Density functional theory has been used in combination with the correlation consistent and polarization consistent basis sets to investigate the structures and energetics for a series of first-row closed shell and several second-row molecules of potential importance in atmospheric chemistry. The impact of basis set choice upon molecular description has been examined, and irregular convergence of molecular properties with respect to increasing basis set size for several functionals and molecules has been observed. The possible reasons and solutions for this unexpected behavior including the effect of contraction and uncontraction, of the basis set diffuse sp basis functions, basis set superposition error (BSSE) and core-valence sets also have been examined.

In this research the validity of various computational techniques has been determined and applied the appropriate techniques to investigate and propose a good catalytic system for C-H bond activation and functionalization. Methane being least reactive and major component of natural gas, its activation and conversion to functionalized products is of great scientific and economic interest in pure and applied chemistry. Thus C-H activation followed by C-C/C-X functionalization became crux of the synthesis. DFT (density functional theory) methods are well suited to determine the thermodynamic as well as kinetic factors of a reaction. The obtained results are helpful to industrial catalysis and experimental chemistry with additional information: since C-X (X = halogens) bond cleavage is important in many metal catalyzed organic syntheses, the results obtained in this research helps in determining the selectivity (kinetic or thermodynamic) advantage. When C-P bond activation is considered, results from chapter 3 indicated that C-X activation barrier is lower than C-H activation barrier. The results obtained from DFT calculations not only gave a good support to the experimental results and verified the experimentally demonstrated Ni-atom transfer mechanism from Ni=E (E = CH2, NH, PH) activating complex to ethylene to form three-membered ring products but also validated the application of late transition metal complexes in respective process. Results obtained supported the argument that increase in metal coordination and electronic spin state increases catalytic activity of FeIII-imido complexes. These results not only encouraged the fact that DFT and multi-layer ONIOM methods are good to determine geometry and thermodynamics of meta-stable chemical complexes, but also gave a great support to spectroscopic calculations like NMR and Mossbauer calculations.

Orientador: Douglas Soares Galvão / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-24T13:39:40Z (GMT). No. of bitstreams: 1 Brunetto_Gustavo_D.pdf: 74304248 bytes, checksum: 1625a1a5cf52fb8ae1bd558d68118c27 (MD5) Previous issue date: 2014 / Resumo: Nas últimas décadas, sucessivas descobertas em materiais baseados em carbono abriram uma nova era na ciência dos materiais. Exemplos destas descobertas são os fulerenos, nanotubos de carbono e, mais recentemente, o grafeno. O grafeno é uma rede bi-dimensional de unidades hexagonais de carbono com ligações do tipo sp2. Grafeno apresenta propriedades mecânicas e eletrônicas não usuais e muito interessantes e devido a estas propriedades é um dos materiais mais promissores para aplicações em diversas áreas da tecnologia tais como eletrônica, militar, aeroespa- cial, dispositivos e outras. Entretanto, há algumas barreiras que devem ser superadas a fim de utilizar o grafeno em aplicações práticas. O grafeno, em sua forma pura, é um semicondutor com gap zero. Esta característica impõe sérias limitações em algumas aplicações em eletrônica, tal como, transistores. Além do mais, é muito difícil a síntese de grandes porções de grafeno que possuam poucos ou nenhum defeito estrutural. Através de simulações de primeiros princípios, propomos uma rota de síntese a partir da de-hidrogenação completa do grafeno poroso para a obtenção de um alótropo de carbono conhecido como BPC. Cálculos de estrutura eletrônica mostraram que o BPC possui um gap da ordem de 0,8 eV e orbitais de fronteira delocalizados, que exercem papel fundamental na mobilidade eletrônica do material. Na área de propriedades mecânicas, estudamos a impermeabilidade de membra- nas de grafeno. Quando depositadas sobre uma cavidade existente em uma superfície de óxido de silício. A membrana é mantida aderida sobre a superfície somente através da interação de van der Waals, entre os átomos da borda da membrana e do substrato. Inicialmente, confinado dentro da cavidade, há um gás (argônio ou hélio) e através de estudos de dinâmica molecular clássica, estudamos o mecanismo envolvido para a re- tenção e o vazamento do gás. Observamos que o gás não é capaz de vazar através da estrutura da membrana e determinamos as condições de pressão para que a membrana se descole da superfície e o gás seja liberado. O comportamento cadeias lineares de carbono confinadas dentro de nanotu- bos de carbono sujeitos a pressões extremamente altas foi analisado. Experimentos de Raman mostram uma diminuição na frequência de vibração das cadeias após todo o sistema ser submetido a altas pressões. Utilizamos o formalismo de campos de força reativo (ReaxFF) para entender a origem da diminuição das frequências de vibração da cadeia. Observamos que após a compressão ocorre uma ligação química entre a ex- tremidade da cadeia e a parede do nanotubo, que se mantém estável mesmo após a diminuição da pressão. Com a reação entre o nanotubo e a cadeia a interação entre alguns átomos da cadeia é alterada causando o enfraquecimento de algumas ligações. Através de cálculos do espectro vibracional, fomos capazes de identificar uma diminui- ção de intensidade no pico de vibração característico da cadeia e o aparecimento de um novo sinal em frequências menores. Além de estudar propriedades de materiais baseados em carbono, estudamos a possibilidade de se alterar o espectro de absorção ótico em moléculas através da uti- lização de fontes externas de laser. Devido a uma grande evolução na área de laseres ultra-rápidos, tornou-se possível estudar e caracterizar o movimento eletrônico durante um processo de excitação, por exemplo. Utilizamos a Teoria do Funcional Densidade Dependente do Tempo (TDDFT) para estudar como o espectro de absorção de molécu- las simples, como hélio e etileno, é alterado durante a interação destas moléculas com uma fonte intensa de laser. Observamos que há o aparecimento de um pico de absorção na região de gap ótico. Utilizamos técnicas de simulação computacional para estudar propriedades de diferentes tipos de sistemas. Para a membrana de grafeno, mostramos que esta é imper- meável aos gases considerados e quais os valores de pressão necessários para desprender a membrana do substrato quando esta é utilizada para selar uma cavidade que possui uma certa quantidade de gás confinado em seu interior. Com relação ao grafeno poroso, mostramos que após a completa remoção dos hidrogênios há uma interconverção para o BPC. Quanto à alteração na frequência de vibração das cadeias lineares de carbono dentro de nanotubos, mostramos que a pressão externa induz a formação de uma ligação química entre a cadeia e a parede do tubo, alterando a ligação entre alguns átomos da cadeia. Esta alteração causa uma diminuição na frequência de vibração dos átomos da cadeia. Por fim, através da metodologia de TDDFT, mostramos a alteração no espectro de absorção, devido a interação entre a amostra e um laser externo intenso / Abstract: In the last decades, successive discoveries in carbon-based materials have opened up a new era in materials science. Examples of these findings are fullerenes, carbon nanotubes, and more recently, graphene. Graphene is a two-dimensional hexagonal array of sp2-bonded carbon atoms. Graphene shows very interesting and unusual mechanical and electronic properties. Due to these special properties graphene is considered one of the most promising materials for applications in diverse areas such as electronics, military, aerospace, and other de- vices. However, there are obstacles that must be overcome in order to use graphene in practical applications. Graphene, in its pure form, is a zero-gap semiconductor. This feature imposes serious limitations in some applications in electronics, such as transis- tors. Moreover, it is very difficult to synthesize large portions of graphene that possess little or no structural defect. In this work, using first principle simulations, we propose a synthesis route from the complete dehydrogenation of porous graphene to obtain an carbon allotrope known as BPC. Electronic structure calculations show that the BPC has a band gap of 0, 8 eV and delocalized frontier orbitals, which has a primary role in material electronic mobility. In mechanical properties area, we studied the impermeability properties of graphene membranes. Graphene membranes were deposited over an existing cavity in a silicon oxide surface. The membrane is kept clamped on the surface only due to van der Waals interaction between the membrane edge atoms and the surface. Initially confined inside the cavity, there is a gas (argon or helium). We carried out classical molecular dynamics simulations in order to study the mechanism involved for the gas leakage. We observed that gas can not pass through the membrane structure and the leakage occurs only when membrane peel off the surface due to the gas high pressure inside the cavity. The behavior of carbon linear chains confined inside carbon nanotubes under extremely high pressure was considered. Experiments show a reduction in the Raman vibrational frequency of the chains after the entire system being subjected to high pressures. We use the formalism of reactive force fields (ReaxFF) to understand the origin of the chain vibrational frequency decrease. We observed that after compression a chemical bond between the end of the chain and the tube walls occurs, and remains stable even after lowering the pressure. The reaction between the nanotube and the chain causes the weakening of some connections between chain atoms. Through calcu- lated vibrational spectrum, we were able to identify a intensity decrease at the peak of characteristic vibration of the chain and the appearance of a new signal at lower frequencies. Besides studying properties of carbon-based materials, we studied the possibil- ity of modifying the optical absorption spectrum of molecules through external laser sources. Due to a great evolution in the area of ultrafast lasers, it has become possible study and characterize the electronic motion during an excitation process, for example. We use the Time-Dependent Density Functional Theory (TDDFT) to study how the absorption spectrum of single molecules such as helium and ethylene changes during due to the action of an intense laser source. We note that there is an appearance of an absorption peak in the optical gap region. We used computer simulation techniques to study properties of different system types. For the graphene membrane, we showed that it is impermeable to the considered gases and which pressure values is necessary to detach membrane from the substrate when it is used to seal a cavity with a certain amount of gas confined. With respect to porous graphene, we showed that after complete hydrogens removal there is an inter- conversion for BPC. Regarding the change in the vibrational frequency of linear carbon chains inside nanotubes, we showed that external pressure induces the formation of a chemical bond between chain and the tube, changing the weakening the bond between some chain atoms. This modification causes a decrease in the vibrational frequency. Finally, through the TDDFT methodology, we showed the change in the absorption spectrum, due to the interaction between the sample and an intense external laser field / Doutorado / Física / Doutor em Ciências

The focus of this thesis is on C-O bonds activation by transition metal atoms. Lignin is a potential alternative energy resource, but currently is an underused biomass species because of its highly branched structure. To aid in better understanding this species, the oxidative cleavage of the Cβ-O bond in an archetypal arylglycerol β-aryl ether (β–O–4 Linkage) model compound of lignin with late 3d, 4d, and 5d metals was investigated. Methoxyethane was utilized as a model molecule to study the activation of the C-O bond. Binding enthalpies (ΔHb), enthalpy formations (ΔH) and activation enthalpies (ΔH‡) have been studied at 298K to learn the energetic properties in the C-O bond cleavage in methoxyethane. Density functional theory (DFT) has become a common choice for the transition metal containing systems. It is important to select suitable functionals for the target reactions, especially for systems with degeneracies that lead to static correlation effects. A set of 26 density functionals including eight GGA, six meta-GGA, six hybrid-GGA, and six hybrid-meta-GGA were applied in order to investigate the performance of different types of density functionals for transition metal catalyzed C-O bond cleavage. A CR-CCSD(T)/aug-cc-pVTZ was used to calibrate the performance of different density functionals.

No description available.

Despite the growing applications of silver nanoparticles, toxicity information on this nanomaterial is still deficient. Conclusions on the toxicity of silver nanoparticles vary and atomic level toxicity mechanisms are not yet achieved. Consequently, our group conducted combined computational and experimental toxicity studies of silver nanoparticles (AgNPs). Toxicity of 10 nm citrate stabilized AgNPs on HepG2 cells were investigated. Experimental results show that the 10 nm citrate stabilized AgNPs begin to be toxic to HepG2 cells at a dosage that exceeds 1 ppm and LD50 was observed at 3 ppm. Elevated reactive oxygen species levels were seen upon exposure to AgNPs with the maximum at the LD50 concentration of 3 ppm. Normal protein regulation of HepG2 cells were affected by exposure to AgNPs. TEM images of HepG2 cells exposed to AgNPs reveal that AgNPs can penetrate and agglomerate inside the cells. Our preliminary computational study was guided by one of the widely accepted toxicity mechanism of AgNPs in which the nanoparticles dissolute to Ag+. The computational model was composed of a 1:1 ratio of silver and phospholipid head. The silver employed are in atomic and anionic form while the phospholipid head are the phosphocholine (PC) and phosphoethanolamine (PE), which are abundant in HepG2 cells. Computational study shows that the presence of Ag+ results in partial oxidation of both the phospholipid heads. Our preliminary experimental and computational studies lead us to develop new computational methods that can accurately predict oxidation potentials (HOMO), reduction potentials (LUMO), and absorption spectra that can be used in studying toxicity mechanism of AgNPs through the oxidation pathway. Thus, computational methods for cyclic voltammetry and absorption spectroscopy that use DFT and TD-DFT, respectively, were improved to provide more accurate electronic and optical properties. Cyclopenta-fused polycyclic hydrocarbons (CP-PAHs) with available experimental data for HOMO, LUMO, ΔEgap and absorption spectra and have potential application as AgNP stabilizers were used in developing the improved computational methods for cyclic voltammetry and absorption spectroscopy. The improved computational method for cyclic voltammetry was developed by accounting for the anion species that occur experimentally and by using B3LYP the best density functional in predicting the HOMO, LUMO and ΔEgap of CP-PAHs with overall MAE of 014 eV. The best absorption spectra otef CP-PAHs were predicted using B3LYP for geometry optimizations followed by TD-CAMB3LYP with MAE of 29 nm. All calculations of CP-PAHs were implemented using the 6-311g (d,p) basis set and tetrahydrofuran (THF) as solvent. These two developed computational methods were tested on a group of methyl triphenyl amine (MTPA) derivatives with available experimental data for HOMO, LUMO, ΔEgap and absorption spectra and have potential application as AgNP stabilizers. The new computational methods for cyclic voltammetry and absorption spectroscopy also provided the most accurate predicted electronic and optical properties of MTPA derivatives. Among the ten density functionals employed, prediction of HOMO, LUMO and ΔEgap were most accurate using B3LYP and B3PW91 with overall MAE of 0.31 eV and 0.27 eV, respectively. Absorption spectra of MTPA derivatives were still best predicted using the B3LYP/TD-CAMB3LYP method with MAE of 13 nm. All calculations of MTPA were implemented using the 6-31+g (d,p) basis set and dichloromethane as solvent.

Density Functional Theory (DFT) method is applied to study the crystal structure of transition metal and lanthanide oxides, as well as molecular magnetic complexes. DFT is a widely popular computational approach because it recasts a many-body problem of interacting electrons into an equivalent problem of non-interacting electrons, greatly reducing computational cost. We show that for certain structural properties like phase stability, lattice parameter and oxygen migration energetics pure DFT can give good agreement with experiments. But moving to more sensitive properties like spin state energetic certain modifications of standard DFT are needed. First we investigated mixed ionic-electronic conducting perovskite type oxides with a general formula ABO3 (where A =Ba, Sr, Ca and B = Co, Fe, Mn). These oxides often have high mobility of the oxygen vacancies and exhibit strong ionic conductivity. They are key materials that find use in several energy related applications, including solid oxide fuel cell (SOFC), sensors, oxygen separation membranes, and catalysts. Different cations and oxygen vacancies ordering are examined using plane wave pseudopotential density functional theory. We find that cations are completely disordered, whereas oxygen vacancies exhibit a strong trend for aggregation in L-shaped trimer and square tetramer structure. On the basis of our results, we suggest a new explanation for BSCF phase stability. Instead of linear vacancy ordering, which must take place before the phase transition into brownmillerite structure, the oxygen vacancies in BSCF prefer to form the finite clusters and preserve the disordered cubic structure. This structural feature could be found only in the first-principles simulations and cannot be explained by the effect of the ionic radii alone. In order to understand vacancy clustering and phase iv stability in oxygen-deficient barium strontium cobalt iron oxide (BSCF), we predict stability and activation energies for oxygen vacancy migration. Using symmetry constrained search and Nudged Elastic Band method, we characterize the transition states for an oxygen anion moving into a nearby oxygen vacancy site that is surrounded by different cations and find the activation energies to vary in the range 30-50 kJ/mol in good agreement with experimental data. Next we study spin alignments of single molecule magnets (SMM). SMMs are a class of polynuclear transition metal complexes, which characterized by a large spin ground state and considerable negative anisotropy. These properties lead to a barrier for the reversal of magnetization. For these reasons SMM are expected to be promising materials for molecular spintronics and quantum computing applications. To design SMM for quantum computation, we need to accurately predict their magnetic properties. The most important property is, Heisenberg exchange coupling constant (J). This constant appears in model Heisenberg Hamiltonian that can be written in general form as here Jij represents the coupling between the two magnetic centers i and j with the spin states Si and Sj. The positive J values indicate the ferromagnetic ground state and the negative ones indicate the antiferromagnetic ground state. We found pure DFT is not accurate enough to predict J values. We employ density functionals with a Hubbard U term that helps to counteract the unphysical delocalization of electrons due to errors in pure exchange-correlation functionals. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the spin density onto acetate ligands due to π-back bonding, inverting spin-polarization of the Jiij −= ∑ S.S.JH v acetate oxygen atoms relative to that predicted from superexchange mechanism. This inversion may affect performance of the models assuming strict localization of the spins on magnetic centers for the complexes with bridging acetate ligands. Next, we apply DFT+U methodology for Mn12(mda) and Mn12(ada) complexes to calculate all six nearest neighbor Jij value. Our result shows both qualitative and quantitative agreement with experiments unlike other DFT studies. Using the optimized geometry of the ground spin state instead of less accurate experimental geometry was found to be crucial for this good agreement. The protocol tested in this study can be applied for the rational design of single-molecule magnets for molecular spintronics and quantum computing applications. Finally we apply hybrid DFT methodology to calculate geometrical parameters for cerium oxides. We review the experimental and computational studies on the cerium oxide nanoparticles, as well as stoichiometric phases of bulk ceria. Electroneutral and nonpolar pentalayers are identified as building blocks of type A sesqioxide structure. The idealized structure of the nanoparticles is described as dioxide covered by a single pentalayer of sesquioxide, which explains the exceptional stability of subsurface vacancies in nanoceria. The density functional theory (DFT) predictions of the lattice parameters and bulk moduli for the Ce(IV) and Ce(III) oxides at the hybrid DFT level are also presented. The calculated values for both compounds agree with experiment and allow to predict changes in the lattice parameter with decreasing size of the nanoparticles. The results validate hybrid DFT as a promising method for future study the structure of oxygen vacancies and catalytic properties of ceria nanoparticles.

No description available.

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Finite element techniques have been applied to a wide variety of problems in electro magnetics, but have been handicapped by the appearance of spurious solutions. Both weighted residual methods and variational methods are the basic finite element techniques that are examined to establish a framework for the discussion of spurious solutions. A simple waveguide example is used to explore the fundamental problem with these spurious solutions. A method is developed that focuses on the functional form as the fundamental cause underlying the difficulties with spurious solutions. By using analytical rather than numerical means, it is shown that the solution form allows for the existence of an improper gradient behavior in a general field expansion. A new functional that satisfies Maxwell's equations and eliminates spurious solutions is introduced. This new functional is shown to be self-adjoint and positive definite, thus providing an error minimization. The analytical form as well as the finite element method is applied to demonstrate the robust nature of the functional. / Ph. D.