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.

Carbon surfaces for the oxidative quantification of pravastatin: glassy-carbon vs. screen-printed carbon electrodes

The electrooxidative behavior of pravastatin (PRV) in aqueous media was studied by square-wave voltammetry at a glassycarbon electrode (GCE) and at a screen-printed carbon electrode (SPCE). Maximum peak current intensities in a pH 5.0 buffer were obtained at +1.3 V vs. AgCl/Ag and +1.0 V vs. Ag for the GCE and SPCE surface respectively. Validation of the developed methodologies revealed good performance characteristics and confirmed their applicability to the quantification of PRV in pharmaceutical products, without significant sample pretreatment. A comparative analysis between the two electrode types showed that SPCEs are preferred as an electrode surface because of their higher sensitivity and the elimination of the need to clean the electrode’s surface for its renewal, which frequently is, if not always, the rate-limiting step in voltammetric analysis.

Logarithmically proportional objective function for planar surfaces recognition in 3D point cloud

3D laser scanning is becoming a standard technology to generate building models of a facility's as-is condition. Since most constructions are constructed upon planar surfaces, recognition of them paves the way for automation of generating building models. This paper introduces a new logarithmically proportional objective function that can be used in both heuristic and metaheuristic (MH) algorithms to discover planar surfaces in a point cloud without exploiting any prior knowledge about those surfaces. It can also adopt itself to the structural density of a scanned construction. In this paper, a metaheuristic method, genetic algorithm (GA), is used to test this introduced objective function on a synthetic point cloud. The results obtained show the proposed method is capable to find all plane configurations of planar surfaces (with a wide variety of sizes) in the point cloud with a minor distance to the actual configurations. © 2014 IEEE.

The effect of metal transfer modes and shielding gas composition on the emission of ultraafine particles in MAG steel welding

The present study aims to characterize ultrafine particles emitted during gas metal arc welding of mild steel and stainless steel, using different shielding gas mixtures, and to evaluate the effect of metal transfer modes, controlled by both processing parameters and shielding gas composition, on the quantity and morphology of the ultrafine particles. It was found that the amount of emitted ultrafine particles (measured by particle number and alveolar deposited surface area) are clearly dependent from the main welding parameters, namely the current intensity and the heat input of the Welding process. The emission of airborne ultrafine particles increases with the current intensity as fume formation rate does. When comparing the shielding gas mixtures, higher emissions were observed for more oxidizing mixtures, that is, with higher CO2 content, which means that these mixtures originate higher concentrations of ultrafine particles (as measured by number of particles. by cubic centimeter of air) and higher values of alveolar deposited surface area of particles, thus resulting in a more hazardous condition regarding welders exposure.

Mono(Eta(5)-cyclopentadienyl)metal(II) complexes with thienyl acetylide chromophores: synthesis, electrochemical studies, and first hyperpolarizabilities

A series of mono(eta(5)-cyclopentadienyl)metal-(II) complexes with nitro-substituted thienyl acetylide ligands of general formula [M(eta(5)-C5H5)(L)(C C{C4H2S}(n)NO2)] (M = Fe, L = kappa(2)-DPPE, n = 1,2; M = Ru, L = kappa(2)-DPPE, 2 PPh3, n = 1, 2; M = Ni, L = PPh3, n = 1, 2) has been synthesized and fully characterized by NMR, FT-IR, and UV-Vis spectroscopy. The electrochemical behavior of the complexes was explored by cyclic voltammetry. Quadratic hyperpolarizabilities (beta) of the complexes have been determined by hyper-Rayleigh scattering (HRS) measurements at 1500 nm. The effect of donor abilities of different organometallic fragments on the quadratic hyperpolarizabilities was studied and correlated with spectroscopic and electrochemical data. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations were employed to get a better understanding of the second-order nonlinear optical properties in these complexes. In this series, the complexity of the push pull systems is revealed; even so, several trends in the second-order hyperpolarizability can still be recognized. In particular, the overall data seem to indicate that the existence of other electronic transitions in addition to the main MLCT clearly controls the effectiveness of the organometallic donor ability on the second-order NLO properties of these push pull systems.

The effect of metal transfer stability (spattering) on fume generation, morphology and composition in short-circuit MAG welding

The main objective of this work was to evaluate the hypothesis that the greater transfer stability leads also to less volume of fumes. Using an Ar + 25%CO2 blend as shielding gas and maintaining constant the average current, wire feed speed and welding speed, bead-on-plate welds were carried out with plain carbon steel solid wire. The welding voltage was scanned to progressively vary the transfer stability. Using two conditions of low stability and one with high stability, fume generation was evaluated by means of the AWS F1.2:2006 standard. The influence of these conditions on fume morphology and composition was also verified. A condition with greater transfer stability does not generate less fume quantity, despite the fact that this condition produces fewer spatters. Other factors such as short-circuit current, arcing time, droplet diameters and arc length are the likely governing factors, but in an interrelated way. Metal transfer stability does not influence either the composition or the size/morphology of fume particulates. (c) 2014 Elsevier B.V. All rights reserved.

Trits(Pyrazol-1-YL)methane metal complexes for catalytic mild oxidative functionalizations of alkanes, alkanes and ketones

This work concerns recent advances (since 2005) in the oxidative functionalization of alkanes, alkenes and ketones, under mild conditions, catalyzed by homoscorpionate tris(pyrazol-1-yl)methane metal complexes. The main types of such homogeneous or supported catalysts are classified, and the critical analysis of the most efficient catalytic systems in the different reactions is presented. These reactions include the mild oxidation of alkanes (typically cyclohexane as a model substrate) with hydrogen peroxide (into alkyl hydroperoxides, alcohols, and ketones), the hydrocarboxylation of gaseous alkanes (with carbon monoxide and potassium peroxodisulfate) into the corresponding Cn+1 carboxylic acids, as well as the epoxidation of alkenes and the Baeyer-Villiger oxidation of linear and cyclic ketones with hydrogen peroxide into the corresponding esters and lactones. Effects of various reaction parameters are highlighted and the preferable requirements for a prospective homogeneous or supported C-scorpionate-M-based catalyst in oxidative transformations of those substrates are identified. (C) 2014 Elsevier B.V. All rights reserved.

The effects of clinical support surfaces on pressure as a risk factor in the development of pressure ulcers, from a radiographical perspective: a narrative literature review

Purpose: Pressure ulcers are a high cost, high volume issue for health and medical care providers, having a detrimental effect on patients and relatives. Pressure ulcer prevention is widely covered in the literature, but little has been published regarding the risk to patients in the radiographical setting. This review of the current literature is to identify findings relevant to radiographical context. Methods: Literature searching was performed using Science Direct and Medline databases. The search was limited to articles published in the last ten years to remain current and excluded studies containing participants less than 17 years of age. In total 14 studies were acquired; three were excluded as they were not relevant. The remaining 11 studies were compared and reviewed. Discussion: Eight of the studies used ‘healthy’ participants and three used symptomatic participants. Nine studies explored interface pressure with a range of pressure mat technologies, two studies measured shear (MRI finite element modelling, and a non-invasive instrument), and one looked at blood flow and haemoglobin oxygenation. A range of surfaces were considered from trauma, nursing and surgical backgrounds for their ability to reduce pressure including standard mattresses, high specification mattresses, rigid and soft layer spine boards, various overlays (gel, air filled, foam). Conclusion: The current literature is not appropriate for the radiographic patient and cannot be extrapolated to a radiologic context. Sufficient evidence is presented in this review to support the need for further work specific to radiography in order to minimise the development of PU in at risk patients.

An experimental study to compare the interface pressure and experience of healthy participants when lying still for 20 minutes in a supine position on two different imaging surfaces

Introduction: Pressure ulcers are a high cost, high volume issue for health and medical care providers, affecting patients’ recovery and psychological wellbeing. The current research of support surfaces on pressure as a risk factor in the development of pressure ulcers is not relevant to the specialised, controlled environment of the radiological setting. Method: 38 healthy participants aged 19-51 were placed supine on two different imaging surfaces. The XSENSOR pressure mapping system was used to measure the interface pressure. Data was acquired over a time of 20 minutes preceded by 6 minutes settling time to reduce measurement error. Qualitative information regarding participants’ opinion on pain and comfort was recorded using a questionnaire. Data analysis was performed using SPSS 22. Results: Data was collected from 30 participants aged 19 to 51 (mean 25.77, SD 7.72), BMI from 18.7 to 33.6 (mean 24.12, SD 3.29), for two surfaces, following eight participant exclusions due to technical faults. Total average pressure, average pressure for jeopardy areas (head, sacrum & heels) and peak pressure for jeopardy areas were calculated as interface pressure in mmHg. Qualitative data showed that a significant difference in experiences of comfort and pain was found in the jeopardy areas (P<0.05) between the two surfaces. Conclusion: A significant difference is seen in average pressure between the two surfaces. Pain and comfort data also show a significant difference between the surfaces, both findings support the proposal for further investigation into the effects of radiological surfaces as a risk factor for the formation of pressure ulcers.

Protein folding, metal ions and conformational states: the case of a di-cluster ferredoxin

Dissertation presented to obtain the PhD degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Noble metal nanoparticles - Au and Ag - for biodetection

Dissertation submitted for obtainment of the Master’s Degree in Biotechnology, by the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Greener Selective Cycloalkane Oxidations with Hydrogen Peroxide Catalyzed by Copper-5-(4-pyridyl)tetrazolate Metal-Organic Frameworks

Microwave assisted synthesis of the Cu(I) compound [Cu(µ4-4-ptz)]n [1, 4-ptz = 5-(4-pyridyl)tetrazolate] has been performed by employing a relatively easy method and within a shorter period of time compared to its sister compounds. The syntheses of the Cu(II) compounds [Cu3(µ3-4-ptz)4(µ2-N3)2(DMF)2]n∙(DMF)2n (2) and [Cu(µ2-4-ptz)2(H2O)2]n (3) using a similar method were reported previously by us. MOFs 1-3 revealed high catalytic activity toward oxidation of cyclic alkanes (cyclopentane, -hexane and -octane) with aqueous hydrogen peroxide, under very mild conditions (at room temperature), without any added solvent or additive. The most efficient system (2/H2O2) showed, for the oxidation of cyclohexane, a turnover number (TON) of 396 (TOF of 40 h−1), with an overall product yield (cyclohexanol and cyclohexanone) of 40% relative to the substrate. Moreover, the heterogeneous catalytic systems 1–3 allowed an easy catalyst recovery and reuse, at least for four consecutive cycles, maintaining ca. 90% of the initial high activity and concomitant high selectivity.

Hydrogenating activity of Pt/zeolite catalysts focusing acid support and metal dispersion influence

Toluene hydrogenation was studied over catalysts based on Pt supported on large pore zeolites (HUSY and HBEA) with different metal/acid ratios. Acidity of zeolites was assessed by pyridine adsorption followed by FTIR showing only small changes before and after Pt introduction. Metal dispersion was determined by H2–O2 titration and verified by a linear correlation with the intensity of Pt0–CO band obtained by in situ FTIR. It was also observed that the electronic properties of Pt0 clusters were similar for the different catalysts. Catalytic tests showed rapid catalyst deactivation with an activity loss of 80–95% after 60 min of reaction. The turnover frequency of fresh catalysts depended both on metal dispersion and the support. For the same support, it changed by a 1.7-fold (HBEA) and 4.0-fold (HUSY) showing that toluene hydrogenation is structure-sensitive, i.e. hydrogenating activity is not a unique function of accessible metal. This was proposed to be due to the contribution to the overall activity of the hydrogenation of adsorbed toluene on acid sites via hydrogen spillover. Taking into account the role of zeolite acidity, the catalysts series were compared by the activity per total adsorbing sites which was observed to increase steadily with nPt/(nPt + nA). An increase of the accessible Pt atoms leads to an increase on the amount of spilled over hydrogen available in acid sites therefore increasing the overall activity. Pt/HBEA catalysts were found to be more active per total adsorbing site than Pt/HUSY which is proposed to be due to an augmentation in the efficiency of spilled over hydrogen diffusion related to the proximity between Pt clusters and acid sites. The intervention of Lewis acid sites in a greater extent than that measured by pyridine adsorption may also contribute to this higher activity of Pt/HBEA catalysts. These results reinforce the importance of model reactions as a closer perspective to the relevant catalyst properties in reaction conditions.