En este trabajo se han realizado cálculos de primeros principios para estudiar las propiedades físicas de superficies y materiales laminares. Los cálculos se basan en la obtención de las propiedades electrónicas por medio de la Teoría del Funcional de la Densidad, con la que se obtienen la energía y fuerzas atómicas para cada sistema estudiado. De esta forma, se realizaron cálculos de optimización estructural y de dinámica molecular, que proporcionan información sobre las estructuras de equilibrio y la dinámica atómica en función de las condiciones externas (tales como presión y temperatura). Los cálculos realizados se han centrado en diferentes sistemas con interés experimental, siempre en estrecha colaboración con distintos grupos experimentales. En el campo de superficies, se han estudiado problemas relacionados con el crecimiento de láminas delgadas de Cobre para metalización de circuitos microelectrónicos, la adsorción de fullerenos sobre superficies de Germanio, y la medición de ondas de densidad de carga mediante microscopía de efecto túnel en bronces azules. En materiales laminares, el trabajo se ha centrado en comprender el efecto de la presión sobre las propiedades estructurales y electrónicas de semiconductores laminares III-VI, así como en explicar la aparición de nuevas fases no-laminares para varios de estos sistemas a altas presiones. / In this work we have made first-principles calculations to study the physical properties of surfaces and layered materials. The calculations are based on obtaining the electronic properties through the Density Functional Theory, with which the energy and atomic forces for each system studied are derived. Thus, structural optimization calculations and molecular dynamics were carried out. They provide information about the equilibrium structure and the atomic dynamic as a function of external conditions (such as temperature and pressure). Calculations have focused on different systems with experimental interest, always in strong collaboration with different experimental groups. In the field of surfaces we have been studied problems associated with the growth of thin films of copper for metallization of microelectronic circuits, the adsorption of fullerenes on Germanium surfaces, and the measurement of charge density waves by scanning tunneling microscopy in bronze blue. In layered materials, the work has focused on understanding the effect of pressure on the structural and electronic properties of layered semiconductor III-VI, as well as explaining the emergence of new no-layered phases for several of these systems at high pressures.

No description available.

This thesis presents ab-initio quantum mechanical calculations at the density functional theory (DFT) level on defect centers hosted by crystalline systems of geologic importance (i.e. fluorite, quartz, stishovite). The research brings new, complementary data to the current understanding of defect structures in minerals and explores the advantages of a theoretical approach in the field of mineral spectroscopy. This present research presents the first ab-initio calculations of the O23- type defects in crystalline solids. New data on the electronic properties and structural characteristics of O23--Y3+ defect in fluorite-type structures (CaF2 and SrF2) were obtained at the DFT level. These results confirm the stability and the molecular character of the O23--Y3+ center, revealing a spin density that is equally distributed between the two oxygen atoms. Our results report an O-O bond distance of 2.47 Å in CaF2 and 2.57 Å in SrF2. The calculated 17O and 19F hyperfine constants for of the O23--Y3+ center are in good agreement with their corresponding experimental values reported by previous electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies, while discrepancies are notable for the 89Y hyperfine constants and are probably attributable to an inadequate basis set for Y.<p> The present study provides a more complete picture of the coupled Al-M substitution for Si in quartz, while investigating the characteristics and electronic properties of the diamagnetic [AlO4/M+]0 (where M = H, Li, Na and K) defects. The diamagnetic [AlO4/M+(a<)]0 defects with M = H, Li and Na have been shown to be more stable than their [AlO4/M+(a>)]0 structural analogues (where a> and a< denote the location of the charge compensating ion on the long-bond and short-bond side, respectively), correctly predicting the common occurrence of paramagnetic [AlO4/M+(a>)]+ centers. The present study confirms previous suggestions that incorporation of the [AlO4/M+]0 defects results in significant structural relaxations that extend at least to the nearest Si atoms. The [AlO4/K+]0 defects have been investigated for the first time and are shown to be stable in quartz. The results of this study have implications for the uptake of Al in quartz.<p> The present research evaluates the structural models of [AlO4/Li] paramagnetic defects in α-quartz. The results confirm the previous experimental findings and propose an additional paramagnetic defect [AlO4/Li+(csmall)]+, with the unpaired electron located on a short-bonded O atom and the Li compensator just off the edge of the small channel. Accordingly we suggest that three distinct Al-Li paramagnetic defects can be can be found in quartz, two of them having the hole located on a short-bonded O and one trapping the hole on a long-bonded O atom. However the structural similarities with the [AlO4/Li+(a>)]+ defect would require detection and measurement of the 17O hyperfine structure for an unequivocal EPR identification.<p> The present work also reports on first-principles quantum-mechanical calculations on the previously proposed [O23--Al3+] defect in stishovite. Our results show that the unpaired spin is 85% localised on one of the six oxygen atoms at an AlO6 octahedron, while the calculated 27Al hyperfine constants are similar to those determined by EPR experiments. Accordingly we propose the Al center to represent an [AlO6]0 defect, and hole hoping among equivalent oxygen atoms is responsible for its detection only at cryogenic temperatures. Theoretical calculations also show that diamagnetic precursors [AlO6/H+]0, [AlO6/Li+]0 and [AlO6/Na+]0 are stable in stishovite. The calculated OH bond distance and orientation are in excellent agreement with those inferred from FTIR spectra and previous theoretical calculations. The calculated [AlO6/Li+]0 and [AlO6/Na+]0 defects suggest that monovalent cations such as Li+ and Na+ are potentially important in accommodating Al in stishovite in the lower mantle.

Metal ions are important for medical, environmental and catalytic applications. They are used as precursor molecules for the manufacture of metal nanocatalysts, which are promising materials for an array of biomedical, industrial, and technological applications. Understanding the effect of the environment upon a metal ion-dendrimer system constitutes a step closer to the understanding of the liquid phase templated synthesis of metal nanoparticles. In this dissertation we have used computational techniques such as abinitio calculations and molecular dynamics (MD) simulations to investigate the complexation of Cu(II) and Pt(II) metal ions to a polyamidoamine (PAMAM) dendritic polymer from structural, thermodynamic, and kinetic viewpoints. First, we analyze the local configuration of a low generation polyamidoamine dendrimer to understand the role of intramolecular interactions. Then, we examine the local configuration of dendrimer outer pockets in order to determine their capacity to encapsulate water within. Next, the complexation of Cu(II) with a small –OH terminated dendrimer in presence of solvent and counterions is investigated. This relatively simple system gives insight on how cationic species bind within a dendrimer. The complexation of potassium tetrachloroplatinate, commonly used precursor salt in dendrimer templated synthesis of platinum and bimetallic platinum-containing nanoparticles, with PAMAM dendrimer has been the subject of several experimental reports. So we investigate the complexation of potassium tetrachloroplatinate within a dendrimer outer pocket in order to understand the effect of dendrimer branches, Pt(II) speciation, pH, solvent and counterions upon it. Our study shows that dendrimer branches can improve the thermodynamics but can also preclude the kinetics by raising the energy barriers. Our study provides an explanation of why, where Pt(II) and how Pt(II) binds. We believe that these molecular level details, unaccessible to experimental techniques, can be a helpful contribution toward furthering our understanding of the complexation of Pt(II) and the starting point to study the next step of dendrimer templated synthesis, the reduction of Pt(II) into platinum nanoparticles inside pockets.

The structure, potential energy functions and vibrational spectra of several cyclic and bicyclic molecules have been investigated using several spectroscopic techniques and high-level ab initio and density functional theory (DFT) calculations. Laser induced fluorescence and Raman spectroscopies were used to study the conformation of 2- indanol in the electronic ground and excited states. These, along with detailed ab initio calculations, confirmed the existence of four different stable conformations with the one undergoing an intermolecular hydrogen bonding being the most stable. A theoretical two-dimensional surface in terms of the ring-puckering and the hydroxyl group internal rotation vibrations was constructed. This work was extended to obtain preliminary insights on the conformations and ring-puckering frequencies of 3-cyclopenten-1-ol using ab initio and DFT calculations. Infrared and Raman spectra were also utilized to study the structures and vibrational spectra of -crotonolactone and 2,3-cyclopentenopyridine (pyrindan). Ab initio results showed that -crotonolactone is rigidly planar in the electronic ground state and has a nearly harmonic ring-puckering potential function. The calculated vibrational levels were shown to be in very good agreement with the experimental ring-puckering frequency from vapor-phase Raman observations. The structures, vibrational spectra, and potential energy functions of several cyclic molecules were reinvestigated using high-level ab initio computations, and detailed vibrational analyses based on DFT-B3LYP calculated frequencies were also carried out. A number of new insights were presented by re-evaluating the available experimental data for several cyclopentenes, silacyclobutanes and silacyclopentenes. It was found that the vibrational spectra of some deuterated cyclopentenes possess extensive coupling between several ring modes and other low-frequency modes. Reassignments of these spectra have been proposed. Frequencies from DFT-B3LYP calculations showed very good agreement with the experimental values for silacyclobutane and its derivatives. The presence of silicon and halogen atoms did not affect the accuracy of the DFT calculations. In addition, the ring-puckering potential energy function for silacyclopent-2-ene was studied and alternative assignments of the far-infrared results were proposed. The new assignments are in good agreement with computational results. Silacyclopent-2-ene and its -1,1-d2 isotopomer were shown to be slightly puckered with barriers of less than 50 cm-1.

No description available.

We have used the first-principle molecular-dynamics method to study the dependence of the sticking property of a C gas-phase atom on C (100) on its initial position. For all the three cases, Cn never penetrates through the dimer layer even when Cn impinges on an opening in the surface. We find Cn becomes bonded with two substrate C atoms and one hydrogen atom with the hydrogen atom moving on the vacuum side.

Gas electron diffraction (GED) is a technique that has been developed to study the molecular structure of species in the gas phase. This thesis focuses on the reconstruction of the Canterbury GED apparatus (moved from Edinburgh, UK) and the requirements for modifying the apparatus to incorporate a mass spectrometer (MS) so diffraction and MS data can be obtained within a single experiment. The combined GED-MS system has been identified in previous work in the Masters group as a necessary development for studying the structure of short-lived species generated in situ. This is particularly true for the study of ketene, which as shown in this thesis, can be generated from several precursors as part of a multiple product pyrolysis system. While GED data for ketene generated from acetic anhydride has been refined, the species formed from the pyrolysis of Meldrum’s acid were determined to be too difficult to deconvolute without additional experimental data from MS. A computational study of possible ketene derivatives that could be studied with a GED-MS apparatus is also presented. Lastly, this thesis details a structural study of the gas-phase structures of tris(chloromethyl)amine and a family of substituted disilane systems which have been determined in the gas phase for the first time. A comprehensive GED, Raman spectroscopy and ab initio study have been undertaken for tris(chloromethyl)amine [N(CH2Cl)3] which is shown to have a different structure in the solid and gas phase. Further work in the form of a molecular dynamics investigation has been identified as necessary to describe the low amplitude motion of one of the CH2Cl groups in the gas phase to allow for the GED refinement to be completed. The work on the substituted disilane systems X3SiSiXMe2 (X = F, Cl, Br, I) and X3SiSiMe3 (X = H, F, Cl, Br) demonstrates the effect of increased halogen substitution on the electronic effects of the disilanes, and the effect that the methyl groups have as larger halogens increase the steric bulk of the system.

The chemical bonds that hold molecules together are composed of electrons, and in order to study these microscopic systems, electronic structure calculations are often employed. This thesis describes the results from several studies that use computational techniques to investigate a variety of bonding interactions. The systems presented range from small water clusters to large DNA quadruplexes. High-level computational techniques, such as ab initio and density functional theory methods, were applied as well as the quantum theory of atoms in molecules (AIM). AIM uses the gradient to analyze the electron density, partitioning the molecule into atomic fragments. Once the system is partitioned, individual atomic contributions to molecular properties can be determined. Furthermore, bonding interactions can be identified by the presence of a specific type of critical point within the topology. These two facets of AIM are exploited throughout this thesis. The first project presented is a theoretical investigation of the exact electronic structure of hydrated electrons. Whether the excess electron resides within a central cavity or is smeared out over the surface of the cluster remains a contentious issue. In an attempt to investigate this dilemma from a novel viewpoint, AIM was used to analyze the electron density of small anionic water clusters up to ten water molecules. The results suggest that the preferred site of binding is dictated by the relative orientation of the non-hydrogen-bonded hydrogen atoms. At the other end of the spectrum, the largest systems investigated were several guanine quadruplexes that can form in telomeric regions of DNA. In light of the attention these structures have received as potential therapeutic agents, a clear understanding of their formation is mandatory. The study presented here is a detailed investigation of the electronic energy changes associated with the folding of the quadruplex from the single-stranded telomere. After devising a novel method to display the atomic energy data, several interesting trends in the energy changes were identified. Ultimately, the data presented could help to guide future drug development endeavours, highlighting one of the many practical applications of computational methods.

In efforts to coordinate carbohydrates to transition metal centres, the coordination of D-(+)-Glucosamine to ruthenium was performed. The product from this reaction was a vibrant blue substance that degraded in a characteristic fashion of blue to green to yellow, indistinguishable to that of the ruthenium coordination precursor “Ruthenium Blue”. The MALDI-ToF-MS spectra of the blue product and subsequent green and yellow degradation products showed the presence of a series of [RuxCly]- ruthenium chloride clusters. Structures of the clusters and their respective electronic excitations were determined using ab initio calculations. Calculations were performed using Density Functional Theory and the CIE1931 colour metric was used to process the electronic excitations into a physically perceived colour. The optimized structures that resulted from the ab initio calculations had the same physically perceived colour as the species found in the product, and thus could be another possibility into the composition of “Ruthenium Blue”.