Étude ab initio des nanotubes de carbone

Le sujet de ce mémoire est l’étude ab initio des nanotubes de carbone. Premièrement, une introduction du sujet est présentée. Elle porte sur l’historique, la structure géométrique et électronique et les applications possibles des nanotubes de carbone. En deuxième lieu, la stabilité énergétique des nanotubes de carbones double parois ainsi que leur structure électronique sont étudiées. On trouve entre autres que le changement d’hybridation provoque une chute de l’énergie du dernier niveau occupé pour les petits nanotubes. Troisièmement, nous présenterons une étude sur la dépendance en diamètre et en métallicité du greffage d’unité bromophényle sur la surface des nanotubes. La principale conclusion est qu’il est plus facile de fonctionnaliser les nanotubes de petit diamètre puisque ceux-ci ont déjà une partie d’hybridation sp3 dans leur structure électronique. Finalement, le dernier chapitre aborde la combustion des nanotubes par le dioxyde de carbone. On constate que cette combustion ne peut pas débuter sur une surface intacte, ni par un pontage d’oxygène dû à la grande quantité d’énergie requise. La réaction privilégiée est alors la combustion par les extrémités du nanotube. Nous proposons une dynamique de réaction qui contient une sélectivité en diamètre.

First-principles study of the inversion thermodynamics and electronic structure of FeM2X4 (thio)spinels (M = Cr, Mn, Co, Ni; X = O, S)

FeM2X4 spinels, where M is a transition metal and X is oxygen or sulfur, are candidate materials for spin filters, one of the key devices in spintronics. We present here a computational study of the inversion thermodynamics and the electronic structure of these (thio)spinels for M = Cr, Mn, Co, Ni, using calculations based on the density functional theory with on-site Hubbard corrections (DFT+U). The analysis of the configurational free energies shows that different behaviour is expected for the equilibrium cation distributions in these structures: FeCr2X4 and FeMn2S4 are fully normal, FeNi2X4 and FeCo2S4 are intermediate, and FeCo2O4 and FeMn2O4 are fully inverted. We have analyzed the role played by the size of the ions and by the crystal field stabilization effects in determining the equilibrium inversion degree. We also discuss how the electronic and magnetic structure of these spinels is modified by the degree of inversion, assuming that this could be varied from the equilibrium value. We have obtained electronic densities of states for the completely normal and completely inverse cation distribution of each compound. FeCr2X4, FeMn2X4, FeCo2O4 and FeNi2O4 are half-metals in the ferrimagnetic state when Fe is in tetrahedral positions. When M is filling the tetrahedral positions, the Cr-containing compounds and FeMn2O4 are half-metallic systems, while the Co and Ni spinels are insulators. The Co and Ni sulfide counterparts are metallic for any inversion degree together with the inverse FeMn2S4. Our calculations suggest that the spin filtering properties of the FeM2X4 (thio)spinels could be modified via the control of the cation distribution through variations in the synthesis conditions.

Semiempirical Study of the Bergman Reaction: Towards a Computationally Efficient and Accurate Method for Modeling Enediyne Anticancer Antibiotics

Over the past 7 years, the enediyne anticancer antibiotics have been widely studied due to their DNA cleaving ability. The focus of these antibiotics, represented by kedarcidin chromophore, neocarzinostatin chromophore, calicheamicin, esperamicin A, and dynemicin A, is on the enediyne moiety contained within each of these antibiotics. In its inactive form, the moiety is benign to its environment. Upon suitable activation, the system undergoes a Bergman cycloaromatization proceeding through a 1,4-dehydrobenzene diradical intermediate. It is this diradical intermediate that is thought to cleave double-stranded dna through hydrogen atom abstraction. Semiempirical, semiempiricalci, Hartree–Fock ab initio, and mp2 electron correlation methods have been used to investigate the inactive hex-3-ene-1,5-diyne reactant, the 1,4-dehydrobenzene diradical, and a transition state structure of the Bergman reaction. Geometries calculated with different basis sets and by semiempirical methods have been used for single-point calculations using electron correlation methods. These results are compared with the best experimental and theoretical results reported in the literature. Implications of these results for computational studies of the enediyne anticancer antibiotics are discussed.

2-pyrazinylnitrene and 4-pyrimidylnitrene. Ring expansion to 1,3,5-triazacyclohepta-1,2,4,6-tetraene and ring opening to (2-isocyanovinyl)carbodiimide

Tetrazolo[1,5-a]pyrazine/2-azidopyrazine 9T/9A undergo photolysis in Ar matrix at cryogenic temperatures to yield 1,3,5-triazacyclohepta-1,2,4,6-tetraene 21 as the first observable intermediate, and 1-cyanoimidazole 11 and (2-isocyanovinyl)carbodiimide 22 as the final products. The latter tautomerizes to 2-(isocyanovinyl)cyanamide 23 on warming to 40 K. The same intermediate 21 and the same final products are obtained on matrix photolysis of the isomeric tetrazolo[1,5-c]pyrimidine/4-azidopyrimidine 24T/24A. These photolysis results as well as those of the previously reported thermal ring contraction of N-15-labeled 2-pyrazinyl- and 4-pyrimidylnitrenes to 1-cyanoimidazoles can all be rationalized in terms of selective ring opening of 21 or nitrine 10 to a nitrile ylide zwitterion 28 prior to formation of the final products, 11 and 22. The results are supported by high-level ab initio and DFT calculations (CASPT2-CASSCF(6,6), G3(MP2), and B3LYP/6-31+G*) of the energies and IR spectra of the intermediates and products.

Theoretical insights on electron donor-acceptor interactions involving carbon dioxide

Electron donor-acceptor (EDA) interactions are widely involved in chemistry and their understanding is essential to design new technological applications in a variety of fields ranging from material sciences and chemical engineering to medicine. In this work, we study EDA complexes of carbon dioxide with ketones using several ab initio and Density Functional Theory methods. Energy contributions to the interaction energy have been analyzed in detail using both variational and perturbational treatments. Dispersion energy has been shown to play a key role in explaining the high stability of a non-conventional structure, which can roughly be described by a cooperative EDA interaction.

Gas-phase solvolysis type reactions of SiCl3+ cations

Gas-phase SiCl3+ ions undergo sequential solvolysis type reactions with water, methanol, ammonia, methylamine and propylene. Studies carried out in a Fourier Transform mass spectrometer reveal that these reactions are facile at 10-8 Torr and give rise to substituted chlorosilyl cations. Ab initio and DFT calculations reveal that these reactions proceed by addition of the silyl cation to the oxygen or nitrogen lone pair followed by a 1,3-H migration in the transition state. These transition states are calculated to lie below the energy of the reactants. By comparison, hydrolysis of gaseous CCl3+ is calculated to involve a substantial positive energy barrier.

Gas-phase solvolysis type reactions of SiCl3+ cations

Gas-phase SiCl3+ ions undergo sequential solvolysis type reactions with water, methanol, ammonia, methylamine and propylene. Studies carried out in a Fourier Transform mass spectrometer reveal that these reactions are facile at 10-8 Torr and give rise to substituted chlorosilyl cations. Ab initio and DFT calculations reveal that these reactions proceed by addition of the silyl cation to the oxygen or nitrogen lone pair followed by a 1,3-H migration in the transition state. These transition states are calculated to lie below the energy of the reactants. By comparison, hydrolysis of gaseous CCl3+ is calculated to involve a substantial positive energy barrier.

Ab-initio determination of x-ray absorption near edge structure (xanes) spectra in an ultrasoft and norm conserving pseudopotentials scheme

X-ray absorption spectroscopy (XAS) is a powerful means of investigation of structural and electronic properties in condensed -matter physics. Analysis of the near edge part of the XAS spectrum, the so – called X-ray Absorption Near Edge Structure (XANES), can typically provide the following information on the photoexcited atom: - Oxidation state and coordination environment. - Speciation of transition metal compounds. - Conduction band DOS projected on the excited atomic species (PDOS). Analysis of XANES spectra is greatly aided by simulations; in the most common scheme the multiple scattering framework is used with the muffin tin approximation for the scattering potential and the spectral simulation is based on a hypothetical, reference structure. This approach has the advantage of requiring relatively little computing power but in many cases the assumed structure is quite different from the actual system measured and the muffin tin approximation is not adequate for low symmetry structures or highly directional bonds. It is therefore very interesting and justified to develop alternative methods. In one approach, the spectral simulation is based on atomic coordinates obtained from a DFT (Density Functional Theory) optimized structure. In another approach, which is the object of this thesis, the XANES spectrum is calculated directly based on an ab – initio DFT calculation of the atomic and electronic structure. This method takes full advantage of the real many-electron final wavefunction that can be computed with DFT algorithms that include a core-hole in the absorbing atom to compute the final cross section. To calculate the many-electron final wavefunction the Projector Augmented Wave method (PAW) is used. In this scheme, the absorption cross section is written in function of several contributions as the many-electrons function of the finale state; it is calculated starting from pseudo-wavefunction and performing a reconstruction of the real-wavefunction by using a transform operator which contains some parameters, called partial waves and projector waves. The aim of my thesis is to apply and test the PAW methodology to the calculation of the XANES cross section. I have focused on iron and silicon structures and on some biological molecules target (myoglobin and cytochrome c). Finally other inorganic and biological systems could be taken into account for future applications of this methodology, which could become an important improvement with respect to the multiscattering approach.

Ab initio study of the electronic and optical properties of sillimanite (Al(2)SiO(5)) crystal

Ab initio calculations based on the density functional theory (DFT) are used to investigate the electronic and optical properties of sillimanite. The geometrical parameters of the unit cell, which contain 32 atoms, have been fully optimized and are in good agreement with the experimental data. The electronic structure shows that sillimanite has an indirect band gap of 5.18 eV. The complex dielectric function and optical constants, such as extinction coefficient, refractive index, reflectivity and energy-loss spectrum, are calculated. The optical properties of sillimanite are discussed based on the band structure calculations. It is shown that the O-2p states and Al-3s, Si-3s states play the major role in optical transitions as initial and final states, respectively. (C) 2011 Elsevier B.V. All rights reserved.

Electronic and optical properties of grossular garnet (Ca(3)Al(2)Si(3)O(12)): An ab initio study

The electronic and optical properties of grossular garnet are investigated using density functional theory (DFT) within generalized gradient approximation (GGA). The calculated lattice parameters are in good agreement with the experiment data. The electronic structure shows that grossular has a direct band gap of 5.22 eV. The dielectric functions, reflective index, extinction coefficient, reflectivity and energy-loss spectrum are calculated. The optical properties of grossular are discussed based on the band structure calculations. The O 2p states and Si 3s play a major role in these optical transitions as initial and final states, respectively. The absorption spectrum is localized in the ultraviolet range between 30 and 250 nm. Finally, we concluded that pure grossular crystal does not absorb radiation in the visible range. (c) 2009 Elsevier B.V. All rights reserved.

Emergence of half-metallicity in suspended NiO chains: Ab initio electronic structure and quantum transport calculations

Contrary to the antiferromagnetic and insulating character of bulk NiO, one-dimensional chains of this material can become half metallic due to the lower coordination of their atoms. Here we present ab initio electronic structure and quantum transport calculations of ideal infinitely long NiO chains and of more realistic short ones suspended between Ni electrodes. While infinite chains are insulating, short suspended chains are half-metallic minority-spin conductors that displays very large magnetoresistance and a spin-valve behavior controlled by a single atom.

Facilitating Realistic and Efficient Applications of Ab Initio Electronic Dynamics for Polyatomic Systems

Thesis (Ph.D.)--University of Washington, 2016-06