Molecular simulations of liquid

Willetts and Rice attempted to develop a continuum model (type II) to calculate the EFISH response of liquid acetonitrile. Their results were compared with accurate calculations and measurements of the hyperpolarizability of the isolated molecule and measured solution for two different cavity radii. One natural choice of cavity radius is based on the van der Waals radius of the compound and with this value of a the discrepancy between the gas and solution measurements is not resolved. A rather smaller value of a can be selected to give much better agreement. The arbitrariness of the choice of cavity radius places a serious limitation on the usefulness of the continuum theories and, in recent years, there has been a considerable effort to develop hyperpolarizability calculations based on discrete molecular simulations of liquid and solution structure. 

M.P. Allen and D.J. Tildesley, Molecular Simulations of Liquids, Oxford University Press, 1987. 

A. G. Kalinichev, Molecular simulations of liquid and supercritical water Thermodynamics, structure and hydrogen bonding, in Molecular Modeling Theory Applications in the Geoscience., R. T. Gygan, J. D. Dubicki (Eds.), Mineralogical Society of America, 2001. 

The molecular simulation of liquids is now a vast field of human endeavour, and we open with a contribution on Simulation of the Liquid State by David Heyes. David captures the spirit of the SPR exactly when he writes ... The ready availability of fast computers has meant that there are many more researchers working in this ever expanding field. .. [and]. .. 1 have restricted my discussion to. .. areas that have interested me . 

In the early 1970s, molecular simulation of liquid crystals started by Monte Carlo simulations of simple shaped models (rigid body ellipses, etc.) to estimate the excluded volume effect [77]. At the same time, there were already attempts to use the so-called Lennard-Jones potential to calculate the anisotropic potential in model liquid crystals [78]. This has developed into the nowadays well-known Gay-Beme potential [79]. 

Force Fields for Molecular Simulations of Liquid Interfaces... 

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. 

R. W. Pastor. Techniques and applications of Langevin dynamics simulations. In G. R. Luckhurst and C. A. Veracini, editors. The Molecular Dynamics of Liquid Crystals, pages 85-138. Kluwer Academic, Dordrecht, The Netherlands, 1994. 

Stillinger F H and A Rahman 1974. Improved Simulation of Liquid Water by Molecular Dynamics. Journal of Chemical Physics 60 1545-1557. 

Fig. 6.2 Radial distribution function determined from a lOOps molecular dynamics simulation of liquid argon at a temperature of 100K and a density of 1.396gcm. ...

Rothlisberger and M Parrinello 1997. Ab Initio Molecular Dynamics Simulation of Liquid Hydroge Fluoride. Journal of Chemical Physics 106 4658-4664. 

M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids Oxford, Oxford (1987). Chemical Applications of Atomic and Molecular Electrostatic Potentials P. Politzer, D. G. Truhlar, Eds., Plenum, New York (1981). 

AB INITIO MOLECULAR DYNAMICS SIMULATIONS OF LIQUID ALLOYS ... 

Eds Ciccotti G., Frenkel D., McDonald I. R.) Simulation of Liquids and Solids Molecular Dynamics and Monte Carlo Methods in Statistical Mechanics (North-Holland Physics Publishing, Amsterdam) (1987). 

This article reviews progress in the field of atomistic simulation of liquid crystal systems. The first part of the article provides an introduction to molecular force fields and the main simulation methods commonly used for liquid crystal systems molecular mechanics, Monte Carlo and molecular dynamics. The usefulness of these three techniques is highlighted and some of the problems associated with the use of these methods for modelling liquid crystals are discussed. The main section of the article reviews some of the recent science that has arisen out of the use of these modelling techniques. The importance of the nematic mean field and its influence on molecular structure is discussed. The preferred ordering of liquid crystal molecules at surfaces is examined, along with the results from simulation studies of bilayers and bulk liquid crystal phases. The article also discusses some of the limitations of current work and points to likely developments over the next few years. 

It is worth noting that much of the development work for the MM force fields has centred on low energy structures of molecules. Consequently, some of the force constants are less applicable to higher energy molecular structures that can occur in molecular dynamics simulations of liquid crystals. 

In contrast to the single molecule case, Monte Carlo methods tend to be rather less efficient than molecular dynamics in sampling phase space for a bulk fluid. Consequently, most of the bulk simulations of liquid crystals described in Sect. 5.1 use molecular dynamics simulation methods. 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

MD simulations also provide an opportunity to detect the structure of molecularly thin films. The most commonly known ordering structure induced by the confinement, the layering, has been revealed that the molecules are packed layer by layer within the film and the atoms would concentrate on several discrete positions. This has been confirmed in the simulations of liquid decane [29]. The density profile of unite atoms obtained from the simulations is given in Fig. 12 where two sharp density peaks appear at the locations near the walls, as a result of adsorption, while in the middle of the film smaller but obvious peaks can be observed on the density profile. The distance between the layers is largely identical to the thickness of the linear chain of decane molecules, which manifests the layered packing of molecules. 

Vassilev P, Hartnig C, Koper MTM, Frechard F, van Santen RA. 2001. Ab initio molecular dynamics simulation of liquid water and water-vapor interface. J Chem Phys 115 9815-9820. 

Raimondi, M., Famulari, A., Gianinetti, E., Sironi, M., Specchio, R. and Vandoni. I. (1998) New ab initio VB interaction potential for molecular dynamics simulation of liquid water, Adv. Quantum Chem., 32, 263-284. 

Yu HB, Geerke DP, Liu HY, van Gunsteren WE (2006) Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. J Comput Chem 27(13) 1494-1504... 

Chang TM, Peterson KA, Dang LX (1995) Molecular-dynamics simulations of liquid, interface, and ionic solvation of polarizable carbon-tetrachloride. J Chem Phys 103(17) 7502-7513... 

English NJ (2005) Molecular dynamics simulations of liquid water using various long range electrostatics techniques. Mol Phys 103(14) 1945-1960... 

Beginning with values of ]r) and ]v) at time 0, one calculates the new positions and then the new velocities. This method is second-order in At, too. For additional details, see Allen, M. R, and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford (1989) Frenkel, D., and B. Smit, Understanding Molecular Simulation, Academic Press (2002) Haile, J. M., Molecular Dynamics Simulation, Wiley (1992) Leach, A. R., Molecular Modelling Principles and Applications, Prentice-Hall (2001) Schlick, T., Molecular Modeling and Simulations, Springer, New York (2002). 

Kumar, S. K. Szleifer, I. Panagiotopoulos, A. Z., Molecular simulation of the pure n-hexadecane vapor-liquid equilibria at elevated temperature, Phys. Rev. Lett. 1991, 66, 2935... 

Finally, a relatively new area in the computer simulation of confined polymers is the simulation of nonequilibrium phenomena [72,79-87]. An example is the behavior of fluids undergoing shear flow, which is studied by moving the confining surfaces parallel to each other. There have been some controversies regarding the use of thermostats and other technical issues in the simulations. If only the walls are maintained at a constant temperature and the fluid is allowed to heat up under shear [79-82], the results from these simulations can be analyzed using continuum mechanics, and excellent results can be obtained for the transport properties from molecular simulations of confined liquids. This avenue of research is interesting and could prove to be important in the future. 

F. H. Stillinger and A. Rahman, Improved simulation of liquid water by molecular... 

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