaction with gold nanoparticles occurs through the amines on the purine/pyrrimidine rings. Also, this typically undesirable interaction between DNA and gold nanoparticles is expected to increase as the particle size decreases. Our analysis suggests that particle size is an important controlling parameter to reduce this interaction. / Singapore-MIT Alliance (SMA)

A long standing global scientific challenge has been the activation of O2 at a single metal center, and use of the subsequent metal-based oxidant for a variety of difficult chemical transformations. Towards this end, computational and synthetic methods have been utilized in an approach to develop model compounds capable of this type of chemistry, and to better understand the electronic and mechanistic properties of the observed catalytic reactivity. We have developed a first generation catalyst that has been shown to be fully functional in utilizing α-keto acids for the catalytic activation of O2 and oxidation of organic substrates in a highly conserved manner. This reactivity takes place at room temperature and standard pressure, and resembles the type of chemistry performed by mononuclear non-heme enzymes, which inspired the design of the catalyst. However, these solution-phase reactions do not benefit from the controlled environment provided by a protein active site, and solution studies and DFT simulations demonstrate an isomeric family of reactive species that ultimately deactivate via a dimerization pathway. A second generation catalyst, which incorporates ligand aromatic functionality, has been developed. This complex has been shown to catalytically oxide methanol to formaldehyde in the presence of α-ketoglutarate using O2. The aromatic group provides a synthetic platform, allowing a variety of substituents geared toward increasing complex solubility and the tuning of the redox properties of the metal center. Additionally, the ligand has been functionalized to allow for the immobilization of the catalyst using an azido-functionalized solid support, by means of 'click' chemistry. A procedure for the immobilization of the catalyst has been developed that sets the stage for the preparation of a material that will diminish dimerization and inactivation. Additional insights into potential reaction pathways of the first generation catalyst have been obtained from DFT studies. These simulations have provided energetic comparisons of proposed intermediates and set the stage for future computational and spectroscopic studies. This synergistic approach will not only allow for detailed electronic and mechanistic descriptions of the intimate mechanism, but will be used in the development of next generation catalysts that that can be tuned for desired reactivity properties.

This thesis uses first principles techniques, mainly the ab initio random structure searching method (AIRSS), to study anode materials for lithium- and sodium- ion batteries (LIBs and NIBs, respectively). Initial work relates to a theoretical structure prediction study of the lithium and sodium phosphide systems in the context of phosphorus anodes as candidates for LIBs and NIBs. The work reveals new Li-P and Na-P phases, some of which can be used to better interpret previous experimental results. By combining AIRSS searches with a high-throughput screening search from structures in the Inorganic Crystal Structure Database (ICSD), regions in the phase diagram are correlated to different ionic motifs and NMR chemical shielding is predicted from first principles. An electronic structure analysis of the Li-P and Na-P compounds is performed and its implication on the anode performance is discussed. The study is concluded by exploring the addition of aluminium dopants to the Li-P compounds to improve the electronic conductivity of the system. The following work deals with a study of tin anodes for NIBs. The structure prediction study yields a variety of new phases; of particular interest is a new NaSn$_2$ phase predicted by AIRSS. This phase plays a crucial role in understanding the alloying mechanism of high-capacity tin anodes, work which was done in collaboration with experimental colleagues. Our predicted theoretical voltages give excellent agreement with the experimental electrochemical cycling curve. First principles molecular dynamics is used to propose an amorphous Na$_1$Sn$_1$ model which, in addition to the newly derived NaSn$_2$ phase, provides help in revealing the electrochemical processes. In the subsequent work, we study Li-Sn and Li-Sb intermetallics in the context of alloy anodes for LIBs. A rich phase diagram of Li-Sn is present, exhibiting a variety of new phases. The calculated voltages show excellent agreement with previously reported cycling measurements and a consistent structural evolution of Li-Sn phases as Li concentration increases is revealed. The study concluded by calculating NMR parameters on the hexagonal- and cubic-Li$_3$Sb phases which shed light on the interpretation of reported experimental data. We conclude with a structure prediction study of the pseudobinary Li-FeS$_2$ system, where FeS$_2$ is considered as a potential high-capacity electrochemical energy storage system. Our first principles calculations of intermediate structures help to elucidate the mechanism of charge storage observed by our experimental collaborators via $\textit{in operando}$ studies.

Orientador: Nelson Henrique Morgon / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-17T17:43:18Z (GMT). No. of bitstreams: 1 Heerdt_Gabriel_M.pdf: 1500564 bytes, checksum: dd39ed6bdcbfe660248d76bcaee6963f (MD5) Previous issue date: 2011 / Resumo: O objetivo principal deste trabalho foi analisar alguns dos mecanismos reacionais de oxidação da molécula de colesterol. Para que isso fosse possível, desenvolveu-se uma metodologia de cálculos à partir da análise de diferentes funcionais de densidade, conjuntos de funções de base e método ONIOM. A metodologia que realiza cálculos no nível ONIOM2(QCISD(T)/6-311++G(2df,p): HF/6-31G(d)//B3LYP/6-31G(d):HF/6-31G(d)) resultou nos menores desvios médios absolutos para afinidades por próton e eletrônica, 5,38 kJ/mol e 0,107 eV, respectivamente, para as 65 moléculas utilizadas no processo de validação. Essa metodologia comparada aos métodos propostos na literatura, G3(MP2) e G3(B3), possui desvios absolutos estatisticamente inferiores e vantagem em tempo computacional. Ao aplicar-se esse nível de teoria no estudo dos mecanismos de autoxidação do colesterol, observa-se uma concordância com dados experimentais que indicam a preferência pela reação através da posição equatorial. As reações de epoxidação seguida pela hidratação, foram realizadas pela transferência de um átomo de oxigênio da molécula de peróxido de hidrogênio para o colesterol, havendo a quebra da insaturação e consequente formação de um triol da molécula de colesterol / Abstract: The main objective of this study was to analyze some oxidation reaction mechanisms involving cholesterol molecule. A calculation methodology considering the analysis of different density functionals, basis sets and ONIOM method. The methodology that performs calculations at the level ONIOM2(QCISD(T)/6-311++G(2df,p):HF/6-31G(d)//B3LYP/6-31G(d):HF/6-31G(d)) resulted in smaller absolute mean deviations for proton and electron affinities, 5.38 kJ/mol and 0.107 eV, respectively, for the 65 molecules used in the validation process. This methodology in comparison with composite methods G3(MP2) and G3(B3), has a lower absolute deviation. Another advantage is the lower computational cost. This methodology when applied to the cholesterol autoxidation mechanisms gives a good agreement with experimental data. The results indicate that the reaction proceeds through the attach at the equatorial position. The next steps involve epoxidation and hidratation reactions. The oxigen is transfered from hydrogen peroxide to cholesterol molecule. The insaturation is broken and the cholesterol triol molecule is formed / Mestrado / Físico-Química / Mestre em Química

Dans les années 1970, Vautherin et Brink ont effectué les premiers calculs auto-consistents du problème à N-corps nucléaire en utilisant une interaction de Skyrme. Aujourd’hui la méthode de la fonctionnelle de densité (EDF) ou la méthode champ-moyen est toujours utilisée à grande échelle pour étudier la structure nucléaire. Le premier point fort de cette méthode est sa simplicité computationnelle qui permet de l'appliquer dans l'entièreté de la charte nucléaire, des noyaux les plus légers aux éléments super lourds à plus que 250 nucléons. Depuis le début des années 1980, les initiales `BFH', représentant Paul Bonche, Hubert Flocard et Paul-Henri Heenen, ont signé un grand nombre des papiers depuis 1984. Ces trois scientifiques sont les auteurs de trois codes numériques iconiques EV8, CR8 et EV4. Des versions évoluées de ces codes sont toujours utilisées fréquemment aujourd’hui par des nombreux chercheurs. Au fil des années, deux désavantages de ces trois codes sont apparus. Le premier désavantage est lié à la physique: bien que EV8, EV4 et CR8 offrent à l'utilisateur accès à une variété de combinaisons de symétries conservées et brisées, un grand nombre n'est pas accessible. De plus en plus souvent, les applications traitant des noyaux exotiques demandent des calculs champ-moyen qui sont moins limités par les symétries imposées. Le deuxième désavantage est d'une nature plus pratique: le maintien au même niveau d'une combinaison de trois codes qui ont des buts comparables est difficile. Le projet de mon doctorat était de construire un code qui unifie et généralise les fonctionnalités de EV8, CR8 et EV4. Aujourd'hui MOCCa, un acronyme de MOdular Cranking Code, est capable de reproduire toutes les fonctionnalités des codes BFH. De plus, il est maintenant possible d'effectuer des calculs champ-moyen pour un nombre des combinaisons de symétries conservées et brisées, offrant un domaine d'applications énorme. Quatre symétries ont été toujours imposées dans les codes BFH, et sont maintenant toutes soumises au choix de l'utilisateur, qui peut les conserver où les briser indépendamment. Ceci résulte en 16 modes d'opération différents du code, dont tous ont des intérêts physiques pour décrire des phénomènes nucléaires. La déformation octupolaire du 224Ra et les bandes chirales du 138Nd sont des exemples récents d'intérêt expérimental, dont la description théorique est maintenant abordable avec un seul outil. Cet outil fait preuve d'une grande complexité: sur le plan physique, des méthodes ont été développées pour résoudre les équations du champ-moyen en l'absence des symétries facilitant le problème, tandis que sur le plan pratique, le traitement d'un nombre de degrés de liberté non-physiques a eté amelioré. La dernière partie de la thèse, la plus importante probablement du point de vue des futurs collaborateurs, est pour cette raison constituée d'un manuel d'utilisateur. Deux applications de la méthode sont ainsi présentées: la description des transitions de forme dans les isotopes de Radium et une étude de l'évolution des rayons de charge dans la chaîne isotopique du mercure démontrent la viabilité de la méthode. / Option Physique du Doctorat en Sciences / info:eu-repo/semantics/nonPublished

In this thesis, we use rst principles density functional theory (DFT) to study the energetics, structural and electronic properties of hydrogenated and lithiated bilayer graphene material systems. The newly developed four variants of the non-local van der Waals (vdW) exchange-correlation functionals (vdW-DF, vdW-DF2, vdW-DF C09x and vdW-DF2 C09x) are employed to explore all the possible con gurations of hydrogen adsorption at 50% and 100% coverage on a 1 1 unit cell. The results obtained are also compared with the GGA PBE functional. For 50% hydrogen coverage, 16 unique con gurations are identi ed in the unrelaxed state. Formation energy analysis reveals six possible energetically favourable con gurations with three low-energy competing con gurations. It is found that the properties of hydrogenated bilayer graphene greatly depend on the hydrogen con guration. For instance, the formation of a hydrogen dimer within the layers decouples the structure, whereas the dimer formation outside surfaces does not have a signi cant in uence on the van der Waals forces; thus the bilayers remain coupled. In this coupled con guration, the vdW-DF C09x functional predicts the lowest formation energy and shortest interlayer separation, whereas the GGA PBE functional gives the highest formation energy and largest interlayer distance. The reasons behind the variation of these functionals are discussed. Two of the three low-energy competing con gurations exhibit semimetallic behaviour, whereas the remaining con guration is a wide band gap material. The wide band gap structure is found to undergo a hydrogen-induced spontaneous phase transformation from hexagonal to tetrahedral (diamond-like) geometry. We conclude that this wide band gap con guration represents a viable template for synthesizing nanodiamonds from graphene by hydrogenation. At 100% coverage, ten unique hydrogen con gurations are identi ed from a 1 1 unit cell. All exchange-correlation functionals predict nine of the structures to have negative formation energies. From these nine structures, three low-energy competing structures are noted and found to be wide band gap semiconductors, whereas the other con gurations exhibit either a semimetallic or metallic character. Although a 1 1 unit-cell is able to present a clear picture for the interaction between hydrogen and graphene, our results reveal that it limits the occurrence of other interesting physics. The cell size was increased to 2 1, to identify other low-energy con gurations that are not possible in a 1 1 cell. The identi ed con gurations have shown physically interesting hydrogen arrangements such as chair-like, zigzag-like and boat-like con gurations. Furthermore, our results reveal that hydrogenation reduces the elastic properties of the pristine structures. We further perform a systematic investigation of the e ects of lithium (Li) on AA and AB stacking sequences of bilayer graphene. Two Li atoms are considered to examine the e ects of the Li-Li interaction on bilayer graphene, and a total of 12 unique con gurations for AB and 9 for AA stackings are identi ed. The vdW-DF consistently predicts the highest formation energies, whereas vdW-DF2 C09x gives the lowest. Unlike in the case of the pristine structures, it is noted that for lithiated bilayer graphene, GGA PBE gives comparable results to the other functionals. One of the Li intercalated con gurations undergoes a spontaneous translation from the AB to AA stacking, and is found to be the most energetically stable con guration. We therefore conclude that Li favours the AA stacking, and that con guration represents a feasible template for experimentally synthesizing and characterizing a Li-based anode material. We noticed that all identi ed Li con gurations exhibit metallic behaviour. Lastly, we found that the intercalated Li dimer weakly interacts with the graphene layers, whereas the intercalated isolated Li atom exhibits strong interaction. / Thesis (PhD)--University of Pretoria, 2014. / gm2014 / Physics / unrestricted

This thesis investigates the wetting of simple liquids using two density functional theory (DFT) models. The first model is a discrete lattice-gas model and the second a continuum DFT model of a hard-sphere reference system with an additional attractive perturbation. The wetting properties of liquids are principally investigated by studying the binding, or interface, potential of the fluid and this thesis presents a method by which a binding potential can be fully calculated from the microscopic DFT. The binding potentials are used to investigate the behaviour of the model fluid depending on the range to which particle interactions are truncated. Long ranged particle interactions are commonly truncated to increase computational efficiency but the work in this thesis shows that in making this truncation some important aspects of the interfacial phase behaviour are changed. It is demonstrated that in some instances by reducing the interaction range of fluid particles a shift in phase behaviour from wetting to non wetting occurs. The binding potential is an input to larger scale coarse grained models and this is traditionally given as an asymptotic approximation of the binding potential. By using the full binding potential, calculated from the DFT model, as an input, excellent agreement can be found between the results from the microscopic DFT model and the larger scale models. This is first verified with the discrete lattice-gas model where the discrete nature of the model causes some non-physical behaviour in the binding potentials. The continuum DFT model is then applied which corrects this behaviour. An adaptation to this continuum model is used to study short ranged systems at high liquid densities at state points below the `Fisher-Widom' line. The form of the decay of the density profiles and binding potentials now switches from monotonic to oscillatory. This model leads to highly structured liquid droplets exhibiting a step-like structure.