QUANTIS: Data quality assessment tool by clustering analysis

Automatically generated kinetic networks are ideally validated against a large set of accurate, reproducible, and easy-to-model experimental data. However, although this might seem simple, it proves to be quite challenging. QUANTIS, a publicly available Python package, is specifically developed to evaluate both the precision and accuracy of experimental data and to ensure a uniform, quick processing, and storage strategy that enables automated comparison of developed kinetic models. The precision is investigated with two clustering techniques, PCA and t-SNE, whereas the accuracy is probed with checks for the conservation laws. First, the developed tool processes, evaluates, and stores experimental yield data automatically. All data belonging to a given experiment, both unprocessed and processed, are stored in the form of an HDF5 container. The demonstration of QUANTIS on three different pyrolysis cases showed that it can help in identifying and overcoming instabilities in experimental datasets, reduce mass and molar balance closure discrepancies, and, by evaluating the visualized correlation matrices, increase understanding in the underlying reaction pathways. Inclusion of all experimental data in the HDF5 file makes it possible to automate simulating the experiment with CHEMKIN. Because of the employed InChI string identifiers for molecules, it is possible to automate the comparison experiment/simulation. QUANTIS and the concepts demonstrated therein is a potentially useful tool for data quality assessment, kinetic model validation, and refinement.     

A Theoretical Model for Release Dynamics of an Antifungal Agent Covalently Bonded to the Chitosan

The aim of the study was to create a mathematical model useful for monitoring the release of bioactive aldehydes covalently bonded to the chitosan by reversible imine linkage, considered as a polymer–drug system. For this purpose, two hydrogels were prepared by the acid condensation reaction of chitosan with the antifungal 2-formyl-phenyl-boronic acid and their particularities; influencing the release of the antifungal aldehyde by shifting the imination equilibrium to the reagents was considered, i.e., the supramolecular nature of the hydrogels was highlighted by polarized light microscopy, while scanning electron microscopy showed their microporous morphology. Furthermore, the in vitro fungicidal activity was investigated on two fungal strains and the in vitro release curves of the antifungal aldehyde triggered by the pH stimulus were drawn. The theoretical model was developed starting from the hypothesis that the imine-chitosan system, both structurally and functionally, can be assimilated, from a mathematical point of view, with a multifractal object, and its dynamics were analyzed in the framework of the Scale Relativity Theory. Thus, through Riccati-type gauges, two synchronous dynamics, one in the scale space, associated with the fungicidal activity, and the other in the usual space, associated with the antifungal aldehyde release, become operational. Their synchronicity, reducible to the isomorphism of two SL(2R)-type groups, implies, by means of its joint invariant functions, bioactive aldehyde compound release dynamics in the form of “kink–antikink pairs” dynamics of a multifractal type. Finally, the theoretical model was validated through the experimental data.     

Biological responses to silicon and nitrogen-rich PVD silicon nitride coatings

Most structural bioceramics are comprised of metallic oxides such as alumina and zirconia. They are generally considered to be completely bioinert, but a non-oxide ceramic, silicon nitride, achieves equivalent levels of mechanical reliability while being bioactive. Silicon nitride can not only stimulate cellular proliferation but it is also antipathogenic with demonstrated efficacy against Gram-positive and Gram-negative bacteria, fungi, and viruses. In this work, three physical vapor deposition coatings with different Si:N ratios (silicon-rich, stoichiometric, and nitrogen-rich) were deposited on mirror-polished silica glass substrates. The coatings were characterized by spectroscopic and microscopic techniques and tested in vitro against E. coli and KUSA-A1 mesenchymal cells. Results showed that nitrogen-enriched Si_xN_y has a strong antibacterial effect against E. coli and contributes to cellular proliferation while silicon-enriched Si_xN_y stimulates the production of bone tissue, with higher indexes for mineralization and quality. These results suggest that Si_xN_y's biological properties can be optimized for specific applications by carefully tuning its surface chemistry.     

Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

Photosensitized Thymine Dimerization via Delocalized Triplet Excited States

A new mechanism of photosensitized formation of thymine (Thy) dimers is proposed, which involves generation of a delocalized triplet excited state as the key step. This is supported by chemical evidence obtained by combining one benzophenone and two Thy units with different degrees of freedom, whereby the photoreactivity is switched from a clean Paternò–Büchi reaction to a fully chemo‐, regio‐, and stereoselective [2+2] cycloaddition.     

The effect of molecular weight distribution on the elongational properties of linear polymers

The elongational properties of a series of six polypropylene and two polystyrene samples have been studied at constant rate of strain. A Wagner-type constitutive equation has been used to fit the experimental data, and the shape of the damping function has been correlated with the polydispersity index of the samples. As the memory function or relaxation function of linear viscoelasticity may be derived from the molecular-weight distribution using either molecular or phenomenological models, it is therefore possible to calculate the stress growth function of a linear polymer in elongation from its molecular-weight distribution.     

Propriétés viscoélastiques linéaires de solutions de polybutadiène en régime semi-dilué et concentré

Résumé L'évolution des propriétés viscoélastiques linéaires de polymères en solution est caractérisée par l'étude des variations des trois paramètres caractéristiques de la viscoélasticité linéaire (viscosité limite ₀, complaisance limiteJ _e ⁰ et module de plateauG _N ⁰ ) en fonction de la concentration dans différents solvants. Les polymères étudiés sont des polybutadiènes linéaires et branchés en étoile, à distribution étroite de masses moléculaires. Les solvants étudiés ont des températures de transition vitreuse inférieure, égale ou supérieure à celle du polybutadiène (respectivement le tétradécane, un polybutadiène de faible masse moléculaire et une huile commerciale). Les résultats obtenus ( ₀ c ^4,0,G _N ⁰ c ^2,25 etJ _e ⁰ c ^–2,25) sont en désaccord avec le comportement conforme aux modèles de champ moyen généralement admis, et semble partiellement en accord avec les modèles récents de la relaxation et de la thermodynamique des longues chaînes flexibles.

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Summary The linear viscoelastic properties of polymer solutions are studied through the concentration dependence of the three characteristic parameters of linear viscoelasticity (zero-shear viscosity ₀, limiting complianceJ _e ⁰ and plateau modulusG _N ⁰ ) in various solvents. The polymers are narrow-distribution linear and starbranched polybutadienes. The glass transition temperatures of the solvents are below, equal to, and above, theT _g of polybutadiene (respectively tetradecane, low molecular weight polybutadiene, and a commercial oil). The results ( ₀ c ^4.0,G _N ⁰ c ^2.25 andJ _e ⁰ c ^–2.25) do not agree with the usual mean field behavior assumed for the viscoelastic properties of polymer solutions, and seem to agree partly with recent models for the relaxation and thermodynamics of long chains.

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Zusammenfassung Das linear-viskoelastische Verhalten von Polymerlösungen wird anhand der Abhängigkeit der drei charakteristischen Parameter (Nullviskosität ₀, NullkomplianzJ _e ⁰ und PlateaumodulG _N ⁰ ) von der Konzentration in verschiedenen Lösungsmitteln untersucht. Bei den Polymeren handelt es sich um lineare und sternförmig verzweigte Polybutadiene mit enger Molmassenverteilung. Die Glasübergangstemperaturen der Lösungsmittel (Tetradecan, niedermolekulares Polybutadien bzw. ein kommerzielles Ol) sind niedriger, gleich oder höher als diejenigen des Polybutadiens. Die Ergebnisse ( ₀ c ^4,0,G _N ⁰ c ^2,25 undJ _e ⁰ c ^–2,25) stimmen nicht mit den Voraussagen der üblicherweise zugrundegelegten, durch Mittelwertbildung gekennzeichneten Theorien überein, sondern scheinen zumindest zum Teil denen neuer thermodynamischer bzw. Relaxationstheorien langkettiger Polymerer zu entsprechen.

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Avec 13 figures et 6 tableaux     

Interaction soliton–sable dans un canal en eau peu profonde

Interaction between solitons and a sandy bed in shallow water is investigated. In our experiments, solitons are generated on the background of a harmonic wave, in a wave flume used in resonant mode. It is found that the sand ripples formed by the solitons propagation induce a significant decrease of solitons amplitude and of the phase shift between the soliton and the harmonic wave. However, the amplitude of the harmonic wave is approximately constant. The possible physical processes of such behaviour for the soliton amplitude and for the harmonic wave amplitude are discussed. To cite this article: F. Marin et al., C. R. Mecanique 333 (2005).     

Multiple Site Hydrogen Isotope Labelling of Pharmaceuticals

Radiolabelling is fundamental in drug discovery and development as it is mandatory for preclinical ADME studies and late-stage human clinical trials. Herein, a general, effective, and easy to implement method for the multiple site incorporation of deuterium and tritium atoms using the commercially available and air-stable iridium precatalyst [Ir(COD)(OMe)]₂ is described. A large scope of pharmaceutically relevant substructures can be labelled using this method including pyridine, pyrazine, indole, carbazole, aniline, oxa-/thia-zoles, thiophene, but also electron-rich phenyl groups. The high functional group tolerance of the reaction is highlighted by the labelling of a wide range of complex pharmaceuticals, containing notably halogen or sulfur atoms and nitrile groups. The multiple site hydrogen isotope incorporation has been explained by the in situ formation of complementary catalytically active species: monometallic iridium complexes and iridium nanoparticles.     

Parametric Model of the Optical Constant Spectra of Hg1 – xCdxTe and Determination of the Compound Composition

Optics and Spectroscopy - A parametric model describing the spectra of optical constants n(λ) and k(λ) of a Hg1 – xCdxTe (MCT) solid solution for the x values in...