The steady march of new technology depends crucially on our ability to discover and design new, advanced materials. Partially due to increases in computing power, computational methods are now having an increased role in this discovery process. Advances in this area speed the discovery and development of advanced materials by guiding experimental work down fruitful paths. Density functional theory (DFT)has proven to be a highly accurate tool for computing material properties. However, due to its computational cost and complexity, DFT is unsuited to performing exhaustive searches over many candidate materials or for extracting thermodynamic information. To perform these types of searches requires that we construct a fast, yet accurate model. One model commonly used in materials science is the cluster expansion, which can compute the energy, or another relevant physical property, of millions of derivative superstructures quickly and accurately. This model has been used in materials research for many years with great success. Currently the construction of a cluster expansion model presents several noteworthy challenges. While these challenges have obviously not prevented the method from being useful, addressing them will result in a big payoff in speed and accuracy. Two of the most glaring challenges encountered when constructing a cluster expansion model include:(i) determining which of the infinite number of clusters to include in the expansion, and (ii) deciding which atomic configurations to use for training data. Compressive sensing, a recently-developed technique in the signal processing community, is uniquely suited to address both of these challenges. Compressive sensing (CS) allows essentially all possible basis (cluster) functions to be included in the analysis and offers a specific recipe for choosing atomic configurations to be used for training data. We show that cluster expansion models constructed using CS predict more accurately than current state-of-the art methods, require little user intervention during the construction process, and are orders-of-magnitude faster than current methods. A Bayesian implementation of CS is found to be even faster than the typical constrained optimization approach, is free of any user-optimized parameters, and naturally produces error bars on the predictions made. The speed and hands-off nature of Bayesian compressive sensing (BCS) makes it a valuable tool for automatically constructing models for many different materials. Combining BCS with high-throughput data sets of binary alloy data, we automatically construct CE models for all binary alloy systems. This work represents a major stride in materials science and advanced materials development.

In the most recent two decades, the development of impurity controls with ultra-high precision in semiconductors motivates people to put more and more attentions on the solotronic devices, whose properties depend on one or a few dopants. One of the most promising applications of solotronic device is the qubit in quantum computing. In the procedure of exploring qubit candidates, the most straightforward challenges we need face include that the qubit must be highly isolated and can be initialized/manipulated efficiently with high fidelities. It has been proved that qubits based on single defects have excellent performances as quits. For instance, the NV center in diamond forms a ground spin triplet which can be manipulated at room temperature with electromagnetic fields. This work focuses on searching for new single defects as qubit candidates with density functional theory. Lanthanides element possesses excellent optical characteristics and extremely long nuclear coherence time. Therefore, combining it into the diamond platform can be possible design for integrated quantum information processing devices in the future. To investigate the stability of lanthanides dopants in the diamond matrix, the formation energies of charge states of complexes are calculated. The broadening of Eu(III) peak in the photoluminescence spectrum can be verified according to the existence of more than stable configuration and steady 4f electron occupation. In the case of transition-metal dopant in the silicon carbide, it is found that both silicon and carbon substituted nickels in 3C-SiC shows a magnetic-antimagnetic transition under applied strains. The virtual hopping rate of electrons strongly depends on the distance between the spin pair residing in the nickel and dangling bonds. Therefore, the Heisenberg exchange coupling between them can be adjusted subtly by controlling the external strain. According to the the spin Hamiltonian of the defect, the spin state can be manipulated universally with strain and electromagnetic fields. In contrast, the nickel dopant in 4H-SiC exhibits a very stable magnetic property. Other than that, the electronic structure of Cr in 4H-SiC implies that optical manipulations of spin states might be realized in the excited state.

Density functional theory (DFT) has become the most widely used first-principles computational method to simulate different atomic, molecular, and solid phase systems based on electron density assumptions. The complexity of describing a many-body system has been significantly reduced in DFT. However, it also brings in potential error when dealing with a system that involves the interactions between metallic and non-metallic species. DFT tends to overly-delocalize the electrons in metallic species and sometimes results in the overestimation of reaction energy, metallic properties in insulators, and predicts relative surface stabilities incorrectly in some instances. There are two approaches to overcoming the failure of DFT using standard exchange-correlation functionals: One can either use a higher level of theory (and thus incur a greater computational cost) or one can apply an efficient correction scheme. However, inaccurate corrections and improper calculation models can also lead to more errors. In the beginning of this dissertation, we introduce the correction methods we developed to accurately model the structure and electron density in material surfaces; then we apply the new methods in surface reactivity studies under experimental conditions to rationalize and solve real life problems. We first investigate the post-DFT correction method in predicting the chemisorption energy (Echem) of a NO molecule on transition metal surfaces. We show that DFT systematically enhances back-donation in NO/metal chemistorption from the metal d-band to NO 2π* orbital, and relate the back-donation charge transfer to the promotion of an electron from the 5σ orbital to the 2π* orbital in the gas-phase NO G2Σ-←X2Π excitation. We establish linear relationships between Echem and ΔEG←X and formulate an Echem correction scheme to the (111) surfaces of Pt, Pd, Rh and Ir. As a precursor to further optimization of DFT corrections on transition metal oxide surfaces, we systematically compare the alumina (α-Al2O3) and hematite (α-Fe2O3) (0001) surfaces to study how the atomic positions treatment during geometry optimizations would affect the electronic structure and modeled reactivity, since they are often reported to have a minimal effect. Our results suggest that both can vary significantly in quantitative and qualitative ways between partially constrained or fully relaxed slab models. We continue to use the α-Fe2O3 (0001) surfaces to optimize the Hubbard U method implemented in DFT that determines the Coulomb repulsion correction (Ud) to localize Fe d-electrons. It successfully restores the insulating properties of bulk hematite, but underestimates the stability of the oxygen-terminated surface. It is mainly due to the fact that all the chemically distinct surface Fe atoms were treated the same way. Here we develop a linear response technique to derive specific Ud values for all Fe atoms in several slab geometries. We also find that in a strongly correlated system, the O p-orbitals also need the Hubbard correction (Up) to accurately predict the structural and electronic properties of bulk hematite. Our results show that the site-specific Ud, combined with Up as Ud+p, is crucial in obtaining theoretical results for surface stability that are congruent with the experimental literature results of α-Fe2O3 (0001) surface structure. Besides methodology development, we continue to apply our specific Ud+p method in the engineered application of the Chemical Looping Combustion (CLC) process in which transition metal oxides play the role of oxidizing fuel molecules for full CO2 capture. Current molecular dynamic studies use partially constrained surface models to simulate the CH4 reaction on hematite surfaces without the detailed comparison of the early stage adsorption products. Here we use hematite (α-Fe2O3) and magnetite (Fe3O4) surfaces as analogous to systematically study the early adsorption products of CH4. Our results show that the reaction favors the homolytic pathway on O-terminated surface, and that as a reduced form of hematite, the magnetite surface also shows excellent reactivity on CH4 dissociation. Knowing how to simulate DFT surface model properly we continue to enrich our theoretical methods for more complicated systems under aqueous conditions. We focus on various structures of the lithium-ion battery material, LiCoO2 (LCO) (001) surface, involving hydroxyl groups. We assess the relative stabilities of different surface configurations using a thermodynamic framework, and a second approach using a surface-solvent ion exchange model. We find that for both models the –CoO–H1/2 surface is the most stable structure near the O-rich limit, which corresponds to ambient conditions. We also found that this surface has nonequivalent surface geometry with the stoichiometric –CoO–Li1/2 surface, leading to distinct band structures and surface charge distributions. We go on to probe how those differences affect the surface reactivity in phosphate anion adsorption. All of the work presented in this dissertation reveals the importance of accurately modeled material structures in theoretical studies to achieve correct physical properties and surface reactivity predictions. We hope our DFT correction schemes can continue to contribute to future surface studies and experimental measurements, and to enlighten new ideas in future DFT methodology improvements.

First-principles density functional theory calculations were performed on a number of important energetic molecular crystals, pentaerythritol tetranitrate (PETN), cyclotetramethylene tetranitramine (HMX), cyclotrimethylene trinitramine (RDX), and nitromethane. Simulations of hydrostatic and uniaxial compressions, as well as predictions of ground-state structures at ambient conditions, were performed using the DFT codes CASTEP and VASP. The first calculations done with CASTEP using GGA-PW yielded reasonable agreement with experiment for the calculated isothermal EOS for PETN-I from hydrostatic compression data, yet the EOS for β -HMX shows substantial deviation from experiment. Interesting anisotropic behavior of the shear-stress maxima were exhibited by both crystals upon uniaxial compression. It was predicted that the <100> direction, the least sensitive direction of PETN, has significantly different values for shear stress maxima τyx and τzx, in contrast to the more sensitive directions, <110> and <001>. In addition, non-monotonic dependence of one of the shear stresses as a function of strain was observed upon compression of PETN in the <100> direction. VASP calculations were later performed, and the results yielded good qualitative agreement with available experimental data for the calculated isothermal EOS and equilibrium structures for PETN-I, β-HMX, α-RDX, and nitromethane. Using VASP, uniaxial compression simulations were performed in the <100>, <010>, <001>, <110>, <101>, <011>, and <111> directions for all crystals up to the compression ratio V/V0 = 0.70. The VASP calculations of PETN reproduced the CASTEP results of significantly different values of τyx and τzx for the insensitive <100> compression, and relatively high and equal values of τyx and τzx for the sensitive <110> and <001> compressions. A correlation between this behavior of shear stress upon uniaxial compression and sensitivity was suggested, and predictions of anisotropic sensitivity of HMX, RDX, and nitromethane were made. Further analysis of the VASP results for PETN do not indicate a correlation between sensitivity and shear stress maxima as a function of longitudinal stress, where longitudinal stress is an appropriate experimental independent variable for comparison. The validity of a correlation between shear stress maxima and sensitivity requires further investigation. Further characterization of the anisotropic constitutive relationships in PETN was performed.

We have used ab initio computational simulation techniques to investigate both intra- and intermolecular interactions in a novel family of ionic organophosphonate molecular crystals. We have examined the influence of various numerical approximations on the computed geometry and binding energies of a selection of well-characterised hydrogen bonded systems. It was found that numerical basis sets provided the efficiency required to study the large hydrogen bonded dimer anions present in the organophosphonate system, while also producing accurate geometries and binding energies. We then calculated the relaxed structures and binding energies of phenylphosphonic acid dimer in the two arrangements in which it is present in the bulk crystal. The computed geometries were in excellent agreement with the experimental structures and the binding energies were consistent with those found for other ionic hydrogen bonded systems. Electron density maps were used to gain insight into the nature of the hydrogen bonding interaction between phenylphosphonic acid dimers. We also examined the effect of aromatic ring substituents on the geometry and energetics of the hydrogen bonding interaction. The nitro-substituted dimer was predicted to have a stronger binding energy than its unsubstituted parent while the methyl-substituted dimer was predicted to have a similar binding energy to its unsubstituted parent. An analysis of crystal field effects showed that the structure of the phenylphosphonic acid dimers in the organophosphonates is a complex product of competing intra- and intermolecular forces and crystal field effects. Cooperative effects in the organophosphonate system were also investigated and it was found that the interactions were mostly one-body (local) in nature. We have examined the intramolecular charge-transfer interaction between copper-halogen cations in the organophosphonate materials. The origin of geometric differences between the Cu(I) starting material and Cu(II) product cations was attributed to the electronic configuration of the Cu ion, not crystal field effects. To gain further insight into the difference in electronic structure between the starting material and product, we attempted to simulate the step-by-step dissociation of the [CuI]+ system. Although this investigation was not successful, we were able to expose some of the pitfalls of simulating dissociating odd-electron systems. We also analysed and compared the charge-transfer interaction in the chloro-, bromo- and iodo-forms of the organophosphonate family. The charge-transfer interaction was predicted to increase on going from the chloro- to the iodo-form, consistent with solid-state UV-visible data. Finally, we used the highly accurate Quantum Monte Carlo (QMC) method to investigate the hydrogen bonding interaction in water dimer and to calculate the dissociation energy. The accuracy of the experimental estimate for the dissociation energy has recently been questioned and an alternative value has been put forward. Our results lend support to the validity of the alternative value and are also in excellent agreement with those from other high-level calculations. Our results also indicate that QMC techniques are a promising alternative to traditional wavefunction techniques in situations where both high accuracy and efficiency are important.

<p>Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms.</p><p>The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions.</p><p>Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.</p>

<p>Computational methods are combined with synchrotron-based techniques to analyze the structure and bonding of water and water plus hydroxyl at metal surfaces under UHV and at near-ambient conditions. Water-metal interaction plays a crucial role in a multitude of cosmic, atmospheric and biological phenomena as well as heterogeneous catalysis, electrochemistry and corrosion. A spotlight of renewed interest has recently been cast on water-metal systems due to their relevance for surface chemical reactions related to the production and utilization of hydrogen as a clean energy carrier. In particular, H2O and OH are essential reaction intermediates in the renewable production of hydrogen from sunlight and water and in fuel cell electrocatalysis.</p><p>Fuel cells are considered one of the most promising power generation technologies for a sustainable energy future. A mechanistic understanding of the oxygen reduction reaction (ORR) pathway, including the role of electronic and geometric structure of the catalyst, is essential to the design of more efficient fuel cell catalysts. This is intimately connected to fundamental factors that affect the ability to form water-metal bonds as well as the site occupation and orientation of the adsorbed H2O and OH at active metal surfaces.</p><p>Key relationships related to critical issues in the fuel cell reaction are illuminated by the synergy of theory and experiment in this thesis. We emerge with a detailed understanding of the structure of the water-metal interface and the factors that rule the wettability of a metal surface, including geometric and electronic structure effects and the influence of coadsorbed species. We show that the preferred microscopic orientation of the water monolayer has consequences for macroscopic properties, and reveal the origin of the hydrophobic water layer. Finally, we identify a cooperativity effect that drives the stability of the mixed water/hydroxyl layer at metal surfaces, an important ORR intermediate.</p>

Aujourd'hui il est possible d'étudier à partir des premier principes la réponse sous excitation de matériaux utilisés dans des applications modernes très variés. En effet, grâce à de récents développements théoriques, ainsi qu'à l'optimisation des algorithmes de calcul, les simulations ab initio ne sont plus seulement limitées à des systèmes idéaux simplifiés, mais elles ont finalement l'ambition de capturer toute la complexité de l'échantillon testé dans l'expérience. Dans ce contexte, ce mémoire porte sur l'étude, à l'aide de différentes approches ab initio, des excitations électroniques dans une gamme de matériaux complexes et nanostructurés. Pour accéder aux excitations électroniques, la connaissance de la densité de l'état fondamental du système n'est plus suffisante, ce qui signifie que l'on doit trouver le moyen approprié d'aller au-delà de la théorie de la fonctionnelle de la densité (DFT) standard. Deux voies ont été intensivement explorées: l'une est basée sur la densité dépendante du temps et l'autre sur les fonctions de Green. La théorie de la fonctionnelle de la densité dépendante du temps (TDDFT) a été proposée en 1984 par Runge et Gross, qui ont dérivé un théorème du type Hohenberg-Kohn pour l'équation de Schrödinger en fonction du temps. Le champ d'application de cette généralisation de la théorie de la fonctionnelle de la densité inclut le calcul des spectres de photo-absorption ou, plus généralement, l'étude de l'interaction de la matière avec des champs électromagnétiques ou des particules qui la perturbent. À présent, l'application la plus populaire de cette théorie est l'extraction des propriétés de l'état électronique excité, et en particulier des fréquences d'excitation électroniques. En appliquant la TDDFT, après avoir déterminé l'état fondamental d'une molécule ou un agrégat, nous pouvons explorer et comprendre son spectre d'absorption, ayant en même temps des informations extrêmement détaillées sur le comportement du système excité. La complexité du problème à plusieurs corps en TDDFT est cachée dans le potentiel d'échange et de corrélation dépendant du temps qui apparaît dans les équations de Kohn- Sham et pour lequel il est primordial de trouver une bonne approximation. Beaucoup d'approximations ont été proposées et testées pour les systèmes finis, où même la très simple approximation TDLDA a souvent donné de très bons résultats. En général, les approximations existantes pour la fonctionnelle d'échange et corrélation fonctionnent assez bien pour certaines propriétés, mais elles se montrent insuffisantes pour d'autres. Dans le cas des matériaux solides, la TDDLA ne parvient pas à reproduire les spectres d'absorption optique, qui sont par contre bien décrits par la résolution de l'équation de Bethe-Salpeter en combinaison avec l'approximation GW pour les états de quasi-électron. D'autre part, la TDLDA peut déjà conduire à des résultats excellents pour la fonction de perte d'énergie d'un solide. La solution de l'équation de Bethe-Salpeter est beaucoup plus onéreuse du point de vue numérique. Ainsi, on poursuit encore la recherche d'approximations fiables en TDDFT, et au fil du temps, on espère atteindre la même maturité qu'on trouve maintenant dans la DFT pour l'état fondamental. En particulier, de nouvelles perspectives (et ses limites) ont étés révélées pendant ces dernières années grâce à la combinaison de deux théories distinctes : la TDDFT et l'approche des fonctions de Green (dont l'approximation GW et l'équation de Bethe- Salpeter font partie). Ces deux approches peuvent partager dans la pratique le point de départ commun de la théorie de la fonctionnelle de la densité pour le calcul de l'état fondamental électronique. Leur combinaison permet d'allier la simplicité de l'une (TDDFT) avec la précision de l'autre (GW et Bethe-Salpeter), afin d'en déduire des noyaux d'échange et de corrélation pour les solides. À partir de ces noyaux nous avons aussi travaillé sur le développement de noyaux modèles pour des applications efficaces à des systèmes de grande taille. Le présent mémoire contient une vue d'ensemble relativement condensée de la TDDFT et des approches basées sur la théorie des fonctions de Green, avec des applications aux domaines des nanotechnologies, aux matériaux photovoltaïques et au stockage de données. Ces applications ont constitué notre principal sujet de recherche au cours des dernières années. Ce mémoire est organisée comme suit. Avant d'entrer dans le domaine des approches pour les états excités, nous donnons dans le chapitre 1 un bref aperçu des idées de base de la DFT pour l'état fondamental, ce qui nous permet d'expliquer pourquoi il faut aller au-delà de la DFT standard, d'introduire quelques concepts-clés et de fixer la notation de base qui sera utilisée dans ce mémoire. Les chapitres suivants font un point sur la théorie formelle, avec une brève présentation des approches théoriques utilisées pour étudier les excitations électroniques: le chapitre 2 est dédié aux approches GW et à l'équation de Bethe-Salpeter, tandis que la TDDFT et la théorie de la réponse linéaire sont décrites dans le chapitre 3. Les noyaux dérivés à partir de l'équation de Bethe-Salpeter et notre travail sur les noyaux modèles sont discutés dans le chapitre 4. Le chapitre 5 contient des applications de la TDDFT dans le domaine de la réponse linéaire aux nanostructures. L'objectif principal est d'obtenir des spectres fiables (en général des spectres d'absorption) à partir de calculs de premiers principes. En comparant ces spectres avec des courbes expérimentales, on peut normalement déduire des informations importantes qui ne sont pas directement accessibles dans les expériences. D'autre part, la connaissance détaillée des propriétés d'excitation électronique contribue à une meilleure compréhension de la physique de ces systèmes dans leur généralité. Le chapitre 6 présente des applications à des matériaux solides d'intérêt technologique. En particulier, nous nous sommes intéressé aux propriétés optiques des matériaux à changement de phase, utilisés dans le DVD re-inscriptibles, ainsi que aux états électroniques des absorbeurs et des oxydes transparents conducteurs pour les cellules solaires à couches minces. Le chapitre 7 est dédié aux cruciales interactions de van der Waals et au calcul – via la TDDFT – des paramètres qui les décrivent. Nous discutons à la fois des interactions entre deux agrégats, et entre un agrégat et une surface semi-conductrice. Le dernier chapitre 8 fait le point sur les résultats de notre réflexion.

La réduction de taille réalisée dans les hétérostructures mène à des états électroniques, fondamental et excité, largement différents de ceux du cristal en volume, et a ouvert la voie à une nouvelle génération de dispositifs optoélectroniques et photonique. Les super-réseaux diélectriques sont par exemple développés pour leurs propriétés non linéaires. Ces effets sont également trouvés dans des hétérostructures de semi-conducteur basées sur GaAs, qui a par lui-même les propriétés optiques non linéaires importantes. Dans la recherche de nouvelles sources optiques, l'anisotropie optique des super-réseaux de GaAs/AlAs-oxidé a été exploitée pour produire la conversion des fréquences optiques. Les super-réseaux de type GaAs/AlAs constituent donc un prototype pour la compréhension des structures artificielles, et leurs propriétés optiques ont été à fond étudiées expérimentalement et théoriquement. En particulier, la réduction de la symétrie cubique initiale de la structure diamant ou zinc-blende provoque une anisotropie optique. Le comportement des composents du tenseur diélectrique du super-réseaux GaAs/AlAs en fonction de la période de barrière/puits est une question qui suscite un très grand intérêt. Expérimentalement, on a observé une baisse remarquable de la biréfringence quand la période décroît. Pour étudier la réponse optique de ces systèmes, les détails de la structure électronique doivent être pris en considération, y compris des effets comme le repliement des bandes et le confinement. Une analyse simple en termes de particules indépendantes est insuffisante: les effets à plusieurs corps peuvent jouer un rôle crucial et tendent à être particulièrement importants quand l'échelle du système est réduite. Les calculs utilisant des pseudopotentiels semi-empiriques sur de super-réseaux de grande période ont récemment fourni une analyse détaillée des effets du repliement des bandes et du confinement. Néanmoins, il n'y avait aucun accord quantitatif avec l'expérience au sujet de la biréfringence statique, et ces calculs n'ont pas pu expliquer l'augmentation de cette quantité avec l'augmentation de la période du super-réseau même qualitativement. Aussi, nous avons calculé la biréfringence statique de super-réseaux (001) (GaAs)$_n$/(AlAs)$_n$ pour une période de barrière/puits variant de n=1 à n=8, en utilisant la théorie de la fonctionnelle de densité dépendante du temps (TDDFT). Nous confirmons les résultats des calculs semi-empiriques précédents basés sur un calcul à particules indépendantes, en exécutant des calculs ab initio dans la même approximation. Cependant, nous montrons que l'inclusion des effets de champs locaux change complètement les composants du tenseur diélectrique: la biréfringence théorique en maintenant en bon accord avec l'expérience. En fait, on obtient l'accord qualitatif, et quantitatif avec l'expérience, en incluant les effets de champs locaux. On montre en particulier que l'anisotropie des champs locaux explique les tendances expérimentales observées. Étonnamment, l'utilisation de l'approche de milieu effectif, ou le super-réseau est modelisé par un empilement de couches ayant la permittivité GaAs ou AlAs, est justifiée dans la direction d'empilement même pour les petites périodes, car les effets de champs locaux et de confinement s'annulent. Par contraste, les effets de confinement sont trouvés plus grands dans le plan perpediculaire à la direction d'empilement, et la théorie de milieu effectif est insuffisante.

<p>The main purpose of this thesis is to implement the Gauss--Legendre quadrature for the dispersion coefficient. This has been done and can be now be made with different number of points. The calculations with this implementation has shown that the relativistic impact on helium, neon, argon and krypton is largest for krypton, that has the highest charge of its nucleus. It was also seen that the polarizability of neon as a function of the imaginary angular frequency decreases monotonically from a static value.</p>