Molecular dynamics, liquids

B.-C. Perng and B. M. Ladanyi, Longitudinal dielectric properties of molecular liquids molecular dynamics simulation studies of CH3CN, C6H6, and C02, J. Chem. Phys., 110 (1999) 6389-405. 

The Relative Performances of Several Scientific Computers for a Liquid Molecular Dynamics Simulation... 

The Effects of Pressure on Structural and Dynamical Properties of Associated Liquids Molecular Dynamics Calculations for the Extended Simple Point Charge Model of Water. 

K. Bagchi, S. Balasubramanian, and M. L. Klein,/. Chem. Phys., 107, 8561 (1997). The Effects of Pressure on Structural and Dynamical Properties of Associated Liquids Molecular Dynamics Calculations for the Extended Simple Point Charge Model of Water. 

Keywords Homogeneous nucleation Ionic liquid Molecular dynamics... 

The local features are essential whenever we want to choose an optimal polymer for a given practical application. If we want to improve the fabrication of rubbers, we need a good understanding of the local motions of a rubber chain—i.e., how they depend on temperature, the influence of steric constraints between neighboring monomers, and so forth. The experimental methods for local probing of a polymer chain are not very different from those used for small molecules (such as infrared and Raman measurements). Similarly, the theoretical methods are (or will become) related to those which are used for conventional liquids molecular dynamics, Monte Carlo methods, etc. 

Zhao W, Leroy F, Heggen B, Zahn S, Kirchner B, Balasubramanian S, Miiller-Plathe F (2009) Are there stable ion-pairs in room temperature ionic liquids Molecular dynamics of l-butyl-3-methylimidazoliun hexafluorophosphate. J Am Chem Soc 131 15825-15833... 

Siqueira LJ, Ribeiro MC (2009) Alkoxy chain effect on the viscosity of a quaternary ammonium ionic liquid molecular dynamics simulations. J Phys Chem B 113 1074-1079... 

Zhao, W., Leroy, R, Heggen, B., Zahn, S., Kirchner, B., Balasubramanian, S. Muller-Plathe, R (2009). Are there stable ion-pairs in room-temperature ionic liquids molecular dynamics simulations of l-n-butyl-3-methylimidazolium hexafluorophosphate, J. Am. Chem. Soc. 131(43) 15825-15833. 

Two simulation methods—Monte Carlo and molecular dynamics—allow calculation of the density profile and pressure difference of Eq. III-44 across the vapor-liquid interface [64, 65]. In the former method, the initial system consists of N molecules in assumed positions. An intermolecule potential function is chosen, such as the Lennard-Jones potential, and the positions are randomly varied until the energy of the system is at a minimum. The resulting configuration is taken to be the equilibrium one. In the molecular dynamics approach, the N molecules are given initial positions and velocities and the equations of motion are solved to follow the ensuing collisions until the set shows constant time-average thermodynamic properties. Both methods are computer intensive yet widely used. 

In Fig. III-7 we show a molecular dynamics computation for the density profile and pressure difference P - p across the interface of an argonlike system [66] (see also Refs. 67, 68 and citations therein). Similar calculations have been made of 5 in Eq. III-20 [69, 70]. Monte Carlo calculations of the density profile of the vapor-liquid interface of magnesium how stratification penetrating about three atomic diameters into the liquid [71]. Experimental measurement of the transverse structure of the vapor-liquid interface of mercury and gallium showed structures that were indistinguishable from that of the bulk fluids [72, 73]. 

There is, of course, a mass of rather direct evidence on orientation at the liquid-vapor interface, much of which is at least implicit in this chapter and in Chapter IV. The methods of statistical mechanics are applicable to the calculation of surface orientation of assymmetric molecules, usually by introducing an angular dependence to the inter-molecular potential function (see Refs. 67, 68, 77 as examples). Widom has applied a mean-held approximation to a lattice model to predict the tendency of AB molecules to adsorb and orient perpendicular to the interface between phases of AA and BB [78]. In the case of water, a molecular dynamics calculation concluded that the surface dipole density corresponded to a tendency for surface-OH groups to point toward the vapor phase [79]. 

Both the Monte Carlo and the molecular dynamics methods (see Section III-2B) have been used to obtain theoretical density-versus-depth profiles for a hypothetical liquid-vapor interface. Rice and co-workers (see Refs. 72 and 121) have found that density along the normal to the surface tends to be a... 

It was noted in connection with Eq. III-56 that molecular dynamics calculations can be made for a liquid mixture of rare gas-like atoms to obtain surface tension versus composition. The same calculation also gives the variation of density for each species across the interface [88], as illustrated in Fig. Ill-13b. The density profiles allow a calculation, of course, of the surface excess quantities. 

Molecular dynamics and density functional theory studies (see Section IX-2) of the Lennard-Jones 6-12 system determine the interfacial tension for the solid-liquid and solid-vapor interfaces [47-49]. The dimensionless interfacial tension ya /kT, where a is the Lennard-Jones molecular size, increases from about 0.83 for the solid-liquid interface to 2.38 for the solid-vapor at the triple point [49], reflecting the large energy associated with a solid-vapor interface. 

It is possible to use the quantum states to predict the electronic properties of the melt. A typical procedure is to implement molecular dynamics simulations for the liquid, which pemiit the wavefiinctions to be detemiined at each time step of the simulation. As an example, one can use the eigenpairs for a given atomic configuration to calculate the optical conductivity. The real part of tire conductivity can be expressed as... 

Figure Al.3.30. Theoretical frequency-dependent conductivity for GaAs and CdTe liquids from ab initio molecular dynamics simulations [42].

Progress in the theoretical description of reaction rates in solution of course correlates strongly with that in other theoretical disciplines, in particular those which have profited most from the enonnous advances in computing power such as quantum chemistry and equilibrium as well as non-equilibrium statistical mechanics of liquid solutions where Monte Carlo and molecular dynamics simulations in many cases have taken on the traditional role of experunents, as they allow the detailed investigation of the influence of intra- and intemiolecular potential parameters on the microscopic dynamics not accessible to measurements in the laboratory. No attempt, however, will be made here to address these areas in more than a cursory way, and the interested reader is referred to the corresponding chapters of the encyclopedia. 

Batista V S and Coker D F 1996 Nonadiabatic molecular dynamics simulation of photodissociation and geminate recombination of liquid xenon J. Chem. Phys. 105 4033-54... 

Rosenberg R O, Berne B J and Chandler D 1980 Isomerization dynamics in liquids by molecular dynamics Chem. Phys. Lett. 75 162... 

Cong P, Simon J D and Yan Y 1995 Probing the molecular dynamics of liquids and solutions Ultrafast Processes in Chemistry and Photobiology ed M A El-Sayed, I Tanaka and Y Molln (Oxford Blackwell) pp 53-82... 

Anta J A, Jesson B J and Madden P A 1998 Ion-electron correlations In liquid metals from orbital-free ab initio molecular dynamics Phys. Rev. B 58 6124-32... 

Figure B3.3.12. Sulphur atoms in liquid iron at the Earth s core conditions, simnlated by first-principle Car-Parrinello molecular dynamics, (a) Initial conditions, showing a mannally-prepared initial cluster of snlphur atoms, (b) A short tune later, indicating spontaneous dispersal of the snlphur atoms, which mingle with the surroundmg iron atoms. Thanks are dne to D Alfe and M J Gillan for this figure. For fiirtlier details see [210. 211].

Allen M P, Warren M A, Wilson M R, Sauron A and Wiliam S 1996 Molecular dynamics calculation of elastic constants in Gay-Berne nematic liquid crystals J. Chem. Phys. 105 2850-8... 

Wilson M R 1997 Molecular dynamics simulations of flexible liquid crystal molecules using a Gay-Berne/Lennard-Jones model J. Chem. Phys. 107 8654-63... 

The parameter /r tunes the stiffness of the potential. It is chosen such that the repulsive part of the Leimard-Jones potential makes a crossing of bonds highly improbable (e.g., k= 30). This off-lattice model has a rather realistic equation of state and reproduces many experimental features of polymer solutions. Due to the attractive interactions the model exhibits a liquid-vapour coexistence, and an isolated chain undergoes a transition from a self-avoiding walk at high temperatures to a collapsed globule at low temperatures. Since all interactions are continuous, the model is tractable by Monte Carlo simulations as well as by molecular dynamics. Generalizations of the Leimard-Jones potential to anisotropic pair interactions are available e.g., the Gay-Beme potential [29]. This latter potential has been employed to study non-spherical particles that possibly fomi liquid crystalline phases. 

The most important molecular interactions of all are those that take place in liquid water. For many years, chemists have worked to model liquid water, using molecular dynamics and Monte Carlo simulations. Until relatively recently, however, all such work was done using effective potentials [4T], designed to reproduce the condensed-phase properties but with no serious claim to represent the tme interactions between a pair of water molecules. 

Rahman, A., Stillinger, F.H. Molecular dynamics study of liquid water. J. Chem. Phys. 55 (1971) 3336-3359. 

Postma, J.P.M., Berendsen, H.J.C., Straatsma, T.P. Intramolecular vibrations from molecular dynamics simulations of liquid water. Journal de Physique C7 (1984) 31-40. 

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