Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3624408]

Polarization effects in molecular dynamics simulations of glass-formers Ca(NO(3))(2)center dot nH(2)O, n=4, 6, and 8

Thermodynamics, equilibrium structure, and dynamics of glass-forming liquids Ca(NO(3))(2)center dot nH(2)O, n=4, 6, and 8, have been investigated by molecular dynamics (MD) simulations. A polarizable model was considered for H(2)O and NO(3)- on the basis of previous fluctuating charge models for pure water and the molten salt 2Ca(NO(3))(2)center dot 3KNO(3). Similar thermodynamic properties have been obtained with nonpolarizable and polarizable models. The glass transition temperature, T(g), estimated from MD simulations was dependent on polarization, in particular the dependence of T(g) with electrolyte concentration. Significant polarization effects on equilibrium structure were observed in cation-cation, cation-anion, and water-water structures. Polarization increases the diffusion coefficient of H(2)O, but does not change significantly the diffusion coefficients of ions. Viscosity decreases upon inclusion of polarization, but the conductivity calculated with the polarizable model is smaller than the nonpolarizable model because polarization enhances anion-cation interactions.

Understanding solvation

The effects of solvents on different chemical phenomena, including reactivity, spectroscopic data, and swelling of biopolymers can be rationalized by use of solvatochromic probes, substances whose UV-vis spectra, absorption, or emission are sensitive to the properties of the medium. Thermo-solvatochromism refers to the effect of temperature on solvatochromism. The study of both phenomena sheds light on the relative importance of the factors that contribute to solvation, namely, properties of the probe, those of the solvent (acidity, basicity, dipolarity/polarizability, and lipophilicity), and the temperature. Solvation in binary solvent mixtures is complex because of ""preferential solvation"" of the probe by some component of the mixture. A recently introduced solvent exchange model is based on the presence in the binary solvent mixture of the organic component (molecular solvent or ionic liquid), S, water, W, and a 1:1 hydrogen-bonded species (S-W). Solvation by the latter is more efficient than by its precursor solvents, due to probe-solvent hydrogen-bonding and hydrophobic interactions; dimethyl sulfoxide (DMSO)-W is an exception. Solvatochromic data are employed in order to explain apparently disconnected phenomena, namely, medium effect on the pH-independent hydrolysis of esters, (1)H NMR data of water-ionic liquid (IL) mixtures, and the swelling of cellulose.

The enzymatic nature of fungal bioluminescence

The uncertainty about the possible involvement of a luciferase in fungal bioluminescence has not only hindered the understanding of its biochemistry but also delayed the characterization of its constituents. The present report describes how in vitro light emission can be obtained enzymatically from the cold and hot extracts assay using different species of fungi, which also indicates a common mechanism for all these organisms. Kinetic data suggest a consecutive two-step enzymatic mechanism and corroborate the enzymatic proposal of Airth and Foerster. Finally, overlapping of light emission spectra from the fungal bioluminescence and the in vitro assay confirm that this reaction is the same one that occurs in live fungi.

Fragility and glassy dynamics of 2Ca(NO(3))(2)center dot 3KNO(3) under pressure: Molecular dynamics simulations

Molecular dynamics simulations of the glass-forming liquid 2Ca(NO(3))(2)center dot 3KNO(3) (CKN) were performed from high temperature liquid states down to low temperature glassy states at six different pressures from 10(-4) to 5.0 GPa. The temperature dependence of the structural relaxation time indicates that the fragility of liquid CKN changes with pressure. In line with recent proposal [Scopigno , Science 302, 849 (2003)], the change on liquid fragility is followed by a proportional change of the nonergodicity factor of the corresponding glass at low temperature. (c) 2008 American Institute of Physics.

Polymer matrix sensitizing effect on photoluminescence properties of Eu(3+)-beta-diketonate complex doped into poly-beta-hydroxybutyrate (PHB) in film form

In this work is reported the sensitization effect by polymer matrices on the photoluminescence properties of diaquatris(thenoyltrifluoroacetonate)europium(III), [Eu(tta)(3)(H(2)O)(2)], doped into poly-beta-hydroxybutyrate (PHB) with doping percentage at 1, 3, 5, 7 and 10% (mass) in film form. TGA results indicated that the Eu(3+) complex precursor was immobilized in the polymer matrix by the interaction between the Eu(3+) complex and the oxygen atoms of the PHB polymer when the rare earth complex was incorporated in the polymeric host. The thermal behaviour of these luminescent systems is similar to that of the undoped polymer, however, the T(onset) temperature of decomposition decreases with increase of the complex doping concentration. The emission spectra of the Eu(3+) complex doped PHB films recorded at 298 K exhibited the five characteristic bands arising from the (5)D(0) -> (7)F(J) intraconfigurational transitions (J = 0-4). The fact that the quantum efficiencies eta of the doped film increased significantly revealed that the polymer matrix acts as an efficient co-sensitizer for Eu(3+) luminescent centres and therefore enhances the quantum efficiency of the emitter (5)D(0) level. The luminescence intensity decreases, however, with increasing precursor concentration in the doped polymer to greater than 5% where a saturation effect is observed at this specific doping percentage, indicating that changes in the polymeric matrix improve the absorption property of the film, consequently quenching the luminescent effect.

Validation of dot blot hybridization and denaturing high performance liquid chromatography as reliable methods for TP53 codon 72 genotyping in molecular epidemiologic studies

Background: Mutations in TP53 are common events during carcinogenesis. In addition to gene mutations, several reports have focused on TP53 polymorphisms as risk factors for malignant disease. Many studies have highlighted that the status of the TP53 codon 72 polymorphism could influence cancer susceptibility. However, the results have been inconsistent and various methodological features can contribute to departures from Hardy-Weinberg equilibrium, a condition that may influence the disease risk estimates. The most widely accepted method of detecting genotyping error is to confirm genotypes by sequencing and/or via a separate method. Results: We developed two new genotyping methods for TP53 codon 72 polymorphism detection: Denaturing High Performance Liquid Chromatography (DHPLC) and Dot Blot hybridization. These methods were compared with Restriction Fragment Length Polymorphism (RFLP) using two different restriction enzymes. We observed high agreement among all methodologies assayed. Dot-blot hybridization and DHPLC results were more highly concordant with each other than when either of these methods was compared with RFLP. Conclusions: Although variations may occur, our results indicate that DHPLC and Dot Blot hybridization can be used as reliable screening methods for TP53 codon 72 polymorphism detection, especially in molecular epidemiologic studies, where high throughput methodologies are required.

Molecular and morphological characterization of Amathia distans Busk and Amathia brasiliensis Busk (Bryozoa: Ctenostomata) from the tropical and subtropical Western Atlantic

Morphological and molecular analyses have proven to be complementary tools of taxonomic information for the redescription of the ctenostome bryozoans Amathia brasiliensis Busk, 1886 and Amathia distans Busk, 1886. The two species, originally described from material collected by the `Challenger` expedition but synonymized by later authors, now have their status fixed by means of the selection of lectotypes, morphological observations and analyses of DNA sequences described here. The morphological characters allowing the identification of living and/or preserved specimens are (1) A. brasiliensis: whitish-pale pigment spots in the frontal surface of stolons and zooids, and a wide stolon with biserial zooid clusters growing in clockwise and anti-clockwise spirals along it, the spirality direction being maintained from maternal to daughter stolons; and (2) A. distans: bright yellow pigment spots in stolonal and zooidal surfaces including lophophores, and a slender stolon, thickly cuticularized, with biserial zooid clusters growing in clockwise and anti-clockwise spirals along it and the spirality direction not maintained from maternal to daughter stolons. Pairwise comparisons of DNA sequences of the mitochondrial genes cytochrome c oxidase subunit I and large ribosomal RNA subunit revealed deep genetic divergence between A. brasiliensis and A. distans. Finally, analyses of those sequences within a Bayesian phylogenetic context recovered their genealogical species status.

Effect of some essential oils on in vitro methane emission

The objectives of this study were to characterise four essential oils (EO) chemically and to evaluate their effect on ruminal fermentation and methane emission in vitro. The investigated EO were isolated from Achillea santolina, Artemisia judaica, Schinus terebinthifolius and Mentha microphylla, and supplemented at four levels (0, 25, 50 and 75 l) to 75ml of buffered rumen fluid plus 0.5 g of substrate. The main components of the EO were piperitone (49.1%) and camphor (34.5%) in A. judaica, 16-dimethyl 15-cyclooactdaiene (60.5%) in A. santolina, piperitone oxide (46.7%) and cis-piperitone oxide (28%) in M. microphylla, and -muurolene (45.3%) and -thujene (16.0%) in S. terebinthifolius. The EO from A. santolina (at 25 and 50 l), and all levels of A. judaica increased the gas production significantly, but S. terebinthifolius (at 50 and 75 l), A. santolina (at 75 l) and all levels of M. microphylla decreased the gas production significantly in comparison with the control. The highest levels of A. santolina and A. judaica, and all doses from M. microphylla EO inhibited the methane production along with a significant reduction in true degradation of dry matter and organic matter, protozoa count and NH3-N concentration. It is concluded that the evaluated EO have the potential to affect ruminal fermentation efficiency and the EO from M. microphylla could be a promising methane mitigating agent.

Simultaneous preconcentration of copper, zinc, cadmium, and nickel in water samples by cloud point extraction using 4-(2-pyridylazo)-resorcinol and their determination by inductively coupled plasma optic emission spectrometry

A procedure for simultaneous separation/preconcentration of copper. zinc, cadmium, and nickel in water samples, based on cloud point extraction (CPE) as a prior step to their determination by inductively coupled plasma optic emission spectrometry (ICP-OES), has been developed. The analytes reacted with 4-(2-pyridylazo)-resorcinol (PAR) at pH 5 to form hydrophobic chelates, which were separated and preconcentrated in a surfactant-rich phase of octylphenoxypolyethoxyethanol (Triton X-I 14). The parameters affecting the extraction efficiency of the proposed method, such as sample pH, complexing agent concentration, buffer amount, surfactant concentration, temperature, kinetics of complexation reaction, and incubation time were optimized and their respective values were 5, 0.6 mmol L(-1). 0.3 mL, 0.15% (w/v), 50 degrees C, 40 min, and 10 min for 15 mL of preconcentrated solution. The method presented precision (R.S.D.) between 1.3% and 2.6% (n = 9). The concentration factors with and without dilution of the surfactant-rich phase for the analytes ranged from 9.4 to 10.1 and from 94.0 to 100.1, respectively. The limits of detection (L.O.D.) obtained for copper, zinc, cadmium, and nickel were 1.2, 1.1, 1.0. and 6.3 mu g L(-1), respectively. The accuracy of the procedure was evaluated through recovery experiments on aqueous samples. (C) 2009 Published by Elsevier B.V.

Variation in the Distribution of Trace Elements in Renal Cell Carcinoma

The development of cancer is a complex, multistage process during which a normal cell undergoes genetic changes that result in phenotypic alterations and in the acquisition of the ability to invade other sites. Inductively coupled plasma optical emission spectroscopy was used to estimate the contents of Al, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, P, Pb, and Zn in healthy kidney and renal cell carcinoma (RCC), and significant differences were found for all elements. Along with the progression of the malignant disease, a progressive decrease of Cd and K was observed. In fact, for Cd, the concentration in stage T4 was 263.9 times lower than in stage T1, and for K, the concentration in stage T4 was 1.73 times lower than in stage T1. Progressive accumulation was detected for P, Pb, and Zn in stage T4. For P, the concentration in stage T4 was 11.1 times higher than in stage T1; for Pb, the concentration in stage T4 was 232.7 times higher than in T1; and for Zn, the concentration in T4 was 8.452 times higher than in T1. This study highlights the marked differences in the concentrations of selected trace metals in different malignant tumor stages. These findings indicate that some trace metals may play important roles in the pathogenesis of RCC.

Sources of particulate matter: emission profile of biomass burning

Biomass burning is an important source of atmospheric Particulate Matter (PM) in Brazil: the burning of forests in the northwest and of sugar cane plantations in the southeast are important examples. The objective of this work is the measurement of the PM emission profile of burning of sugar cane and other characteristic vegetative burning in the region of Sao Carlos-SP/Brazil. Samples of PM(10) and PM(2.5) were collected in different conditions, including small laboratory controlled burnings and real ones. The samples were analysed by X-Ray Fluorescence (XRF) and 14 chemical elements quantified. t-Student tests were performed to compare the obtained profiles, using as a reference a vegetative burn profile taken from the USEPA data bank SPECIATE. All measured profiles presented significant amounts of Cl and K, which are confirmed as tracers of sugar cane foliage burning.

Evaluation of the use of multiple lines for determination of metals in water by inductively coupled plasma optical emission spectrometry with axial viewing

Inductively coupled plasma optical emission spectrometers (ICP DES) allow fast simultaneous measurements of several spectral lines for multiple elements. The combination of signal intensities of two or more emission lines for each element may bring such advantages as improvement of the precision, the minimization of systematic errors caused by spectral interferences and matrix effects. In this work, signal intensities for several spectral lines were combined for the determination of Al, Cd, Co, Cr, Mn, Pb, and Zn in water. Afterwards, parameters for evaluation of the calibration model were calculated to select the combination of emission lines leading to the best accuracy (lowest values of PRESS-Predicted error sum of squares and RMSEP-Root means square error of prediction). Limits of detection (LOD) obtained using multiple lines were 7.1, 0.5, 4.4, 0.042, 3.3, 28 and 6.7 mu g L(-1) (n = 10) for Al, Cd. Co, Cr, Mn, Pb and Zn, respectively, in the presence of concomitants. On the other hand, the LOD established for the most intense emission line were 16. 0.7, 8.4, 0.074. 23, 26 and 9.6 mu g L(-1) (n = 10) for these same elements in the presence of concomitants. The accuracy of the developed procedure was demonstrated using water certified reference material. The use of multiple lines improved the sensitivity making feasible the determination of these analytes according to the target values required for the current environmental legislation for water samples and it was also demonstrated that measurements in multiple lines can also be employed as a tool to verify the accuracy of an analytical procedure in ICP DES. (C) 2009 Elsevier B.V. All rights reserved.

Partial microwave-assisted wet digestion of animal tissue using a baby-bottle sterilizer for analyte determination by inductively coupled plasma optical emission spectrometry

A procedure for partial digestion of bovine tissue is proposed using polytetrafluoroethylene (PTFE) microvessels inside a baby-bottle sterilizer under microwave radiation for multi-element determination by inductively coupled plasma optical emission spectrometry (ICP OES). Samples were directly weighed in laboratory-made polytetrafluoroethylene vessels. Nitric acid and hydrogen peroxide were added to the uncovered vessels, which were positioned inside the baby-bottle sterilizer, containing 500 mL of water. The hydrogen peroxide volume was fixed at 100 mu L The system was placed in a domestic microwave oven and partial digestion was carried out for the determination of Ca, Cu, Fe. Mg, Mn and Zn by inductively coupled plasma optical emission spectrometry. The single-vessel approach was used in the entire procedure, to minimize contamination in trace analysis. Better recoveries and lower residual carbon content (RCC) levels were obtained under the conditions established through a 2(4-1) fractional factorial design: 650 W microwave power, 7 min digestion time, 50 mu L nitric acid and 50 mg sample mass. The digestion efficiency was ascertained according to the residual carbon content determined by inductively coupled plasma optical emission spectrometry. The accuracy of the proposed procedure was checked against two certified reference materials. (C) 2009 Elsevier B.V. All rights reserved.

Exploring the emission intensities of ICP OES aided by chemometrics in the geographical discrimination of mineral waters

A rapid method for classification of mineral waters is proposed. The discrimination power was evaluated by a novel combination of chemometric data analysis and qualitative multi-elemental fingerprints of mineral water samples acquired from different regions of the Brazilian territory. The classification of mineral waters was assessed using only the wavelength emission intensities obtained by inductively coupled plasma optical emission spectrometry (ICP OES), monitoring different lines of Al, B, Ba, Ca, Cl, Cu, Co, Cr, Fe, K, Mg, Mn, Na, Ni, P, Pb, S, Sb, Si, Sr, Ti, V, and Zn, and Be, Dy, Gd, In, La, Sc and Y as internal standards. Data acquisition was done under robust (RC) and non-robust (NRC) conditions. Also, the combination of signal intensities of two or more emission lines for each element were evaluated instead of the individual lines. The performance of two classification-k-nearest neighbor (kNN) and soft independent modeling of class analogy (SIMCA)-and preprocessing algorithms, autoscaling and Pareto scaling, were evaluated for the ability to differentiate between the various samples in each approach tested (combination of robust or non-robust conditions with use of individual lines or sum of the intensities of emission lines). It was shown that qualitative ICP OES fingerprinting in combination with multivariate analysis is a promising analytical tool that has potential to become a recognized procedure for rapid authenticity and adulteration testing of mineral water samples or other material whose physicochemical properties (or origin) are directly related to mineral content.