Metastable (Ti,Si)N alloy and TiN/SiNx multilayer thin solid films as well as SiNx/TiN surfaces have been explored. Cubic Ti1-xSixN (0≤x≤0.14) films deposited onto cemented carbide (WC-Co) substrates by arc evaporation exhibited a competitive columnar growth mode where the structure transforms to a feather-like nanostructure with increasing Si content as revealed by x-ray diffraction and transmission electron microscopy. X-ray photoelectron spectroscopy revealed the presence of Ti-N and Si-N bonding, but no amorphous Si3N4. Band structure calculations showed that phase separation of NaClstructure Ti1-xSixN solid solution into cubic SiN and TiN phases is energetically favorable. The metastable microstructure, however, was maintained for the Ti0.86Si0.14N film annealed at 900°C, while recrystallization in the cubic state took place at 1100°C annealing during 2h. The Si content influenced the film hardness close to linearly, by combination of solid-solution hardening in the cubic state and defect hardening. For x=0 and x=0.14, nanoindentation gave a hardness of 29.9±3.4 GPa and 44.7±1.9 GPa, respectively. The hardness was retained during annealing at 900°C. Nanostructured materials, e.g., nanocomposites and nanolaminates, are defined by internal interfaces, of which the nature is still under debate. In this work two-phase model systems were explored by depositing SiNx/TiN nanolaminate films, including superlattices containing cubic SiNx, by dual target reactive magnetron sputtering. It is demonstrated that the interfacial phase of SiNx onto TiN(001) and TiN(111) can be crystalline, and even epitaxial with complex surface reconstructions. Using in situ structural analyses combined with ab initio calculations, it is found that SiNx layers grow epitaxially, giving rise to strong interfacial bonding, on both TiN(001) and TiN(111) surfaces. In addition, TiN overlayers grow epitaxially on SiNx/TiN(001) bilayers in nanolaminate structures. These results provide insight into the development of design rules for novel nanostructured materials. / Report code: LiU-TEK-LIC-2006:51.

Computer modeling of enzymes is a valuable complement to experiments. Quantum chemical studies of enzymatic reactions can provide a detailed description of the reaction mechanism and elucidate the roles of various residues in the active site. Different reaction pathways can be analyzed, and their feasibility be established based on calculated energy barriers. In the present thesis, density functional theory has been used to study the active sites and reaction mechanisms of three different enzymes, cytosine deaminase (CDA) from Escherichia coli, ω-transaminase from Chromobacterium violaceum (Cv-ωTA) and dinitrogenase reductase-activating glycohydrolase (DraG) from Rhodospirillum rubrum. The cluster approach has been employed to design models of the active sites based on available crystal structures. The geometries and energies of transition states and intermediates along various reaction pathways have been calculated, and used to construct the energy graphs of the reactions. In the study of CDA (Paper I), two different tautomers of a histidine residue were considered. The obtained reaction mechanism was found to support the main features of the previously proposed mechanism. The sequence of the events was established, and the residues needed for the proton transfer steps were elucidated. In the study of Cv-ωTA (Paper II and Paper III), two active site models were employed to study the conversion of two different substrates, a hydrophobic amine and an amino acid. Differences and similarities in the reaction mechanisms of the two substrates were established, and the role of an arginine residue in the dual substrate recognition was confirmed. In the study of DraG (Paper IV), two different substrate-binding modes and two different protonation states of an aspartate residue were considered. The coordination of the first-shell ligands and the substrate to the two manganese ions in the active site was characterized, and a possible proton donor in the first step of the proposed reaction mechanism was identified. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

A coupling-limited approach for the Ullmann reaction-like on-surface synthesis of a two-dimensional covalent organic network starting from a halogenated metallo-porphyrin is demonstrated. Copper-octabromo-tetraphenylporphyrin molecules can diffuse and self-assemble when adsorbed on the inert Au(111) surface. Splitting-off of bromine atoms bonded at the macrocyclic core of the porphyrin starts at room temperature after the deposition and is monitored by X-ray photoelectron spectroscopy for different annealing steps. Direct coupling between the reactive carbon sites of the molecules is, however, hindered by the molecular shape. This leads initially to an ordered non-covalently interconnected supramolecular structure. Further heating to 300 °C and an additional hydrogen dissociation step is required to link the molecular macrocycles via a phenyl group and form large ordered polymeric networks. This approach leads to a close-packed covalently bonded network of overall good quality. The structures are characterized using scanning tunneling microscopy. Different kinds of lattice defects and, furthermore, the impact of polymerization on the HOMO–LUMO gap are discussed. Density functional theory calculations corroborate the interpretations and give further insight into the adsorption of the debrominated molecule on the surface and the geometry and coupling reaction of the polymeric structure. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

An understanding of the fundamental mechanism behind the relief of shear stress in single-crystal silicon subject to loading by shock-waves has to this day remained elusive. What is known is that this material undergoes a first-order pressure-induced polymorphic phase transition from its ambient pressure cubic-diamond (cd) crystal structure to its first stable high-pressure phase, known as &beta;-Sn, at a pressure of about 120 kbar under hydrostatic compression. By investigating the evolution of the transition parameters for this phase transition as a function of increasing uniaxial shear stress representative of the effects of shock-compression via ab-initio Density Functional Theory computational techniques, we predict a significant lowering of the stress at which the phase transition occurs. This raises the question as to whether the onset of plastic response at the material's Hugoniot Elastic Limit (HEL) reported in experiments corresponds in fact to the phase transition itself, a very plausible possibility which has never been considered before. Furthermore, we present molecular dynamics simulations using a Tersoff-like potential of shock-compressed single crystals of silicon. We find an elastic response up to a critical stress, above which the shear stress is relieved by an inelastic response associated with a partial transformation to a new high-pressure phase, where both the new phase (Imma) and the original cubic diamond phase are under close to hydrostatic conditions. We note that these simulations are also consistent with shear stress relief provided directly by the shock-induced phase transition itself, without an intermediate state of plastic deformation of the cubic diamond phase.

Ground state destabilization is a hypothesis to explain enzyme catalysis. The most popular interpretation of it is the entropic effect, which states that enzymes accelerate biochemical reactions by bringing the reactants to a favorable position and orientation and the entropy cost of this is compensated by enthalpy of binding. Once the enzyme-substrate complex is formed, the reaction could proceed with negligible entropy cost. Deamination of cytidine catalyzed by E.coli cytidine deaminase appears to agree with this hypothesis. In this reaction, the chemical transformation occurs with a negligible entropy cost and the initial binding occurs with a large entropy penalty that is comparable to the entropic cost of the uncatalyzed reaction. Our calculations revealed that this reaction occurs with different mechanisms in the cytidine deaminase and water. The uncatalyzed reaction involves a concerted mechanism and the entropy cost of this reaction appears to be dominated by the reacting fragments and first solvation shell. The catalyzed reaction occurs via a stepwise mechanism in which a hydroxide ion acts as the nucleophile. In the active site, the entropy cost of hydroxide ion formation is eliminated due to pre-organization of the active site. Hence, the entropic effect in this reaction is due to a pre-organized active site rather than ground state destabilization. In the second part of this thesis, we investigated peptide bond formation and peptidyl-tRNA hydrolysis at the peptidyl transferase center of the ribosome. Peptidyl-tRNA hydrolysis occurs by nucleophilic attack of a water molecule on the ester carbon of peptidyl-tRNA. Our calculations showed that this reaction proceeds via a base catalyzed mechanism where the A76 O2’ is the general base and activates the nucleophilic water. Peptide bond formation occurs by nucleophilic attack of the α-amino group of aminoacyl-tRNA on the ester carbon of peptidyl-tRNA. For this reaction we investigated two mechanisms: i) the previously proposed proton shuttle mechanism which involves a zwitterionic tetrahedral intermediate, and ii) a general base mechanism that proceeds via a negatively charged tetrahedral intermediate. Although both mechanisms resulted in reasonable activation energies, only the proton shuttle mechanism found to be consistent with the pH dependence of peptide bond formation.

Downscaling of the contact length Lc of a side-contacted carbon nanotube field-effect transistor (CNTFET) is challenging because of the rapidly increasing contact resistance as Lc falls below 20–50 nm. If in agreement with existing experimental results, theoretical work might answer the question, which metals yield the lowest CNT–metal contact resistance and what physical mechanisms govern the geometry dependence of the contact resistance. However, at the scale of 10 nm, parameter-free models of electron transport become computationally prohibitively expensive. In our work we used a dedicated combination of the Green function formalism and density functional theory to perform an overall ab initio simulation of extended CNT–metal contacts of an arbitrary length (including infinite), a previously not achievable level of simulations. We provide a systematic and comprehensive discussion of metal–CNT contact properties as a function of the metal type and the contact length. We have found and been able to explain very uncommon relations between chemical, physical and electrical properties observed in CNT–metal contacts. The calculated electrical characteristics are in reasonable quantitative agreement and exhibit similar trends as the latest experimental data in terms of: (i) contact resistance for Lc = ∞, (ii) scaling of contact resistance Rc(Lc); (iii) metal-defined polarity of a CNTFET. Our results can guide technology development and contact material selection for downscaling the length of side-contacts below 10 nm.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

The swelling properties of Bentonite are highly affected by clay content and the clay-water interactions that arise from the ion distribution in the diffuse double layer formed near the charged montmorillonite (or smectite) surfaces. Existing continuum models describing the electric double layers, such as classical Poisson-Boltzmann and DLVO theory, ignore the ion-ion correlations, which are especially important for multivalent ions at high surface charge and ionic strength. To better understand the clay-water interactions, atomistic models were developed using both density functional theory of fluids (DFT) as well as classical molecular dynamics (MD) methods. In order to increase our understanding of water-saturated, swelling smectite clays, a DFT, technique was initially developed that allowed more accurate predictions of important thermodynamic properties of the diffuse double layers. This DFT approach was then extended to handle systems with mixtures of different sizes and charges. The extended DFT model was verified against experiments and Monte-Carlo simulations. One practical application was to predict the ion exchange equilibria in Bentonite clays, which have wide practical usage in different areas. Nevertheless, in the DFT work it was realized that DFT demands that the particles, ions in this case, which are described as hard spheres, realistically cannot be described as such at low water loadings, when ion specific hydration forces govern the electric double layer properties. To study how the deformation of the hydration shells of Ca2+ influences the properties of compacted smectite clays, MD simulations using the CLAYFF forcefield were employed in order to account for the deformation of the hydration shells. Comparisons of DFT and MD modeling then allowed to demonstrate under which conditions DFT modeling becomes increasingly inaccurate and when it still can give accurate results. / Under senare år har mycket forskning ägnats åt att förstå egenskaperna hos svällande leror som används för att skydda mot läckage av föroreningar från kontaminerade områden och från framtida slutförvar av radionuklider. Den fria svällningen förorsakas av de starka osmotiska krafter som uppstår när vatten tränger in mellan de tunna elektriskt negativt laddade lermineralskikten och löser de laddningskompenserande jonerna i det diffusa dubbelskiktet. I flera arbeten användandes av sk. kontinuum-teori har vattenmolekylens form, specifika orientering och bindning till katjonerna i de nanometerstora utrymmen mellan lerpartiklarna ej beaktats samt ej heller hur de hydratiserade jonerna orienteras på de atomärt ojämna ytorna. Detta möjliggörs dock genom modellering av de enskilda atomernas och jonernas interaktioner med molekyldynamik simuleringar, MD. I detta arbete har programmet Gromacs använts tillsammans med kraftfältet CLAYFF för att studera dessa fenomen i montmorillonitleror med natrium- och kalciumjoner. Simuleringarna visar att natrium bildar transienta innersfärkomplex vilka orienterar sig i bi-triangulära fördjupningar på ytan, ungefär 3.8 Å från mitt-planet mellan lerytorna. Denna orientering observeras ända upp till att avståndet mellan ytorna ökat till större än motsvarande fem lager vattenmolekyler mellan lerpartiklarnas ytor. Detta sker inte med kalcium, oberoende av avståndet mellan ytorna. Natriumjoner koordineras med fyra vattenmolekyler och en syreatom på leran vid ett lager vatten mellan ytorna och med fem till sex vattenmolekyler, ortogonalt orienterade med ökande mängd vatten mellan ytorna, och med en hydratiserad jon-radie av 3.1 Å. Kalcium koordinerar till sju vattenmolekyler vid ett vattenlager mellan ytorna, men ökar till åtta ortogonalt orienterade vattenmolekyler med en jonradie på 3.3 Å vid större avstånd. Generellt visas att när avståndet mellan lerytorna är mindre än ca 10 Å, deformeras de annars symmetriskt hydratiserade jonerna. En jämförelse mellan MD simuleringar och med klassisk täthetsfunktionalteori, DFT, visar att den senare inte kan beskriva hur yttersfärkomplexen samverkar med laddningarna bundna närmast ytan, dvs i Stern-lagret. / <p>QC 20170403</p>

Nuclear magnetic resonance (NMR) is a popular spectroscopic method and has widespread use in many fields. Recent developments in solid-state NMR have increased interest in experiment and, alongside simultaneous developments in computational theory, have led to the field dubbed 'NMR crystallography.' This is a suite of methodologies, complementing the capabilities of other crystallographic methods in the determination of atomic structure, especially when large crystals cannot be made and when exploring materials with phenomena such as compositional, positional and dynamic disorder. NMR J-coupling is the indirect coupling between nuclear spins, which, when measured, can reveal a wealth of information about structure and bonding. This thesis develops and applies the method of Joyce for the prediction of NMR J-coupling in condensed matter systems using plane-wave pseudopotential density-functional theory, an important requirement for efficient treatment of finite and infinite periodic systems. It describes the first-ever method for the use of ultrasoft pseudopotentials and inclusion of special relativistic effects in J-coupling prediction, allowing for the treatment of a wider range of materials systems and overall greater user friendliness, thus making the method more accessible and attractive to the wider scientific community.

À l'heure actuelle, le développement dans les piles à combustible gagne un regard considérable pour la cogénération de l'énergie propre. Plus particulièrement, les piles à combustible à conduction protonique dont leurs électrolytes sont des oxydes de type pérovskite. Nous nous sommes intéressés aux électrolytes des piles de type PCFC « Proton Ceramic Fuel Cell » dont la température de fonctionnement est intermédiaire. L'intérêt porté pour l'amélioration de la diffusion du proton au sein de ces matériaux implique une compréhension fondamentale de l'interaction du proton avec son environnement. Cette problématique a conduit à une étude systématique en appliquant l'approche de la théorie de la fonctionnelle de la densité sur les matériaux de BaMxZr1-xO3 (M=Y, In et Sc ; x=12,5, 25 et 37,5%). Dans un premier temps, la validation de la méthode appliquée sur le système idéal de BaZrO3 et BaZr0,625Y0,375O3 a été nécessaire afin de reproduire les propriétés électroniques, structurales et de vibration de phonon en bon accord avec les résultats expérimentaux. Dans un deuxième temps, la variation des propriétés électroniques et structurales en fonction de la nature du dopant accepteur (M=Y, In et Sc), sa répartition dans le réseau, et sa concentration ont été étudiées. Une distorsion locale autour de l'atome dopant dans le réseau a été obtenue. Par conséquent, une baisse de symétrie du réseau a été déterminée. Cette distorsion est remarquée quel que soit la nature du dopant. La différence la plus marquée de l'effet de la nature du dopant est trouvée sur les charges atomiques des ions oxygène selon trois environnement possible : Zr-O(1)-Zr, Zr-O(2)-M et M-O(3)-M. Une diminution de la charge (et donc diminution de la basicité) sur le site O3 est bien remarquée dans BaMxZr1-xO3. On attribue cette diminution de charge à la formation d'une liaison covalente à caractère anti-liant Y-O2 (O3). La liaison est ionique pour Sc-O2(O3) et covalente de faible caractère liant pour In-O2 (O3). Nous avons poursuivi nos investigations sur l'insertion d'hydrogène dans les matériaux étudiés. L'analyse des propriétés électroniques, structurales, des vibrations de phonon et l'énergie d'interaction de l'hydrogène des structures BaMxZr1-xO3H, nous ont permis d'établir une corrélation entre le caractère de la liaison chimique M-O, l'insertion du proton et la force de la liaison O-H. L'insertion de H sur le site O3 dans BaYxZr1-xO3 (x=0,25 et 0,375) n'est pas obtenue, probablement à cause de la faible basicité de l'ion oxygène dans la configuration Y-O3-Y. L'insertion du H sur le site O3 pour les deux configurations In-O-In et Sc-O-Sc est obtenue dans BaInxZr1-xO3 (x=0,25 et 0,375) et BaScxZr1-xO3 (x=0,25 et 0,375) respectivement. La variation de l'énergie d'interaction de l'hydrogène avec son environnement dévoile une stabilisation des défauts protoniques significativement plus importante dans le cas de l'atome dopant accepteur yttrium que dans le cas des dopants In et Sc. L'analyse des fréquences de vibration de valence de la liaison O-H a montrée que cette liaison est plus forte dans BaInxZr1-xO3 et BaScxZr1-xO3 que dans BaYxZr1-xO3. En conclusion, nos résultats démontrent que le matériau BaZrO3 dopé en Y favorise plus la formation des défauts protoniques avec une liaison O-H moins forte que dans les matériaux baryum zirconates dopés en In et Sc. / At the present, the development of fuel cells gains a significant interest for their application in clean energy technologies, more specifically, the proton conducting fuel cells. We are interested in the perovskite oxides electrolytes used in PCFC fuel cell “Proton Ceramic Fuel Cell” which operates at intermediate temperature. The interest for the improvement of proton diffusion in these materials necessitates a fundamental systematic understanding of the proton interaction with its environment. Therefore we applied Density Functional Theory based approach on ideal BaZrO3 and doped barium zirconates BaMxZr1-xO3 (M=Y, Sc and In ; x=12.5, 25 and 37.5%), currently known among the best candidates for PCFC electrolytes. First, the validation of the method applied to the ideal system and BaY0.375Zr0.625O3 was necessary in order to reproduce the electronic, structural and phonon vibration in good agreement with the experimental results. Second, the variation of electronic and structural properties and of the phonon vibration was studied as a function of acceptor dopant nature, positions in the lattice and concentration. A local distortion around the dopant atom in the lattice was obtained. Therefore a reduction of the symmetry system has been determined. This distortion is noticeable regardless of the nature of the dopant. The most striking difference due to the dopant nature is found for the atomic charges on three possible oxygen environments : Zr-O(1)-Zr, Zr-O(2)-M and M-O(3)-M. A decrease in the atomic charge of O3 site (decrease of basicity) is well observed in BaYxZr1-xO3. This decrease in the charge can be attributed to the formation of a covalent anti-binding Y-O2(O3) bond. The binding is ionic for Sc-O2 and slightly covalent with a maximum of 15% covalency for In-O2. Our next investigations were focused on the insertion of hydrogen in the studied materials. The analysis of the computed electronic and structural properties, phonon vibrations and hydrogen interaction energies allowed us to establish a correlation between the nature of the chemical bonding M-O, the insertion energy of the proton and the O-H bond strength. The insertion of hydrogen in O3 site in BaYxZr1-xO3 (x=0.25 and 0.375) is not obtained, probably due to the low basicity of the oxygen ion in the configuration Y-O-Y. The insertion of H at the oxygen site for both In-O3-In and Sc-O3-Sc configurations found to be energetically favored in BaInxZr1-xO3 (x=0.25 and 0.375) and BaScxZr1-xO3 (x=0.25 and 0.375) respectively. The variation of hydrogen interaction energy with its environment reveals a significantly stronger stabilization of proton defects in the case of yttrium acceptor dopant than in the two other barium zirconates doped with In and Sc. The analysis of O-H stretching vibration frequencies has shown that the O-H bond is stronger in BaInxZr1-xO3 and BaScxZr1-xO3 than in BaYxZr1-xO3. In conclusion, our results show that the Y doped barium zirconate material favors the formation of proton defects, with a weaker O-H bond than in In and Sc doped oxides.