Solvent description

The interaction with the solvent is of similar importance as the intramolecuiar energy contributions and a correct representation of the solvent is therefore es.sential. If an explicit solvent description is chosen, averaging over many different solvent configurations is necessary in order to obtain converged statistical averages. Advantageous in this respect is describing the solvent as... 

The study of slow protein dynamics is a fascinating field with still many unknowns. We have presented a number of computational techniques that are currently being used to tackle those questions. Most promising for our case seems the development of methods that combine an implicit solvent description with techniques to induce conformational transitions. 

Microscopic models aim at describing the charge-charge and charge-solvent interaction in full molecular detail, thus circrrmventing the use of a dielectric corrstant (Warshel and Rnssell, 1984 Russel and Warshel, 1985 van Belle et al, 1987). Although this may seem like the proper approach, practical limitations on computer capacity and speed make approximations unavoidable, especially in the solvent description. 

The need of mixed noethods (in which a small part of a biomolecule is treated at high ab initio level, while the remaining part is described less accurately) is now commonly acknowledged for many apphcations, and several models have been proposed. Of course also the solvent description must be adapted to such... 

In microscopic approaches the solvent molecules are described as true discrete entities but in some simplified form, generally based on fotee-field methods (Allinger, 1977). These theories may be of the semicontinuum type if the distant bulk solvent is accounted for, or of the fully discrete type if the solvent description includes a large number of molecules. As an example, the spectrum of formaldehyde in water has been examined using a combination of classical molecular dynamics and ab initio quantum chemical methods and sampling the calculated spectrum at different classical conformations (Blair et al., 1989 Levy et al., 1990). These calculations predict most of the solvent shift as well as the line broadening. 

Simulations with molecular solvent description can only be performed in the concentration range above about 0.5 mol/liter, much higher than the concentrations of many electrochemical experiments. 

In this chapter, we have covered some of the basic elements of the Poisson-Boltzmann implicit solvent description of biomolecular electrostatics. Specifically, we have focused on the application of these methods to basic problems in computational biology. The discussion presented here is necessarily incomplete—electrostatics is a very broad field and continually changing. For additional background and more in-depth discussions of some of the principles and limitations of continuum electrostatics, interested readers should see the general continuum electrostatics texts by Jackson" and Landau et al., " the electrochemistry text of Bockris et al., the colloid theory treatise by Verwey and Overbeek, " and the fantastic collection of condensed matter electrostatics articles assembled by Holm et al. ... 

In reality, these experimental results are not wholly inconsistent with the Debye-HOckel model, whereby the mean activity coefficient decreases as the molality increases. This comes down to taking into account the fact that a usual solute/solvent description is no longer satisfactory for concentrated electrolytes. Indeed, when dealing with concentrated electrolytes, the number of solvent molecules involved in the solvation sphere, close to the ions, cannot be ignored when compared to the total number of solvent molecules. Once one takes this phenomenon into account, then three types of adjustment emerge, each of which are laid out in detail below. 

BD simulation is similar to MD simulations [26]. However it introduees a few new approximations that allow one to perform simulations on the mieroseeond timescale whereas MD simulation is known up to a few nanoseeonds. In BD the explicit description of solvent molecules used in MD is replaced with an implicit continuum solvent description. Besides, the internal motions of molecules are typically ignored, allowing a much larger time step than that of MD. Therefore, BD is particularly useful for systems where there is a large gap of time scale governing the motion of different components. For example, in polymer-solvent mixture, a short time-step is required to resolve the fast motion of the solvent molecules, whereas the evolution of the slower modes of the system requires a larger time-step. However, if the detailed motion of the solvent molecules is concerned, they may be removed from the simulation and their effects on the polymer are represented by dissipative (-yP) and random (o C (0) force... 

J E House, K A House, in Adds, Bases, and Nonaqueous Solvents. Descriptive Inorganic Chemistry. 

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