Dielectric constants of binary mixtures of propylene carbonate with dimethyl carbonate and ethylene carbonate from molecular dynamics simulation: comparison between non-polarizable and polarizable force fields

Using non-polarizable and polarizable molecular dynamics simulations, binary mixtures of propylene carbonate?+?dimethyl carbonate and propylene carbonate?+?ethylene carbonate with various compositions were investigated. The polarizable model produces more reasonable estimation of dielectric constants than the non-polarizable model; however, combining the electronic continuum model with the non-polarizable MD improves the comparison between the two models. Fair agreement was found between the results from these simulations and available experimental data. In addition, for a better understanding of the mixing behaviour, the excess dielectric constants over the entire composition were calculated. By comparison of the two mixtures in various mole fractions, distinctive mixing behaviours of propylene carbonate?+?dimethyl carbonate (poorly symmetric mixture) and propylene carbonate?+?ethylene carbonate (highly symmetric mixture) were observed.     

Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD–PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.     

The collapsing bubble in a liquid by molecular dynamics simulations

Molecular dynamics simulations have been made of a collapsing bubble or cavity in a simple liquid. Simulations of a Lennard-Jones liquid reveal that the collapsing process takes place in a series of stages. First, the ‘hottest’ molecules from the high kinetic energy tail in the Maxwell—Boltzmann distribution diffuse into the empty cavity. This is followed by a gradual filling in of the cavity until the density in the centre is a little lower than that of the bulk liquid. The system eventually reaches a final new equilibrium liquid state through a subsequent slower equilibration phase. The bubble fills in an oscillatory manner, by partly filling in, and then partially emptying, and so on, with ever decreasing amplitude towards the final uniform liquid state. These density oscillations are more obvious in systems with a larger bubble. Similar oscillations are observed in the kinetic energy of the molecules at selected radii from the centre of the initial bubble. The maximum temperature occurs typically at the end of the initial fillingin stage during which the density of the core undergoes a vapour-to-liquid phase transition, the released latent heat probably contributing to the temperatures achieved in this region. The average maximum temperature found in the smallest system examined is about nine times the critical temperature, which is about 6000 K for water, thus suggesting a simple mechanism for producing molecules with the sorts of kinetic energies and lifetimes required for sonoluminescence.     

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.     

Molecular dynamics study on water self-diffusion in aqueous mixtures of methanol,ethylene glycol and glycerol: investigations from the point of view of hydrogen bonding

Molecular dynamics simulations have been performed to investigate the aqueous binary mixtures of alcohols, including methanol, ethylene glycol (EG) and glycerol of molalities ranging from 1 to 5 m at the temperatures of 273, 288 and 298 K, respectively. The primary purpose of this paper is to investigate the mechanism of water self-diffusion in water-alcohol mixtures from the point of view of hydrogen bonding. The effects of temperature and concentration on water self-diffusion coefficient are evaluated quantitatively in this work. Temperature and concentration to some extent affect the hydrogen bonding statistics and dynamics of the binary mixtures. It is shown that the self-diffusion coefficient of water molecules decreases as the concentration increases or the temperature decreases. Moreover, calculations of mean square displacements of water molecules initially with different number n of H-bonds indicate that the water self-diffusion coefficient decreases as n increases. We also studied the aggregation of alcohol molecules by the hydrophobic alkyl groups. The largest cluster size of the alkyl groups clearly increases as the concentration increases, implying the emergence of a closely connected network of water and alcohols. The clusters of water and alcohol that interacted could block the movement of water molecules in binary mixtures. These findings provide insight into the mechanisms of water self-diffusion in aqueous binary mixtures of methanol, EG and glycerol.     

基于混合液晶分子动力学模拟比较液晶分子旋转黏度大小

提高液晶波前校正器的响应速度是增加液晶自适应光学系统校正带宽的关键, 而研究设计低旋转黏度的液晶分子是提高液晶波前校正器响应速度的根本方法. 利用原子水平上的分子动力学方法获得了目标分子的液相、向列相以及近晶相, 给出了理论计算液晶分子序参数以及旋转黏度的方法. 与此同时, 结合实验方法, 提出利用混合液晶分子动力学模拟来比较液晶分子旋转黏度的大小, 通过多次模拟、多起始点数据处理最大限度消除了因边界尺寸效应带来的数据波动, 最后给出了两种高性能液晶分子的具体比较结果. 这种分子动力学模拟方法能够探查分子结构细微差别对液晶相态以及旋转黏度的影响, 为设计低旋转黏度的液晶分子提供了理论支持, 必将为快速响应液晶材料的设计提供帮助.     

乙二醇均相及其TX-100胶束溶液中光敏分子菲醌的激光光解研究

用时间分辨电子自旋共振（TR-ESR）和瞬态吸收光谱技术,研究了菲醌在乙二醇均相及其TX-100含水胶束溶液中的光化学反应机理。化学诱导动态电子极化（CIDEP）谱和瞬态吸收光谱都表明,在乙二醇均相溶液中,菲醌光激发三重态3PAQ* 夺取氢原子形成中性自由基PAQH.,三重态机理是CIDEP形成的主要机理。在TX-100含水胶束溶液中,光解主要得到菲醌负离子基PAQ-．,PAQ-．由PAQH.解离形成,解离过程中伴随着极化转移。     

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TMU. The lifetime and structural relaxation time of water–water and NMA–water hydrogen bonds show a strong increase with the addition of TMAO and TMU in the solution, whereas the change is nominal in case of urea solution. It is also found that the translational and rotational dynamics of water and NMA slowdown with increasing the concentration of these osmolytes. The slower dynamics of water and NMA is more pronounced in case of TMAO and TMU solution, as these co-solutes strengthen the average hydrogen bond energies between water–water and NMA–water, whereas urea has a little effect on the hydrogen bonding structure and dynamics of aqueous NMA solution. The calculated self-diffusion coefficient values for water and these co-solutes are in similar pattern with experimental observations.     

Studies on the structures and interactions of glutathione in aqueous solution by molecular dynamics simulations and NMR spectroscopy

All-atom molecular simulations and temperature-dependent NMR have been used to investigate the conformations and hydrogen bonds of glutathione (GSH) in aqueous solution. The simulations start from three different initial conformations. The properties are characterized by intramolecular distances, radius of gyration, root-mean-square deviation, and solvent-accessible surface. GSH is highly flexible in aqueous solutions in the simulations. Moreover, conformations can covert between “extended” and “folded” states. Interestingly, the two different hydrogen atoms in cysteine (H_N2) and glycin (H_N3) show different capabilities in forming NH?OW hydrogen bonds. The temperature-dependent NMR results of the different amide hydrogen atoms also show agreements with the MD simulations. Competing formation of GSH hydrogen-bonding interactions in aqueous solutions leads to hydrogen-bonding networks and the distribution of conformations. These changes will affect the activity of GSH under physiological conditions.     

A molecular dynamics method for simulations in the canonical ensemble

A molecular dynamics simulation method which can generate configurations belonging to the canonical (T, V, N) ensemble or the constant temperature constant pressure (T, P, N) ensemble, is proposed. The physical system of interest consists of N particles (f degrees of freedom), to which an external, macroscopic variable and its conjugate momentum are added. This device allows the total energy of the physical system to fluctuate. The equilibrium distribution of the energy coincides with the canonical distribution both in momentum and in coordinate space. The method is tested for an atomic fluid (Ar) and works well.     

Acoustic non-linearity parameter B/A and related molecular properties of binary organic liquid mixtures

Acoustic non-linearity parameter B/A is calculated for binary mixtures using four different methods. The interactions in the liquid mixtures are explained on the basis of excess non-linearity parameter and excess adiabatic compressibility. Sehgal's relations for calculating molecular properties of pure liquids are extended to binary mixtures.     

基于分子动力学模拟流体输运性质的稳定性分析

利用线性响应理论对Ar流体输运参数进行了分子动力学模拟,结果发现:导热系数和黏度会随着自相关积分函数积分时间的增加而产生剧烈波动,而扩散系数却相对稳定. 针对积分稳定性这一问题,对导热系数和黏度中的热流密度和应力张量进行了分解分析,发现含分子间作用力项是影响稳定性的最大因素. 从牛顿力学出发对作用力项的影响机理进行了分析,指明减小这种影响的最主要方法是使在体系进行统计输运参数前达到稳定平衡状态,即最小的预平衡步数应该满足使体系达到该状态下熵最大或者能量最低,并尽量减小温度对体系的影响. 同时,还对模拟盒尺寸、统计步长等因素对积分稳定性的影响进行了分析,给出了保持稳定性的建议. 关键词： 分子动力学 输运性质 自相关函数 稳定性     

A new method for the determination of surface tension from molecular dynamics simulations applied to liquid droplets

For the determination of surface tension of liquid droplets by molecular dynamics simulations, the most time-consuming part is the calculation of pressure tensor in the transition layer, which makes it difficult to enhance the precision of the computation. A new method for the calculation of surface tension of liquid droplets to reduce the calculation quantity of pressure tensor in transition layer to the minimum is proposed in this paper. Two thousand particles are taken as example to show how to carry out our scheme.     

Calculation of the nonlinearity parameter for some types of gaseous and liquid mixtures

Relations that allow one to calculate the nonlinearity parameters for some types of multicomponent systems from the parameters involved in the equations of state are presented. Relations for estimating the derivatives of the speed of sound with respect to temperature and pressure in a two-component mixture from the data on the properties of pure components are obtained. The calculated values of the aforementioned derivatives agree well with the values obtained from the experimental dependences of the speed of sound on temperature and pressure in a two-component mixture.     

Orientation sensitivity of focused ion beam damage in pure zirconium: direct experimental observations and molecular dynamics simulations

A high-purity predominantly single crystalline zirconium was subjected to controlled focused ion beam (FIB) damage. Damage estimates were obtained from electron backscattered diffraction (EBSD) and nano-indentation measurements on exactly the same area/orientation. The damage kinetics, between different crystallographic orientations, differed by one order of magnitude and a clear hierarchy of orientation sensitive ion damage emerged. Use of a simple geometric approach, linear density of atoms and corresponding scattering cross-sections to impinging gallium ions, could differentiate between extreme damage kinetics; but failed when such differences were relatively minor. Numerically intensive molecular dynamics (MD) simulations, on the other hand, were more effective. However, MD simulations or direct EBSD observations failed to justify anisotropic irradiation hardening (AIH): 3–8 times more hardening for near basal. Though explanation for AIH is indirect, evidence and rationalization for orientation-sensitive radiation damage appears clear and statistically reproducible.     

Quantum molecular dynamics simulations for the nonmetal-to-metal transition in fluid helium

We have performed quantum molecular dynamics simulations for dense helium to study the nonmetal-to-metal transition at high pressures. We present new results for the equation of state and the Hugoniot curve in the warm dense matter region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity is derived. The nonmetal-to-metal transition is identified at about 1 g/cm(3). We compare with experimental results as well as with other theoretical approaches, especially with predictions of chemical models.     

Orientational correlations in liquid and supercritical CO2: neutron diffraction experiments and molecular dynamics simulations

Neutron diffraction data from sub- and supercritical CO₂, collected over three different experimental runs, are analysed together, in order to investigate the evolution of the microscopic structure with the thermodynamic parameters. The relative orientations of neighbouring molecules are analysed also in terms of the angular radial correlation function, obtained by molecular dynamics simulation runs compatible with the total neutron weighted radial distribution function. Orientational correlations between neighbouring molecules are seen to persist across the whole thermodynamic range investigated. However, these are limited to the first neighbouring shell, and mainly ascribable to the quadrupolar interaction.     

Atomic structure and diffusivity in liquid Al80Ni20 by ab initio molecular dynamics simulations

The atomic structure and diffusivity in liquid Al₈₀Ni₂₀ are studied by ab initio molecular dynamics simulations. The local structures are analyzed by the pair correlation function, structure factor, coordinate number, Honneycutt–Anderson bond pair, and Voronoi tessellation methods. It is observed that the amount of icosahedral clusters increases, and the liquid becomes more ordered as the temperature decreases. The predicted self-diffusion coefficients of Al and Ni via the mean square displacements are very close to each other and agree well with the quasi-elastic neutron scattering measurements in the literature. The observation of equal self-diffusivity of Al and Ni is attributed to the formation of local solute-centered polyhedra, coupling the migration of Al and Ni. The Manning dynamic correlation factor is evaluated and found to be close to unity. The predicted interdiffusion coefficients using the Darken equation agree well with experimental data in the literature.     

A comparison of effective and polarizable intermolecular potentials in simulations: liquid water as a test case

A comparison of polarizable and effective intermolecular potentials has been carried out by employing simulated properties of liquid water at different temperatures. The effective potentials were obtained by adding a fixed fraction (~80%) of the induced dipole moments of the polarizable potential to the permanent dipole moment of the water molecule. The fraction was fitted to reproduce one structural (the height of the first peak of the oxygen-oxygen radial distribution function) and one dynamic (the self-diffusion coefficient) liquid property predicted by the polarizable potential. The two properties were well reproduced simultaneously by the effective potential at 273 K and 303 K, but less accurately at 373 K. The effective dipole moments were 2.79, 2.75, and 2.68 D at the three respective temperatures. In order to examine the effective potentials further, other liquid properties have been considered, and we found that the molecular rotational relaxation times and the hydrogen bonding properties are reproduced well by the effective potentials, whereas the velocity autocorrelation function, the pressure, the dielectric constant, and the Debye relaxation time are reproduced less accurately.     

Importance of poly(ethylene glycol) conformation for the synthesis of silver nanoparticles in aqueous solution

Silver nanoparticles (NPs) were prepared using silver nitrate (AgNO₃) as a precursor in an aqueous solution of poly(ethylene glycol) (PEG), which acted as both a reducing and stabilizing agent. The UV/Vis spectra showed that PEG 100 (100 kg/mol) has a remarkable capability to produce silver NPs at 80 °C, but the production of silver NPs by both PEG 2 (2 kg/mol) and PEG 35 (35 kg/mol) was negligible. This difference was explained by the conformation of PEG in the reaction solution: the entangled conformation for PEG 100 and the single-coiled conformation for PEG 2 and PEG 35, which were confirmed by pulse-field-gradient ¹H NMR and viscosity measurements. In an aqueous solution, the entangled conformation of PEG 100 facilitated the reduction reaction by caging silver ions and effectively prevented the agglomeration of formed NPs. The reaction in an aqueous PEG 100 solution was observed to be stable under the conditions of a prolonged reaction time or an increased temperature, while no reduction reaction occurred in the PEG 2 solution. The synthesis of silver NPs by PEG 100 was well controlled to produce fine silver NPs with 3.68 ± 1.03 nm in diameter, the size of which remained relatively constant throughout the reaction.