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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. 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. 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.

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. 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. 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.

Hydrogen is abundant, uniformly distributed throughout the Earth's surface and its oxidation product (water) is environmentally benign. Owing to these features, it is considered as an ideal synthetic fuel for a new world energetic matrix (renewable, secure and environmentally friendly) that could allow a sustainable future development. However, for this prospect to become a reality, efficient ways to produce, transport and store hydrogen still need to be developed. In the present thesis, theoretical studies of a number of potential hydrogen storage materials have been performed using density functional theory. In NaAlH4 doped with 3d transition metals (TM), the hypothesis of the formation of Ti-Al intermetallic alloy as the main catalytic mechanism for the hydrogen sorption reaction is supported. The gateway hypothesis for the catalysis mechanism in TM-doped MgH2 is confirmed through the investigation of MgH2 nano-clusters. Thermodynamics of Li-Mg-N-H systems are analyzed with good agreement between theory and experiments. Besides chemical hydrides, the metal-organic frameworks (MOFs) have also been investigated. Li-decorated MOF-5 is demonstrated to possess enhanced hydrogen gas uptake properties with a theoretically predicted storage capacity of 2 wt% at 300 K and low pressure. The metal-hydrogen systems undergo many structural and electronic phase transitions induced by changes in pressure and/or temperature and/or H-concentration. It is important both from a fundamental and applied viewpoint to understand the underlying physics of these phenomena. Here, the pressure-induced structural phase transformations of NaBH4 and ErH3 were investigated. In the latter, an electronic transition is shown to accompany the structural modification. The electronic and optical properties of the low and high-pressure phases of crystalline MgH2 were calculated. The temperature-induced order-disorder transition in Li2NH is demonstrated to be triggered by Li sub-lattice melting. This result may contribute to a better understanding of the important solid-solid hydrogen storage reactions that involve this compound.

Diamond is an important material in many industrial applications (e.g., machining of hard materials, bio-electronics, optics, electronics, etc.) because of its exceptional properties such as hardness, tolerance to aggressive environments, compatibility with human tissues, and high carrier mobility. However, a highly controlled method for growing artificial high-purity diamond on a range of different substrates is needed to exploit these exceptional properties. The Chemical Vapour Deposition (CVD) method is a useful tool for this purpose, but the process still needs to be developed further to achieve better control of growth. In this context, the introduction of dopant species into the gas phase has been shown to strongly influence growth rate and surface morphology. Density Functional Theory (DFT) methods are used to deepen our atomic-level understanding of the effect of dopants on the mechanism for CVD growth on diamond. More specifically, the effect of four dopants (N, P, B and S) has been studied on the important reaction steps in the growth mechanism of diamond. Substitution of N into the diamond lattice has generally been found to disfavour critical reaction steps in the growth of the 100-face in diamond. This negative effect has been related to electron transfer from the N dopant into an empty surface state, e.g., a surface carbon radical. In addition, strong surface stabilization is observed for N substitution in certain sites via a beta-scission reconstruction, with the formation of sp2 carbon. These observations correlate well with observed surface degradation and decrease in growth rate when a high concentration of nitrogen gas is introduced into the CVD growth process. The effect of co-adsorbed P, S and B onto the diamond surface has also been investigated for two reaction steps: CH3 adsorption and H abstraction. While P and B are observed to influence these reaction steps, the effect of S is rather limited.

Nanowire heterostructures play a crucial role in nanoscale electronics, i.e., one-dimensional electronics derives benefits from the growth of heterostructures along the nanowire axis. We use first-principles plane-wave calculations within density functional theory with the localized density approximation (LDA) to get information about the structural and electronic properties of bare and hydrogen passivated GaAs/AlAs nanowire heterostructures. We also take into account the reconstruction of the nanowire surfaces. Modeled nanowire heterostructures are constructed using bulk atomic positions along [001] and [111] direction of zinc-blende structures and cutting out wires from this GaAs/AlAs heterostructure crystal with a diameter of 1 nm. We study for the effects of the surface passivation on the band gap and the band offsets for the planar GaAs/AlAs bulk heterostructure system and GaAs/AlAs nanowire heterostructure system. It is possible to control the potential that carriers feel in semiconductor heterostructures. For the planar lattice-matched heterostructures, the macroscopic average of potential of the two materials is constant far from the interface and there is a discontinuity at the interface depending on the composition of the heterostructure. In order to obtain the valence band offset in the heterostructure system, the shift in the macroscopic potential at the interface and the difference between the valence band maximum values of the two constituents must be added. In nanoscale heterostructures, the potential profile presents a more complex picture. The results indicate that while the discontinuity remains close to the planar limit right at the interface, there are fluctuations on the average potential profile beyond the interface developed by the inhomogeneous surface termination, that is, there are variations of the band edges beyond the interface. We report a first-principles study of the electronic properties of surface dangling-bond (SDB) states in hydrogen passivated GaAs/AlAs nanowire heterostructures with a diameter of 1 nm, where the SDB is defined as the defect due to an incomplete passivation of a surface atom. The charge transition levels of SDB states serve as a common energy reference level, such that charge transition level value for group III and V atoms is a constant value and a periodic table atomic property. We have carried out first-principles electronic structure and total energy calculations of aluminum nanowires for a series of different diameters ranging from 3 Angtrom-10 Angstrom, which is cut out from a slab of ideal bulk structure along the [001] direction. First-principles calculations of aluminum nanowires have been carried out within the density-functional theory. We use the norm-conserving pseudopotentials that are shown to yield successful results for ultrathin nanowire regime. Our results show that the number of bands crossing the Fermi level decreases with decreasing wire diameter and all wires studied are metallic.

Environmentally Assisted cracking (EAC) is a very critical materials science problem that concerns many technological areas such as petrochemical engineering, aerospace operations and nuclear power generation, in which cracking or sudden failure of materials may happen at stress far below the tensile strength. This type of corrosion is initiated at the microscopic level and is complicated due to the combination of chemistry (reaction caused by corrosive agents) and mechanics (varying load). As EAC is generally related to the segregation of impurity elements to defects (mainly grain boundaries), the symptoms of risk may not be apparent from the exterior of the metal components: hence EAC remains latent and gives no sign of warning until the failure occurs. Due to its intricate nature, conducting experiments on this phenomenon involves difficulties and requires much effort. In this work, we employed advanced molecular simulation techniques to study EAC in order to give insight into its atomistic behavior. First, Density-Functional Theory (DFT) method was used to investigate the fundamental processes and mechanism of EAC-related issues at the nanoscale level, with two case studies concerning the stress corrosion in iron and hydrogen embrittlement in palladium. When segregating to the grain boundary (GB) of iron, different impurity elements such as sulfur, phosphorus and nitrogen raise corrosion failures in a variety of ways. Hydrogen atoms, due to their mobility and small atomic size, are able to form high occupation at crystal defects, but show different interactions to vacancy and GB. Then, we used the classical Molecular Dynamics (MD) method to gain an understanding of the dynamic response of materials to mechanical load and the effects of temperature, strain and extreme conditions (high pressure shock compression) on structural properties. The MD simulations show that hydrogen maintains the highest localization at grain boundaries in the vicinity of ambient temperatures, and grain boundaries are the preferred nucleation sites for dislocations and voids. This computational work, using DFT and MD techniques, is expected to contribute to the better understanding on chemistry and mechanisms of complex environment-assisted cracking phenomenon at a fundamental level in order to beneficially complement conventional laboratory approaches.

This thesis concerns methods for electronic structure calculations and some applications of the methods. The augmented planewave (APW) basis set and it’s relatives LAPW (linearised APW) and APW+lo (local orbitals) have been widely used for electronic structure calculations. Here a modification of the APW basis set based on a transformation of the basis functions from a curvilinear coordinate system. Applications to a few test systems show that the modified basis set may speed up electronic structure calculations of sparse systems. The local density approximation (LDA) is used in density functional theory. Although it is the simplest possible approximation possible for the unknown exchange-correlation energy functional, it has proven to give quite accurate results for a wide range of systems. LDA fails in systems where the non-local effects are important. By including non-local effects by adding an orbital dependent term to the energy functional, through for example the LDA+U method, the calculated properties of many materials are closer to experimental observations. In the thesis the most general formulation of the LDA+U method is presented and a new way of interpreting the results of a calculations by formulating the orbital dependent part of the energy functional in terms of multipole momentum tensors. Applications to some early actinide systems leads to a reformulations of Hund’s rules for polarisations associated with the spin and orbital magnetic moment and a suggestion for similar rules, Katt’s rules, valid in the strong spin orbit coupling regime.

Density functional theory has been used to investigate cathode materials for rechargeable batteries, carbon nanotube interactions with catalyst particles and transition metal catalyzed hydrogen release in magnesium hydride nanoclusters. An effort has been made to the understand structural and electrochemical properties of lithium iron silicate (Li2FeSiO4) and its manganese-doped analogue. Starting from the X-ray measurements, the crystal structure of Li2FeSiO4 was refined, and several metastable phases of partially delithiated Li2FeSiO4 were identified. There are signs that manganese doping leads to structural instability and that lithium extraction beyond 50% capacity only occurs at impractically high potentials in the new material. The chemical interaction energies of single-walled carbon nanotubes and nanoclusters were calculated. It is found that the interaction needs to be strong enough to compete with the energy gained by detaching the nanotubes and forming closed ends with carbon caps. This represents a new criterion for determining catalyst metal suitability. The stability of isolated carbon nanotube fragments were also studied, and it is argued that chirality selection during growth is best achieved by exploiting the much wider energy span of open-ended carbon nanotube fragments. Magnesium hydride nanoclusters were doped with transition metals Ti, V, Fe, and Ni. The resulting changes in hydrogen desorption energies from the surface were calculated, and the associated changes in the cluster structures reveal that the transition metals not only lower the desorption energy of hydrogen, but also seem to work as proposed in the gateway hypothesis of transition metal catalysis.

The purpose of this thesis has been to investigate the elastic properties of an fcc FeMg alloy with 10 at.% magnesium under high pressure. Recent research has shown that magnesium can be a possible candidate for light element impurities in the Earth’s inner core, something that was previously not considered possible because of the low miscibility of magnesium in iron at ambient pressure. Gaining knowledge about the composition of the Earth’s core can help us better understand such phenomena as seismic activity and the fluctuations of the Earth’s magnetic field. The elastic constants of the FeMg alloy was calculated using ab-initio methods based on Density Functional Theory. The Exact Muffin-Tin Orbitals method was used in conjunction with the Coherent Potential Approximation. The FeMg alloy was found to be overall considerably softer than pure iron, and the softening effect on the elastic constants was also found to increase with pressure. The results also showed that 10% Mg alloying increased the anisotropy with about 40% compared to pure iron.