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.

The development of science and technology have provided a lifestyle completely dependent on energy consumption. Devices such as computers and mobile phones are good examples of how our daily life depends on electric energy. In this scenario, energy storage technologies emerge with strategic importance providing efficient ways to transport and commercialize the produced energy. Rechargeable batteries come as the most suitable alternative to fulfill the market demand due to their higher energy- and power- density when compared with other electrochemical energy storage systems. In this context, during the production of this thesis, promising compounds for advanced batteries application were investigated from the theoretical viewpoint. The framework of the density functional theory has been employed together with others theoretical tools to study properties such as ionic diffusion, redox potential, electronic structure and crystal structure prediction. Different organic materials were theoretically characterized with quite distinct objectives. For instance, a protocol able to predict the redox potential in solution of long oligomers were developed and tested against experimental measurements. Strategies such as anchoring of small active molecules on polymers backbone have also been investigated through a screening process that determined the most promising candidates. Methods such as evolutionary simulation and basin-hopping algorithm were employed to search for global minimum crystal structures of small molecules and inorganic compounds working as a cathode of advanced sodium batteries. The crystal structure evolution of C6Cl4O2 upon Na insertion was unveiled and the main reasons behind the lower specific capacity obtained in the experiment were clarified. Ab initio molecular dynamics and the nudged elastic band method were employed to understand the underlying ionic diffusion mechanisms in the recently proposed Alluaudite and Eldfellite cathode materials. Moreover, it was demonstrated that electronic conduction in Na2O2, a byproduct of the Na-O2 battery, occurs via hole polarons hopping. Important physical and chemical insights were obtained during the production of this thesis. It finally supports the development of low production cost, environmental friendliness and efficient electrode compounds for advanced secondary batteries.

Computational chemistry has led to the greater understanding of the molecular world, from the interaction of molecules, to the composition of molecular species and materials. Of the families of computational chemistry approaches available, the main families of electronic structure methods that are capable of accurate and/or reliable predictions of energetic, structural, and spectroscopic properties are ab initio methods and density functional theory (DFT). The focus of this dissertation is to improve the accuracy of predictions and computational efficiency (with respect to memory, disk space, and computer processing time) of some computational chemistry methods, which, in turn, can extend the size of molecule that can be addressed, and, for other methods, DFT, in particular, gain greater insight into which DFT methods are more reliable than others. Much, though not all, of the focus of this dissertation is upon transition metal species – species for which much less method development has been targeted or insight about method performance has been well established. The ab initio approach that has been targeted in this work is the correlation consistent composite approach (ccCA), which has proven to be a robust, ab initio computational method for main group and first row transition metal-containing molecules yielding, on average, accurate thermodynamic properties, i.e., within 1 kcal/mol of experiment for main group species and within 3 kcal/mol of experiment for first row transition metal molecules. In order to make ccCA applicable to systems containing any element from the periodic table, development of the method for second row transition metals and heavier elements, including lower p-block (5p and 6p) elements was pursued. The resulting method, the relativistic pseudopotential variant of ccCA (rp-ccCA), and its application are detailed for second row transition metals and lower p-block elements. Because of the computational cost of ab initio methods, DFT is a popular choice for the study of transition metals. Despite this, the most reliable density functionals for the prediction of energetic properties (e.g. enthalpy of formation, ionization potential, electron affinity, dissociation energy) of transition metal species, have not been clearly identified. The examination of DFT performance for first and second row transition metal thermochemistry (i.e., enthalpies of formation) was conducted and density functionals for the study of these species were identified. And, finally, to address the accuracy of spectroscopic and energetic properties, improvements for a series of density functionals have been established. In both DFT and ab initio methods, the harmonic approximation is typically employed. This neglect of anharmonic effects, such as those related to vibrational properties (e.g. zero-point vibrational energies, thermal contributions to enthalpy and entropy) of molecules, generally results in computational predictions that are not in agreement with experiment. To correct for the neglect of anharmonicity, scale factors can be applied to these vibrational properties, resulting in better alignment with experimental observations. Scale factors for DFT in conjunction with both the correlation and polarization consistent basis sets have been developed in this work.

The dry reforming of methane (DRM) has received critical attention because it converts two major greenhouse gases, methane and carbon dioxide, into molecular hydrogen and carbon monoxide, known as synthesis gas (syngas). Syngas is an important feedstock to produce various chemicals. A major drawback of the DRM process is the high deactivation rates of conventional nickel and cobalt catalysts. Experimental findings indicate that treating nickel and cobalt catalysts with boron reduces deactivation rates and enhances the catalytic activity. This study investigates the mechanism through which boron promotes catalytic stability using density functional theory calculations. First, the location of boron in nickel and cobalt catalysts is explored. Boron is found to be more stable occupying on-surface and substitutional sites in the catalysts. However, during DRM operation, carbon dioxide is able to oxidize on-surface and substitutional boron. The formed boron oxide units may react with each other and form diboron trioxide or react with hydrogen to form boric acid, and eventually leave the catalyst, which means they cannot have an effect on deactivation rates. This study argues that interstitial boron plays the major role since it is protected from getting oxidized by carbon dioxide. Geometric optimization indicates that interstitial boron leads to spontaneous surface reconstruction in both extended surfaces and nanoparticles. The effect of interstitial boron on the binding energies of methyl, hydrogen, carbon monoxide, and oxygen on extended surfaces and nanoparticles is studied and utilized using the Brønsted-Evans-Polanyi principle to give an insight about how boron reduces deactivation rates. Our analysis indicates that interstitial boron lowers the activation energies of methane and carbon dioxide. On (100) surfaces, boron lowers C–H activation energies in methane more than it lowers C=O activation energies in carbon dioxide, which means catalytic deactivation rates due to metal oxidation are lowered. On (111) surfaces, boron lowers carbon dioxide activation energies more than it lowers methane activation energies, which means catalytic deactivation rates due to coke formation are lowered. The computational study is consistent with experimental findings and gives an atomistic understanding of the beneficial role of boron on the DRM process catalyzed by nickel and cobalt.