液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Molecular dynamics simulation of liquid sulfur dioxide

A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k).     

Molecular dynamics simulation of liquid water between two walls

A molecular dynamics simulation, lasting ≈25 ps, has been performed with 150 ST2 water molecules between two quasi-hard repulsive walls, at a temperature of 302 K. A number of static and dynamic properties have been computed as a function of the distance from the walls, showing that water near the walls is in general more “ordered” than in the bulk, and that this bulk water behaves like ordinarv liquid ST2 water.     

Molecular dynamics simulation of liquid mixtures of benzene with chlorobenzene

A molecular dynamics method is used to simulate liquid mixtures of benzene and chlorobenzene at different concentrations. Radial angular distribution functions (RADFs) for distances between the benzene ring planes and the angle between them were calculated to analyze the structure of pure components and mixtures. In chlorobenzene, the highest RADF maximum at a distance between the mass centers of the benzene rings of about 4 Å corresponds to the stacked configurations of molecules, and at 5–7 Å the number of stacked contacts are much less than that at 4 Å and is comparable with the orthogonal ones. In liquid benzene, the number of stacked and orthogonal configurations is approximately equal in a range from 4 Å to 7 Å. RADF for benzene reveals extended regions of correlation, which gives evidence of the occurrence of agglomerates bound by specific interactions between the benzene rings. These agglomerates are not characteristic of chlorobenzene, but the presence of maxima on the radial distribution function for the distances between chlorine atoms indicates chlorine aggregation. The effect of halogen aggregation on the structure of benzene-chlorobenzene mixtures is considered. The obtained results are compared with the data on molecular light scattering.     

Molecular dynamics simulation of the free surface of liquid formamide

Molecular dynamics simulations of liquid formamide (HCONH₂) were carried out using the GROMOS software. The formamide molecule is represented by all of its atoms with all internal degrees of freedom. In contrast to other simulations dealing with bulk properties, this study focuses on the interface liquid–vacuum for the first time. We show that the molecular plane is tilted out of the surface, exposing the HCO group to the vacuum. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63 : 1123–1131, 1997     

Molecular dynamics simulation of the homogeneous crystallization of liquid rubidium

The homogeneous crystallization of liquid rubidium models containing 500, 998, and 1968 particles in the basic cube was studied by the molecular dynamics method. The liquid crystallized over the temperature range 70–182.5 K predominantly with the formation of a body centered cubic (BCC) structure. The mechanism of crystallization was different from that accepted in classic nucleation theory. Crystallization developed as an increase in the number of atoms with Voronoi polyhedra of the 0-6-0-8 and 0-4-4-6 types, the formation of bound groups (clusters) from these atoms, and growth of these groups as in the coagulation of an impurity from a supersaturated solution. At the initial stage, bound groups had a very loose structure and included a fairly large number of atoms with polyhedra of other types. The linear dimension of the largest group rapidly approached the basic cube size. The atoms with the 0-6-0-8 and 0-4-4-6 Voronoi polyhedra played a leading role in crystallization and activated the transition of bound group atoms with other coordination types into a BCC coordination. The probability of formation of a bound group of a given size was found to be independent of the volume of the liquid model. Cluster size fluctuations especially strong over the temperature range 180–185 K played an important role in the formation of 0608 clusters of a threshold (“critical”) size.     

Molecular dynamics simulation of liquid water: hybrid density functionals

The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.     

Molecular dynamics simulation of liquid methylene dichloride (EMLG Publication)

The molecular dynamics and interactions of liquid methylene dichloride (CH₂Cl₂) have been computer simulated with atom—atom interaction potentials, with and without charges, at three EMLG pilot project state points, 293K 1 bar; 177K, 1 bar; and 323K, 5 k bar. A wide variety of static and dynamic results have been lodged in the EMLG data bank and in this paper we summarise the work to date and suggest areas of further investigation.     

Molecular dynamics simulation of nanostructural organization in ionic liquid/water mixtures

Molecular dynamics simulations have been carried out to investigate nanostructural organization in mixtures of 1-octyl-3-methylimidazolium nitrate ionic liquid and water at multiple water concentrations. Evolution of the polar network, water network, and micelle structures is visualized and analyzed via partial radial distribution functions. The calculated static partial structure factors show that within the range of water contents examined, polar networks, water networks, and micelles possess an approximately invariant characteristic length at around 20 A. Furthermore, the above calculations point out that, as the amount of water increases, the polar network is continuously broken up (screened) by the intruding water, while the structural organization of the water network and the micelle exhibits a turnover. At the turnover point, the most ordered micelle (cation-cation) structure and water (water-anion-water) network are formed. Thereafter, the structural organization abates drastically, and only loose micelle structure exists due to the dominant water-water interactions. The simulated turnover of structural organization agrees with the sharpest peak in the experimentally obtained structure factor in aqueous solutions of similar ionic liquids; the simulated water structure reveals that water can form liquidlike associated aggregates due to the planar symmetry and strong basicity of NO(3)-, in agreement with experiment. The turnover of structural organization of micelles results from the persistent competition between the hydrophobic interactions of the nonpolar groups and the breakup of the charged polar network with increasing water content, whereas the turnover of the water network results from the competition between the water-water and water-anion interactions.     

Molecular alignment in a liquid induced by a nonresonant laser field: Molecular dynamics simulation

We carried out molecular dynamics (MD) simulations for a dilute aqueous solution of pyrimidine in order to investigate the mechanisms of field-induced molecular alignment in a liquid phase. An anisotopically polarizable molecule can be aligned in a liquid phase by the interaction with a nonresonant intense laser field. We derived the effective forces induced by a nonresonant field on the basis of the concept of the average of the total potential over one optical cycle. The results of MD simulations show that a pyrimidine molecule is aligned in an aqueous solution by a linearly polarized field of light intensity I approximately 10(13) W/cm2 and wavelength lambda = 800 nm. The temporal behavior of field-induced alignment is adequately reproduced by the solution of the Fokker-Planck equation for a model system in which environmental fluctuations are represented by Gaussian white noise. From this analysis, we have revealed that the time required for alignment in a liquid phase is in the order of the reciprocals of rotational diffusion coefficients of a solute molecule. The degree of alignment is determined by the anisotropy of the polarizability of a molecule, light intensity, and temperature. We also discuss differences between the mechanisms of optical alignment in a gas phase and a liquid phase.     

Molecular dynamics simulation of polymer dispersed liquid crystal droplets under competing boundary conditions

This paper is devoted to the molecular dynamics simulation of structural organization inside a polydispersed liquid crystal (LC) droplet under competing boundary conditions. The droplet is assumed to be placed at the liquid crystal interface between two different regions of the solid polymer matrix, which accordingly separates the droplet into two hemispheres: the first of these is under radial boundary conditions; the second hemisphere is under bipolar boundary conditions. The droplet is considered as a jagged sphere filled with LC molecules, modelled as classical spins (unit vectors), whose centres of mass are associated with sites of a cubic lattice inside the cavity. The orienting action of the polymer matrix, and hence the resulting boundary conditions, are modelled by the interaction between the internal LC molecules (possessing only orientational degrees of freedom), and those of a delimiting surface layer (a jagged spherical shell), whose orientations are fixed, radial or bipolar, respectively. All interactions are modelled by the short range McMillan pair potential. The molecular orientation inside the LC droplet has been determined for various anchoring strengths of the interaction between internal spins and boundary layers. We have investigated the structure of the spherical defect resulting in the central region of the droplet, as well as of the boojum ‐ like defects existing near the poles of the droplet. It has been found that a change of relative radial and bipolar anchoring strengths can affect both central and boojum ‐ like defects. The effect of an external field on the molecular orientation inside the droplet has also been investigated. It has been found that a sufficiently strong external field increases the radius of the spherical defect placed in the central region of the droplet.     

Molecular dynamics simulation of polymer dispersed liquid crystal droplets under competing boundary conditions

This paper is devoted to the molecular dynamics simulation of structural organization inside a polydispersed liquid crystal (LC) droplet under competing boundary conditions. The droplet is assumed to be placed at the liquid crystal interface between two different regions of the solid polymer matrix, which accordingly separates the droplet into two hemispheres: the first of these is under radial boundary conditions; the second hemisphere is under bipolar boundary conditions. The droplet is considered as a jagged sphere filled with LC molecules, modelled as classical spins (unit vectors), whose centres of mass are associated with sites of a cubic lattice inside the cavity. The orienting action of the polymer matrix, and hence the resulting boundary conditions, are modelled by the interaction between the internal LC molecules (possessing only orientational degrees of freedom), and those of a delimiting surface layer (a jagged spherical shell), whose orientations are fixed, radial or bipolar, respectively. All interactions are modelled by the short range McMillan pair potential. The molecular orientation inside the LC droplet has been determined for various anchoring strengths of the interaction between internal spins and boundary layers. We have investigated the structure of the spherical defect resulting in the central region of the droplet, as well as of the boojum - like defects existing near the poles of the droplet. It has been found that a change of relative radial and bipolar anchoring strengths can affect both central and boojum - like defects. The effect of an external field on the molecular orientation inside the droplet has also been investigated. It has been found that a sufficiently strong external field increases the radius of the spherical defect placed in the central region of the droplet.     

Molecular level structure of the liquid/liquid interface. Molecular dynamics simulation and ITIM analysis of the water-CCl4 system

The molecular level properties of the liquid/liquid interface between water and CCl(4) are analysed in detail on the basis of molecular dynamics computer simulation. This analysis requires a full list of the molecules that are right at the interface in both phases. Such a list can be provided by the novel method for identifying truly interfacial molecules (ITIM). The full list of the truly interfacial molecules various properties (e.g., width, molecular level roughness) of the interface can be meaningfully analysed. The residence time of the molecules at the interface, the percolation of the water molecules at the interfacial layer as well as in the second layer beneath the surface, the preferred orientations of the interfacial water molecules and the dependence of these orientational preferences on the local curvature of the interface are also analysed and discussed in detail.     

Molecular dynamics simulation of liquid methanol. I. Molecular modeling including C-H vibration and Fermi resonance

A flexible and polarizable methanol model has been developed on the basis of charge response kernel (CRK) theory. The present CRK methanol model well reproduces bulk liquid and interfacial properties, including density, enthalpy of vaporization, diffusion coefficient, surface tension, and radial distribution functions. The modeling of intramolecular potential incorporates the anharmonic coupling effects pertinent to the Fermi resonance of stretching and bending overtones, with its effective quantum correction. Therefore, the present methanol model can describe the vibrational spectroscopic features of infrared, Raman, and sum frequency generation spectra of C-H or C-D stretching region of methanol or deuterated methanol on the same footing. This model allows for further detailed analysis of C-H vibrations of alkyl moieties by molecular dynamics simulation.     

Molecular dynamics simulation of semirigid polymers

The chain rigidity of poly(p-hydroxybenzoate) was estimated through the theoretical evaluation of its persistence length (L_p). A non-Brownian molecular dynamics (MD) simulation of an isolated chain with 20 monomeric units was performed. The sampled conformational population was analyzed and the orientational correlation function between monomeric units along the chain was calculated. An algorithm based on the worm-like chain model was applied to evaluate the persistence length. The results were compared with those obtained from equilibrium models like the freely-rotating-chain and the rotational-matrix method with fluctuations. Equilibrium models give different results depending on the degree of accuracy used in describing the monomeric unit. The inclusion of thermal fluctuations is crucial to obtain realistic results. These coincide with those given by MD simulation when only nearest-neighbour orientational correlations are taken into account: inclusion of higher-order correlation terms leads to lower values of the persistence length. The origin of this discrepancy was investigated. The MD simulation results are characterized by an overrepresentation of conformations with a short end-to-end distance resulting from an anomalous energy concentration in the first bending mode of the chain. In analogy with previous simulation results from systems characterized by a week coupling amoung their degrees of freedom, failure in the energy equipartition is proposed as a likely explanation of the anomalous dynamical behaviour.     

Molecular flexibility effects upon liquid dynamics

Simulation results for the diffusive behavior of polymer chain/penetrant systems are analyzed. The attractive range and flexibility of simple chain molecules were varied in order to gauge the effect on dynamics. In all cases, the dimensionless diffusion coefficient, D*, is found to be a smooth, single-valued function of the packing fraction, eta. The functions D*(eta) are found to be power laws with exponents that are sensitive to both chain stiffness and particle type. For a specific system type, the D*'s for both penetrant and chain-center-of-mass extrapolate to zero at the same packing fraction, eta0. This limiting packing fraction is interpreted to be the location of the glass transition, and (eta0-eta), the distance to the glass transition.     

Molecular dynamics simulation of liquid water confined inside graphite channels: dielectric and dynamical properties

Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.     

Molecular dynamics simulation of cellobiose in water

The conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.