Implicit solvation,

The GB equation is suitable for the description of solvent effects in molecular mechanics and dynamics [16], as well as in quantum mechanical calculations (17,18]. An excellent review of implicit solvation models, with more than 900 references, is given by Cramer and Truhlar [19]. 

D Cregut, J-P Liautard, L Chiche. Homology modeling of annexm I Implicit solvation improves side-chain prediction and combination of evaluation criteria allows recognition of different types of conformational eiTor. Protein Eng 7 1333-1344, 1994. 

Presently, only the molecular dynamics approach suffers from a computational bottleneck [58-60]. This stems from the inclusion of thousands of solvent molecules in simulation. By using implicit solvation potentials, in which solvent degrees of freedom are averaged out, the computational problem is eliminated. It is presently an open question whether a potential without explicit solvent can approximate the true potential sufficiently well to qualify as a sound protein folding theory [61]. A toy model study claims that it cannot [62], but like many other negative results, it is of relatively little use as it is based on numerous assumptions, none of which are true in all-atom representations. 

Jaramillo A, Wodak SJ. Computational protein design is a challenge for implicit solvation models. Biophys J 2005 88 156-71. 

A. Schiiurmann, G. COSMO a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc., Perkins Trans. 1993, 799-805. (c) Klamt, A. Jonas, V. Burger, T. Lohrenz, J. C. W. Refinement and parametrization of COSMO-RS. J. Phys. Chem. A 1998, 102, 5074—5085. (d) For a more comprehensive treatment of solvation models, see Cramer, C. J. Truhlar, D. G. Implicit solvation models equilibria, structure, spectra, and dynamics. Chem. Rev. 1999, 99, 2161— 2200. 

Schaefer, M., Bartels, C., and Karplus, M. (1998). Solution conformations and thermodynamics of structured peptides Molecular dynamics simulation with an implicit solvation model./. Mol. Biol. 284, 835-848. 

New horizons for treating computationally challenging problems opened with the emergence of reliable implicit solvation models. For example, Simonson et al. [119]... 

A key element of many simplified free energy methods is the use of an implicit description of the solvent. Implicit solvent models are based on the concept of a PMF, presented briefly in this section see [11] for a detailed review see Chap. 4 for applications of the PMF concept that are not related to implicit solvation. 

At the antipodes of the latter description, there is a continuous need for better low-resolution models that involve, for instance, coarse graining of molecules, or implicit solvation. This need is motivated by the expectation that the free energy of a large system can be calculated with sufficient accuracy without requiring that all its components be described at the atomic level. In many cases, this is equivalent to the assumption that a mean-field approximation works, or that many fast degrees of freedom can be removed from the system, yet without any appreciable loss of... 

C. J. Cramer and D. G. Truhlar, Implicit solvation models equilibria, structure, spectra,... 

In the development of solvation models, Cramer and Tmhalar have made several noteworthy contributions [8-11]. Most of the implicit solvation models do not include the effect of first solvation shell on the solute properties. This can be satisfactorily treated by finding the best effective radii within implicit models. In addition to the first-solvent-shell effects, dispersion interactions and hydrogen bonding are also important in obtaining realistic information on the solvent effect of chemical systems. 

Some work has also appeared describing MD with implicit solvation for solutes described at the DFT level. Fattebert and Gygi (2002) have proposed making the external dielectric constant a function of the electron density, thereby achieving a smooth transition from solute to solvent instead of adopting a sudden change in dielectric constant at a particular cavity surface. Non-electrostatic components of the solvation free energy have not been addressed in this model. 

Cramer, C. J. and Truhlar, D. G. 1999. Implicit Solvation Models Equilibria, Structure, Spectra, and Dynamics , Chem. Rev., 99, 2160. 

You can conduct your reaction experiment in a solution-like environment. One of the options in the set-up window of a program is to let you to turn on an implicit solvation model (48). Such models attempt to account for the mutual interaction of the dipoles of the water molecules and the electron distribution in the solute molecule, as well as to account for the energy required to create a cavity in the bulk solvent to accommodate the solute. A very dilute solution is assumed, so the solute molecules do not see each other. Several implicit solvation modeling schemes have been proffered in the literature and are incorporated in various quantum mechanical programs. 

We will look at two important processes which have been studied by implicit solvation techniques ... 

Hybrid solvation Implicit solvation plus Explicit solvation microsolvation subjected to the continuum method. Here the solute molecule is associated with explicit solvent molecules, usually no more than a few and sometimes as few as one, and with its bound (usually hydrogen-bonded) solvent molecule(s) is subjected to a continuum calculation. Such hybrid calculations have been used in attempts to improve values of solvation free energies in connection with pKp. [42], and also [45] and references therein. Other examples of the use of hybrid solvation are the hydration of the environmentally important hydroxyl radical [52] and of the ubiquitous alkali metal and halide ions [53]. Hybrid solvation has been surveyed in a review oriented toward biomolecular applications [54]. 

Explicit and implicit solvation, benzylic organolithiums. Deora N, Carlier PR, J Org Chem, (2010), 75 1061... 

Ideally, the solvent molecules, as well as the solute molecules, should be subjected to geometry optimization in microsolvation (implicit solvation) in a perfect calculation all components of the system, in this case the solution, would be handled exactly. This is feasible for most quantum mechanical (AMI or PM3, ab initio, DFT) microsolvation calculations, since these usually use only a few solvent molecules (see e.g. Chapter 8, [14]). Forcefield (molecular mechanics) calculations on biopolymers surround the solute with a large number of molecules when implicit solvation is used, and it may not be practical to optimize these. 

Implicit solvation models have proved themselves very effective in providing a computationally feasible way to simulate the microscopic environment of molecules in solution [1-3] accurate free energy of solvation can be computed, and the spectroscopic properties of solutes can be corrected to take into account solvent effects. 

A functional even more general than that in Equation (1.77) was given by Marcus [29] in order to describe a system where only a portion of the polarization is in equilibrium. However, also in this case, the functional is in terms of three-dimensional polarization fields and thus it cannot be readily introduced in an ASC implicit solvation model. 

The aim of this contribution was to review the efforts that have been made so far in the formulation of a Lagrangian for the implicit solvation model. The goal is to provide a simple and computationally efficient way to describe the very complex phenomenon of solvation, which involve a large number of molecules, by using a strongly reduced set of degrees of freedom. 

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