Continuum, solvent

As pointed out earlier, the contributions of the hard cores to the thennodynamic properties of the solution at high concentrations are not negligible. Using the CS equation of state, the osmotic coefficient of an uncharged hard sphere solute (in a continuum solvent) is given by... 

D. D. Humphreys, R. A. Friesner, and B. J. Berne. Simulated annealing of a protein in a continuum solvent by multiple-time-step molecular dynamics. J. Phys. Chem., 99 10674-10685, 1995. 

It is often the case that the solvent acts as a bulk medium, which affects the solute mainly by its dielectric properties. Therefore, as in the case of electrostatic shielding presented above, explicitly defined solvent molecules do not have to be present. In fact, the bulk can be considered as perturbing the molecule in the gas phase , leading to so-called continuum solvent models [14, 15]. To represent the electrostatic contribution to the free energy of solvation, the generalized Bom (GB) method is widely used. Wilhin the GB equation, AG equals the difference between and the vacuum Coulomb energy (Eq. (38)) ... 

The Stokes-Einstein equation has already been presented. It was noted that its vahdity was restricted to large solutes, such as spherical macromolecules and particles in a continuum solvent. The equation has also been found to predict accurately the diffusion coefficient of spherical latex particles and globular proteins. Corrections to Stokes-Einstein for molecules approximating spheroids is given by Tanford. Since solute-solute interactions are ignored in this theory, it applies in the dilute range only. 

In continuum boundary conditions the protein or other macromolecule is treated as a macroscopic body surrounded by a featureless continuum representing the solvent. The internal forces of the protein are described by using the standard force field including the Coulombic interactions in Eq. (6), whereas the forces due to the presence of the continuum solvent are described by solvation tenns derived from macroscopic electrostatics and fluid dynamics. 

Another variant that may mrn out to be the method of choice performs the alchemical free energy simulation with a spherical model surrounded by continuum solvent, neglecting portions of the macromolecule that lie outside the spherical region. The reaction field due to the outer continuum is easily included, because the model is spherical. Additional steps are used to change the dielectric constant of that portion of the macromolecule that lies in the outer region from its usual low value to the bulk solvent value (before the alchemical simulation) and back to its usual low value (after the alchemical simulation) the free energy for these steps can be obtained from continuum electrostatics [58]. 

If the Brownian particles were macroscopic in size, the solvent could be treated as a viscous continuum, and the particles would couple to the continuum solvent through appropriate boundary conditions. Then the two-particle friction may be calculated by solving the Navier-Stokes equations in the presence of the two fixed particles. The simplest approximation for hydrodynamic interactions is through the Oseen tensor [54],... 

In an early work by Mertz and Pettitt, an open system was devised, in which an extended variable, representing the extent of protonation, was used to couple the system to a chemical potential reservoir [67], This method was demonstrated in the simulation of the acid-base reaction of acetic acid with water [67], Recently, PHMD methods based on continuous protonation states have been developed, in which a set of continuous titration coordinates, A, bound between 0 and 1, is propagated simultaneously with the conformational degrees of freedom in explicit or continuum solvent MD simulations. In the acidostat method developed by Borjesson and Hiinenberger for explicit solvent simulations [13], A. is relaxed towards the equilibrium value via a first-order coupling scheme in analogy to Berendsen s thermostat [10]. However, the theoretical basis for the equilibrium condition used in the derivation seems unclear [3], A test using the pKa calculation for several small amines did not yield HH titration behavior [13],... 

Kuhn B, Kollman PA, Stahl M (2004) Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. J Comput Chem 25 1865-1872. 

We can exploit the new results for packing contributions to reconsider the outer shell contribution in Eq. (33). For ionic solutes, the outer shell term would represent the Born contribution because it describes a hard ion stripped of any inner shell ligands. A Born model based on a picture of a dielectric continuum solvent is reasonable (see Section III,B, and Fig. 9, color insert). With that motivation, we first separate the outer shell term into an initial packing contribution and an approximate electrostatic contribution as... 

Realizing that the screening charges, q, must be positioned so as to minimize the energy of the system, differentiation and simplification gives the amount of stabilization energy, AE, due to the presence of the continuum solvent ... 

Zhou, R. Friesner, R.A. Ghosh, A. Rizzo, R.C. Jorgensen, W.L. Levy, R.M., New linear interaction method for binding affinity calculations using a continuum solvent model, J. Phys. Chem. B 2001,105,10388-10397... 

Incorporation of Continuum Solvent Models Using a Generalized Born Approach... 

An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models, J. Med. Chem. 43 3786 (2000). 

We have also studied the coordination of the monocarbonate, bicarbonate, and tricarbonate complexes of neptunyl in water, by using both explicit water molecules and a continuum solvent model.84 The monocarbonate complex was shown to have a pentacoordinated structure, with three water molecules in the first coordination shell, and the bicarbonate complex has a hexacoordinated structure, with two water molecules in the first coordination shell. Overall good agreement with experimental results was obtained. 

Quantitative models of solute-solvent systems are often divided into two broad classes, depending upon whether the solvent is treated as being composed of discrete molecules or as a continuum. Molecular dynamics and Monte Carlo simulations are examples of the former 8"11 the interaction of a solute molecule with each of hundreds or sometimes even thousands of solvent molecules is explicitly taken into account, over a lengthy series of steps. This clearly puts a considerable demand upon computer resources. The different continuum models,11"16 which have evolved from the work of Bom,17 Bell,18 Kirkwood,19 and Onsager20 in the pre-computer era, view the solvent as a continuous, polarizable isotropic medium in which the solute molecule is contained within a cavity. The division into discrete and continuum models is of course not a rigorous one there are many variants that combine elements of both. For example, the solute molecule might be surrounded by a first solvation shell with the constituents of which it interacts explicitly, while beyond this is the continuum solvent.16... 

Values of AGsolvation and Its Components in Two Different Solvents, in kcal/mol, As Predicted by a Hybrid Discrete Molecular/Continuum Solvent... 

General Comments Discrete Molecular and Continuum Solvent Models... 

The Bom equation does not take into account the mutually polarizing effect that the solute and solvent have upon each other. This can be done, within the framework of continuum solvent... 

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