Adapted Gaussian basis sets for atoms from Li through Xe generated with the generator coordinate Hartree-Fock method

Utiliza-se o método coordenada geradora Hartree-Fock para gerar bases Gaussianas adaptadas para os átomos de Li (Z=3) até Xe (Z=54). Neste método, integram-se as equações de Griffin-Hill-Wheeler-Hartree-Fock através da técnica de discretização integral. Comparam-se as funções de ondas geradas neste trabalho com as funções de ondas Roothaan-Hartree-Fock de Clementi e Roetti (1974) e com outros conjuntos de bases relatados na literatura. Para os átomos estudados aqui, os erros em nossas energias totais relativos aos limites numéricos Hartree-Fock são sempre menores que 7,426 milihartree.

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Desarrollo de materiales nanocristalinos de base hierro por aleado mecánico

Two alloys, Fe80Nb10B10 and Fe70Ni14Zr6B10, were produced by mechanical alloying. The formation of thenanocrystallites (about 7-8 nm at 80h MA) was detected by X-ray diffraction. After milling for 80 h, differentialscanning calorimetry scans show low-temperature recovery processes and several crystallization processes related with crystal growth and reordering of crystalline phases. The apparent activation energy values are 315 ± 40 kJ mol–1 for alloy A, and 295 ± 20 kJ mol–1 and 320 ± 25 kJ mol–1 for alloy B. Furthermore, a melt-spun Fe-based ribbon was mechanically alloyed to obtain a powdered-like alloy. The increase of the rotation speed and the ball-to-powderweight ratio reduces the necessary time to obtain the powdered form

Defect study of SnO2 nanostructures by cathodoluminescence analysis: Application to nanowires

Defects in SnO2 nanowires have been studied by cathodoluminescence, and the obtained spectra have been compared with those measured on SnO2 nanocrystals of different sizes in order to reveal information about point defects not determined by other characterization techniques. Dependence of the luminescence bands on the thermal treatment temperatures and pre-treatment conditions have been determined pointing out their possible relation, due to the used treatment conditions, with the oxygen vacancy concentration. To explain these cathodoluminescence spectra and their behavior, a model based on first-principles calculations of the surface oxygen vacancies in the different crystallographic directions is proposed for corroborating the existence of surface state bands localized at energy values compatible with the found cathodoluminescence bands and with the gas sensing mechanisms. CL bands centered at 1.90 and 2.20 eV are attributed to the surface oxygen vacancies 100° coordinated with tin atoms, whereas CL bands centered at 2.37 and 2.75 eV are related to the surface oxygen vacancies 130° coordinated. This combined process of cathodoluminescence and ab initio calculations is shown to be a powerful tool for nanowire defect analysis.

Surface structure and stability of PdZn and PtZn alloys: Density-functional slab model studies

Geometric parameters of binary (1:1) PdZn and PtZn alloys with CuAu-L10 structure were calculated with a density functional method. Based on the total energies, the alloys are predicted to feature equal formation energies. Calculated surface energies of PdZn and PtZn alloys show that (111) and (100) surfaces exposing stoichiometric layers are more stable than (001) and (110) surfaces comprising alternating Pd (Pt) and Zn layers. The surface energy values of alloys lie between the surface energies of the individual components, but they differ from their composition weighted averages. Compared with the pure metals, the valence d-band widths and the Pd or Pt partial densities of states at the Fermi level are dramatically reduced in PdZn and PtZn alloys. The local valence d-band density of states of Pd and Pt in the alloys resemble that of metallic Cu, suggesting that a similar catalytic performance of these systems can be related to this similarity in the local electronic structures.

Effect of tow-drop gaps on the damage resistance and tolerance of Variable-Stiffness Panels

This paper presents an experimental study of the effects of tow-drop gaps in Variable Stiffness Panels under drop-weight impact events. Two different configurations, with and without ply-staggering, have been manufactured by Automated Fibre Placement and compared with their baseline counterpart without defects. For the study of damage resistance, three levels of low velocity impact energy are generated with a drop-weight tower. The damage area is analysed by means of ultrasonic inspection. Results of the analysed defect configurations indicate that the influence of gap defects is only relevant under small impact energy values. However, in the case of damage tolerance, the residual compressive strength after impact does not present significant differences to that of conventional straight fibre laminates. This indicates that the strength reduction is driven mainly by the damage caused by the impact event rather than by the influence of manufacturing-induced defects

Conservation Laws in Cellular Automata

Conservation laws in physics are numerical invariants of the dynamics of a system. In cellular automata (CA), a similar concept has already been defined and studied. To each local pattern of cell states a real value is associated, interpreted as the “energy” (or “mass”, or . . . ) of that pattern.The overall “energy” of a configuration is simply the sum of the energy of the local patterns appearing on different positions in the configuration. We have a conservation law for that energy, if the total energy of each configuration remains constant during the evolution of the CA. For a given conservation law, it is desirable to find microscopic explanations for the dynamics of the conserved energy in terms of flows of energy from one region toward another. Often, it happens that the energy values are from non-negative integers, and are interpreted as the number of “particles” distributed on a configuration. In such cases, it is conjectured that one can always provide a microscopic explanation for the conservation laws by prescribing rules for the local movement of the particles. The onedimensional case has already been solved by Fuk´s and Pivato. We extend this to two-dimensional cellular automata with radius-0,5 neighborhood on the square lattice. We then consider conservation laws in which the energy values are chosen from a commutative group or semigroup. In this case, the class of all conservation laws for a CA form a partially ordered hierarchy. We study the structure of this hierarchy and prove some basic facts about it. Although the local properties of this hierarchy (at least in the group-valued case) are tractable, its global properties turn out to be algorithmically inaccessible. In particular, we prove that it is undecidable whether this hierarchy is trivial (i.e., if the CA has any non-trivial conservation law at all) or unbounded. We point out some interconnections between the structure of this hierarchy and the dynamical properties of the CA. We show that positively expansive CA do not have non-trivial conservation laws. We also investigate a curious relationship between conservation laws and invariant Gibbs measures in reversible and surjective CA. Gibbs measures are known to coincide with the equilibrium states of a lattice system defined in terms of a Hamiltonian. For reversible cellular automata, each conserved quantity may play the role of a Hamiltonian, and provides a Gibbs measure (or a set of Gibbs measures, in case of phase multiplicity) that is invariant. Conversely, every invariant Gibbs measure provides a conservation law for the CA. For surjective CA, the former statement also follows (in a slightly different form) from the variational characterization of the Gibbs measures. For one-dimensional surjective CA, we show that each invariant Gibbs measure provides a conservation law. We also prove that surjective CA almost surely preserve the average information content per cell with respect to any probability measure.

Composição centesimal do leite humano e caracterização das propriedades físico-químicas de sua gordura

Human milk fat is essential for development of newborn infants. Many studies detail chemical characteristics of human milk fat; however there are no studies about its physical properties. The objective of this work was to analyze the centesimal composition of human milk and to compare the calculated energy value with the estimated energy by the creamatocrit method. Chemical composition and physical properties of human milk lipids and Betapol - a structured lipid - were also studied. The results showed that energy values of human milk estimated by creamatocrit and calculated by the centesimal composition didn't present significant correlation. Human milk lipids and Betapol presented distinct physico-chemical properties.

Metodologia AGOA: a modelagem de clusters de hidratação no complexo aziridina···ácido fluorídrico

We present a theoretical study of solvent effect on C2H5N···HF hydrogen-bonded complex through the application of the AGOA methodology. By using the TIP4P model to orientate the configuration of water molecules, the hydration clusters generated by AGOA were obtained through the analysis of the molecular electrostatic potential (MEP) of solute (C2H5N···HF). Thereby, it was calculated the hydration energies on positive and negative MEP fields, which are maxima (PEMmax) and minima (PEMmin) when represent the -CH2- methylene groups and hydrofluoric acid, respectively. By taking into account the higher and lower hydration energy values of -370.6 kJ mol-1 and -74.3 kJ mol-1 for PEMmax and PEMmin of the C2H5N···HF, our analysis shows that these results corroborate the open ring reaction of aziridine, in which the preferential attack of water molecules occurs at the methylene groups of this heterocyclic.

TUNGSTOPHOSPHORIC ACID HETEROGENIZED ONTO NH4ZSM5 AS AN EFFICIENT AND RECYCLABLE CATALYST FOR THE PHOTOCATALYTIC DEGRADATION OF DYES

Materials based on tungstophosphoric acid (TPA) immobilized on NH4ZSM5 zeolite were prepared by wet impregnation of the zeolite matrix with TPA aqueous solutions. Their concentration was varied in order to obtain TPA contents of 5%, 10%, 20%, and 30% w/w in the solid. The materials were characterized by N2 adsorption-desorption isotherms, XRD, FT-IR, 31P MAS-NMR, TGA-DSC, DRS-UV-Vis, and the acidic behavior was studied by potentiometric titration with n-butylamine. The BET surface area (SBET) decreased when the TPA content was raised as a result of zeolite pore blocking. The X-ray diffraction patterns of the solids modified with TPA only presented the characteristic peaks of NH4ZSM5 zeolites, and an additional set of peaks assigned to the presence of (NH4)3PW12O40. According to the Fourier transform infrared and 31P magic angle spinning-nuclear magnetic resonance spectra, the main species present in the samples was the [PW12O40]3- anion, which was partially transformed into the [P2W21O71]6- anion during the synthesis and drying steps. The thermal stability of the NH4ZSM5TPA materials was similar to that of their parent zeolites. Moreover, the samples with the highest TPA content exhibited band gap energy values similar to those reported for TiO2. The immobilization of TPA on NH4ZSM5 zeolite allowed the obtention of catalysts with high photocatalytic activity in the degradation of methyl orange dye (MO) in water, at 25 ºC. These can be reused at least three times without any significant decrease in degree of degradation.

Influence of temperature on the respiration rate of minimally processed organic carrots (Daucus Carota L. cv. Brasília)

The objective of this work was to study the influence of temperature on the respiration rate of minimally processed organic carrots (Daucus Carota L. cv. Brasília) with and without the application of a gelatin film. The samples were packed in flexible bags and stored at 1, 5 and 10 °C. During the five days of storage, the CO2 and O2 concentrations in the headspace of the package were monitored by gas chromatography, and the mathematical model based on enzymatic kinetics was used to estimate the respiration rate of minimally processed organic carrots. The effect of temperature on the respiration rate was evaluated by the Arrhenius equation. The results showed that the O2 concentration decreased during the storage period and the CO2 concentration increased. The lowest O2 concentrations of 2.59 and 2.66% were found for the samples stored at 10 °C with and without the film, respectively. For the CO2 concentration, the highest concentrations of 16.25 and 16.32% were again found for the temperature of 10 °C with and without the application of the film, respectively. At the temperature of 1 °C, the maximum respiratory rates for the samples without and with the film were 10.82 and 10.44 mL CO2.kg-1/hour, respectively, after 72 hours of storage. The greatest respiratory rate was obtained at 10 °C, the maximum peak being reached after 50 hours. Activation energy values were of 50.59 kJ.mol-1, for the samples with the film, and 51.88 kJ.mol-1 for the samples without the film.

Color degradation kinetics in low-calorie strawberry and guava jellies

The purpose of this study was to follow-up color changes in low-calorie strawberry and guava jellies during storage. To this end, one formulation of each flavor was prepared varying the application of hydrocolloids (pectin and modified starch). The jellies were studied regarding pH, soluble solids, water activity and syneresis. In order to follow-up color changes, the samples remained stored for 180 days in chambers with controlled temperatures of 10 °C (control) and 25 °C (commercial), and color instrumental analyses (L*, a*, and b*) were performed every 30 days. Arrhenius model was applied to reaction speeds (k) at different temperatures, where light strawberry and guava jellies showed greater color changes when stored at 25 °C compared to the samples stored at 10 °C. Activation energy values between 13 and 15 kcal.mol-1 and Q10 values between 2.1 and 2.3 were obtained for light strawberry jelly and light guava jelly, respectively. Therefore, it was concluded that, with respect to color changes, every 10 °C temperature increase reduces light jellies shelf-life by half.

Crystallinity, Magnetic and Electrical Properties of Bi doped LaVO3

We report the results of crystal structure, magnetization and resistivity measurements of Bi doped LaVO3. X-ray diffraction (XRD) shows that if doping Bi in the La site is less than ten percent, the crystal structure of La1-xBixVO3 remains unchanged and its symmetry is orthorhombic. However, for higher Bi doping (>10%) composite compounds are found where the XRD patterns are characterized by two phases: LaVO3+V2O3. Energy-dispersive analysis of the x-ray spectroscopy (EDAX) results are used to find a proper atomic percentage of all samples. The temperature dependence of the mass magnetization of pure and single phase doped samples have transition temperatures from paramagnetic to antiferromagnetic region at TN=140 K. This measurement for bi-phasic samples indicates two transition temperatures, at TN=140 K (LaVO3) and TN=170 K (V2O3). The temperature dependence of resistivity reveals semiconducting behavior for all samples. Activation energy values for pure and doped samples are extracted by fitting resistivity versus temperature data in the framework of thermal activation process.

Surface structure and stability of PdZn and PtZn alloys: Density-functional slab model studies

Geometric parameters of binary (1:1) PdZn and PtZn alloys with CuAu-L10 structure were calculated with a density functional method. Based on the total energies, the alloys are predicted to feature equal formation energies. Calculated surface energies of PdZn and PtZn alloys show that (111) and (100) surfaces exposing stoichiometric layers are more stable than (001) and (110) surfaces comprising alternating Pd (Pt) and Zn layers. The surface energy values of alloys lie between the surface energies of the individual components, but they differ from their composition weighted averages. Compared with the pure metals, the valence d-band widths and the Pd or Pt partial densities of states at the Fermi level are dramatically reduced in PdZn and PtZn alloys. The local valence d-band density of states of Pd and Pt in the alloys resemble that of metallic Cu, suggesting that a similar catalytic performance of these systems can be related to this similarity in the local electronic structures.

Investigations on the electrical and structural properties of polyaniline doped with camphor sulphonic acid

Polyaniline is chemically synthesised and doped with camphor sulphonic acid. FTIR studies carried out on these samples indicate that the aromatic rings are retained after polymerisation. The percentage of crystallinity for polyaniline doped with camphor sulphonic acid has been estimated from the X-ray diffraction studies and is around 56% with respect to polyaniline emeraldine base. The change in dielectric permittivity with respect to temperature and frequency is explained on the basis of interfacial polarisation. AC conductivity is evaluated from the observed dielectric permittivity. The values of AC and DC conductivity and activation energy are calculated. The activation energy values suggested that the hopping conduction is the prominent conduction mechanism in this system.