Molecular dynamics simulation solvent effect

Hydrophobic Interaction from Molecular Dynamics Simulations the Effects of Solute and Solvent Polarizability. 

Wang W, Nelson K A, Xiao L and Coker D F 1994 Molecular dynamics simulation studies of solvent cage effects on photodissociation in condensed phases J. Chem. Phys. 101 9663-71... 

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

Langevin dynamics simulates the effect of molecular collisions and the resulting dissipation of energy that occur in real solvents, without explicitly including solvent molecules. This is accomplished by adding a random force (to model the effect of collisions) and a frictional force (to model dissipative losses) to each atom at each time step. Mathematically, this is expressed by the Langevin equation of motion (compare to Equation (22) in the previous chapter) ... 

The concentration of salt in physiological systems is on the order of 150 mM, which corresponds to approximately 350 water molecules for each cation-anion pair. Eor this reason, investigations of salt effects in biological systems using detailed atomic models and molecular dynamic simulations become rapidly prohibitive, and mean-field treatments based on continuum electrostatics are advantageous. Such approximations, which were pioneered by Debye and Huckel [11], are valid at moderately low ionic concentration when core-core interactions between the mobile ions can be neglected. Briefly, the spatial density throughout the solvent is assumed to depend only on the local electrostatic poten-... 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

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]. 

Sudholt W, Staib A, Sobolewski AL, Domcke W (2000) Molecular-dynamics simulations of solvent effects in the intramolecular charge transfer of 4-(N, N-dimethylamino) benzonitrile. Phys Chem Chem Phys 2(19) 4341-4353... 

Phelps, D. K., Weaver, M. J. and Ladanyi, B. M. Solvent dynamic effects in electron transfer molecular dynamics simulations of reactions in methanol, Chem. Phys., 176 (1993), 575-588... 

An interesting combined use of discrete molecular and continuum techniques was demonstrated by Floris et al.181,182 They used the PCM to develop effective pair potentials and then applied these to molecular dynamics simulations of metal ion hydration. Another approach to such systems is to do an ab initio cluster calculation for the first hydration shell, which would typically involve four to eight water molecules, and then to depict the remainder of the solvent as a continuum. This was done by Sanchez Marcos et al. for a group of five cations 183 the continuum model was that developed by Rivail, Rinaldi et al.14,108-112 (Section III.2.ii). Their results are compared in Table 14 with those of Floris et al.,139 who used a similar procedure but PCM-based. In... 

TvaroSka, KoS r and Hricovini in this book). One way to account for the effect of solvent on conforxnation might be to represent the molecule without environmental influences, and then explicitly include the solvent or other environmental molecules in the calculation. While avoiding built-in influences of environment is a satisfying concept, it is difficult to obtain by experiment parameters that lack those influences. Several methods have been used to study solvation effects, including continuum descriptions (24) and the explicit treatment of solvent molecules in Monte Carlo and molecular dynamics simulation. 

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