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.

Microstructure, mechanical properties and chemical degradation of brazed AISI 316 stainless steel/alumina systems

The main aims of the present study are simultaneously to relate the brazing parameters with: (i) the correspondent interfacial microstructure, (ii) the resultant mechanical properties and (iii) the electrochemical degradation behaviour of AISI 316 stainless steel/alumina brazed joints. Filler metals on such as Ag–26.5Cu–3Ti and Ag–34.5Cu–1.5Ti were used to produce the joints. Three different brazing temperatures (850, 900 and 950 °C), keeping a constant holding time of 20 min, were tested. The objective was to understand the influence of the brazing temperature on the final microstructure and properties of the joints. The mechanical properties of the metal/ceramic (M/C) joints were assessed from bond strength tests carried out using a shear solicitation loading scheme. The fracture surfaces were studied both morphologically and structurally using scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and X-ray diffraction analysis (XRD). The degradation behaviour of the M/C joints was assessed by means of electrochemical techniques. It was found that using a Ag–26.5Cu–3Ti brazing alloy and a brazing temperature of 850 °C, produces the best results in terms of bond strength, 234 ± 18 MPa. The mechanical properties obtained could be explained on the basis of the different compounds identified on the fracture surfaces by XRD. On the other hand, the use of the Ag–34.5Cu–1.5Ti brazing alloy and a brazing temperature of 850 °C produces the best results in terms of corrosion rates (lower corrosion current density), 0.76 ± 0.21 μA cm−2. Nevertheless, the joints produced at 850 °C using a Ag–26.5Cu–3Ti brazing alloy present the best compromise between mechanical properties and degradation behaviour, 234 ± 18 MPa and 1.26 ± 0.58 μA cm−2, respectively. The role of Ti diffusion is fundamental in terms of the final value achieved for the M/C bond strength. On the contrary, the Ag and Cu distribution along the brazed interface seem to play the most relevant role in the metal/ceramic joints electrochemical performance.

Electrodeposition and characterization of nikel-copper metallic foams for application as electrodes for supercapacitors

Nickel-copper metallic foams were electrodeposited from an acidic electrolyte, using hydrogen bubble evolution as a dynamic template. Their morphology and chemical composition was studied by scanning electron microscopy and related to the deposition parameters (applied current density and deposition time). For high currents densities (above 1 A cm(-2)) the nickel-copper deposits have a three-dimensional foam-like morphology with randomly distributed nearly-circular pores whose walls present an open dendritic structure. The nickel-copper foams are crystalline and composed of pure nickel and a copper-rich phase containing nickel in solid solution. The electrochemical behaviour of the material was studied by cyclic voltammetry and chronopotentiometry (charge-discharge curves) aiming at its application as a positive electrode for supercapacitors. Cyclic voltammograms showed that the Ni-Cu foams have a pseudocapacitive behaviour. The specific capacitance was calculated from charge-discharge data and the best value (105 F g(-1) at 1 mA cm(-2)) was obtained for nickel-copper foams deposited at 1.8 A cm(-2) for 180 s. Cycling stability of these foams was also assessed and they present a 90 % capacitance retention after 10,000 cycles at 10 mA cm(-2).

Chemical composition and antioxidante activity of Tunisian Origanum glandulosum Desf. essential oil and volatile oil obtain by supercritical CO2 extraction

Dried flowers and leaves of Origanum glandulosum Desf. were submitted to hydrodistillation (HD) and supercritical fluid extraction with CO2 (SFE). The essential oils isolated by HD and volatile oils obtained by SFE were analysed by GC and GC/MS. Total phenolics content and antioxidant effectiveness were performed. The main components of the essential oils from Bargou and Nefza were: p-cymene (40.4% and 39%), thymol (38.7% and 34.4%) and γ- terpinene (12.3% and 19.2%), respectively. The major components obtain by SFE in the volatile oil, from Bargou and Nefza, were: p-cymene (32.3% and 36.2%), thymol (41% and 40%) and γ-terpinene (20.3% and 13.3%). Total phenolic content, expressed in gallic acid equivalent (GAE) g kg-1 dry weight, varied from 12 to 27 g kg-1 dw, and the ability to scavenge the DPPH radicals, expressed by IC50 ranged from 44 to143 mg L-1.

Cooperative effects in the detection of a nitroaliphatic liquid explosive and na explosive taggant in the vapor phase by calix[4]arene-based carbazole-containing conjugated polymers

Two fluorescent molecular receptor based conjugated polymers were used in the detection of a nitroaliphatic liquid explosive (nitromethane) and an explosive taggant (2,3-dimethyl-2,3-dinitrobutane) in the vapor phase. Results have shown that thin films of both polymers display remarkably high sensitivity and selectivity toward these analytes. Very fast, reproducible, and reversible responses were found. The unique behavior of these supramolecular host systems is ascribed to cooperativity effects developed between the calix[4] arene hosts and the phenylene ethynylene-carbazolylene main chains. The calix[4]-arene hosts create a plethora of host-guest binding sites along the polymer backbone, either in their bowl-shaped cavities or between the outer walls of the cavity, to direct guests to the area of the transduction centers (main chain) at which favorable photoinduced electron transfer to the guest molecules occurs and leads to the observed fluorescence quenching. The high tridimensional porous nature of the polymers imparted by the bis-calixarene moieties concomitantly allows fast diffusion of guest molecules into the polymer thin films.

Chemical reaction network of flavylium ions in heterogeneous media

Dissertação apresentada para a obtenção do Grau de Doutor em Química, especialidade em Química-Física, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

InOx thin films deposited by plasma assisted evaporation: application in light shutters

An integration of undoped InOx and commercial ITO thin films into laboratory assembled light shutter devices is made. Accordingly, undoped transparent conductive InOx thin films, about 100 nm thick, are deposited by radiofrequency plasma enhanced reactive thermal evaporation (rf-PERTE) of indium teardrops with no intentional heating of the glass substrates. The process of deposition occurs at very low deposition rates (0.1-0.3 nm/s) to establish an optimized reaction between the oxygen plasma and the metal vapor. These films show the following main characteristics: transparency of 87% (wavelength, lambda = 632.8 nm) and sheet resistance of 52 Omega/sq; while on commercial ITO films the transparency was of 92% and sheet resistance of 83 Omega/sq. The InOx thin film surface characterized by AFM shows a uniform grain texture with a root mean square surface roughness of Rq similar to 2.276 nm. In contrast, commercial ITO topography is characterized by two regions: one smoother with Rq similar to 0.973 nm and one with big grains (Rq similar to 3.617 nm). For the shutters assembled using commercial ITO, the light transmission coefficient (Tr) reaches the highest value (Tr-max) of 89% and the lowest (Tr-min) of 1.3% [13], while for the InOx shutters these values are 80.1% and 3.2%, respectively. Regarding the electric field required to achieve 90% of the maximum transmission in the ON state (E-on), the one presented by the devices assembled with commercial ITO coated glasses is 2.41 V/mu m while the one presented by the devices assembled with InOx coated glasses is smaller, 1.77 V/mu m. These results corroborate the device quality that depends on the base materials and fabrication process used. (C) 2014 Elsevier Ltd. All rights reserved.

Increasing the wear resistance of molds for injection of glass fiber reinforced plastics

Abrasion by glass fibers during injection molding of fiber reinforced plastics raises new challenges to the wear performance of the molds. In the last few decades, a large number of PVD and CVD coatings have been developed with the aim of minimizing abrasion problems. In this work, two different coatings were tested in order to increase the wear resistance of the surface of a mold used for glass fiber reinforced plastics: TiAlSiN and CrN/CrCN/DLC. TiAlSiN was deposited as a graded monolayer coating while CrN/CrCN/DLC was a nanostructured coating consisting of three distinct layers. Both coatings were produced by PVD unbalanced magnetron sputtering and were characterized using scanning electron microscopy (SEM) provided with energy dispersive spectroscopy (EDS), atomic force microscopy (AFM), micro hardness (MH) and scratch test analysis. Coating morphology, thickness, roughness, chemical composition and structure, hardness and adhesion to the substrate were investigated. Wear resistance was characterized through industrial tests with coated samples and an uncoated reference sample inserted in a feed channel of a plastic injection mold working with 30 wt.% glass fiber reinforced polypropylene. Results after 45,000 injection cycles indicate that the wear resistance of the mold was increased by a factor of 25 and 58, by the TiAlSiN and CrN/CrCN/DLC coatings, respectively, over the uncoated mold steel.

Fabrication of the three-dimensional dendritic Ni-Co films by electrodeposition on stainless steel substrates

Co-deposition of nickel and cobalt was carried out on austenitic stainless steel (AISI 304) substrates by imposing a square waveform current in the cathodic region. The innovative procedure applied in this work allows creating a stable, fully developed, and open porous three-dimensional (3D) dendritic structure, which can be used as electrode for redox supercapacitors. This study investigates in detail the influence of the applied current density on the morphology, mass, and chemical composition of the deposited Ni-Co films and the resulting 3D porous network dendritic structure. The morphology and the physicochemical composition were studied by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS) and X-ray diffraction (W). The electrochemical behavior of the materials was evaluated by cyclic voltammetry (CV). The results highlight the mechanism involved in the coelectrodeposition process and how the lower limit current density tailors the film composition and morphology, as well as its electrochemical activity.

Acylated cyanoimido-complexes trans-[Mo(NCN){NCN(O)R}(DPPE)(2)]Cl and their reactons with electrophiles: Chemical, electrochemical and theoretical study

Treatment of a dichloromethane solution of trans-[Mo(NCN){NCNC(O)R}(dppe)(2)]Cl [R = Me (1a), Et (1b)] (dppe = Ph2PCH2CH2PPh2) with HBF4, [Et3O][BF4] or EtC(O)Cl gives trans-[Mo(NCN)Cl-(dppe)(2)]X [X = BF4 (2a) or Cl (2b)] and the corresponding acylcyanamides NCN(R')C(O)Et (R' = H, Et or C(O)Et). X-ray diffraction analysis of 2a (X = BF4) reveals a multiple-bond coordination of the cyanoimide ligand. Compounds 1 convert to the bis(cyanoimide) trans-[Mo(NCN)(2)(dppe)(2)] complex upon reaction with an excess of NaOMe (with formation of the respective ester). In an aprotic medium and at a Pt electrode, compounds 1 (R = Me, Et or Ph) undergo a cathodically induced isomerization. Full quantitative kinetic analysis of the voltammetric behaviour is presented and allows the determination of the first-order rate constants and the equilibrium constant of the trans to cis isomerization reaction. The mechanisms of electrophilic addition (protonation) to complexes 1 and the precursor trans[Mo(NCN)(2)(dppe)(2)], as well as the electronic structures, nature of the coordination bonds and electrochemical behaviour of these species are investigated in detail by theoretical methods which indicate that the most probable sites of the proton attack are the oxygen atom of the acyl group and the terminal nitrogen atom, respectively.

Solid-state sensory properties of Calix-Poly(Phenylene Ethynylene)s toward nitroaromatic explosives

This study is primarily focused in establishing the solid-state sensory abilities of several luminescent polymeric calix[4]arene-based materials toward selected nitroaromatic compounds (NACs), creating the foundations for their future application as high performance materials for detection of high explosives. The phenylene ethynylene-type polymers possessing bis-calix[4]arene scaffolds in their core were designed to take advantage of the known recognition abilities of calixarene compounds toward neutral guests, particularly in solid-state, therefore providing enhanced sensitivity and selectivity in the sensing of a given analyte. It was found that all the calix[4]arene-poly(para-phenylene ethynylene)s here reported displayed high sensitivities toward the detection of nitrobenzene, 2,4-dinitrotoluene and 2,4,6-trinitrotoluene (TNT). Particularly effective and significant was the response of the films (25-60 nm of thickness) upon exposure to TNT vapor (10 ppb): over 50% of fluorescence quenching was achieved in only 10 s. In contrast, a model polymer lacking the calixarene units showed only reduced quenching activity for the same set of analytes, clearly highlighting the relevance of the macrocyclics in promoting the signaling of the transduction event. The films exhibited high photostability (less than 0.5% loss of fluorescence intensity up to 15 min of continuous irradiation) and the fluorescence quenching sensitivity could be fully recovered after exposure of the quenched films to saturated vapors of hydrazine (the initial fluorescence intensities were usually recovered within 2-5 min of exposure to hydrazine).

Three-Dimensional patchy lattice model for empty fluids

The phase diagram of a simple model with two patches of type A and ten patches of type B (2A10B) on the face centred cubic lattice has been calculated by simulations and theory. Assuming that there is no interaction between the B patches the behavior of the system can be described in terms of the ratio of the AB and AA interactions, r. Our results show that, similarly to what happens for related off-lattice and two-dimensional lattice models, the liquid-vapor phase equilibria exhibit reentrant behavior for some values of the interaction parameters. However, for the model studied here the liquid-vapor phase equilibria occur for values of r lower than 1/3, a threshold value which was previously thought to be universal for 2AnB models. In addition, the theory predicts that below r = 1/3 (and above a new condensation threshold which is < 1/3) the reentrant liquid-vapor equilibria are so extreme that it exhibits a closed loop with a lower critical point, a very unusual behavior in single-component systems. An order-disorder transition is also observed at higher densities than the liquid-vapor equilibria, which shows that the liquid-vapor reentrancy occurs in an equilibrium region of the phase diagram. These findings may have implications in the understanding of the condensation of dipolar hard spheres given the analogy between that system and the 2AnB models considered here.

Hexachlorophene as a topically applied chemical for prophylaxis against Schistosoma mansoni infections in mice

Treatment of mouse tail skins with hexachlorophene (1.25% w/v) in absolute methanol or 70% isopropanol suppressed Schistosoma mansoni infections by more than 95% even when the application was performed up to three days prior to exposure to cercarial suspensions by tail immersion. Treatment with concentrations of 0.313% or higher one day prior to exposure provided at least 98% protection when the treated surface was not subjected to water washes of greater duration than 1/2 hour. Tail immersion application of 1.25% hexachlorophene one day prior to exposure still provided 87-92% protection after 3 hours water wash. Wipe application of 1.25% hexachlorophene three days prior to exposure still provided 93% protection following 3 hours water wash. High cercarial recoveries from exposure tubes at the end of exposure periods indicated high antipenetrant activity for hexachlorophene. Sufficient hexachlorophene leached from treated tail skins into the surrounding water to affect subsequently added cercariae so that they were no longer infective to untreated mice.

Influence of the deposition pressure on the properties of transparent and conductive ZnO: Ga thin-film produced by r.f. sputtering at room temperature

Thin Solid Films, vol. 427, nº 1-2

Modeling radionuclides dispersion and deposition downwind of a coal-fired power plant

In this study the inhalation doses and respective risk are calculated for the population living within a 20 km radius of a coal-fired power plant. The dispersion and deposition of natural radionuclides were simulated by a Gaussian dispersion model estimating the ground level activity concentration. The annual effective dose and total risk were 0.03205 mSv/y and 1.25 x 10-8, respectively. The effective dose is lower than the limit established by the ICRP and the risk is lower than the limit proposed by the U.S. EPA, which means that the considered exposure does not pose any risk for the public health.