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.

Emerging contaminants are defined as synthetic or naturally occurring chemicals or microorganisms that are not currently regulated but have the potential to enter the environment and cause adverse ecological and/or human health effects. With recent development in analytical techniques, emerging contaminants have been detected in wastewater, source water, and finished drinking water. These environmental occurrence data have raised public concern about the fate and ecological impacts of such compounds. Concerns regarding emerging contaminants and the many chemicals that are in use or production necessitate a task to assess their potential health effects and removal efficiency during water treatment. Advanced oxidation processes (AOPs) are attractive and promising technologies for emerging contaminant control due to its capability of mineralizing organic compound via reactions with highly active hydroxyl radicals. However, the nonselective reactivity of hydroxyl radicals and the radical chain reactions make AOPs mechanistically complex processes. In addition, the diversity and complexity of the structure of a large number of emerging contaminants make it difficult and expensive to study the degradation pathways of each contaminant and the fate of the intermediates and byproducts. The intermediates and byproducts that are produced may pose potential effects to human and aquatic ecosystems. Consequently, there is a need to develop first-principle based mechanistic models that can enumerate reaction pathway, calculate concentrations of the byproducts, and estimate their human effects for both water treatment and reuse practices. This dissertation develops methods to predict reaction rate constants for elementary reactions that are identified by a previously developed computer-based reaction pathway generator. Many intermediates and byproducts that are experimentally identified for HO* induced reactions with emerging contaminants include common lower molecular weight organic compounds on the basis of several carbons. These lower carbon intermediates and byproducts also react with HO* at relatively smaller reaction rate constants (i.e., k < 109 M-1s-1) and may significantly affect overall performance of AOPs. In addition, the structures of emerging contaminants with various functional groups are too complicated to model. As a consequence, the rate constant predictors are established based on the conventional organic compounds as an initial approch. A group contribution method (GCM) predicts the aqueous phase hydroxyl radical reaction rate constants for compounds with a wide range of functional groups. The GCM is a first comprehensive tool to predict aqueous phase hydroxyl radical reaction rate constants for reactions that include hydrogen-atom abstraction from a C-H bond and/or a O-H bond by hydroxyl radical, hydroxyl radical addition to a C=C unsaturated bond in alkenes and aromatic compounds, and hydroxyl radical interaction with sulfur-, nitrogen-, or phosphorus-atom-containing compounds. The GCM shows predictability; factor of difference of 2 from literature-reported experimental values. The GCM successfully predicts the hydroxyl radical reaction rate constants for a limited number of emerging contaminants. Linear free energy relationships (LFERs) bridge a kinetic property with a thermochemical property. The LFERs is a new proof-of-concept approach for Ab initio reaction rate constants predictors. The kinetic property represents literature-reported and our experimentally obtained hydroxyl radical reaction rate constants for neutral and ionized compounds. The thermochemical property represents quantum mechanically calculated aqueous phase free energy of activation. Various Ab initio quantum mechanical methods and solvation models are explored to calculate the aqueous phase free energy of activation of reactantas and transition states. The quantum mechanically calculcated aqueous phase free energies of activation are within the acceptable range when compared to those that are obtained from the experiments. These approaches may be applied to other reaction mechanisms to establish a library of rate constant predictions for the mechanistic modeling of AOPs. The predicted kinetic information enables one to identify important pathways of AOP mechanisms that are initiated by hydroxyl radical, and can be used to calculate concentration profiles of parent compounds, intermediates and byproducts. The mechanistic model guides the design of experiments that are used to examine the reaction mechanisms of important intermediates and byproducts and the application of AOPs to real fields.