Further evidence that interfacial water is the main "driving force" of protein dynamics: a neutron scattering study on perdeuterated C-phycocyanin

The fundamental role of hydration water (also called interfacial water) is widely recognized in protein flexibility, especially in the existence of the so-called protein "dynamical transition" at around 220 K. In the present study, we take advantage of perdeuterated C-phycocyanin (CPC) and elastic incoherent neutron scattering (EINS) to distinguish between protein dynamics and interfacial water dynamics. Powders of hydrogenated (hCPC) and perdeuterated (dCPC) CPC protein have been hydrated, respectively, with D(2)O or H(2)O and measured by EINS to separately probe protein dynamics (hCPC/D(2)O) and water dynamics (dCPC/H(2)O) at different time- and length-scales. We find that "fast" (<20 ps) local mean-square displacements (MSD) of both protein and interfacial water coincide all along the temperature range, with the same dynamical transition temperature at ~220 K. On higher resolution (<400 ps), two different types of motions can be separated: (i) localized motions with the same amplitude for CPC and hydration water and two transitions at ~170 and ~240 K for both; (ii) large scale fluctuations exhibiting for both water molecules and CPC protein a single transition at ~240 K, with a significantly higher amplitude for the interfacial water than for CPC. Moreover, by comparing these motions with bulk water MSD measured under the same conditions, we show no coupling between bulk water dynamics and protein dynamics all along the temperature range. These results show that interfacial water is the main "driving force" governing both local and large scale motions in proteins.     

Fragility by elastic incoherent neutron scattering

The present work furnishes an operative definition for the fragility degree by using elastic incoherent neutron scattering (EINS). Such a definition is based on the relation between viscosity, a macroscopic quantity, and the atomic mean-square displacement, which refers to a nanoscopic property. This procedure has been used to analyze a set of glass-forming systems and it allows to obtain a linear dependence of the fragility parameter M, obtained by EINS, on the fragility parameter m, obtained by viscosity measurements.     

The Normalization of the Micropore-Size Distribution Function in the Polanyi-Dubinin Type of Adsorption Isotherm Equations

The problem of the normalization of the micropore-size distribution (MSD) based on the gamma-type function is presented. Three cases of the integration range (widely known in the literature) of MSD, characterizing the geometric heterogeneity of a solid, are considered (val( identical withB, E(0), and/or x)) i.e., from zero to infinity, from val(min) to infinity, and the finite range from val(min) up to val(max)-due to the boundary setting of an adsorbate-adsorbent system. The physical meaning of the parameters of the gamma-type function (rho and nu) is investigated for the mentioned intervals. The behavior and properties of this MSD function are analyzed and compared with the fractal MSD proposed by Pfeifer and Avnir. The general conclusion is that if adsorption proceeds by a micropore filling mechanism and the structural heterogeneity is described in the finite region (val(min), val(max)), for all cases of the possible values of the parameters of the MSD functions, the generated isotherms belong to the first class of the IUPAC classification (i.e., Langmuir-type behavior is observed). For the other cases (valin<0, infinity) and valin相似文献   

基质固相分散-超高效液相色谱-质谱检测器测定牛奶中9种类固醇激素残留

利用基质固相分散技术(MSPD),建立了超高效液相色谱-质谱检测器(MSD)同时分析牛奶中9种类固醇激素残留的方法。便携式MSD的灵敏度和准确度优于紫外检测器;相比传统的质谱仪,MSD不需质谱参数优化,操作简便,开机抽真空时间短(只要5 min),即开即用。分别考察了流动相比例、萃取溶剂和固相萃取小柱净化对MSD灵敏度和牛奶样品基质效应的影响。结果表明,MSD正离子模式对吸电子基团化合物的灵敏度更高,受外界条件影响大。经MSPD净化后,9种类固醇激素的基质效应由84%~160%降低为80%~121%。方法学研究结果表明,9种类固醇激素的日内精密度和日间精密度分别为0.87%~1.78%和1.82%~3.79%,加标回收率为68.7%~94.7%,相对标准偏差(RSD)小于10%,方法检出限(LOD)为0.5~10 μ g/kg,定量限(LOQ)为2~20 μ g/kg。该方法适合日常大批量样品的检测。     

String-like propagation of the 5-coordinated defect state in supercooled water: molecular origin of dynamic and thermodynamic anomalies

We find that at low temperature water, large amplitude (~60°) rotational jumps propagate like a string, with the length of propagation increasing with lowering temperature. The strings are formed by mobile 5-coordinated water molecules which move like a Glarum defect (J. Chem. Phys., 1960, 33, 1371), causing water molecules on the path to change from 4-coordinated to 5-coordinated and again back to 4-coordinated water, and in the process cause the tagged water molecule to jump, by following essentially the Laage-Hynes mechanism (Science, 2006, 311, 832-835). The effects on relaxation of the propagating defect causing large amplitude jumps are manifested most dramatically in the mean square displacement (MSD) and also in the rotational time correlation function of the O-H bond of the molecule that is visited by the defect (transient transition to the 5-coordinated state). The MSD and the decay of rotational time correlation function, both remain quenched in the absence of any visit by the defect, as postulated by Glarum long time ago. We establish a direct connection between these propagating events and the known thermodynamic and dynamic anomalies in supercooled water. These strings are found largely in the regions that surround the relatively rigid domains of 4-coordinated water molecules. The propagating strings give rise to a noticeable dynamical heterogeneity, quantified here by a sharp rise in the peak of the four-point density response function, χ(4)(t). This dynamics heterogeneity is also responsible for the breakdown of the Stokes-Einstein relation.     

Optimization of analytical quality control for long-term monitoring of metals and volatile organic compounds in groundwater

Statistical analysis of historical results for matrix spikes (MS), matrix spike duplicates (MSD), and laboratory control samples (LCS) from aqueous samples analyzed for metals and volatile organic compounds was performed to determine whether the MS/MSD provided substantive information apart from that provided by the LCS. The statistical analysis showed that the mean recovery of all analytes from MS/MSD closely approximated the mean recovery of all analytes from the LCS. Average bias, skewness, and kurtosis were also assessed for both data sets. The evaluation provided strong evidence for the use of LCS recoveries as performance indicators of probable MS/MSD recoveries of metals and volatile organic compounds from groundwater.     

Determination of two oxy-pyrimidine metabolites of diazinon in urine by gas chromatography/mass selective detection and liquid chromatography/electrospray ionization/mass spectrometry/mass spectrometry

An analytical method was developed for the determination in urine of 2 metabolites of diazinon: 6-methyl-2-(1-methylethyl)-4(1H)-pyrimidinone (G-27550) and 2-(1-hydroxy-1-methylethyl)-6-methyl-4(1H)-pyrimidinone (GS-31144). Two of the urine sample preparation procedures presented rely on gas chromatography/mass selective detection (GC/MSD) in the selected ion monitoring mode for determination of G-27550. For fast sample preparation and a limit of quantitation (LOQ) of 1.0 ppb, urine samples were purified by using ENV+ solid-phase extraction (SPE) columns. For analyte confirmation at an LOQ of 0.50 ppb, classical liquid/liquid partitioning was used before further purification in a silica SPE column. An SPE sample preparation procedure and liquid chromatography/electrospray ionization/mass spectrometry/mass spectrometry (LC/ESI/MS/MS) were used for both G-27550 and GS-31144. The limit of detection was 0.01 ng for G-27550 with GC/MSD, and 0.016 ng when LC/ESI/MS/MS was used for both G-27550 and GS-31144. The LOQ was 0.50 ppb for G-27550 when GC/MSD and the partitioning/SPE sample preparation procedure were used, and 1.0 ppb for the SPE only sample preparation procedure. The LOQ was 1.0 ppb for both analytes when LC/ESI/MS/MS was used.     

Refinements in the characterization of the heterogeneous dynamics of Li ions in lithium metasilicate

We have performed the molecular dynamics simulations of ionically conducting lithium metasilicate, Li(2)SiO(3), to get a more in depth understanding of the heterogeneous ion dynamics by separating out the partial contributions from localized and diffusive ions to the mean square displacement (MSD) , the non-Gaussian parameter alpha(2)(t), and the van Hove function G(s)(r,t). Several different cage sizes l(c) have been used for the definition of localized ions. Behaviors of fast ions are obtained by the subtraction of the localized component from the r(2)(t) of all ions, and accelerated dynamics is found in the resultant subensemble. The fractional power law of MSD is explained by the geometrical correlation between successive jumps. The waiting time distribution of jumps also plays a role in determining but does not affect the exponent of its fractional power law time dependence. Partial non-Gaussian parameters are found to be instructive to learn how long length-scale motions contribute to various quantities. As a function of time, the partial non-Gaussian parameter for the localized ions exhibits a maximum at around t(x2), the onset time of the fractional power law regime of . The position of the maximum is slightly dependent on the choice of l(c). The power law increases in the non-Gaussian parameter before the maximum are attributed to the Levy distribution of length scales of successive (long) jumps. The decreases with time, after the maximum has been reached, are due to large back correlation of motions of different length scales. The dynamics of fast ions with superlinear dependence in their MSD also start at time around the maximum. Also investigated are the changes of the characteristic times demarcating different regimes of on increasing temperatures from the glassy state to the liquid state. Relation between the activation energies for short time and long time regimes of is in accord with interpretation of ion dynamics by the coupling model.     

Molecular simulation of binary colloidal mixtures: Gelation and aging phenomena

We investigate the aging dynamics of colloidal depletion gel by computer simulation. In this study, we employ an alternative approach using the effective pair potential to avoid the slow convergence in binary mixtures due to cage effect, and the structural formation of colloidal depletion gels is then clarified. We study the mean square displacement (MSD) of each segment in depletion gels by stochastic molecular dynamic simulations. It is shown that the MSD obeys a power-law, indicating sub-diffusive behavior of depletion gels. We also observe aging phenomena of the colloidal depletion gels from intermediate scattering functions. Power-law behavior of a characteristic time in this system, as a function of a waiting time, is also clarified.     

An efficient algorithm for multistate protein design based on FASTER

Most of the methods that have been developed for computational protein design involve the selection of side‐chain conformations in the context of a single, fixed main‐chain structure. In contrast, multistate design (MSD) methods allow sequence selection to be driven by the energetic contributions of multiple structural or chemical states simultaneously. This methodology is expected to be useful when the design target is an ensemble of related states rather than a single structure, or when a protein sequence must assume several distinct conformations to function. MSD can also be used with explicit negative design to suggest sequences with altered structural, binding, or catalytic specificity. We report implementation details of an efficient multistate design optimization algorithm based on FASTER (MSD‐FASTER). We subjected the algorithm to a battery of computational tests and found it to be generally applicable to various multistate design problems; designs with a large number of states and many designed positions are completely feasible. A direct comparison of MSD‐FASTER and multistate design Monte Carlo indicated that MSD‐FASTER discovers low‐energy sequences much more consistently. MSD‐FASTER likely performs better because amino acid substitutions are chosen on an energetic basis rather than randomly, and because multiple substitutions are applied together. Through its greater efficiency, MSD‐FASTER should allow protein designers to test experimentally better‐scoring sequences, and thus accelerate progress in the development of improved scoring functions and models for computational protein design. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Molecular dynamics simulation of ionic transport on molten Li–KCl interface

A molecular dynamics study is performed to determine the dynamics and transport properties of the ions on the molten interface between anode metal Li and electrolyte KCl. Radial distribution function of the ionic pair and the behavior of the mean‐square displacement (MSD) as a function of time (t) indicate that KCl and metal Li are in the molten state at 2,200 K in the canonical ensemble. The dynamics of the ionic transport are characterized by studying MSD for the centers of mass of the ions at different temperatures. Diffusion coefficient is evaluated from the linear slope of the MSD (t) function in the range of 0–500 ps. The MSD and diffusion coefficient of the Li⁺ ions are much larger than those of the Cl^? and K⁺ ions due to the difference in ionic characteristic. The transport process has been dominated by the Li⁺ ions on the molten interface and the Li⁺ ions are main charge carriers. The energy barrier of the Li⁺ ions transporting into the molten KCl is fitted to be 5.28 kcal/mol in the light of the activation model. The electrical conductivity of the Li⁺ ions transporting into the molten KCl are calculated from the Nernst–Einstein formula to be in the range of 0.2–0.3 S cm^?1. The current density resulted from the Li⁺ ions through the interface are estimated to be an order of 10⁶ A cm^?2, which may be the value corresponding to a larger concentration gradient of the Li⁺ ions. Simulated results at different temperatures show that the diffusion coefficient, conductivity and current density have increased with the temperature. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Gas and liquid chromatography and enzyme linked immuno sorbent assay in pesticide monitoring of surface water from the western mediterranean (Comunidad Valenciana,Spain)

Summary A monitoring programme based on gas chromatography (NPD, ECD) using MSD for confirmatory purposes and coupled-column liquid chromatography was applied to the analysis of pesticide residues in surface water from a predominantly agricultural area of Spain (Comunidad Valenciana). Samples analysed by means of enzyme-linked immunosorbent assay gave similar results to those obtained by GC (MSD) for the determination of total triazines. The test employed had the advantages of a simple test procedure, short analysis time and high confirmatory value. Nevertheless, the multiresidue character, accuracy and unequivocal identification of individual pesticide residues of GC (MSD) make this technique the most appropriate for environmental monitoring programmes. In this monitoring programme about 200 samples were analysed between 1993–1994. 27 different pesticides were detected in 91 of these samples. The pesticides more frequently detected were dimethoate, methidathion, endosulfan A and B, endosulfan sulphate and pirimicarb. The highest concentrations found were 39.9 g L^–1 of dimethoate, 10.6 of pirimicarb and 10.6 of methidathion.     

Mechanism of Oxygen Adsorption on Partially K Exchanged Na-A Type Zeolite

Accordingly, the observation of oxygen selectivity on Na-K-A would indicate that nitrogen has a greater steric hindrance at the window than does oxygen. Using single crystal X-ray diffraction (SCXD), it was confirmed that K at 8-member rings was relocated to 6-member rings and that the location of Na at 8-member rings became uncertain with calcination. It was also observed that Na-K-A was thermally more stable than Na-A. Using magic angle spin nuclear magnetic resonance (MAS-NMR), it was confirmed that Na at 8-member rings irreversibly changed location from a symmetric position to an asymmetric position with calcination.Using the atomic positions determined by SCXD, the mean square displacements (MSD) of oxygen and nitrogen inside the crystal of Na-A and Na-K-A were estimated by means of molecular dynamic simulation (MD). When temperature was decreased, the MSD of nitrogen was reduced to a greater extent than that of oxygen and the MSD of nitrogen inside Na-K-A was reduced by a greater margin than that inside Na-A.     

Dissimilar bouncy walkers

We consider the dynamics of a one-dimensional system consisting of dissimilar hardcore interacting (bouncy) random walkers. The walkers' (diffusing particles') friction constants ξ(n), where n labels different bouncy walkers, are drawn from a distribution ?(ξ(n)). We provide an approximate analytic solution to this recent single-file problem by combining harmonization and effective medium techniques. Two classes of systems are identified: when ?(ξ(n)) is heavy-tailed, ?(ξ(n))?ξ(n) (-1-α)?(0<α<1) for large ξ(n), we identify a new universality class in which density relaxations, characterized by the dynamic structure factor S(Q, t), follows a Mittag-Leffler relaxation, and the mean square displacement (MSD) of a tracer particle grows as t(δ) with time t, where δ = α∕(1 + α). If instead ? is light-tailed such that the mean friction constant exist, S(Q, t) decays exponentially and the MSD scales as t(1/2). We also derive tracer particle force response relations. All results are corroborated by simulations and explained in a simplified model.     

Improved microwave steam distillation apparatus for isolation of essential oils. Comparison with conventional steam distillation

Steam distillation (SD) is routinely used by analysts for the isolation of essential oils from herbs, flowers and spices prior to gas chromatographic analysis. In this work, a new process design and operation for an improved microwave steam distillation (MSD) of essential oils from aromatic natural products was developed. To demonstrate its feasibility, MSD was compared with the conventional technique, SD, for the analysis of volatile compounds from dry lavender flowers (Lavandula angustifolia Mill., Lamiaceae). Essential oils isolated by MSD were quantitatively (yield) and qualitatively (aromatic profile) similar to those obtained by SD, but MSD was better than SD in terms of rapidity (6 min versus 30 min for lavender flowers), thereby allowing substantial savings of costs in terms of time and energy. Lavender flowers treated by MSD and SD were observed by scanning electron microscopy. Micrographs provide evidence of more rapid opening of essential oil glands treated by MSD, in contrast to conventional SD.     

Multiresidue determination of organophosphorus and organochlorine pesticides in human biological fluids by capillary gas chromatography

Two multiresidue analytical methods for the simultaneous determination of organophosphorus and organochlorine pesticides in human urine and serum samples are described. The first approach is based on liquid-liquid microextraction with dichloromethane, and the second uses solid-phase extraction with C18. In both methods, the extracts are analyzed by capillary gas chromatography using nitrogen-phosphorus detection (NPD) and electron-capture detection (ECD). Limits of detection of the overall procedure of analysis are at the low ng mL(-1) level. Stability experiments have been performed with spiked urine and serum samples stored at 4 degrees C for 1 month. Finally, the solid-phase extraction procedure was applied to real-world samples. Quantification was performed by NPD or ECD, and peak identity was confirmed by use of mass-selective detection (MSD).     

Mechanochemical solid-state polymerization (X): the influence of copolymer structure in copolymeric prodrugs on the nature of drug release

From the standpoint of the mechanism of mechanochemical polymerization, two kinds of copolymeric prodrug, whose monomer sequence distribution (MSD) is different from each other, can be prepared by this polymerization under appropriate operational conditions: one is a random copolymer abundant in the longer block consisting of the same repeating units (multi-block copolymer), and the other is a block copolymer. To confirm the difference of MSD, the 13C-NMR spectra of poly(acrylamide-co-sodium acrylate) prepared by mechanochemical polymerization were measured and compared with the spectrum of that synthesized by a conventional radical-initiated solution polymerization, which produces the random copolymer normally. The results show that MSD in copolymers depends on the polymerization method (operational condition). We prepared three kinds of copolymeric prodrug consisting of acrylamide and vinyl monomer of 5-fluorouracil, whose MSD is different from one another. These copolymeric prodrugs had almost the same number average molecular weight, particle diameter and composition, and differed only in MSD. We compared the rate of drug release of these copolymeric prodrugs. The rate of drug release was the highest with the random copolymer, followed by the mechanochemically produced multi-block copolymer and the block copolymer. This result suggests that the rate of drug release depends on MSD of copolymeric prodrugs. These results are useful as they give a fundamental insight into the synthesis of copolymeric prodrugs having the desired rate of drug release.     

Determination of the plasticizer N-butylbenzenesulfonamide and the pharmaceutical Ibuprofen in wastewater using solid phase microextraction (SPME)

A rapid, inexpensive and solvent-free method for the simultaneous determination of the polyamide plasticizer N-butylbenzenesulfonamide (NBBS) and the widely used pharmaceutical Ibuprofen by solid phase microextraction (SPME) combined with gas chromatography/mass spectrometry (GC/MSD) in wastewater samples was developed. Besides the optimized analytical conditions, results of investigations with varying analytical parameters are reported. Problems, which may occur during the analytical procedure (e.g. salt deposits, adsorption phenomena, carry-over), are discussed. For the determination of Ibuprofen, it is important to carry out the extraction under acidic conditions with sufficiently buffered samples; the GC/MSD system must be very clean and well maintained. SPME allows an extraction of Ibuprofen without derivatization of its carboxylic group. For quantification in complex matrices, the standard addition technique is necessary. Limit of detection and limit of determination are 0.1 μg/L for both analytes. NBBS and Ibuprofen were detected in several raw and treated wastewater samples from municipal wastewater treatment plants in the range from < 0.1 to 3.5 μg/L.     

Particle tracking microrheology of lyotropic liquid crystals

We present comprehensive results on the microrheological study of lyotropic liquid crystalline phases of various space groups constituted by water-monoglyceride (Dimodan) mixtures. In order to explore the viscoelastic properties of these systems, we use particle tracking of probe colloidal particles suitably dispersed in the liquid crystals and monitored by diffusing wave spectroscopy. The identification of the various liquid crystalline phases was separately carried out by small-angle X-ray scattering. The restricted motion of the particles was monitored and identified by the decay time of intensity autocorrelation function and the corresponding time-dependent mean square displacement (MSD), which revealed space group-dependent behavior. The characteristic time extracted by the intersection of the slopes of the MSD at short and long time scales, provided a characteristic time which could be directly compared with the relaxation time obtained by microrheology. Further direct comparison of microrheology and bulk rheology measurements was gained via the Laplace transform of the generalized time-dependent MSD, yielding the microrheology storage and loss moduli, G'(ω) and G'(ω), in the frequency domain ω. The general picture emerging from the microrheology data is that all liquid crystals exhibit viscoelastic properties in line with results from bulk rheology and the transition regime (elastic to viscous) differs according to the specific liquid crystal considered. In the case of the lamellar phase, a plastic fluid is measured by bulk rheology, while microrheology indicates viscoelastic behavior. Although we generally find good qualitative agreement between the two techniques, all liquid crystalline systems are found to relax faster when studied with microrheology. The most plausible explanation for this difference is due to the different length scales probed by the two techniques: that is, microscopical relaxation on these structured fluids, is likely to occur at shorter time scales which are more suitably probed by microrheology, whereas bulk, macroscopic relaxations occurring at longer time scales can only be probed by bulk rheology.     

疏水改性聚丙烯酰胺溶液的分子模拟

设计了几种不同的非离子型改性聚丙烯酰胺(HM-PAM)和阴离子型改性聚丙烯酰胺(HM-HPAM). 通过分子动力学模拟(MD)方法研究了在聚合物链上加入不同疏水改性单体对提高聚丙烯酰胺耐盐性的影响, 考察了盐浓度对疏水改性聚丙烯酰胺的回旋半径(R_g)、 特性黏数([η])、 径向分布函数(RDF)和均方位移(MSD)的影响以及聚合物的微观结构与特性黏数之间的关系. 研究结果表明, 引入疏水改性单体后, 改性聚丙烯酰胺具有较好的耐盐性. 通过研究非键作用与氢键相互作用可知, 体系中溶质和溶剂间的相互作用及氢键作用越弱, 溶液的特性黏数越大. O-H原子对的RDF结果表明, 聚合物链的伸展与聚合物链及官能团间的相互作用有关. 当RDF峰较弱时, 聚合物链与水的作用越弱, 越有利于聚合物链保持舒展状态, 溶液的特性黏数也就越大. 另外, 从聚合物链的MSD曲线发现, 聚合链的移动性与特性黏数呈负相关.