Potentials of mean force for hydrophobic interactions between hydrocarbons in water solution: dependence on temperature,solute shape,and solute size

We carried out molecular dynamics (MD) simulations with the AMBER force field for four pairs of spherical dimers of different size (neopentane, bicyclooctane, adamantane, and fullerene‐C₆₀) using the TIP3P model of water as solvent. For comparison, we performed MD simulations for a linear molecule of n‐pentane at the same conditions. To assess the entropy contribution to the Gibbs free energy, MD simulations were run at three different temperatures of 273 K, 323 K, and 348 K, respectively, using umbrella‐sampling/the WHAM method. The stability of dimers is described by a potential of mean force (PMF). The shape of PMF curves for hydrophobic interactions is characteristic, and entails a contact minimum, a solvent‐separated minimum, and a desolvation maximum. The depth and position of the contact minimum for each pair change with the size of the nonpolar particle, and are consequently shifted to a larger distance for larger molecules. Additionally, the Lennard–Jones contribution to the PMF increases simultaneously with an increase in particle size. For a linear dimer, the contact minimum is shifted to a shorter distance than it is for spherical systems with the same number of carbon atoms. The contact minima on PMF curves increase with temperature, suggesting that the association entropy is positive. Dimensionless PMF curves showed a low dependency (near contact minima regions) on temperature, as the association entropy is low. Copyright © 2014 John Wiley & Sons, Ltd.     

离子配对动力学不一定遵循Eigen-Tamm机理

Eigen-Tamm模型认为水溶液中的离子对从单水分子桥链离子对到紧密离子对是离子对溶剂化平衡的动力学控制性步骤,两态之间自由能垒最高,相互转化速率最慢. 设计了两类带有单位电荷的离子对模型(2.0:x和x:2.0,固定离子对中的阳离子或阴离子的半径为2 ?,另一个为不同半径的阴阳离子),通过计算离子对不同距离的平均力势来获取自由能曲线,发现2.0:x系列离子对由于溶剂水的作用,从单水分子桥链离子对到紧密离子对转化的自由能垒有明显减低,并不是离子成对动力学平衡中的最慢步骤,与Eigen-Tamm 模型描述存在偏差.     

PMD分析中的PMF级联模型研究

PMF级联模型是进行PMD研究广泛采用的模型.从PMD矢量在Stokes空间的运动入手,推导出了PMF级联模型的DGD的统计分布并给出了整体特性与局部特性之间的关系,所得结果用JME法验证是正确的.最后通过误差分析,提出了该模型的级联段数的选取原则.所得结论可为PMD的仿真提供理论依据.     

Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.     

Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones （LJ） or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.     

THEORETICAL ANALYSIS OF POLARIZATION MODE DISPERSION EMULATOR

The PMF (Polarization Maintaining Fiber) concatenation model is an important model in studying PMD (Polarization Mode Dispersion). In this paper, two numerical models are established based on Jones matrix and Mueller matrix. Then we perform the numerical simulation. The results indicate that the statistical probability distribution of PMD approximates the Maxwell distribution more closely with the increasing of the number of degree of freedom. The efficiency of the two ways is also discussed.     

基于偏振度椭球的PMD补偿的前馈信息提取方法

通过建立一个简单的模型推导了偏振模色散与偏振度椭球的关系式,可以直接从偏振度椭球的长轴和短轴得到偏振模色散的大小.将得到的一阶偏振模色散大小与理论上从琼斯矩阵中计算的结果进行比较,发现在差分群时延小于20 ps时,模拟结果与理论计算值较好相符.分析了如何从偏振度椭球的长轴判断偏振模色散矢量的方向.因此,从得到的偏振模色散矢量的大小和方向信息可以为一阶偏振模色散补偿提供前馈信息.     

Microscopic structure of liquid dimethyl sulphoxide and its electrolyte solutions: molecular dynamics simulations

Molecular dynamics (MD) simulations of pure dimethyl sulphoxide (DMSO) and solutions of Na⁺, Ca²⁺, Cl^?, NaCl and CaCl₂ in DMSO have been performed at 298.15 K and 398.15 K in NVT ensembles by using a four-interaction-site model of DMSO and reaction field method for Coulombic interactions. The structure of solvent, ion-solvation shells and ion-pairs have been analysed by employing a concept of coordination centres and characteristic vectors of the solvent molecule. Results are given for atom-atom (corresponding to DMSO), ion-atom and ion-ion radial distribution functions (RDFs), orientation of the DMSO molecules and their geometrical arrangements in the first solvation shells of the ions (Na⁺, Ca²⁺, Cl^?). A preferential formation of cyclic dimers with antiparallel alignment between dipole moments of nearest-neighbour molecules in the pure solvent is found. Geometrical models of the first coordination shells of the ions in ‘infinitely dilute solutions’ are proposed. Ion-ion RDFs in NaCl-DMSO and CaCl₂-DMSO solutions reveal the presence of both solvent separated (SSIP) and contact (CIP) ion pairs. The structures of the solvation shells of such ion pairs are also discussed.     

Analysis and Compensation of Polarization Mode Dispersion in Single Channel,WDM and 32-channel DWDM Fiber Optic System

One of the most serious impairments which limit the data rate in long distance and high speed transmission systems is Polarization Mode Dispersion (PMD). PMD is negligible when data rate is low (i.e. in Mb/s or few Gb/s) but it will affect the high data rate transmission systems (10^s of Gb/s, Tb/s etc.), as the pulse broadening severely distorts the signal during transmission. Thus it is necessary to compensate the PMD in both single and multichannel fiber optic transmission system due to increase in the traffic demand. This paper deals with a Deterministic Differential Group Delay (DDGD) method to compensate the PMD in single channel, by delaying the fast polarization component and wavelength independent Polarization Maintaining Fiber (PMF) method for multichannel PMD compensation. The DDGD method efficiently compensates the PMD upto 45 ps in single channel 40 Gb/s transmission systems. The State of Polarization (SOP) before and after the PMD and after compensation is analyzed by means of Poincare Sphere. By using PM Fiber method, simultaneous and effective compensation of PMD in multichannel system is achieved. Here, the simulation has been carried out for 4-channel (40 Gb/s), 8-channel (80 Gb/s), 16-channel (160 Gb/s) WDM systems and 32-channel (320 Gb/s) DWDM fiber optic system with each channel having the data rate of 10 Gb/s and the results of PMD compensation for all the channels are analyzed. It is seen that the PMD compensation is achieved upto 90 ps 87 ps, 84 ps and 80 ps in 4-channel, 8-channel, 16-channel WDM systems and 32-channel DWDM systems respectively. As very high data rate of 100 Gb/s and above are in practice now-a-days, compensation of PMD is enhanced to 1.6 Tb/s (16 × 100 Gb/s) data rate for 16-channel by PMF method and 74 ps of broadening is compensated effectively.     

计算平均力势的理论方法

提出了一个用于计算平均力势的普适性的理论框架,方法克服了以前的方法的缺陷,仅仅需要溶剂粒子在单个溶质粒子附近的密度分布作为输入.计算了两个大尺寸溶质粒子浸在小尺寸硬球溶剂浴中的平均力势,理论预言与可能的模拟数据符合.调查了溶剂-溶质相互作用势、溶剂密度、溶质粒子尺寸对过量平均力势的影响.结论是:溶剂粒子在单个溶质粒子附近的减少导致吸引的过量平均力势,而溶剂粒子在单个溶质粒子附近的聚集导致排斥的过量平均力势,高溶剂密度与大溶质粒子尺寸能强化这种趋势.讨论了这种空耗吸引-聚集排斥与生物学中的疏水吸引-水化排斥的联系.     

基于偏振模色散矢量的偏振模色散补偿方案的研究

在研究局部偏振模色散矢量与整体偏振模色散矢量关系的基础上，从理论上得到完全补偿偏振模色散的关系，结论是至少利用两段保偏光纤才能完全补偿。提出了基于偏振模色散矢量的偏振模色散补偿方案和调节控制的算法原理及改进的方向。这些结果对正确进行偏振模色散补偿是很有帮助的。     

Emulator with inverse trend in first-order and second-order polarisation mode dispersion

We design a polarisation mode dispersion (PMD) emulator through subdividing a polarisation maintaining fibre (PMF) of 22 m in length. The aim of this emulator design is to show that first-order and second-order PMD can be inversely proportional to each other. Furthermore, the emulator is also used to show that the magnitude of PMD is independent to whether its statistics approach theoretical distributions or not, of most importance is the degree of mode coupling. The same (as former) applies to its autocorrelation function (ACF). The PMD control mechanism for the emulator is not in real time.     

Polarization mode dispersion of spun fibers: an analytical solution

A simple analytical solution is derived from coupled-mode theory to describe the evolution of polarization mode dispersion (PMD) in spun fibers. For practical fibers with a beat length greater than a few meters, the solution is valid for a whole category of periodic spin profiles. We find that the PMD change factor is independent of the intrinsic birefringence of the fiber and the fiber PMD scales linearly with the fiber length in the short length regime. This solution allows us to determine phase-matching conditions for spun fibers, in which the PMD evolves periodically along the fiber. An example of determining the phase-matching conditions of sinusoidal-type spin profiles is given.     

Impact of polarization dependent loss on degree of polarization as feedback signal of polarization mode dispersion

Polarization dependent loss (PDL) has been recognized as a critical issue because various inline optical components may have nonnegligible PDL effect that interacts with polarization mode dispersion (PMD).We investigated the impact of PMD-PDL interaction on degree of polarization (DOP), which is the most commonly used feedback signal in PMD compensation. The simulation results of a 40-Gb/s NRZ code optical transmission system show that the maximum PMD increases from approximately 40 ps to more than 45 ps, while minimum DOP declines from approximately 0.6 to approximately 0.2. The interaction of PMD and PDL also induces residual PMD underestimation of 5-8 ps, which causes degradation of PMD compensation performance.     

Ultrafast experiments on intermolecular electron transfer in the benzene - bromine atom charge transfer complex

Ultrafast pump - probe measurements have been made on the benzene - bromine atom charge transfer (CT) complex in CCl₄ and cyclohexane solutions. Ultrafast optical excitation of the CT band of the complex yields an ion pair, which is comprised of a benzene cation and a bromide anion. The rate of charge recombination between the bromide and the benzene cation in the ion pair has been observed to be much faster than the rate of diffusion apart. The charge recombination rate is accelerated at high benzene concentrations as a result of the formation of a benzene dimer cation - bromide ion pair which undergoes much faster charge recombination than the benzene cation - bromide ion pair.     

Biphotonic photochemistry of benzophenones in dimethylsulphoxide: a flash photolysis EPR study

Benzophenone and its derivatives in dimethylsulphoxide (DMSO) exhibit biphotonic photochemistry under 355 nm laser photolysis. Flash photolysis electron paramagnetic resonance experiments demonstrate that a single laser pulse is capable of producing and exciting benzophenone triplets, which can sensitize dimethylsulphoxide and subsequently lead to photodecomposition. In decafluorobenzophenone, electron transfer is the dominant process of the highly excited triplet state. Despite the rapid radiationless decay of 2-hydroxybenzophenone (2OHbenzophenone) in non-polar solvents, radical signals are observed from the photoexcitation of 2OHbenzophenone in DMSO. This is attributed to the sufficiently rapid excitation of the triplet state, which competes with the radiationless decay process, aided by the unique solvent properties of DMSO. It is concluded, in contrast to literature data, that the excited triplet state of DMSO is reactive, and can produce methyl radicals that show triplet mechanism polarization via the biphotonic photoexcitation of benzophenone.     

Calculations of potential of mean force: application to ion-pairs and host–guest systems

ABSTRACT

We report the calculation of the potential of mean force (PMF) of different types of associations by various techniques: two no biased methods (thermodynamic integration and finite difference thermodynamic integration), a constraint biased technique (adaptive biasing force) and an umbrella biased method (umbrella sampling). We apply these methodologies to the association between two methane molecules in water, to the formation of an ion pair in water and to the formation of an insertion complex between a macrocycle and a cation. The different PMFs are compared to each other on the basis of the depth of the free energy minimum and on the location of different specific points.     

Dielectric studies of some binary liquid mixtures using microwave cavity techniques

The excess parameter studies in the microwave frequency region (X-band) on complex dielectric permittivity for the binary mixtures are reported. The methods employed are fixed cavity perturbation technique and adjustable plunger cavity technique. Also Gopalakrishna method is used to calculate the relaxation time of the polar solute in a non-polar solvent. The samples under study are acetonitrile, chlorobenzene, dimethyl formamide, carbon tetrachloride and benzene.     

Model for ion-initiated trench etching

We model the plasma etching of trenches by Langmuir kinetics for neutral molecules and bombarding ions. The parallel combination of an isotropic etch rate for the neutrals and an anisotropic etch rate for the ions gives an effective etch rate. The ion etch rate is proportional to the normal surface component of the ion energy flux. An approximate analytical expression for the composite etch rate offers a new approach to the computation of etch profiles for these mixed systems. Etch profiles are displayed for three cases: the nearly ion flux-limited regime, an intermediate case, and the nearly neutral-flux limited regime for the trench bottom. The numerical calculation of the etch profiles follows from the integration of three characteristic strip equations which are nonlinear first-order ordinary differential equations (ODE's)