Molecular dynamics computation of solvent contribution to work of ion solvation

Clusters of water with various (charged and neutral) solute particles were simulated by molecular dynamics, and the radial profiles of local density, energy, electric potential, normal pressure, and polarization were obtained. The work of cluster formation was calculated. On the basis of an estimate of the surface potential for the vacuum-liquid and liquid-solid interfaces, the linear contribution of the ion charge to the chemical work of solvation was determined. In the case of the K⁺ ion, the linear contribution to the total work of solvation proved to be practically negligible.     

Molecular dynamics study of electron gas models for liquid water

The frozen density electron gas model proposed by Gordon and Kim for rare gas systems has been implemented in a molecular dynamics code. This code has been applied to investigate various options for extending this scheme to inter-molecular interactions in liquid water. We have compared a number of gradient corrections to the Thomas-Fermi kinetic energy. We also explored a more empirical approach based on adaptation of the frozen molecular electron density to the condensed phase environment. Consistent with experience from force field methods, enhancement of the molecular dipole moment proved to be necessary to reproduce the properties of the liquid. The best models we investigated are a gradient corrected expansion of the simple local density Hamiltonian applied in the original Gordon and Kim model. In addition, these models observed a modified molecular electron density carrying the same dipole moment of 2.95 D as has been observed by recent ab initio molecular dynamics studies based on fully self-consistent Kohn-Sham methods. Possible implications of this finding for force field models are discussed.     

Molecular dynamics simulation of C8E5 micelle in explicit water: structure and hydrophobic solvation thermodynamics

Results are presented from a large scale molecular dynamics (MD) simulation of a non-ionic micelle comprising 80 C₈E₅ surfactant molecules in 9798 explicit TIP3P waters. The results are consistent with the conventional static picture of a simple spherical micelle (‘hydrophilic heads out, hydrophobic tails in’). In addition, the MD simulation reveals structural details that show clearly the dynamic nature of the micellar aggregate. The micelle is roughly spherical with thermal fluctuations leading to instantaneous shapes that are significantly non-spherical. The individual surfactant molecules adopt various nonlinear conformations, predominately in the hydrophilic segment, thereby leading to the overall compact globular shape of the micelle aggregate. Atomic distribution functions and dihedral angle distributions show that the micelle interior is similar to liquid n-octane. Although no water penetration in the micelle hydrophobic core is observed, there is considerable exposure of the hydrophobic tails of the surfactant molecules to water in the interfacial region. The excess chemical potentials of hydrophobic Lennard-Jones (LJ) solutes and their WCA analogs show a preference for the michelle core relative to bulk water. Interestingly, the solvation energies of LJ solutes show a minimum in the interfacial region. A qualitative explanation for this behaviour based on different packing tendencies of water and chain-like molecules is presented.     

Real-time measurement of the orientational dynamics of aqueous solvation shells in bulk liquid water

We present a study of the orientational dynamics of aqueous solvation shells of halogenic anions in bulk water solution with femtosecond two-color midinfrared spectroscopy. These orientational dynamics have time constants between 2.5 and 12 ps, depending on the type of anion and the temperature. We find that the solvation shell of the larger ion I- shows faster dynamics than that of the smaller ions Cl- and Br-.     

Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

Several time dependent fluorescence Stokes shift (TDFSS) experiments have reported a slow power law decay in the hydration dynamics of a DNA molecule. Such a power law has neither been observed in computer simulations nor in some other TDFSS experiments. Here we observe that a slow decay may originate from collective ion contribution because in experiments DNA is immersed in a buffer solution, and also from groove bound water and lastly from DNA dynamics itself. In this work we first express the solvation time correlation function in terms of dynamic structure factors of the solution. We use mode coupling theory to calculate analytically the time dependence of collective ionic contribution. A power law decay in seen to originate from an interplay between long-range probe–ion direct correlation function and ion–ion dynamic structure factor. Although the power law decay is reminiscent of Debye–Falkenhagen effect, yet solvation dynamics is dominated by ion atmosphere relaxation times at longer length scales (small wave number) than in electrolyte friction. We further discuss why this power law may not originate from water motions which have been computed by molecular dynamics simulations. Finally, we propose several experiments to check the prediction of the present theoretical work.     

Molecular dynamics computation of clusters in liquid Fe–Al alloy

By means of constant pressure molecular dynamics (MD) simulation technique, a series of simulations of the Fe₅₀Al₅₀ alloy have been carried out. The atoms interact via semi-empirical n-body noncentral potential. The pair correlation functions and the pair analysis technique is applied to reveal the cluster evolution in the process of quick solidification. By using the bond orientation order parameters, we have measured both local and extended orientation symmetries for computer-generated models of dense liquid and glass. A lot of polyhedra in liquid system, for example, icosahedra, are also obtained. In order to test the reliance of the computation results, corresponding X-ray diffraction experiments have been performed on the material.     

两种扩展Harper模型的波包动力学

本文通过二次矩M₂(t)和概率分布W_n(t)数值地研究了两种扩展Harper模型的波包动力学,得到了这两种模型中各个相、各条临界线以及三相点的波包扩散情况.对于第一种扩展Harper模型,发现两个金属相中波包是弹道扩散的,在绝缘体相中波包不扩散,而在三相点以及各条临界线上波包是反常扩散的.同时,发现金属相—金属相转变的临界线上的波包动力学行为与金属相—绝缘体相转变的临界线上的相同,但三相点的动力学行为与各临 关键词： 金属绝缘体转变 扩展Harper模型 波包动力学     

Quantum chemical studies of the solvation of the hydroxide ion

Abstract

To understand and model the solvation of the hydroxide ion, OH(H₂O)^? _n clusters, n = 1?5, are studied using ab initio quantum chemical techniques, largely at the MP2 level of theory using a double zeta plus polarization functions basis extended by diffuse functions. Energies and vibrational frequencies, together with thermodynamic quantities such as enthalpies, entropies and Gibbs free energies, are computed. This permits comparison with experimental estimates of the successive thermodynamic changes associated with the reaction OH(H₂O)^? _n + H₂O → OH(H₂O)^? _n+1. The theoretical values are in good agreement with experiment. The free energy of hydration of OH^? is modelled by a composite discrete-continuum method where the effects of the first hydration shell (n = 3) are obtained from the gas phase cluster calculation, while the long-range effects are modelled using self consistent reaction field theory, namely by calculating the solvation energy of OH(H₂O)^? _n in a dielectric continuum. The best estimate of the solvation (free) energy at 298 K is ?84·5 kcal mol^?1, compared to the experimental value of ?102·8 kcal mol^?1.     

Molecular dynamics study on the field effect ion transport in carbon nanotube

We investigated potassium ion transport in the (5, 5) carbon nanotube by using classical molecular dynamics simulations under applying external force fields. This can be applied to nanoscale ionic-field-effect devices. As the applying external force field increases, the potassium ions rapidly go through the nanochannel. Under the low external force fields, the thermal fluctuation of the nanochannel affected on the tunneling of the potassium ions, whereas the effects of the thermal fluctuation were negligible under the high external force fields.     

分子动力学模拟压水反应堆中联氨对水的影响

本文采用分子动力学方法模拟在常温常压下(1 atm,298 K)和在压水堆环境下(155 atm,626 K),水分子数为256,联氨(N₂H₄)分子数为0,25,50,75等不同数目时,水和联氨粒子系统的动力性质和微观结构.同时探讨了联氨分子的引入对水中溶解氧的影响.从模拟结果可知,在常温常压下,当联氨的分子数为0,25,50,75时,粒子系统的均方位移会随联氨分子数的增加而增加;联氨分子数为0与为25,50,75比较时会少一个数量级;压水堆环境下,联氨分子数 关键词： 分子动力学 压水堆 联氨     

分子动力学模拟压水反应堆中氢气对水的影响

通过分子动力学方法模拟了在常温常压下(1 atm, 298 K)和在压水堆环境下(155 atm, 626 K), 水分子数为256, 氢分子数为0, 25, 50, 75和100等不同数目时, 粒子系统的动力学性质和微观结构, 分析了不同氢气对水中溶解氧的影响. 从模拟结果可知, 在常温常压和压水堆环境下, 当氢粒子数分别为0, 25, 50, 75和100时, 粒子系统的均方位移会随氢分子数增加而增加, 并且常温常压下的增长幅度远小于压水堆环境下的增长幅度, 如压水堆环境下氢分子数为75时系统的均方位移约是常温常压下氢分子数为75时系统的均方位移的6.02倍, 比压水堆环境下氢分子数0时系统的均方位移增加了131.88%. 此外, 粒子系统的微观结构, 从径向分布函数看, 在常温常压下随着氢分子数目的增加而小幅度增加, 这与常温常压下因氢气溶解在水中增大了氧离子周围的粒子密度相符合. 而在压水堆环境下, 氢分子数为75, 50, 25与为0时的水比较, 其径向分布均不会有太大的变化, 而分子数为100时会出现明显增加, 与为0时的水比较其径向分布增加了22.00%. 模拟结果表明, 往压水堆中的水加入氢气能明显地抑制水中的溶解氧.     

Molecular dynamics study of particle emission by reactive cluster ion impact

Molecular dynamics (MD) simulations of sputtering process with fluorine cluster impact onto silicon targets were performed. By iterating collisional simulations on a same target, accumulation of incident atoms and evolution of surface morphology were examined as well as emission process of precursors. When (F₂)₃₀₀ clusters were sequentially irradiated on Si(1 0 0) target at 6 keV of total incident energy, column-like surface structure covered with F atoms was formed. As the number of incident clusters increased, sputtering yield of Si atoms also increased because the target surface was well fluoridised to provide SiF_x precursors. Size distribution of emitted particles showed that SiF₂ was the major sputtered particle, but various types of silicon-fluoride compounds such like Si₂F_x, Si₃F_x and very large molecules consists of 100 atoms were also observed. This size distribution and kinetic energy distribution of desorbed materials were studied, which showed that the sputtering mechanism with reactive cluster ions is similar to that under thermal equilibrium condition at high-temperature.     

棱形石墨烯纳米孔道内离子传输性能的分子动力学模拟

纳米通道的尺寸、结构和表面化学对其内部溶液的分布结构和输运性质有着重大影响.本文研究了一种全新的菱形石墨烯纳米通道.这种理想的通道与最近被广泛研究的金属有机框架材料(MOF)的内部结构类似,有着与传统的碳纳米管截然不同的内部结构.本文使用分子动力学模拟的方法研究在不同尺寸的菱形石墨烯纳米通道内的KCl溶液的性质,并将其与同尺寸的单壁碳纳米管进行了比较.研究结果表明在小孔道内(<20?)其内部的溶液结构呈现若干个密度极高的聚集区域,即出现了结晶化的趋势．这一研究结果,将为MOF的结构设计提供思路,从而有望实现类似于生物离子通道的高选择性和高传输能力.     

Molecular dynamics investigation of water adsorption on rutile surfaces

Born-Oppenheimer molecular dynamics (MD) simulations were performed in the framework of the semi-empirical molecular orbital method MSINDO to study water adsorption on rutile surfaces. Monolayer and doublelayer water coverage was considered on the rutile (1 1 0) and (1 0 0) surfaces and the adsorbate structures were determined. Vibrational density of states of hydrogen atoms were calculated by constant temperature MD simulations at 100 K. These were used to interpret the experimental vibrational spectrum by assigning all peaks to the particular types of hydrogen atoms.     

Molecular dynamics simulation of ice nanocluster in supercooled water

The properties of the interface between an ice nanocluster and the surrounding water shell were investigated by the molecular simulation method for the SPC/E model in the temperature interval from 200 to 230?K. The melting point of the ice core was determined on the basis of the caloric curve and the behaviour of the diffusion coefficient. The change of the local structure was described by the orientational distribution functions and by the radial profiles of the local density, energy, and normal pressure.     

Molecular dynamics studies of the interaction between water and oxide surfaces

The water-surface interaction is a research target of great importance for a broad spectrum of technological applications and fundamental scientific disciplines. In the present study, a comparative analysis is performed to clarify the structural and diffusion properties of water on a number of oxide surfaces. Based on the molecular dynamics (MD) simulation method, the water-surface interaction mechanism was investigated for the oxide materials TiO₂ (anatase), Al₂O₃ (corundum), and Fe₂O₃ (hematite). A comparison of the water-TiO₂ interaction with the water-Al₂O₃ and water-Fe₂O₃ systems demonstrates the specificity of the adsorption and layer formation on the atomic/molecular level scale. The obtained MD analysis data point to a considerable enhancement of water-TiO₂ surface adsorption and a relatively high density distribution profile near the surface. The novel data on water structure and diffusion on oxide surfaces are discussed from the point of view of possible material innovation and design.     

Molecular dynamics computer simulation of the hydration of two simple organic solutes

The hydration of two simple organic solutes has been studied using the molecular dynamics (MD) computer simulation method. Results of the simulations of a single 1,4-dioxane or 1,3-dioxane molecule dissolved in 122 water molecules are compared with those of a MD simulation of an empty cavity of corresponding size in 216 water molecules. This yields the opportunity to trace the specific effects of the polar and dispersion solute-solvent interactions on the properties of the water molecules in the hydration shell of the solute.

The hydration shell properties of 1,4-dioxane (μ) = 0·14 D) are very similar to those of the corresponding cavity, whereas those of 1,3-dioxane (μ) = 1·91 D) show significant deviations. Earlier conclusions that water structure-making and water structure-breaking properties of 1,4-dioxane are about equally balanced, while 1,3-dioxane is definitely structure-breaking, are confirmed. Moreover, it is shown that a slower self-diffusion and reorientation of water molecules upon addition of a cosolvent does not necessarily point at structure-making properties, additional to those that are already induced by the cavity formation. The introduction of an empty cavity also slows down self-diffusion and molecular reorientation in the hydration shell.     

Molecular dynamics simulation of the ion bombardment of interlayer Cu13 clusters in graphite

The normal bombardment of interlayer Cu₁₃ clusters in graphite by 100, 200, and 400-eV argon ions is examined by means of molecular dynamics simulation employing many-body potentials. The formation frequencies of cluster fragments of different sizes are quantified. The dynamics of the process is studied. The main directions of atom displacements are detected. Changes in the atomic structure of targets are discussed.