Isothermal diffusion studies of water-choline chloride-hydrogen chloride system

Sets of four diffusion coefficients were obtained for the water-choline chloridehydrogen chloride system at 25°C. The cross-term diffusion coefficients were found to be very large, and the electrostatic force is the dominant factor for these cross-term diffusion coefficients.     

电势法测定KI在CH3OH-H2O混合溶剂中的活度系数

用无液接电势电池测定了303.15 K时,KI在甲醇-水混合溶剂中的电动势,用扩展的Debye-Hückel方程及Pitzer方程关联不同溶剂组成下电动势的实验值,得到电池的标准电动势E°和KI在混合溶剂中的活度系数.结果表明,在一定的溶剂比例下,随KI浓度的增大,其平均活度系数先随它的浓度增加而下降,经过一个最低点后又上升;或者随浓度增加而单调递减.当KI浓度固定时,它的平均活度系数随溶剂中甲醇的含量增加而下降.表明KI在甲醇中有微弱的缔合.     

Rotational mechanism for vibrational relaxation in rigid media. Interaction potentials

Using the assumption of pairwise additive forces we derive the interaction potential acting upon a substantial impurity in a crystalline lattice. The angle dependent parts of the force on the impurity internal vibrations are represented in the form of a Fourier series. Numerical calculations of the Fourier coefficients of the force are presented for a model system employing empirical argon—argon interactions. The higher Foutier coefficients are shown to decrease rapidly in conformity with the simple model potential used to describe the vibrational relaxation in a preceding paper.     

气体在无定型聚异戊二烯中扩散的分子动力学模拟

采用分子动力学模拟方法研究了多个温度下氧气、氮气及甲烷在无定型顺式1,4-聚异戊二烯中的扩散系数。在模拟过程中,使用COMPASS力场作为分子力场。应用COMPASS力场的势能函数,聚合物的密度及玻璃化转变温度的计算结果与实验值有较好吻合。在278-378 K的温度范围内,通过3或1.5 ns时长的正则系综动力学模拟,计算了不同温度下氧气、氮气及甲烷的扩散系数。结果表明,根据爱因斯坦关系式计算得到的扩散系数与实验结果比较接近。对气体扩散系数与温度的关系进一步研究,发现在278-378 K温度范围内,甲烷的扩散系数随温度变化的半对数曲线图是非线性的,而氧气和氮气的扩散系数随温度变化的半对数曲线图是线性的。本文研究结果有助于理解温度对气体扩散的影响机制,并为高温下气体在天然橡胶中扩散系数的测定及天然橡胶热氧老化建模分析提供依据。     

Separated internal force constants for the ethylene and ethane molecules and their use for calculation of the force field for the propylene molecule

We consider the question of separation of linear combinations of force constants for ethylene and ethane. Introduction of a perturbation into the matrix of the kinematic coefficients allows us to solve the inverted vibrational problem using the matrix method of successive approximations without eliminating dependent coordinates. Such an approach makes it possible to obtain a sufficient system of equations for determining the separated internal force constants. The separated internal force constants determined for ethylene and ethane are used to calculate the force field for propylene. The calculated separated internal force constants for propylene reproduce its vibrational spectrum and the spectrum or propylene-d₆ with average deviation from experimental frequencies of 8 cm^–1. The numerical influence coefficients for stretching vibrations of the C-H bond are linearly related to the lengths of these bonds.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 22, No. 1, pp. 118–122, Janauary–February, 1986.     

Limiting diffusion coefficients of ionic liquids in water and methanol: a combined experimental and molecular dynamics study

Mutual diffusion coefficients D(12) of the ionic liquids 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C(2)MIM][NTf(2)]) and [C(4)MIM][NTf(2)] in highly diluted solutions of water and methanol have been measured at different temperatures between 288 K and 313 K using the Taylor dispersion technique. Tracer diffusion coefficients of the two cations [C(2)MIM](+) and [C(4)MIM](+) as well as the anion [NTf(2)](-) in these solutions have been obtained by molecular dynamics (MD) simulations. For our simulations we used well established force fields for the solvents water and methanol and a recently developed force field for imidazolium-based ionic liquid [C(n)MIM][NTf(2)]. Mutual diffusion coefficients D(12) have been calculated from the tracer diffusion coefficients using the Nernst-Hartley equation strictly valid only at low ionic concentration. The agreement between the diffusion coefficients reported in the literature, the experimental data obtained in this work and the MD results is excellent.     

A new method to evaluate force constants from experimental spectral data

An iterative procedure is proposed to facilitate the determination of molecular vi-brational force constants from the experimental fundamental frequencies. Proper restrictions are introduced to the force constants based on physical considerations for getting reasonable results. The experimental data of Coriolis coupling coefficients and isotopic frequency shifts are utilized to reduce the uncertainty of the calculated force constants when they are available. A series of various kinds of molecules have been calculated by this method and the results are satisfactory.     

Effect of pendent chains on the interfacial properties of thin polydimethylsiloxane (PDMS) networks

The interfacial properties of end-linked polydimethylsiloxane (PDMS) films on silicon are examined. Thin cross-linked PDMS films (～10 μm thick) were synthesized over a self-assembled monolayer supported on a silicon wafer. By systematically varying the concentration of monofunctional PDMS in a mixture with telechelic precursor molecules, structures ranging from near-ideal elastic networks to poorly cross-linked networks composed of a preponderance of dangling/pendent chains were synthesized. Lateral force microscopy (LFM) employing bead probes was used to quantify the effect of network structure on the interfacial friction coefficient and residual force. Indentation measurements employing an AFM in force mode were used to characterize the elastic modulus and the pull-off force for the films as a function of pendent chain content. These measurements were complemented with conventional mechanical rheometry measurements on similar thick network films to determine their bulk rheological properties. All networks studied manifested interfacial friction coefficients substantially lower than that of bare silicon. PDMS networks with the lowest pendent chain content displayed friction coefficients close to 1 order of magnitude lower than that of bare silicon, whereas networks with the highest pendent chain content manifested friction coefficients about 3 times lower than that of bare silicon. At intermediate sliding velocities, a crossover in the interfacial friction coefficient was observed, wherein cross-linked PDMS films with the least amount of pendent chains exhibit the highest friction coefficient. These observations are discussed in terms of the structure of the films and relaxation dynamics of elastic strands and dangling chains in tethered network films.     

Modeling van der Waals interactions between proteins and inorganic surfaces from time-dependent density functional theory calculations

In this work we show how the ab initio determination of van der Waals coefficients within time-dependent density functional theory can be used to build efficient and accurate atomistic models that describe the long-range interactions of proteins with other proteins and of proteins with semi-conducting surfaces. The model parameters are fitted so that they reproduce the ab initio van der Waals coefficients of amino acids and dipeptides. We then assess the quality of our results by comparing ab initio van der Waals coefficients for larger peptides with the coefficients yielded by the models. The different sets of parameters can be easily incorporated in current empirical force field methods, thus providing an essential ingredient for molecular dynamics simulations of proteins close to surfaces.     

Approche du phénomène de galop par un modèle d'effort retardé et validation expérimentale

We consider the case of elongated cylinders submitted to a cross-flow. We propose a time delayed force model for the galloping oscillations for which the linear study allows to calculate the critical velocity with quasi-steady coefficients. The phase delay between force and position is based on the Strouhal number of the cylinder measured in static conditions. The experimental validation is presented on square and rectangular sections cylinders.     

Combined AFM and two-focus SFCS study of raft-exhibiting model membranes.

Dioleoylphosphatidylcholine/sphingomyelin/cholesterol (DOPC/SM/cholesterol) model membranes exhibit liquid-liquid phase separation and therefore provide a physical model for the putative liquid-ordered domains present in cells. Here we present a combination of atomic force microscopy (AFM) imaging, force measurements, confocal fluorescence imaging and two-focus scanning fluorescence correlation spectroscopy (two-focus SFCS) to obtain structural and dynamical information about this model membrane system. Partition coefficients and diffusion coefficients in the different phases were measured with two-focus SFCS for numerous fluorescent lipid analogues and proteins, while being directly related to the lateral organization of the membrane and its mechanical properties probed by AFM. Moreover we show how the combination of these different approaches is effective in reducing artifacts resulting from the use of a single technique.     

Application of fractal geometry for studies of heterogeneity properties of nanomaterials

Calculations based on the fractal geometry in the estimation of surface heterogeneity are superior compared with conventional calculation methods (e.g. from the data of gas adsorption or X-ray radiation scattering) as they can be applied without limitation as far as the range of surface sizes of the studied structures is concerned. This paper presents structural characteristics of carbon and carbon- free nanomaterials based on the determined surface and volumetric fractal coefficients. Fractal coefficients were determined from the data obtained by means of two independent methods: sorptometry and atomic force microscopy (AFM). Correlation between porosity parameters and fractal coefficients is presented.     

Communication: Turnover behavior of effective mobility in a tube with periodic entropy potential

Using Brownian dynamics simulations, we study the effective mobility and diffusion coefficient of a point particle in a tube formed from identical compartments of varying diameter, as functions of the driving force applied along the tube axis. Our primary focus is on how the driving force dependences of these transport coefficients are modified by the changes in the compartment shape. In addition to monotonically increasing or decreasing behavior of the effective mobility in periodic entropy potentials reported earlier, we now show that the effective mobility can even be nonmonotonic in the driving force.     

Analytical treatment of biased diffusion in tubes with periodic dead ends

Effective mobility and diffusion coefficient of a particle in a tube with identical periodic dead ends characterize the motion on large time scale, when the particle displacement significantly exceeds the tube period. We derive formulas that show how these transport coefficients depend on the driving force and the geometric parameters of the system. Numerical tests show that values of the transport coefficients obtained from Brownian dynamics simulations are in excellent agreement with our theoretical predictions.     

Brownian dynamics simulation of a model simple electrolyte in solvents of low dielectric constant

Brownian dynamics simulations are performed to investigate the ionic transport of model simple electrolytes, in which ions are interacting with each other through the repulsive core and Coulombic interactions. The equivalent conductivity and self-diffusion coefficient show minima as the function of the number density of ions when the dielectric constant of the solvent is low. Although the minimum of the former is in harmony with various experiments, no experiment has ever been reported on that of the latter. The analysis of time-dependent transport coefficients reveals that the presence of the minima is ascribed to the slow dynamics, rather than to static association models. The inclusion of a model function that resembles the short-range part of the potential of mean force induced by solvent affects the transport coefficients qualitatively, which suggests the importance of solvent-induced potential of mean force in the conduction mechanism of electrolytes in solvents of low dielectric constant.     

Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform‐to‐water partition coefficients

Nucleic acid force fields have been shown to reproduce structural properties of DNA and RNA very well, but comparative studies with respect to thermodynamic properties are rare. As a test for thermodynamic properties, we have computed hydration free energies and chloroform‐to‐water partition coefficients of nucleobases using the AMBER‐99, AMBER‐gaff, CHARMM‐27, GROMOS‐45a4/53a6 and OPLS‐AA force fields. A mutual force field comparison showed a very large spread in the calculated thermodynamic properties, demonstrating that some of the parameter sets require further optimization. The choice of solvent model used in the simulation does not have a significant effect on the results. Comparing the hydration free energies obtained by the various force fields to the adenine and thymine experimental values showed a very large deviation for the GROMOS and AMBER parameter sets. Validation against experimental partition coefficients showed good agreement for the CHARMM‐27 parameter set. In view of mutation studies, differences in partition coefficient between two bases were also compared, and good agreement between experiments and calculations was found for the AMBER‐99 parameter set. Overall, the CHARMM‐27 parameter set performs best with respect to the thermodynamic properties tested here. © 2012 Wiley Periodicals, Inc.     

Ultrathin film characterization: photoreactive polyacrylamide

The structure and properties of photoreactive polyacrylamide thin films suitable for medical devices are presented. Using a solution deposition process, we report on the influences of polymer concentration, substrate residence time in solution and UV illumination upon the film structure, wettability and frictional properties. Ellipsometry, atomic force microscopy and lateral force microscopy show that increasing polymer concentration and illumination increased the film thickness and uniformity. Dynamic contact angles and frictional coefficients of the modified surfaces depend upon the film structure and thickness for films less than 40Å thick. We also demonstrate the potential of lateral force microscopy for investigating tribology at the nanoscale level.     

Physical meaning of the rheological coefficients in the generalized Casson model

The coefficients of the previously proposed generalized flow model of structured systems have been interpreted. The cohesive force between particles in disperse systems has been calculated from rheological data. The number of aggregated particles in a disperse system is estimated using the kinetic equation method.     

Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions

The existence of length-scale dependence of hydrophobic solvation has important implications in the equilibrium of disordered, partially folded, and folded protein conformations. Neglecting this dependence, such as in popular solute surface-area based implicit solvent models with fixed surface tension coefficients, severely limits the ability to accurately model protein conformational equilibrium. We illustrate such fundamental limitations by examining the potentials of mean force of forming dimeric and trimeric nonpolar clusters and propose a new empirical model that effectively captures the context dependence of the local effective surface tension. Further optimization of the new model with other components of the implicit solvent force fields provides promise to significantly improve one's ability to simulate protein folding and conformational transitions. The existence of length-scale dependence of hydrophobic solvation has important implications in the equilibrium of disordered, partially folded, and folded protein conformations. Neglecting this dependence, such as in popular solute surface-area based implicit solvent models with fixed surface tension coefficients, severely limits the ability to accurately model protein conformational equilibrium. We illustrate such fundamental limitations by examining the potentials of mean force of forming dimeric and trimeric nonpolar clusters and propose a new empirical model that effectively captures the context dependence of the local effective surface tension. Further optimization of the new model with other components of the implicit solvent force fields provides promise to significantly improve one's ability to simulate protein folding and conformational transitions.     

Activity Coefficients of Potassium Chloride and Sodium Chloride in the Quaternary System KCl-NaCl-Water-Ethanol

Activity coefficients of KCl and NaCl were determined in the quaternary system KCl-NaCl-water-ethanol, for 10 and 20% (w/w) ethanol in the solvent, from experimental electromotive force data. The molalities varied from 0.1 mol kg^–1 to near saturation and measurements were taken in the temperature range 20 to 50°C. The Pitzer-Simonson equations were used to describe the nonideal behavior of both electrolytes and the corresponding activity coefficients were determined for each solvent and temperature.