Computational methodologies were employed to study a supramolecular micellar structure and its application, nanoreactor. This task was done through rigorous scale-up procedure using both atomistic and mesoscopic simulations. Primarily, density functional theory (DFT) calculation was used to characterize the smallest unit of complex molecules in the multicomponent mixture system. The following step involved transferring the information achieved by DFT calculation to larger scale simulation, such as molecular dynamics (MD) simulation. Lastly, based on the atomistic simulation results, we performed a series of dissipative particle dynamics (DPD) simulations to study a full body of polymeric multicompartment micelle. In the course of research, we built a systematic procedure to minimize the complexity of computation and efficiently characterize macromolecular structures and its application.

Carbon nanotubes have been envisioned to become a very important material in various applications. This is due to the unique properties of carbon nanotubes which can be exploited in applications on length scales spanning from the nano world to our macroscopic world. For example, the electronic properties of carbon nanotubes makes them utterly suitable for nano electronics while the strength of them makes them suitable for reinforcements in plastics. Both of these applications do however require... mer the ability for systematic production of carbon nanotubes with certain properties. This is called selective carbon nanotube growth and today this has not been achieved with total success. In the work presented in the thesis several different computational methods have been applied in our contribution to the systematic search for selective carbon nanotube growth. Put in a context of previous knowledge about carbon nanotube growth our results provide valuable clues to which parameters that control the carbon nanotube growth. In association with the latest results we even dare to, with all modesty, speculate about a plausible control mechanism. The studies presented in the thesis addressed different stages of carbon nanotube growth, spanning from the properties affecting the initiation of the growth to the parameters affecting the termination of the growth. In some more detail this included studies of the melting temperatures of nanoscaled metal clusters. The expected size dependence of the melting temperatures was confirmed and the melting temperatures of clusters on substrates were seen to depend both on the material and shape of the surface. As this constitute the premises prior to the carbon nanotube growth it was followed by studies of the interaction between carbon nanotubes and metal clusters of different size and constitution. This was done using different computational methods and at different temperatures. It soon became apparent that the clusters adapted to the carbon nanotube and not vice versa. This held true irrespectively of the constitution of the cluster, that is for both pure metal and metal carbide. It was also seen that there exist a minimum cluster size that prevent the carbon nanotube end from closing. Closure of the carbon nanotube end is likely to lead to the termination of the growth which lead to studies of other reasons for growth termination, e.g., Ostwald ripening of the catalyst particles. This was investigated with the result that the rate of the Ostwald ripening may depend on both the chirality and diameter of the carbon nanotubes. It is suggested that this may provide some answers to the controlled growth of carbon nanotubes. / <p>Disputationen sker fredagen den 3 december 2010, kl. 10:15, Kollektorn, Kemivägen 9</p>

<p>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.</p><p>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.</p><p>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.</p>

<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>

No description available.

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>