Ce travail de thèse a porté sur l'étude des réactions unimoléculaires de décomposition des alcènes à basse température. L'oxydation de ces molécules est primordiale dans la compréhension des mécanismes de combustion, car elles peuvent être présentes initialement dans des carburants usuels ou formées en tant qu'intermédiaires dans le processus d'oxydation. L’étude théorique menée peut se décomposer en deux parties : - L’étude des réactions de décomposition des radicaux hydroxyalkylperoxyles (HOROO•) obtenus à partir de l’addition d’un radical •OH sur l’alcène, suivi par une addition du radical •ROH sur l’oxygène moléculaire. Cette étude a été conduite de façon systématique sur un ensemble de radicaux représentatifs d'alcènes afin de mettre en évidence l'influence de l'environnement intramoléculaire sur les constantes de vitesse. Les résultats obtenus ont montré l’influence très nette de certains paramètres comme la présence d'un groupement hydroxyle en position β par rapport à l'atome de carbone réactif, la nature des atomes de carbone portant les hydrogènes transférés, la taille des cycles de transition ou encore la présence d'une liaison hydrogène intramoléculaire. - L’étude des réactions de décomposition unimoléculaires des radicaux allylperoxyles obtenus à partir de l’addition des radicaux allyliques sur l’oxygène. La grande complexité de ces systèmes a été mise en avant au cours de ce travail. Il a ainsi pu être mis en évidence que la formation d'un composé de type 1-alcenyloxirane est favorisée à basse température ce qui montre l'importance de ces réactions, souvent négligées dans les modèles / This work focused on the study of the unimolecular decomposition of the low-temperature reactions of alkenes. The oxidation of these molecules is essential in the understanding of the mechanisms of combustion, because they are initially present in conventional fuels or formed as intermediates in the oxidation process. The theoretical study can be divided in two parts: - The study of the decomposition of hydroxyalkylperoxyl radicals (HOROO•) obtained from the addition of an •OH radical on the alkene, followed by a subsequent addition of the formed radical •ROH on molecular oxygen. This study was conducted in a systematic way on a set of representative radicals of alkenes in order to highlight the influence of the intramolecular environment on the rate constants. The results clearly showed the major influence of parameters such as the presence of a hydroxyl group in β position with respect to the reactive carbon atom, the nature of the carbon atoms bearing the transferred hydrogen, the size of the transition state ring and the presence of intramolecular hydrogen bonds. - The study of the unimolecular decomposition of the allylperoxy radicals obtained from the addition of a resonance-stabilized radical on molecular oxygen. The complexity of these systems, specifically induced by the mesomeric structures of heavy allyl radicals and the role of cis and trans conformations alkenes parents, have been highlighted in this work. It has been shown that the formation of a compound 1-alkenyloxirane is favored at low-temperatures, which shows the importance of these reactions, usually neglected in the kinetic models for the combustion of alkenes

In recent years, advances in computer technology combined with new ab initio computational methods have allowed for dramatic improvement in the prediction of energetic properties. Unfortunately, even with these advances, the extensive computational cost, in terms of computer time, memory, and disk space of the sophisticated methods required to achieve chemical accuracy - defined as 1 kcal/mol from reliable experimental data effectively - limits the size of molecules [i.e. less than 10-15 non-hydrogen atoms] that can be studied. Several schemes were explored to help reduce the computational cost while still maintaining chemical accuracy. Specifically, a study was performed to assess the accuracy of ccCA to compute atomization energies, ionization potentials, electron affinities, proton affinities, and enthalpies of formation for third-row (Ga-Kr) containing molecules. Next, truncation of the correlation consistent basis sets for the hydrogen atom was examined as a possible means to reduce the computational cost of ab initio methods. It was determined that energetic properties could be extrapolated to the complete basis set (CBS) limit utilizing a series of truncated hydrogen basis sets that was within 1 kcal/mol of the extrapolation of the full correlation consistent basis sets. Basis set truncation for the hydrogen atom was then applied to ccCA in the development of two reduced basis set composite methods, ccCA(aug) and ccCA(TB). The effects that the ccCA(aug) and ccCA(TB) methods had upon enthalpies of formation and the overall percent disk space saved as compared to ccCA was examined for the hydrogen containing molecules of the G2/97 test suite. Additionally, the Weizmann-n (Wn) methods were utilized to compute the several properties for the alkali metal hydroxides as well as the ground and excited states of the alkali monoxides anion and radicals. Finally, a multi-reference variation to the correlation consistent Composite Approach [MR-ccCA] was presented and utilized in the computation of the potential energy surfaces for the N2 and C2 molecules.

Neste trabalho foram estudadas as moléculas conhecidas corno cetonas-gaiola de Cookson e seus derivados pelo uso de técnicas computacionais de modelagem molecular. Estas moléculas participam de cicloadições [2+2], urna classe de reações cujo mecanismo ainda é estudado. As técnicas usadas foram as do Conjunto Completo de Funções de Base (CBS-4), Hartree-Fock, métodos de Teoria do Funcional de Densidade pBP e B3LYP e semi-empírico PM3. As técnicas foram usadas com diferentes conjuntos de base para analisar as conformações das moléculas e avaliar a exatidão do método em reproduzir resultados experimentais de termodinâmica e ressonância magnética nuclear. Com base na concordância dos resultados e com as caraterísticas do método, procura-se inferir quais as características estruturais e interações atômicas que explicam os resultados experimentais e os calculados. Foi estudada também a solvatação das espécies. Os programas empregados foram o Gaussian 94, Spartan 5.0, MOPAC e Amsol 6.6. Os resultados mostraram as interações interatômicas mais relevantes para a determinação das estabilidades relativas das moléculas. Foi considerado o efeito da estrutura no resultado de cálculos de energias e avaliado o método de reações isodésmicas para moléculas de estrutura complexa. / In this work the molecules known as Cookson\'s cage ketones and similar adducts were studied with the use of computational molecular modelling techniques. These molecules participate in cycloadditions [2+2], a class of reactions whose mechanism is still being studied. Toe techniques used were the Complete Basis Set (CBS-4), Hartree-Fock, Density Functional Theory methods pBP and B3LYP and semi-emprical PM3. The techniques were used with some basis sets to analise the molecular conformations and evaluate the agreement of the calculated with the experimental results of thermodynamics and NMR spectroscopy. Based on the agreement between the results and on the characteristics of the methods, it is sought to determine the structural characteristics and atomic interactions that explain the results. The solvation of the species was also studied. The programs used were the Gaussian 94, Spartan 5.0, MOPAC and Amsol 6.6. The results show the more important interactions that determine the relative stabilities of the molecules. The effect of the molecular structure on the energy calculation was studied and the method of isodesmic reactions was evaluated for complex molecules.

O entendimento das propriedades de complexos metálicos é de fundamental importância para o desenvolvimento de fármacos. No entanto, tanto do ponto de vista experimental quanto no de modelagem teórica, ainda temos muitas dificuldades de simular e mensurar as mudanças que a complexação com um metal causa em um composto. Este trabalho apresenta estudos de simulacões ab initio de complexos de Epiisopiloturina com Cu e Zn. Foram realizadas otimizações de estrutura, simulaçoes de espectroscopia vibracional, NMR e EPR além de estudos de reatividade. Obtivemos uma geometria otimizada condizente com a da forma cristalizada. Além disso, os resultados espectroscópicos mostram que as estruturas dos com plexos permanecem intactas em solução. Por fim, os estudos de reatividade conrmam que o complexo de Cobre aumenta a reatividade da molécula. / Understanding the properties of metal complexes is fundamental goal in the development of drugs. However, both from the experimental point of view and theoretical modeling, many diculties in the simulation and evaluatio of the changes that the metal causes upon complexation still remains. This work presents ab initio computational simulations of Epiisopiloturin com plexes with Cu and Zn. We make structural optimizations, simulations of vibrational spectroscopy, NMR and EPR, as well as reactivity studies. We obtain an optimized geometry that corresponds to that of the crystallized form. In addition, the spectroscopic results conrm that the complexes remain intact in solution. Finally, the reactivity studies conrm that the copper complex increases the reactivity of the molecule.

Greater understanding and accurate predictions of structural, thermochemical, and spectroscopic properties of chemical compounds is critical for the advancements of not only basic science, but also in applications needed for the growth and health of the U.S. economy. This dissertation includes new ab initio composite approaches to predict accurate energetics of lanthanide-containing compounds including relativistic effects, and optimization of parameters for semi-empirical methods for transition metals. Studies of properties and energetics of chemical compounds through various computational methods are also the focus of this research, including the C-O bond cleavage of dimethyl ether by transition metal ions, the study of thermochemical and structural properties of small silicon containing compounds with the Multi-Reference correlation consistent Composite Approach, the development of a composite method for heavy element systems, spectroscopic of compounds containing noble gases and metals (ArxZn and ArxAg+ where x = 1, 2), and the effects due to Basis Set Superposition Error (BSSE) on these van der Waals complexes.

PhD (Chemistry) / Department of Chemistry

MSc (Chemistry) / Department of Chemistry

In the recent years, interest in TM oxides with 5d valence electrons has grown immensely due to the realization of novel spin-orbit coupled ground states. In these compounds, e.g., iridates and osmates, the intriguing situation arises where the spin-orbit and electron-electron interactions meet on the same energy scale. This has created a new window of interest in these compounds since the interplay of crystal field effects, local multiplet physics, spin-orbit couplings, and intersite hopping can offer novel types of correlated ground states and excitations. In 5d5 iridates, a spin-orbit entangled j = 1/2 Mott insulating state has been realized recently. A remarkable feature of such a ground state is that it gives rise to anisotropic magnetic interactions. The 2D honeycomb-lattice 213 iridium oxides, A2IrO3 (A=Li,Na), have been put forward to host highly anisotropic bond-dependent spin-spin interactions that resemble the Kitaev spin model, which supports various types of topological phases relevant in quantum computing. The 2D square-lattice 214 iridates Sr2IrO4 and Ba2IrO4 are, on the other hand, appealing because of their perceived structural and magnetic simi- larity to La2CuO4, the mother compound of the cuprate high-Tc superconductors. This has promoted the latter iridium oxide compounds as novel platforms for the search of high-Tc superconductivity. To put such considerations on a firm footing, it is essential to quantify the different coupling strengths and energy scales, as they for instance appear in effective Hamiltonian descriptions of these correlated systems. Moreover, it is important to correctly describe their effects. In this thesis, the electronic structure and magnetic properties of 5d5 (mainly 214 and 213) iridates are studied using wave-function-based quantum chemistry methods. These methods are fully ab initio and are capable of accurately treating the electron-electron interactions without using any ad hoc parameters. The spin-orbit entangled j = 1/2 ground state in 214, 213 and other lower symmetry Sr3CuIrO6 and Na4Ir3O8 iridates is first analyzed in detail, by studying the local electronic structure of the 5d5 Ir4+ ion. We establish that the longer-range crystal anisotropy, i.e., low-symmetry fields related to ionic sites beyond the nearest neighbor oxygen cage, strongly influence the energies of Ir d levels. The ground state in all the compounds studied is j = 1/2 like with admixture from j ≃ 3/2 states ranging from 1 – 15 %. Further, the average j ≃ 1/2 → j ≃ 3/2 excitation energy we find is around 0.6 eV. The NN magnetic exchange interactions we computed for 214 iridates are predominantly isotropic Heisenberg-like with J ~ 60 meV, 3 – 4 times smaller than found in isostructural copper oxides. However, the anisotropic interactions are an order of magnitude larger than those in cuprates. Our estimates are in excellent agreement with those extracted from experiments, e.g., resonant inelastic x-ray scattering measurements. For the 213 honeycomb-lattice Na2IrO3 our calculations show that the relevant spin Hamiltonian contains further anisotropic terms beyond the Kitaev-Heisenberg model. Nevertheless, we predict that the largest energy scale is the Kitaev interaction, 10 to 20 meV, while the Heisenberg superexchange and off-diagonal symmetric anisotropic couplings are significantly weaker. In the sister compound Li2IrO3, we find that the structural inequivalence between the two types of Ir-Ir links has a striking influence on the effective spin Hamiltonian, leading in particular to two very different NN superexchange pathways, one weakly AF (~ 1 meV) and another strongly FM (−19 meV). The latter gives rise to rigid spin-1 triplets on a triangular lattice.

The presence of excess free radicals in the body can result in severe health consequences because of oxidative damage to cells. Spin traps may be used as a probe to examine radical reactions in cells, but there is a need for less toxic and more lipid soluble examples. Melatonin is one of the numerous antioxidants used to scavenge free radicals in the body and reportedly one of the most efficient radical scavengers known. It is relatively nontoxic and easily crosses the lipid bilayer in cell membranes. Melatonin is thought to undergo a multistep oxidation process and this work investigates the potential for it to be used as a spin trap. The presence of electron withdrawing or donating groups added to melatonin may stabilize an intermediate and allow it to function as a spin trap. The essence of this study is to conduct a computational inquiry into the relative stability of melatonin, selected derivatives, and the partial oxidation products formed from the scavenging of hydroxyl radical. To determine this, geometries were optimized for each molecule at the DFT/B3LYP/6-31G(d) and HF/6-31G(d) levels of theory.

This thesis has been focused around the Diels Alder reaction with the goal to design an enzyme catalyzed reaction pathway. To achieve this goal computer aided enzyme design was utilized. Common traditional methods of computational chemistry (B3LYP, MP2) do not do well when calculating reaction barriers or even reaction energies for the Diels Alder reaction. New calcu- lation methods were developed and tested. This was the focus of the first part of the thesis, by choosing a small system, extensive and heavy calculations could be done with CBS-QB3. Then by benchmarking faster methods of calculation (SCS-MP2, M06-2X) against the results, they could be graded by efficiency and cost. This was done anticipating that the same accuracy could be applied to larger systems where CBS-QB3 cannot be used. In the second part activating groups were investigated for both the diene and the dienophile, along with their effects on reaction rates. A qualitative analysis was done. This is important not only for the uncatalyzed reaction, but also interesting when searching for possible substrates for the enzyme reaction. In the last part the thesis presents a designed enzyme that catalyzes Diels Alder in silico using ∆5−3−Keto steroid isomerase. Using empirical calculations, the enzyme was scanned for catalytic activity. The catalytic effect was then showed with ab initio Quantum chemical calculations.