Estudos teóricos da reação de alquilação desracemizante em enaminas quirais

Utilizando métodos ab initio no nível RHF/6-311G**, combinado com conceitos do Princípio de Curtin-Hammett e da lei de distribuição de Maxwell-Boltzmann, este trabalho teve como objetivo elucidar os mecanismos implicados na reação de Michael assimétrica via o equilíbrio tautomérico imina/enamina quirais, também conhecida como alquilação desracemizante. Estão descritos novas abordagens e metodologias para uma extensiva Análise Conformacional e Análise dos Estados de Transição para moléculas com razoável número de átomos, envolvendo um alto número de graus de liberdade. Essas novas abordagens e metodologias envolvendo o Estado de Transição, proporcionaram gerar resultados com desvio de apenas 10,1% para o valor do excesso diastereoisomérico dos produtos Re/Si envolvendo a enamina (R,R) 5; consideramos ainda neste caso, contribuições de entropia e entalpia (ZPE) para a energia livre absoluta de ativação. Tais resultados obtidos evidenciaram a importância da consideração de um maior número de confôrmeros na obtenção de geometrias no estado de transição, para a correta descrição dos processos cinéticos envolvidos nas reações químicas.

Novo formalismo semi-empírico para cálculos químico-quânticos

Realizou-se a dedução de um formalismo básico, útil para o desenvolvimento de novas implementações semi-empíricas, partindo de primeiros princípios. A abordagem utilizada é inspirada nos métodos da família HAM, e visa possibilitar o desenvolvimento de uma implementação semi-empírica de última geração que não esteja sujeita às di culdades que ocorrem com métodos da família ZDO. São apresentadas as expressões para a energia total e para os elementos da matriz de Fock segundo este formalismo básico. O emprego de expoentes variáveis nas funções de base (orbitais atômicos) é proposto e modelado com esquemas tipo HAM/3, HAM/4 e polinomial, tomando-se como referência resultados obtidos por cálculo ab initio. Além disso, uma contribuição para produção de conjuntos de dados de referência por cálculo ab initio é fornecida. Esta contribuição permite que sejam produzidos resultados de alto nível para energias eletrônicas a um custo computacional moderado, por meio da extrapola- ção da energia de correlação eletrônica em cálculos com bases correlation consistent de Dunning.

Estudo do genoma do vírus causador da mionecrose infecciosa em camarões e desenvolvimento de métodos para detecção de diferentes variantes

Shrimp farming is one of the activities that contribute most to the growth of global aquaculture. However, this business has undergone significant economic losses due to the onset of viral diseases such as Infectious Myonecrosis (IMN). The IMN is already widespread throughout Northeastern Brazil and affects other countries such as Indonesia, Thailand and China. The main symptom of disease is myonecrosis, which consists of necrosis of striated muscles of the abdomen and cephalothorax of shrimp. The IMN is caused by infectious myonecrosis virus (IMNV), a non-enveloped virus which has protrusions along its capsid. The viral genome consists of a single molecule of double-stranded RNA and has two Open Reading Frames (ORFs). The ORF1 encodes the major capsid protein (MCP) and a potential RNA binding protein (RBP). ORF2 encodes a probable RNA-dependent RNA polymerase (RdRp) and classifies IMNV in Totiviridae family. Thus, the objective of this research was study the IMNV complete genome and encoded proteins in order to develop a system differentiate virus isolates based on polymorphisms presence. The phylogenetic relationship among some totivirus was investigated and showed a new group to IMNV within Totiviridae family. Two new genomes were sequenced, analyzed and compared to two other genomes already deposited in GenBank. The new genomes were more similar to each other than those already described. Conserved and variable regions of the genome were identified through similarity graphs and alignments using the four IMNV sequences. This analyze allowed mapping of polymorphic sites and revealed that the most variable region of the genome is in the first half of ORF1, which coincides with the regions that possibly encode the viral protrusion, while the most stable regions of the genome were found in conserved domains of proteins that interact with RNA. Moreover, secondary structures were predicted for all proteins using various softwares and protein structural models were calculated using threading and ab initio modeling approaches. From these analyses was possible to observe that the IMNV proteins have motifs and shapes similar to proteins of other totiviruses and new possible protein functions have been proposed. The genome and proteins study was essential for development of a PCR-based detection system able to discriminate the four IMNV isolates based on the presence of polymorphic sites

Predição de promotores de Bacillus subtilis usando técnicas de aprendizado de máquina

One of the most important goals of bioinformatics is the ability to identify genes in uncharacterized DNA sequences on world wide database. Gene expression on prokaryotes initiates when the RNA-polymerase enzyme interacts with DNA regions called promoters. In these regions are located the main regulatory elements of the transcription process. Despite the improvement of in vitro techniques for molecular biology analysis, characterizing and identifying a great number of promoters on a genome is a complex task. Nevertheless, the main drawback is the absence of a large set of promoters to identify conserved patterns among the species. Hence, a in silico method to predict them on any species is a challenge. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. In this work, we present an empirical comparison of Machine Learning (ML) techniques such as Na¨ýve Bayes, Decision Trees, Support Vector Machines and Neural Networks, Voted Perceptron, PART, k-NN and and ensemble approaches (Bagging and Boosting) to the task of predicting Bacillus subtilis. In order to do so, we first built two data set of promoter and nonpromoter sequences for B. subtilis and a hybrid one. In order to evaluate of ML methods a cross-validation procedure is applied. Good results were obtained with methods of ML like SVM and Naïve Bayes using B. subtilis. However, we have not reached good results on hybrid database

Propriedades física de molécilas orgânicas e compostos do tipo perovskita CdSiO3 e CaPbO3

In the first part of this work our concern was to investigate the thermal effects in organic crystals using the theory of the polarons. To analyse such effect, we used the Fröhlich s Hamiltonian, that describes the dynamics of the polarons, using a treatment based on the quantum mechanics, to elucidate the electron-phonon interaction. Many are the forms to analyzing the polaronic phenomenon. However, the measure of the dielectric function can supply important information about the small polarons hopping process. Besides, the dielectric function measures the answer to an applied external electric field, and it is an important tool for the understanding of the many-body effects in the normal state of a polaronic system. We calculate the dielectric function and its dependence on temperature using the Hartree-Fock decoupling method. The dieletric function s dependence on the temperature is depicted by through a 3D graph. We also analyzed the so called Arrhenius resistivity, as a functionof the temperature, which is an important tool to characterize the conductivity of an organic molecule. In the second part we analyzed two perovskita type crystalline oxides, namely the cadmium silicate triclinic (CdSiO3) and the calcium plumbate orthorhombic (CaPbO3), respectively. These materials are normally denominated ABO3 and they have been especially investigated for displaying ferroelectric, piezoelectric, dielectrics, semiconductors and superconductors properties. We found our results through ab initio method within the functional density theory (DFT) in the GGA-PBE and LDA-CAPZ approximations. After the geometry optimization for the two structure using the in two approximations, we found the structure parameters and compared them with the experimental data. We still determined further the angles of connection for the two analyzed cases. Soon after the convergence of the energy, we determined their band structures, fundamental information to characterize the nature of the material, as well as their dielectrics functions, optical absorption, partial density of states and effective masses of electrons and holes

A theoretical analysis on the intramolecular proton transfer of alpha-alanine in an aqueous medium

Intramolecular proton transfer from oxygen to nitrogen atoms in the alpha-alanine amino acid has been studied by ab initio methods at the HF/6-31G*, HF/6-31 ++ G** and MP2/6-31 ++ G** levels of calculation including the solvent effects by means of self-consistent reaction field theory. An analysis of the results based on the natural bond orbital charges shows that the transition structure presents an imbalance in the sense that the charge shift lags behind the proton transfer and that the bond formation is always in advance with respect to the bond cleavage. All calculation levels show that the barrier height associated with the conformational change on alpha-alanine is larger than the proton transfer process. (C) 1998 Elsevier B.V. B.V. All rights reserved.

Transporte eletrônico e propriedades termodinâmicas de nanobiomoléculas

We use a tight-binding formulation to investigate the transmissivity and the currentvoltage (I_V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare theresults for the genomic DNA sequence with those of arti_cial sequences (the long-range correlated Fibonacci and RudinShapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same _rst neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I_V curves seem to be mostly inuenced by the short-range correlations. We also analyze in this work the electronic and thermal properties along an _-helix sequence obtained from an _3 peptide which has the uni-dimensional sequence (Leu-Glu-Thr- Leu-Ala-Lys-Ala)3. An ab initio quantum chemical calculation procedure is used to obtain the highest occupied molecular orbital (HOMO) as well as their charge transfer integrals, when the _-helix sequence forms two di_erent variants with (the so-called 5Q variant) and without (the 7Q variant) _brous assemblies that can be observed by transmission electron microscopy. The di_erence between the two structures is that the 5Q (7Q) structure have Ala ! Gln substitution at the 5th (7th) position, respectively. We estimate theoretically the density of states as well as the electronic transmission spectra for the peptides using a tight-binding Hamiltonian model together with the Dyson's equation. Besides, we solve the time dependent Schrodinger equation to compute the spread of an initially localized wave-packet. We also compute the localization length in the _nite _-helix segment and the quantum especi_c heat. Keeping in mind that _brous protein can be associated with diseases, the important di_erences observed in the present vi electronic transport studies encourage us to suggest this method as a molecular diagnostic tool

Structural characterization of 0.5PbMg(1/3)Nb(2/3)O(3)-0.5Ba(x)Pb((1-x))TiO(3) powders

The present work reports the effects caused by barium on phase formation, morphology and sintering of lead magnesium niobate-lead titanate (PMN-50PT). Ab initio study of 0.5PbMg(1/3)Nb(2/3)O(3)-0.5Ba(x)Pb((1-x))TiO(3) ceramic powders, with x = 0, 0.20, and 0.40 was proposed, considering that the partial substitution of lead by barium can reestablish the equilibrium of monoclinic-tetragonal phases in the system. It was verified that even for 40 mol% of barium, it was possible to obtain pyrochlore-free PMN-PT powders. The increase of the lattice parameters of PMN-PT doped-powders confirmed dopant incorporation into the perovskite phase. The presence of barium improved the reactivity of the powders, with an average particle size of 120 nm for 40 mol% of barium against 167 mn for the pure sample. Although high barium content (40 mol%) was deleterious for a dense ceramic, contents up to 20 mol% allowed 95% density when sintered at 1100 degrees C for 4 h. (c) 2007 Elsevier Ltd. All rights reserved.

Nonzero Gap Two-Dimensional Carbon Allotrope from Porous Graphene

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

On the photoluminescence behavior of samarium-doped strontium titanate nanostructures under UV light. A structural and electronic understanding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo da série iso-eletrônica do átomo de hélio pelo método hiperesférico

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Binding energies of excitons trapped by ionized donors in semiconductors

Using the hyperspherical adiabatic approach in a coupled-channel calculation, we present precise binding energies of excitons trapped by impurity donors in semiconductors within the effective-mass approximation. Energies for such three-body systems are presented as a function of the relative electron-hole mass sigma in the range 1 less than or equal to1/sigma less than or equal to6, where the Born-Oppenheimer approach is not efficiently applicable. The hyperspherical approach leads to precise energies using the intuitive picture of potential curves and nonadiabatic couplings in an ab initio procedure. We also present an estimation for a critical value of sigma (sigma (crit)) for which no bound state can be found. Comparisons are given with results of prior work by other authors.

Spectroscopic studies of the Eu3+ and Er3+ ions in the fluorozirconate LaZr2F11 matrix

An investigation by optical spectroscopy of the Eu3 + and Er3 + active ions in the crystallized fluorozirconate matrix LaZr2F11 is presented. The D-5(1) --> F-7(0-5) emission lines of Eu3 + are used to extract the F-7(0-5) energy scheme and the observed extinctions permit the deduction of irreducible representations (IRREPS) associated with corresponding sub-levels in the D-2 symmetry. The crystal field analysis was carried out on a 387 x 387 basis set, comprising the F-7, D-5(1,2,3) F-5(1,2), (5)G(1,2,3) and P-3(1,2,3,4,5,6) terms of the Eu-3 (+) 4f(6) configuration. The deviation and rms are 6.8 and 7.9 cm (-1), respectively for 38 levels and ten parameters. The experimental crystal field parameters are in good agreement with the ab-initio ones. Moreover, the relative intensities of the D-5(0) --> F-7(2,3,4) emissions are well reproduced by an 'ab-initio' calculation, except for three lines. The Er3 + ions introduced in LaZr2F11, microcrystals also lie in an unique crystallographic site. A total of 31 energy levels were recorded and the crystal field analysis led to 6.6 and 7.8 cm (-1) for the deviation and rms, respectively, for nine variable parameters taken into account. The experimental CF parameters for Er3 + and Eu3 + are very similar, which seems to show that the host lattice contracts around the smaller Er3 + ion. The informations given by both Eu3 + and Eu3 + optical probes in LaZr2F11 are very consistent with the structure previously determined for the isotypic PrZr2F11 fluoride. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Er3+ as marker for order-disorder determination in the PbTiO3 system

Er3+ ions were added to the PbTiO3 network using the polymeric precursor method to characterize the order-disorder transformation found in this material by means of experimental and theoretical approach. The disordered and ordered material structures were studied by photoluminescence measurements, X-ray diffraction (XRD) and U-V-visible spectroscopy. The Er3+ ions served as a marker to identify the structural short-range order beginning in the PbTiO3 matrix. From photoluminescence results it was concluded that disordered PbTiO3 powders have a certain short range order in the network that are undetected by XRD measurements. The electronic structures were calculated by the ab initio periodic method in DFT level with the non-local B3LYP hybrid approximation for the Ti atom site interpretation using density of states (DOS) results. This analysis enabled understanding that Ti atom sphere coordination can create possible states for radioactive return and trap of electron-holes pair. (c) 2007 Elsevier B.V. All rights reserved.

Correlation among order-disorder, electronic levels, and photoluminescence in amorphous CT : Sm

Ca0.95Sm0.05TiO3 (CT:Sm) powder was prepared by the polymeric precursor method (PPM). Order-disorder at short and long range has been investigated by means of Raman spectroscopy, X-ray diffraction (XRD), and photoluminescence emission (PL) experimental techniques. The broad PL band and the Sm emission spectrum measured at room temperature indicate the increase of structural order with annealing temperature. The measured PL emission reveals that the PL intensity changes with the degree of disorder in the CT: Sm. The electronic structures were performed by the ab initio periodic method in the DFT level with the hybrid nonlocal B3LYP approximation. Theoretical results are analyzed in terms of DOS, charge densities, and Mulliken charges. Localized levels into the band gap of the CT: Sm material favor the creation of the electron-hole pair, supporting the observed room-temperature PL phenomenon.