<p>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. </p><p>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. </p><p>Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the <i>cis</i> isomer where competition between intra- and inter-molecular interactions increases flexibility. </p><p>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. </p><p>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. </p><p>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 S<i>N</i>1 type of mechanism seems the most efficient one.</p>

A summary of research conducted since September 2007 at the University of Toronto in the laboratory of Professor Robert A. Batey is presented in this thesis, which is divided into four chapters. The first chapter contains a two-part introduction, where aryl- and aliphatic-Claisen rearrangements are discussed in part 1, and the nucleophilic addition of organoboron reagents to unsaturated C–N functionalities is described in part 2. Chapter 2 contains research involving synthetic and theoretical studies of aryl-Claisen rearrangements and other sigmatropic reactions. The work towards developing the lanthanide-catalyzed domino aryl-Claisen rearrangement for the synthesis of contiguous aryl–C(sp³) moieties is presented first. This is followed by computational studies involving E/Z-selectivity differences for the aryl-Claisen rearrangement, which was an issue noted for the domino aryl-Claisen reaction of a linear substrate. The mechanistic origins of E/Z-selectivity differences for the mono aryl-Claisen rearrangement, which was experimentally ambiguous for over 40 years, is resolved through computational methods. A theoretical analysis of selectivity differences for the allylic azide rearrangement is also described. The third section contains a discussion of Eu(fod)3-catalyzed aryl-Claisen rearrangements on vinyl bromide systems and preliminary studies involving application of the substrates in cross-coupling reactions, and other attempted mono- and domino sigmatropic rearrangements are presented in the fourth section. In chapter 3, the search for computational methods that can accurately predict experimental free energy of activation barriers for the aliphatic-Claisen rearrangement through benchmarking studies with a priori kinetic barrier and kinetic isotope effect data is described. Methods were found to predict new valid transition states and predict ΔG‡ values with a mean unsigned error of 0.3 kcal/mol relative to experimental values. In chapter 4, the development of new allylboration reaction is outlined, involving the double allylboration of nitriles and anhydrides, and initial studies towards the first aminoallylboration reactions of N-aluminoaldimines to form 1,2-diamines.

In this work, physical phenomena related to the growth and phase formation of alumina, Al2O3, are investigated by experiments and computer calculations. Alumina finds applications in a wide variety of areas, due to many beneficial properties and several existing crystalline phases. For example, the α and κ phases are widely used as wear-resistant coatings due to their hardness and thermal stability, while, e.g., the metastable γ and θ phases find applications as catalysts or catalyst supports, since their surface energies are low and, hence, they have large surface areas available for catalytic reactions. The metastable phases are involved in transition sequences, which all irreversibly end in the transformation to the stable α phase at about 1050 °C. As a consequence, the metastable aluminas, which can be grown at low temperatures, cannot be used in high temperature applications, since they are destroyed by the transformation into α. In contrast, α-alumina, which is the only thermodynamically stable phase, typically require high growth temperatures (~1000 °C), prohibiting the use of temperature sensitive substrates. Thus, there is a need for increasing the thermal stability of metastable alumina and decreasing the growth temperature of the α phase. In the experimental part of this work, hard and single-phased α-alumina thin films were grown by magnetron sputtering at temperatures down to 280 °C. This dramaticdecrease in growth temperature was achieved by two main factors. Firstly, the nucleation stage of growth was controlled by pre-depositing a chromia “template” layer, which is demonstrated to promote nucleation of α-alumina. Secondly, it is shown that energetic bombardment was needed to sustain growth of the α phase. Energy-resolved mass spectrometry measurements demonstrate that the likely source of energetic bombardment, in the present case, was oxygen ions/atoms originating from the target surface. Overall, these results demonstrate that low-temperature α-alumina growth is possible by controlling both the nucleation step of growth as well as the energetic bombardment of the growing film. In addition, the mass spectrometry studies showed that a large fraction of the deposition flux consisted of AlO molecules, which were sputtered from the target. Since the film is formed by chemical bonding between the depositing species, this observation is important for the fundamental understanding of alumina thin film growth. In the computational part of the work, the effect of additives on the phase stability of α- and θ-alumina was investigated by density functional theory calculations. A systematic study was performed of a large number of substitutional dopants in the alumina lattices. Most tested dopants tended to reverse the stability between α- and θ-alumina; so that, e.g., Modoping made the θ phase energetically favored. Thus, it is possible to stabilize the metastable phases by additives. An important reason for this is the physical size of the dopant ions with respect to the space available within the alumina lattices. For example, large ions induced θ stabilization, while ions only slightly larger than Al, e.g., Co and Cu, gave a slight increase in the relative stability of the α phase. We also studied the stability of some of these compounds with respect to pure alumina and other phases, containing the dopants, with the result that phase separations are energetically favored and will most likely occur at elevated temperatures.

The work presented in this thesis deals with experimental and theoretical studies related to the growth of crystalline alumina thin films. Alumina, Al2O3, is a polymorphic material utilized in a variety of applications, e.g., in the form of thin films. Many of the possibilities of alumina, and the problems associated with thin film synthesis of the material, are due to the existence of a range of different crystalline phases. Controlling the formation of the desired phase and the transformations between the polymorphs is often difficult. In the experimental part of this work, it was shown that the thermodynamically stable alpha phase, which normally is synthesized at substrate temperatures of around 1000 °C, can be grown using reactive sputtering at a substrate temperature of 500 °C by controlling the nucleation surface. This was done by predepositing a Cr2O3 nucleation layer. Moreover, it was found that an additional requirement for the formation of the α phase is that the depositions are carried out at low enough total pressure and high enough oxygen partial pressure. Based on these observations, it was concluded that energetic bombardment, plausibly originating from energetic oxygen, is necessary for the formation of α alumina (in addition to the effect of the chromia nucleation layer). Further, the effects of impurities, especially residual water, on the growth of crystalline films were investigated by varying the partial pressure of water in the ultra high vacuum (UHV) chamber. Films deposited onto chromia nucleation layers exhibited a columnar structure and consisted of crystalline α-alumina if deposited under UHV conditions. However, as water to a partial pressure of 1x10-5 Torr was introduced, the columnar growth was interrupted. Instead, a microstructure consisting of small, equiaxed grains was formed, and the gamma-alumina content was found to increase with increasing film thickness. When gamma-alumina was formed under UHV conditions, no effects of residual water on the phase formation was observed. Moreover, the H content was found to be low (&lt; 1 at. %) in all films. Consequently, this shows that effects of residual gases during sputter deposition of oxides can be considerable, also in cases where the impurity incorporation in the films is found to be low. In the modeling part of the thesis, density functional theory based computational studies of adsorption of Al, O, AlO, and O2 on different alpha-alumina (0001) surfaces have been performed. The results give possible reasons for the difficulties in growing the α phase at low temperatures through the identification of several metastable adsorption sites, and also provide insights related to the effects of hydrogen on alumina growth. / Report code: LiU-TEK-LIC-2007:1.

Numerous enzymatic reactions are controlled by the chemistry of metallic ions. This dissertation investigates the electronic properties of three transition metal (copper, chromium, and nickel) complexes and describes modeling studies performed on glutathione synthetase. (1) Copper nitrene complexes were computationally characterized, as these complexes have yet to be experimentally isolated. (2) Multireference calculations were carried out on a symmetric C2v chromium dimer derived from the crystal structure of the [(tBu3SiO)Cr(µ-OSitBu3)]2 complex. (3) The T-shaped geometry of a three-coordinate β-diketiminate nickel(I) complex with a CO ligand was compared and contrasted with isoelectronic and isosteric copper(II) complexes. (4) Glutathione synthetase (GS), an enzyme that belongs to the ATP-grasp superfamily, catalyzes the (Mg, ATP)-dependent biosynthesis of glutathione (GSH) from γ-glutamylcysteine and glycine. The free and reactant forms of human GS (wild-type and glycine mutants) were modeled computationally by employing molecular dynamics simulations, as these currently have not been structurally characterized.

To accelerate environmentally friendly thin film photovoltaic (PV) technologies, copper-based chalcogenides are attractive as absorber materials. Chalcopyrite copper indium gallium selenide (CIGS ≡ CuIn1–xGaxSe2) is today a commercially important PV material, and it is also in many aspects a very interesting material from a scientific point of view. Copper zinc tin sulfide selenide (CZTSSe ≡ Cu2ZnSn(S1–xSex)4) is considered as an emerging alternative thin film absorber material. Ternary Cu2SnS3 (CTS) is a potential absorber material, thus its related alloys Cu2Sn1–xGexS3 (CTGS) and Cu2Sn1–xSixS3 (CTSS) are attractive due to the tunable band gap energies. CuSb(Se1–xTex)2 and CuBi(S1–xSex)2 can be potential as ultra-thin (≤ 100 nm) film absorber materials in the future. In the thesis, analyses of these Cu-based chalcogenides are based on first-principles calculations performed by means of the projector augmented wave method and the full-potential linearized augmented plane wave formalisms within the density functional theory as implemented in the VASP and WIEN2k program packages, respectively. The electronic and optical properties of CIGS (x = 0, 0.5, and 1) are studied, where the lowest conduction band (CB) and the three uppermost valence bands (VBs) are parameterized and analyzed in detail. The parameterization demonstrates that the corresponding energy dispersions of the topmost VBs are strongly anisotropic and non-parabolic even very close to the Γ-point. Moreover, the density-of-states and constant energy surfaces are calculated utilizing the parameterization, and the Fermi energy level and the carrier concentration are modeled for p-type CIGS. We conclude that the parameterization is more accurate than the commonly used parabolic approximation. The calculated dielectric function of CuIn0.5Ga0.5Se2 is also compared with measured dielectric function of CuIn0.7Ga0.3Se2 collaborating with experimentalists. We found that the overall shapes of the calculated and measured dielectric function spectra are in good agreement. The transitions in the Brillouin zone edge from the topmost and the second topmost VBs to the lowest CB are responsible for the main absorption peaks. However, also the energetically lower VBs contribute significantly to the high absorption coefficient. CTS and its related alloys are explored and investigated. For a perfectly crystalline CTS, reported experimental double absorption onset in dielectric function is for the first time confirmed by our calculations. We also found that the band gap energies of CTGS and CTSS vary almost linearly with composition over the entire range of x. Moreover, those alloys have comparable absorption coefficients with CZTSSe. Cu2XSnS4 (X = Be, Mg, Ca, Mn, Fe, Ni, and Zn) are also studied, revealing rather similar crystalline, electronic, and optical properties. Despite difficulties to avoid high concentration of anti-site pairs disordering in all compounds, the concentration is reduced in Cu2BeSnS4 partly due to larger relaxation effects. CuSb(Se1–xTex)2 and CuBi(S1–xSex)2 are suggested as alternative ultra-thin film absorber materials. Their maximum efficiencies considering the Auger effect are ~25% even when the thicknesses of the materials are between 50 and 300 nm. / <p>QC 20170523</p>

<p>Density functional theory is a formally exact theory to describe ground state properties due to the existence of the exact functional. In practice, the usefulness of density functional theory relies on the accuracy of density functional approximations. After decades of effort of functional developments, the present-day state-of-the-art density functional approximations have achieved reasonably good accuracy for small systems. However, the error grows with system size. One of the dominant errors intrinsic in the mainstream density functional approximations is the delocalization error, which arises because of the violation of Perdew-Parr-Levy-Balduz (PPLB) linearity condition. The PPLB condition governs the formulation of the density functional theory for fractional-charge systems, for which the ground state energy for the exact functional, as a function of the fractional electron number, should yield a series of line-segments across the integer points. In this dissertation, by imposing the PPLB condition in a local, size-consistent way, we develop the local scaling correction (LSC) and its updated version, the localized orbital scaling correction (LOSC), which largely improve upon the mainstream density functional approximations across system sizes. With the LOSC, we open a door towards a systematic elimination of delocalization error. Besides the ground state functional development, we also develop a gentlest ascent dynamics approach for accessing the excited states via time-independent ground state density functionals. This is also useful for exploring Kohn-Sham energy landscapes of approximate density functionals. I will also review the PPLB formulation of density functional theory for fractionally charged systems, and show that it is equivalent to the formulation normally used for fractional system calculations under certain assumptions. Furthermore, I will examine the behavior of the fractional system energy as a function of the fractional number of electrons for different mainstream functionals, and relate it to their errors for integer systems.</p> / Dissertation

The warm dense matter regime (WDM), defined by temperatures of a few electron volts and densities comparable with solids, is a complex state of matter where multi-body particle correlations and quantum effects play an important role in determining the overall structure and equation of state. The study of WDM states represents the laboratory analogue of the astrophysical environments found in the cores of planets and in the crusts of old stars, but also has practical applications for controlled thermonuclear fusion. Time resolved X-ray diffraction is used to study the temporal evolution of a sample from solid state towards WDM, either after irradiation with an intense proton/electron beam, in carbon samples, or direct laser illumination, in thin gold nanofoils. The electron-ion equilibration time is extracted through the use of the two-temperature model and in highly excited carbon shown to be longer than previously thought, this is attributed to strong ion-ion coupling screening the interaction (coupled mode theory). Calculation of the dynamic ion-ion structure factor is performed using orbital-free density functional theory (OF-DFT) and shown to compare well with Kohn-Sham DFT in both the static and dynamic cases. Experimental verification of these results is vital and measurement of the microscopic dynamics of warm dense aluminium have been successfully demonstrated through inelastic X-ray scattering. Using the self-seeded beam at the linear coherent light source (LCLS) scattering at a small momentum exchange allowed the first direct measurement of ion acoustic waves in WDM. This data provides the basis for a direct experimental test of many dense plasma theories through direct comparison with the ion-ion dynamic structure factor.

This thesis combines solid-state nuclear magnetic resonance (NMR) spectroscopy, X-ray diffraction (XRD), chemical synthesis, isotopic enrichment and density-functional theory (DFT) calculations to provide insight into a number of microporous materials. The first class of materials studied is metal-organic frameworks (MOFs), where the presence of paramagnetic ions has a range of effects on the ¹³C NMR spectra, depending on the nature of the ligand-metal interactions. For the Cu²⁺-based MOFs, HKUST-1 and STAM-1, the assignment of the NMR spectra is non-intuitive, and unambiguous assignment requires specific ¹³C labelling of the organic linker species. It is shown that ¹³C NMR spectra of these two MOFs could act as a sensitive probe of the nature of “guest” molecules bound to the Cu²⁺. The second class of materials is aluminophosphates (AlPOs). It is shown that, using a series of relatively simple linear relationships with the crystal structure, the NMR parameters calculated by DFT (with calculation times of several hours) can be predicted, often with experimentally-useful accuracy, in a matter of seconds using the DIStortion analysis COde (DISCO), which is introduced here. The ambient hydration of the AlPO, JDF-2, to AlPO-53(A) is shown to occur slowly, with incomplete hydration after ~3 months. The resulting AlPO-53(A) is disordered and some possible models for this disorder are investigated by DFT. The final class of materials is gallophosphates (GaPOs), particularly GaPO-34 and related materials. The two as-prepared forms of GaPO-34 are characterised by solid-state NMR, and their calcination investigated by TGA and in-situ powder XRD. An unusual dehydrofluorinated intermediate phase is isolated and characterised for the first time by solid-state NMR. The fully calcined material is shown to be stable under anhydrous conditions, but hydrates rapidly in air. The hydrated material is stable under ambient conditions, but collapses upon heating. Partial dehydration without collapse is achieved by gentle heating or room-temperature evacuation. The impurity phases, GaPO₄ berlinite and GaPO-X are investigated by solid-state NMR and, while the structure of GaPO-X remains unknown, much structural information is obtained.

Theoretical studies using the Kohn-Sham density functional formalism have been carried out to identify and investigate the stability of a variety of atomic clusters for their use in cluster assembled materials. The stable behavior found in a cluster system provides a way to classify inorganic clusters. The clusters in this study can be categorized in one of the following, jellium, all-metal aromatic, Zintl analogue or as a covalent metal-carbide. By understanding the electronic structure and ultimately the stable nature of a cluster first, it is proposed one can construct assemblies based on the stable cluster. The methodology presented is a viable way to design future nanomaterials with a variety of architectures and precise control over properties based on stable cluster motifs.