An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: application to water

An efficient parallelization scheme for classical molecular dynamics simulations with flexible, polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during molecular dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128 to 512 molecules employing two flexible polarizable water models [DC(F) and TTM2.1-F] containing 1 and 3 polarizable sites, respectively. The time-to-solution for these two polarizable models is compared with the one for a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculation of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed. To the best of our knowledge, this is the first reported results of parallel scaling and performance for simulations of liquid water with a polarizable potential under periodic boundary conditions.     

Adsorption of an endoglucanase from the hyperthermophilic Pyrococcus furiosus on hydrophobic (polystyrene) and hydrophilic (silica) surfaces increases protein heat stability

The interaction of an endoglucanase from the hyperthermophilic microorganism Pyrococcus furiosus with two types of surfaces, that is, hydrophobic polystyrene and hydrophilic silica, was investigated, and the adsorption isotherms were determined. The adsorbed hyperthermostable enzyme did not undergo loss of biological activity. A model was proposed for the mechanism of interaction of the enzyme with the surface based on the shape of the adsorption isotherm, the morphological characteristics of the enzyme, and the thermodynamic parameters of the system. The enzyme was irreversibly immobilized at the solid/liquid interface even at high temperatures, and most interestingly, it acquired further heat stabilization upon adsorption. The denaturation temperature increased from 108 degrees C in solution to 116 degrees C upon adsorption on hydrophilic silica particles. Adsorption on the hydrophobic polystyrene surface even shifted the denaturation temperature to 135 degrees C, the most extreme experimentally determined protein denaturation temperature ever reported. Maintenance of the biological function particularly at high temperatures is important for the development of solid substrate immobilized enzymes for applications in biocatalysis and biotechnology. This also presents an additional stabilization mechanism employed by nature where the extracellular hyperthermostable enzyme remains folded and active at the extreme temperatures of its natural environment by adsorption on the surface of rocks and other materials appearing in the surroundings of the microorganism.     

Interaction of Fe(III) with herbicide-carboxylato ligands – Di-, tri- and tetra-nuclear compounds: Structure and magnetic behavior

The iron complexes with the phenoxyalkanoic acids 3,4-D, 2,3-D and 2,4,5-T in the presence or not of a nitrogen donor heterocyclic ligand, phen, were prepared and characterized. Interaction of Fe(III) with phenoxyalkanoic acids and phen leads to dinuclear neutral complexes while the absence of phen favours trinuclear cationic or tetranuclear neutral forms. The crystal structure of hexakis(2,3-dichlorophenoxyacetato)tris(methanol)oxotri-iron(III) chloride–methanol(1/3), [Fe₃O(2,3-D)₆(MeOH)₃]Cl · 3MeOH (2), and tetrakis(dimethyl-sulfoxide)octakis(2,4,5-trichlorophenoxyacetato)dioxotetra-iron(III) methanol(1/2)–water(1/1)–dimethylsulfoxide(1/0.8), {[Fe₄O₂(2,4,5-T)₈(dmso)₄] · 2MeOH · H₂O · 0.8dmso} (3), have been determined and refined by least-squares methods using three-dimensional Mo Kα data.     

Synthesis, structural characterization, and biological studies of six- and five-coordinate organotin(IV) complexes with the thioamides 2-mercaptobenzothiazole, 5-chloro-2-mercaptobenzothiazole, and 2-mercaptobenzoxazole

Organotin(IV) complexes with the formulas [(C6H5)3Sn(mbzt)] (1), [(C6H5)3Sn(cmbzt)] (3), and [(C6H5)2Sn(cmbzt)2] (4) (Hmbzt = 2-mercaptobenzothiazole and Hcmbzt = 5-chloro-2-mercaptobenzothiazole) have been synthesized and characterized by elemental analysis; FT-IR, Raman, 1H, 13C, and 119Sn NMR, and M?ssbauer spectroscopic techniques; and X-ray crystallography at various temperatures. The crystal structures of complexes 1, 3, and 4 were determined by X-ray diffraction at room temperature [295(1) or 293(2) K]. The complexes [(C6H5)3Sn(mbzo)] (2) and [(n-C4H9)2Sn(cmbzt)2] (5) (Hmbzo = 2-mercaptobenzoxazole) were synthesized by new improved methods, and their structures were determined at low temperature [100(1) K] and compared to those solved at room temperature. Comparison with {(CH3)2Sn(cmbzt)2]} (6), already reported, was also attempted. The influence of temperature on the geometry of the complexes is discussed. In the cases of complexes 1-3, three carbon atoms from phenyl groups and one sulfur atom and one nitrogen atom from thione ligands form a tetrahedrally distorted trigonal-bipyramidal geometry around the five-coordinate tin(IV) ion. In complexes 4-6, two carbon atoms from aryl groups and two sulfur atoms and two nitrogen atoms from thione ligands form a distorted tetrahedral geometry, tending toward octahedral, around the six-coordinate tin(IV) ions, with trans-C2, cis-N2, and cis-S2 configurations. Although the C-Sn and S-Sn bond distances are found to be constant in compounds 1-6, their N-Sn bond lengths vary significantly (from 2.635 to 3.078 A), with the longer distances found in the cases of five-coordinate complexes 1-3.     

Infrared spectrum of NH4+(H2O): evidence for mode specific fragmentation

The gas phase infrared spectrum (3250-3810 cm-1) of the singly hydrated ammonium ion, NH4+(H2O), has been recorded by action spectroscopy of mass selected and isolated ions. The four bands obtained are assigned to N-H stretching modes and to O-H stretching modes. The N-H stretching modes observed are blueshifted with respect to the corresponding modes of the free NH4+ ion, whereas a redshift is observed with respect to the modes of the free NH3 molecule. The O-H stretching modes observed are redshifted when compared to the free H2O molecule. The asymmetric stretching modes give rise to rotationally resolved perpendicular transitions. The K-type equidistant rotational spacings of 11.1(2) cm-1 (NH4+) and 29(3) cm-1 (H2O) deviate systematically from the corresponding values of the free molecules, a fact which is rationalized in terms of a symmetric top analysis. The relative band intensities recorded compare favorably with predictions of high level ab initio calculations, except on the nu3(H2O) band for which the observed value is about 20 times weaker than the calculated one. The nu3(H2O)/nu1(H2O) intensity ratios from other published action spectra in other cationic complexes vary such that the nu3(H2O) intensities become smaller the stronger the complexes are bound. The recorded ratios vary, in particular, among the data collected from action spectra that were recorded with and without rare gas tagging. The calculated anharmonic coupling constants in NH4+(H2O) further suggest that the coupling of the nu3(H2O) and nu1(H2O) modes to other cluster modes indeed varies by orders of magnitude. These findings together render a picture of a mode specific fragmentation dynamic that modulates band intensities in action spectra with respect to absorption spectra. Additional high level electronic structure calculations at the coupled-cluster singles and doubles with a perturbative treatment of triple excitations [CCSD(T)] level of theory with large basis sets allow for the determination of an accurate binding energy and enthalpy of the NH4+(H2O) cluster. The authors' extrapolated values at the CCSD(T) complete basis set limit are De [NH4+-(H2O)]=-85.40(+/-0.24) kJ/mol and DeltaH(298 K) [NH4+-(H2O)]=-78.3(+/-0.3) kJ/mol (CC2), in which double standard deviations are indicated in parentheses.     

In situ coating of flame-made TiO2 particles with nanothin SiO2 films

Rutile TiO2 particles made by flame spray pyrolysis (FSP) were coated in a single step with SiO2 layers in an enclosed flame reactor. This in situ particle coating was accomplished by a hollow ring delivering hexamethyldisiloxane (HMDSO) vapor (precursor to SiO2) through multiple jets in swirl cross-flow to Al-doped nanostructured rutile TiO2 aerosol freshly made by FSP of a solution of titanium tetraisopropoxide and aluminum sec-butoxide in xylene. The as-prepared powders were characterized by (scanning) transmission electron microscopy (STEM and TEM), energy dispersive X-ray analysis, X-ray diffraction, nitrogen adsorption, electrophoretic mobility, DC plasma optical emission (DCP-OES), and Fourier transform infrared (FT-IR) spectroscopy. The coating quality was assessed further by the photocatalytic oxidation of isopropyl alcohol to acetone. The effect of HMDSO injection point and vapor concentration on product particle morphology was investigated. The titania particles were uniformly SiO2-coated with controlled and uniform thickness at a production rate of about 30 g h(-1) and exhibited limited, if any, photoactivity. In contrast, spraying and combusting equivalent mixtures of the above Si/Al/Ti precursors in the above reactor (without delivering HMDSO through the hollow ring) resulted in particles segregated in amorphous (SiO2) and crystalline (TiO2) domains which exhibited high photocatalytic activity.     

Monitoring the Dynamics of Concentrated Suspensions by Enhanced Backward Light Scattering

The shear-induced flocculation of kaolin-polymer flocs in a stirred tank is investigated at medium to high solids concentrations (ϕ=1−10% w/w). The evolution of the average floc size is monitored by the change in intensity of laser light scattered in the 180° direction. The measurements reflect the change in particle number concentration as flocculation proceeds. As flocculation begins, coagulation dominates and the floc size increases (total particle number decreases) and then levels off at a steady state value as fragmentation becomes significant and balances coagulation. At steady state, the measurements indicate the extent of flocculation. Increasing the shear rate increases the coagulation and fragmentation rates, resulting in smaller floc sizes at steady state. Increasing the flocculant concentration increases the steady state floc size by strengthening the bonds between primary particles to resist fragmentation. At constant shear rate and flocculant concentration, increasing the solids fraction decreases the steady state floc size indicating formation of weakly bonded flocs. Flocculant mixing was the most important factor for flocculation efficiency at high solids concentrations.     

A Multi-Method Survey on the Use of Sentiment Analysis in Multivariate Financial Time Series Forecasting

In practice, time series forecasting involves the creation of models that generalize data from past values and produce future predictions. Moreover, regarding financial time series forecasting, it can be assumed that the procedure involves phenomena partly shaped by the social environment. Thus, the present work is concerned with the study of the use of sentiment analysis methods in data extracted from social networks and their utilization in multivariate prediction architectures that involve financial data. Through an extensive experimental process, 22 different input setups using such extracted information were tested, over a total of 16 different datasets, under the schemes of 27 different algorithms. The comparisons were structured under two case studies. The first concerns possible improvements in the performance of the forecasts in light of the use of sentiment analysis systems in time series forecasting. The second, having as a framework all the possible versions of the above configuration, concerns the selection of the methods that perform best. The results, as presented by various illustrations, indicate, on the one hand, the conditional improvement of predictability after the use of specific sentiment setups in long-term forecasts and, on the other, a universal predominance of long short-term memory architectures.     

Organotin adducts with pyrimidinethione: crystal structure of dimethyldi(pyrimidine‐2‐thiolato)tin(IV) and diphenyldi(pyrimidine‐2‐thiolato)tin(IV)

The complexes dimethyldi(pyrimidine‐2‐thiolato)tin(IV) ( 1 ) and diphenyldi(pyrimidine‐2‐thiolato)tin(IV) ( 2 ) have been structurally ­characterized by means of X‐ray crystallography. Complex 1 exhibits strong π–π stacking interactions and adduct 2 is self‐assembled via intermolecular hydrogen bonds, C H–π and π–π stacking interactions. Partial solvolysis occurs in organic solvents for 1 and 2 . Copyright © 2000 John Wiley & Sons, Ltd.