This thesis presents and uses the techniques of computational chemistry to explore two different processes induced in human skin by ultraviolet light. The first is the transformation of urocanic acid into a immunosuppressing agent, and the other is the enzymatic action of the 8-oxoguanine glycosylase enzyme. The photochemistry of urocanic acid is investigated by time-dependent density functional theory. Vertical absorption spectra of the molecule in different forms and environments is assigned and candidate states for the photochemistry at different wavelengths are identified. Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the cis isomer where competition between intra- and inter-molecular interactions increases flexibility. A model to explain the observed gas phase photochemistry of urocanic acid is developed and it is shown that a reinterpretation in terms of a mixture between isomers significantly enhances the agreement between theory and experiment , and resolves several peculiarities in the spectrum. A model for the photochemistry in the aqueous phase of urocanic acid is then developed, in which two excited states governs the efficiency of photoisomerization. The point of entrance into a conical intersection seam is shown to explain the wavelength dependence of photoisomerization quantum yield. Finally some mechanistic aspects of the DNA repair enzyme 8-oxoguanine glycosylase is investigated with density functional theory. It is found that the critical amino acid of the active site can provide catalytic power in several different manners, and that a recent proposal involving a SN1 type of mechanism seems the most efficient one.

Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO2 cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding. This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified. Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.

The present thesis deals with the application of ab-initio electronic structure calculations based on density functional theory for material design. The correlation between magnetic properties and electronic structures has been investigated in detail for diluted magnetic semiconductors (DMS), which have promising application for spintronics devices. The point defects, acting as electron donor or electron acceptor, have been studied for their key role in mediating the long ranged ferromagnetic interaction between transition metal (TM) ions. The electron holes induced by electron acceptor are completely spin polarized in semiconductor and exhibit a very significant efficiency to the ferromagnetic coupling between TM ions. While the electron donor shows a negative effect to the ferromagnetism in the system. The common trend of magnetic interaction and electron charge transfer between TM ions and electron acceptors or electron donators have been outlined. The Coulomb correlation U of d electrons, which could change the energy levels of TM d band respective to the host semiconductor band, also shows a significant influence on the magnetic behavior in DMS. The crystallography phase transition under high pressure has also been studied for the iron doped with light element, carbon. Our calculated results show that interstitial carbon defect has little effect on the iron's bcc to hcp phase transition under high pressure. The other carbon iron phases, like Fe3C, has also been studied in a wide pressure range. We also present a first-principles description on the temperature dependence of elastic constant for solids. The total temperature effects are approximated as a sum of two separated parts, the thermal expansion contribution, which gives the normal linearly decreasing effect on the elastic constant with increasing temperature, and the electronic band contribution, which could lead anomalous behavior for thermal elastic constants.

The electronic and geometrical structure of free neutral clusters and liquids have been studied using synchrotron-radiation based photoelectron and Auger electron spectroscopy in combination with lineshape modeling. A novel experimental setup has been developed for studies of liquids, based on the liquid microjet technique. Theoretical lineshapes have been computed using both classical (molecular dynamics) and quantum mechanical (mainly density functional theory) methods. Clusters are finite ensembles of atoms or molecules, ranging in size from a few to several thousand atoms. Apart from being fundamentally interesting, clusters are also promising as building blocks for nano-technology. In this thesis results are presented for rare-gas and molecular clusters, ranging from weakly van-deer-Waals bonded to hydrogen bonded. It is shown that the combination of core-level photoelectron spectroscopy (XPS) and lineshape modeling can be used to estimate the sizes of clusters. A model for treating the effect of inter-molecular nuclear relaxation upon ionization is proposed. The structure of single-component molecular clusters are investigated by molecular dynamics simulations, validated against XPS data. Finally, the radial structure of a two-component molecular cluster is investigated by XPS. Liquids have been studied for centuries, but still many questions remain regarding the microscopic properties. With the recent development of the liquid microjet technique, new insight into the atomic structure can be obtained. In this thesis we study aqueous solutions using photoelectron and Auger electron spectroscopy (AES). We investigate the structure of surface active molecules by XPS, study the Auger decay after core-level ionization in aqueous potassium chloride (KCl), and follow the changes in molecular structure of glycine as a function of pH.

Time-dependent density functional theory calculations have been carried out to determine the complex first-order hyperpolarizability in the two-photon resonance region of the molecule IDS-Cab. Calculations show that three strongly absorbing states, in the ultraviolet region, are separated to the extent that no significant interference of the imaginary parts of the tensor elements of the first-order hyper-polarizability occurs. Consequently, and in contrast to experimental findings [27], no reduced imaginary parts of the first-order hyperpolarizability in the two-photon resonant region can be seen.

Quantum chemistry has nowadays become a powerful and efficient tool that can be successfully used for studies of biosystems. It is therefore possibleto model the enzyme active-site and the reactions undergoing into it, as well as obtaining quite accurate energetic profiles. Important conclusions can be drawn from such profiles about the  plausibility of different putative mechanisms. Density Functional Theory is used in the present thesis for investigation of the catalytic mechanism of dioxygenase metallo-enzymes and synthetic model complexes. Three enzymes were studied – Homoprotocatechuate 2,3-dioxygenase isolated from Brevibacterium fuscum (Bf 2,3-HPCD), Manganese-Dependent Homoprotocatechuate 2,3-Dioxygenase (MndD) and Homogentisate Dioxygenase (HGD). Models consisting of 55 to 208 atoms have been built from X-ray crystal structures and used in the calculations. The computed energies were put in energy curves and were used for estimation of the feasibility of the suggested reaction mechanisms. A non-heme [(L4Me4)Fe(III)]+3 complex that mimics the reactivity of intradiol dioxygenases, and a heme [T(o-Cl)PPFe] complex catalyzing the stepwise oxidation of cyclohexane to adipic acid, were also studied. For the enzymes and the non-heme biomimetic complex the reaction was found to follow a mechanism that was previously suggested for extradiol and intradiol dioxygenases – ordered substrates binding and formation of peroxo species, which further undergoes homolytic O-O bond cleavage. Different reaction steps appear to be rate limiting in the particular cases: proton transfer from the substrate to the peroxide in Bf 2,3-HPCD, the formation of the peroxo bridge in HGD and the biomimetic complex, and notably, spin transition in MndD. The catalytic oxidation of cyclohexane to adipic acid in the presence of molecular oxygen as oxidant was studied, a reaction of great importance for the chemical industry. Reaction mechanism is suggested, involving several consecutive oxidative steps. The highest calculated enthalpy of activation is 17.8 kcal/mol for the second oxidative step. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In progress, Paper 5: In progress

The properties of dilute magnetic semiconductors have been studied by combined ab initio, Monte Carlo, and experimental techniques. This class of materials could be very important for future spintronic devices, that offer enriched functionality by making use of both the spin and the charge of the electrons. The main part of the thesis concerns the transition metal doped ZnO. The role of defects on the magnetic interactions in Mn-doped ZnO was investigated. In the presence of acceptor defects such as zinc vacancies and oxygen substitution by nitrogen, the magnetic interactions are ferromagnetic. For dilute concentrations of Mn (~ 5%) the ordering temperature of the system is low, due to the short ranged character of the exchange interactions and disorder effects. The clustering tendency of the Co atoms in a ZnO matrix was also studied. The electronic structure, and in turn the magnetic interactions among the Co atoms, is strongly dependent on the exchange-correlation functional used. It is found that Co impurities tend to form nanoclusters and that the interactions among these atoms are antiferromagnetic within the local spin density approximation + Hubbard U approach. The electronic structure, as well as the chemical and magnetic interactions in Co and (Co,Al)-doped ZnO, was investigated by joined experimental and theoretical techniques. For a good agreement between the two, approximations beyond the local density approximation must be used. It is found that the Co atoms prefer to cluster within the semiconducting matrix, a tendency which is increased with Al co-doping. We envision that it is best to describe the system as superparamagnetic due to the formation of  Co nanoclusters within which the interactions are antiferromagnetic. The magnetic anisotropy and evolution of magnetic domains in Fe81Ni19/Co(001) superlattices were investigated both experimentally, as well as using model spin dynamics. A magnetic reorientation transition was found.

The present thesis deals with a theoretical description of issues regarding chemical bonding, structure and stability of transition metal carbides and multilayered structures. First principles density functional theory has been used extensively to investigate the properties of alloyed solutions of transition metal carbides. Joint theoretical and experimental investigations have shown that there is a driving force for carbon to be released from these ternary carbide systems as a response to the alloying. This release of carbon was shown to yield favorable lubricating properties in the case of alloyed solutions of Ti-Al-C, that were not present in the case of pure TiC, a property that can be used to design new materials that combine high hardness with favorable tribological properties. From calculations of the activation energy of C diffusion in the vicinity of substitutional transition metal impurities (M) in TiC, it is found that the mobility of C atoms is increased due to the presence of the impurities. The lowering of the activation energy barriers suggests that the mobility of C in alloyed solutions of Ti-M-C is increased and will be more pronounced at lower temperature than for C diffusion in TiC. The magnetic properties of alloyed solutions of Ti-Fe-C has been investigated using both theory and experiment. Theoretical calculations reveal that the magnetic moment and the critical temperature increase when increasing the Fe content as well as when lowering the C content in the system. Furthermore, the magnetic exchange parameters between Fe atoms were found to clearly reflect changes in the chemical bonding when varying the C content. Experimentally the magnetic properties were found to be rather substantial. Furthermore, the magnetic properties changes upon annealing due to the formation of Fe-rich and Fe-poor regions in the system. After long enough annealing times precipitates of α-Fe are formed which is consistent with theoretical predictions. The interaction between TiC(111) surfaces and C in the form of graphite has also been investigated. For these systems it was found that graphite was rather strongly bonded to the carbide surface and that the atomic as well as electronic structure at the interface depend on the termination of the carbide surface. This research was motivated by the recent interest in graphene, but also to investigate how carbide grains interacts with C when dispersed in a carbon matrix. A model for the calculation of structural parameters in multilayer structures has been presented and evaluated. The model is based on classical elasticity theory and uses the elastic constants of the materials constituting the multilayer as the only input.

The overall aim of this thesis is to compare different methods for calculation of Core-Level shifts in metallic alloys. The methods compared are the Initial State model, the Complete screening and the Transition state model. Core-level shifts can give information of chemical bonding and about the electronic structure in solids. The basic theory used is the so-called Density-Functional-Theory, in conjunction with the Local-Density Approximation and the Coherent-Potential- Approximation. The metallic alloys used are Silver-Palladium, Copper-Palladium, Copper-Gold and Copper-Platinum, all inface-centered-cubic configuration. The complete screening- and the transition-state model are found to be in better agreement with experimental results than those calculated with the initial state model. This is mainly due to the fact that the two former models includes final-state effects, whereas the last one do not. The screening parameters within the Coherent-Potential approximation are also investigated. It is found that the Screened-Impurity Model can extend the validity of the Coherent-Potential-Approximation and increase it's accuracy.

As the demand for clean and renewable energy sources continues to grow, much attention has been given to solid oxide fuel cells (SOFCs) due to their efficiency and low operating temperature. However, the components of SOFCs must still be improved before commercialization can be reached. Of particular interest is the solid electrolyte, which conducts oxygen ions from the cathode to the anode. Samarium-doped ceria (SDC) is the electrolyte of choice in most SOFCs today, due mostly to its high ionic conductivity at low temperatures. However, the underlying principles that contribute to high ionic conductivity in doped ceria remain unknown, and so it is difficult to improve upon the design of SOFCs. This thesis focuses on identifying the atomistic interactions in SDC which contribute to its favourable performance in the fuel cell. Unfortunately, information as basic as the structure of SDC has not yet been found due to the difficulty in experimentally characterizing and computationally modelling the system. For instance, to evaluate 10.3% SDC, which is close to the 11.1% concentration used in fuel cells, one must investigate 194 trillion configurations, due to the numerous ways of arranging the Sm ions and oxygen vacancies in the simulation cell. As an exhaustive search method is clearly unfeasible, we develop a genetic algorithm (GA) to search the vast potential energy surface for the low-energy configurations, which will be most prevalent in the real material. With the GA, we investigate the structure of SDC for the first time at the DFT+U level of theory. Importantly, we find key differences in our results from prior calculations of this system which used less accurate methods, which demonstrate the importance of accurately modelling the system. Overall, our simulation results of the structure of SDCagree with experimental measurements. We identify the structural significance of defects in the doped ceria lattice which contribute to oxygen ion conductivity. Thus, the structure of SDC found in this work provides a basis for developing better solid electrolytes, which is of significant scientific and technological interest. Following the structure search, we perform an investigation of the electronic properties of SDC, to understand more about the material. Notably, we compare our calculated density of states plot to XPS measurements of pure and reduced SDC. This allows us to parameterize the Hubbard (U) term for Sm, which had not yet been done. Importantly, the DFT+U treatment of the Sm ions also allowed us to observe in our simulations the magnetization of SDC, which was found by experiment. Finally, we also study the SDC surface, with an emphasis on its structural similarities to the bulk. Knowledge of the surface structure is important to be able to understand how fuel oxidation occurs in the fuel cell, as many reaction mechanisms occur on the surface of this porous material. The groundwork for such mechanistic studies is provided in this thesis.