In this thesis I have studied some problems of condensed matter at high pressures and temperatures by means of numerical simulations based on Density Functional Theory (DFT). The stability of MgCO3 and CaCO3 carbonates at the Earth's mantle conditions may play an important role in the global carbon cycle through the subduction of the oceanic crust. By performing ab initio electronic structure calculations, we observed a new high-pressure phase transition within the Pmcn structure of CaCO3. This transformation is characterized by the change of the sp-hybridization state of carbon atom and indicates a change to a new crystal-chemical regime. By performing ab initio Molecular Dynamics simulations we show the new phase to be stable at 250 GPa and 1000K. Thus, the formation of sp3 hybridized bonds in carbonates can explain the stability of MaCO3 and CaCO3 at pressures corresponding to the Earth's lower mantle conditions. We have also calculated phase transition sequence in CaCO3, SrCO3 and BaCO3, and have found that, despite the fact that these carbonates are isostructural and undergo the same type of aragonite to post-aragonite transition, their phase transformation sequences are different at high pressures. The continuous improvement of the high-pressure technique led to the discovery of new composite structures at high pressures and complex phases of many elements in the periodic table have been determined as composite host-guest incommensurate structures. We propose a procedure to accurately describe the structural parameters of an incommensurate phase using ab initio methods by approximating it with a set of analogous commensurate supercells and exploiting the fact that the total energy of the system is a function of structural parameters. By applying this method to the Sc-II phase, we have determined the incommensurate ratio, lattice parameters and Wyckoff positions of Sc-II in excellent agreement with the available experimental data. Moreover, we predict the occurrence of an incommensurate high-pressure phase in Ca from first-principle calculations within this approach. The implementation of DFT in modern electronic structure calculation methods proved to be very successful in predicting the physical properties of a solid at low temperature. One can rigorously describe the thermodynamics of a crystal via the collective excitation of the ionic lattice, and the ab initio calculations give an accurate phonon spectra in the quasi-harmonic approximation. Recently an elegant method to calculate phonon spectra at finite temperature in a self-consistent way by using first principles methods has been developed. Within the framework of self-consistent ab initio lattice dynamics approach (SCAILD) it is possible to reproduce the observed stable phonon spectra of high-temperature bcc phase of Ti, Zr and Hf with a good accuracy. We show that this method gives also a good description of the thermodynamics of hcp and bcc phases of Ti, Zr and Hf at high temperatures, and we provide a procedure for the correct estimation of the hcp to bcc phase transition temperature.

In this thesis a computational complement to experimental observables will be presented. Computational tools such as molecular dynamics and quantum chemical tools will be used to aid in the interpretation of experimentally (NMR) obtained structural data. The techniques are applied to study the dynamical features of biologically important carbohydrates and their interaction with proteins. When evaluating conformations, molecular mechanical methods are commonly used. Paper I, highlights some important considerations and focuses on the force field parameters pertaining to carbohydrate moieties. Testing of the new parameters on a trisaccharide showed promising results. In Paper II, a conformational analysis of a part of the repeating unit of a Shigella flexneri bacterium lipopolysaccharide using the modified force field revealed two major conformational states. The results showed good agreement with experimental data. In Paper III, a trisaccharide using Langevin dynamics was investigated. The approach used in the population analysis included a least-square fit technique to match T1 elaxation parameters. The results showed good agreement with experimental T-ROE build-up curves, and three states were concluded to be involved. In Paper IV, carbohydrate moieties were used in the development of prodrug candidates, to “hide” peptide opioid receptor agonists. Langevin dynamics and quantum chemical methods were employed to elucidate the structural preference of the compound. The results showed a chemical shift difference between hydrogens across the ring for the two isomers as well as a difference in the coupling constant, when taking the dynamics into account. In Paper V, the interaction of the Salmonella enteritidis bacteriophage P22 with its host bacterium, involves an initial hydrolysis of the O-antigenic polysaccharide (O-PS). Docking calculations were used to examine the binding between the Phage P22 tail-spike protein and the O-PS repeating unit. Results indicated a possible active site in conjunction with NMR measurements.

This thesis presents a theoretical study of materials under high pressure using ab initio lattice dynamics based on density functional theory and density functional perturbation theory using both super-cell and linear response approach. Ab initio lattice dynamics using super-cell approach is applied to compare our theoretical predictions with experimental findings. Phonon dispersion curves of fcc α-γ cerium are calculated and compared with inelastic X-ray scattering data. Pressure dependency of phonon density of states in two cubic phases TiO2 allows us to assign the observed cubic phase in experiments to be of fluorite rather than pyrite structure. Dynamical stability of cotunnite TiO2 phase at low pressure can explain the observed quenching phenomena in experiments. Our calculated O2 vibron mode in both ε-ζ phases of solid oxygen supports the hypothesis that both phases are iso-structural. Hydrogen-dense materials attract great attention not only because they open a path to study phenomena related to metallization (superconductivity) of solid hydrogen but also because they are closely related to important industrial applications (hydrogen storage). Using linear response method, we find that metallic fcc-AlH3 is dynamically stabilized in the range of 72-106 GPa and can persist at ambient pressure if finite temperature effects are considered. For SiH4, we test dynamical stability, Raman spectra, zero point energy, and utilize GW calculations for self energy correction. We find that a metallic tetragonal phase of SiH4 can be assigned to the experimentally observed one. Our ab initio lattice dynamics calculations based on density functional perturbation theory predict that fcc-YH3 is a pressure-induced superconductor with a high transition temperature of 40 K at 17.7 GPa. With increasing pressure this material undergoes a superconductor-metal-superconductor transition and the underlying mechanism of this transition can simultaneously explains also the observed metal-insulator transition at 25 GPa in YH3-δ.

The complete and accurate thermodynamic and kinetic description of any systemis crucialfor understanding and predicting its properties. A particular interest is in systemsthat are used for some practical applications and have to be constantly improved usingmodification of their composition and structure. This task can be quite accuratelysolved at a fundamental level by density functional theory methods. Thesemethods areapplied to two practically important systems Fe-Cr and TiC-ZrC.The elastic properties of pure iron and substitutionally disordered Fe-Cr alloy are investigatedas a function of temperature and concentration using first-principles electronicstructurecalculations by the exact muffin-tin orbitals method. The temperature effectson the elastic properties are included via the electronic, magnetic, and lattice expansioncontributions. It is shown that the degree of magnetic order in both pure iron andFe90Cr10 alloy mainly determines the dramatic change of the elastic anisotropy of thesematerials at elevated temperatures. A peculiarity in the concentration dependence ofthe elastic constants in Fe-rich alloys is demonstrated and related to a change in theFermi surface topology.A thermodynamic model for the magnetic alloys is developed from first principles andapplied to the calculation of bcc Fe-Cr phase diagram. Various contributions to the freeenergy (magnetic, electronic, and phonon) are estimated and included in the model. Inparticular, it is found that magnetic short range order effects are important just abovethe Curie temperature. The model is applied for calculating phase equilibria in disorderedbcc Fe-Cr alloys. Model calculations reproduce a feature known as a Nishizawahorn for the Fe-rich high-temperature part of the phase diagram.The investigation of the TiC-ZrC system includes a detailed study of the defect formationenergies and migration barriers of point defects and defect complexes involvedin the diffusion process. It is found, using ab initio atomistic simulations of vacancymediateddiffusion processes in TiC and ZrC, that a special self-diffusion mechanism isoperative for metal atom diffusion in sub-stoichiometric carbides. It involves a noveltype of a stable point defect, a metal vacancy ”dressed” in a shell of carbon vacancies.It is shown that this vacancy cluster is strongly bound and can propagate through thelattice without dissociating. / <p>QC 20120604</p> / HERO-M

Metal ions solvated in aqueous, non-aqueous, and mixtures of solvents occur in many chemical contexts, for example in electrochemical applications and solvent separation. Solvated ions appear in high concentration in the living organisms, where their presence or absence can fundamentally alter the functions of life. In many of these cases, understanding the selective solvation and the dynamics of the ions is essential for the understanding of the processes involved. Computer simulation provides a molecular level of detail of the solvation process usually not available from experiments. The quality of the interaction models employed in the theoretical description is of particular importance, since even rather small changes in the interaction can lead to substantial and qualitative differences. This thesis describes the development of a sequence of increasingly refined analytical ion-solvent potentials from ab initio calculations for the systems Li+(aq), Na+(aq), Mg2+(aq), Al3+(aq), Li+(MeCN), Na+(MeCN), Li+(aq, MeCN), and Na+(aq, MeCN). Molecular dynamics simulations using these potentials were subsequently performed, and some key-properties computed. The reliability of the computed thermodynamical, structural and dynamical properties was scrutinized.

La tesis aborda el estudio teórico de varias reacciones enzimáticas mediante el uso de programas de cálculo de química cuántica. A partir de la localización y caracterización de estructuras de transicion para la etapa química del proceso enzimático, se pretende obtener el mecanimo del mismo, así como información necesaria para deducir el origen del poder catalítico de las enzimas. Cálculos de efectos cinñeticos isotópicos ayudarán a comparar resultados teóricos con los únicos datos experimentales que porporcionan información indirecta de las estructuras de transición.Todos los cálculos han sido realizados utilizando modelos en vacío o simulando el medio con modelos continuos de polarización

The development and improvement of the functionality of metal oxides in heterogeneous catalysis and other surface chemical processes can greatly benefit from an atomic-level understanding of the surface chemistry. Atomistic calculations such as quantum mechanical (QM) calculations and molecular dynamics (MD) simulations can provide highly detailed information about the atomic and electronic structure, and constitute valuable complements to experimental surface science techniques. In this thesis, an embedded-cluster approach for quantum mechanical calculations has been developed to model the surface chemistry of metal oxides. In particular, CO adsorption on the MgO(001) and CeO2(110) surfaces as well as O vacancy formation at the CeO2(110) surface have been investigated. The cluster model has been thoroughly tested by comparison with electronic structure calculations for the periodic slab model. The chemical implications of distorted surface structures arising from the surface dynamics have been investigated by combining the QM embedded-cluster calculations with force-field based MD simulations. Here QM embedded-cluster calculations were performed using surface structures sampled from the MD simulations. This combined MD+QM embedded-cluster procedure was applied to the CO adsorption on MgO(001) at 50 K and the O vacancy formation on CeO2(110) at 300 K. Significant thermal variations of the CO adsorption energy and the O vacancy formation energy were observed. It was found that these variations could be estimated using the force field of the MD simulation as an interaction model. With this approach, the QM results were extrapolated to higher temperature and doped systems.

Ce mémoire traite de la dynamique des molécules envisageant une description classique pour les noyaux et quantique pour la structure électronique. Les approches "Born-Oppenheimer" et "Car-Parrinello" sont discutées et un nouvel algorithme est présenté puis validé de par la bonne conservation de l'énergie totale au cours du temps. Il est ensuiote étendu pour simuler l'ensemble canonique et appliqué à la détermination de caractéristiques spectroscopiques de systèmes moléculaires. L'estimation de quantités, telle l'énergie libre, est considérée à l'aide de la théorie de l'ensemble "blue-moon". Cette méthode est appliquée à deux réactions chimiques, mettant en évidence la mise en défaut de l'approche traditionnelle basée sur l'approximation harmonique. Enfin, l'estimation de l'énergie de point zéro au delà de cette approximation est abordée.

Noncovalent interactions are of pivotal importance in many areas of chemistry, biology, and materials science, and the intermolecular interactions involving aromatic rings in particular, are fundamental to molecular organization and recognition processes. The work detailed in this thesis involves the application of state-of-the-art ab initio electronic structure theory methods to elucidate the nature of pi-pi interactions. The binding energies, and geometrical and orientational preferences of the simplest prototype of aromatic pi-pi interactions, the benzene dimer, are explored. We obtain the first converged values of the binding energies using highly accurate methods and large basis sets. Results from this study predict the T-shaped and parallel-displaced configurations of benzene dimer to be nearly isoenergetic. The role of substituents in tuning pi-pi interaction is investigated. By studying dimers of benzene with various monosubstituted benzenes (in the sandwich and two T-shaped configurations), we surprisingly find that all of the substituted sandwich dimers considered bind more strongly than benzene dimer. We also find that these interactions can be tuned by a modest degree of substitution. Energy decomposition analysis using symmetry-adapted perturbation theory (SAPT) reveals that models based solely on electrostatic effects will have difficulty in reliably predicting substituent effects in pi-pi interactions.

The accuracy of a quantum chemical calculation inherently depends on the ability to account for the completeness of the one- and n-particle spaces. The size of the basis set used can be systematically increased until it reaches the complete one-particle basis set limit (CBS) while the n-particle space approaches its exact full configuration interaction (FCI) limit by following a hierarchy of electron correlation methods developed over the last seventy years. If extremely high accuracy is desired, properly correcting for very small effects such as those resulting the Born-Oppenheimer approximation and the neglect of relativistic effects becomes indispensable. For a series of chemically interesting and challenging systems, we identify the limits of conventional approaches and use state-of-the-art quantum chemical methods along with large basis sets to get the “right answer for the right reasons.” First, we quantify the importance of small effects that are ignored in conventional quantum chemical calculations and manage to achieve spectroscopic accuracy (agreement of 1 cm−1 or less with experimental harmonic vibrational frequencies) for BH, CH+ and NH. We then definitively resolve the global minimum structure for Li₆ , Li₆⁺ , and Li₆- using high accuracy calculations of the binding energies, ionization potentials, electron affinities and vertical excitation spectra for the competing isomers. The same rigorous approach is used to study a series of hydrogen transfer reactions and validate the necessary parameters for the hydrogen abstraction and donation steps in the mechanosynthesis of diamondoids. Finally, in an effort to overcome the steep computational scaling of most high-level methods, a new hybrid methodology which scales as O(N⁵) but performs comparably to O(N⁶) methods is benchmarked for its performance in the equilibrium and dissociation regimes.