Solvation explicit

Tiic Langevin dipole method of Warshel and Levitt [Warshel and Levitt 1976] i.itermediate between a continuum and an explicit solvation model. A three-dimension... 

Protein-DNA complexes present demanding challenges to computational biophysics The delicate balance of forces within and between the protein, DNA, and solvent has to be faithfully reproduced by the force field, and the systems are generally very large owing to the use of explicit solvation, which so far seems to be necessary for detailed simulations. Simulations of such systems, however, are feasible on a nanosecond time scale and yield structural, dynamic, and thermodynamic results that agree well with available experimen-... 

The opposite approach has also been considered to make accuracy paramount, independent of computational cost. For example, these cases typically employ the most accurate methods and complex sampling methods, both of which contribute to the computational complexity of the calculation. Clearly, just because a calculation is computationally demanding does not in itself demonstrate that it will be more accurate. However, elements which contribute to the accuracy of a calculation in terms of more accurate models — e.g., all-atom models, explicit solvation — or enhancing the degree of sampling would clearly be more computationally demanding. 

The reader is referred to review articles concerned with dynamic solvent effects for further discussion of the interesting issues involved in applying continuum and explicit solvation models to dynamical situations [333,381-385],... 

It can be seen from Table 26.1 that various methods used to model the effect of a solvent can be broadly classified into three types (1) those which treat the solvent as continuous medium, (2) those which describe the individual solvent molecules (discrete/explicit solvation), and (3) combinations of (1) and (2) treatments. The following section provides a brief introduction to continuum models. 

In addition to the continuum models, the explicit solvation has also been used to quantify the reactivity [48]. In this study, the effect of solvent on the... 

There is, therefore, a good deal of work for theoretical chemists, dedicated to merging the calculations of the separate steps of extraction of metal ions into a whole. Only such a united approach will allow us to analyze correctly all the factors that affect the thermodynamics of extraction. The greatest challenge stems from the need to evaluate solvent effects by the use of more accurate, explicit solvation models. That will require quantum mechanical calculations on extremely large systems consisting of many hundred molecules, thousands of atoms. 

Various instruments of theoretical chemistry have been widely to describe separate steps of solvent extraction of metal ions. Because of the complexity of solvent extraction systems, there is still no unified theory and no successful approach aimed at merging the extraction steps. It has already been pointed out that the challenging problem for theoreticians dealing with solvent extraction of metals, in particular with thermodynamic calculations, is to evaluate correctly solvent effects by the use of the most accurate explicit solvation models and QM calculations. However, such calculations on extremely large sets consisting of hundreds or even thousands of molecules, necessary to model all aspects of the extraction systems, are still impossible due to both hardware and software limitations. 

On balance, the FF derived from a reasonably large and diverse training set gives accurate structures (Fig. 11). Any significant discrepancies suggest interesting behavior due to environmental effects. In such cases, explicit solvation improves the computed results (45). 

In sum, the generation of accurate PMFs from probability distributions for processes with free energies of activation in excess of a few kilocalories per mole continues to be a significant challenge for modern simulation methods. Some alternative approaches, using both continuum and explicit solvation models, are discussed in Section 15.4. 

DFT was employed to study the mechanism of ammonolysis of phenyl formate in the gas phase, and the effect of various solvents on the title reaction was assessed by the polarizable continuum model (PCM). The calculated results show that the neutral concerted pathway is the most favourable one in the gas phase and in solution.24 The structure and stability of putative zwitterionic complexes in the ammonolysis of phenyl acetate were examined using DFT and ab initio methods by applying the explicit, up to 7H20, and implicit PCM solvation models. The stability of the zwitterionic tetrahedral intermediate required an explicit solvation by at least five water molecules with stabilization energy of approximately 35 kcalmol-1 25... 

Crown ethers continue to be one of the most useful parts of supramolecular chemistry/91 From the beginning computations of metal ions complexes with synthetic ionophores/101 which have been aptly reviewed/111 emphasized the importance of including explicitly solvation in free energy calculations, also with ab initio calculations on calixarene complexes/121 Molecular dynamics simulations of 18-crown-6 ether complexes in aqueous solutions predict too low affinities, but at least correctly reproduce the sequence trend K+ > Rb+ > Cs+ > Na+. However, only the selection of K+ over Rb+ and Cs+ is ascribed to the cation size relative to that of the crown cavity, whereas K+ appears in these calculations to be selected over Na+ as consequence of the greater free energy penalty involved in displacing water molecules ftomNa/1131... 

Abstract For some purposes solution-phase computations are necessary, e.g. for understanding certain reactions, and for the prediction of p/ in solution. For introducing the effects of solvation there are two methodologies (and a hybrid of these two) explicit solvation and continuum solvation. 

There are two basic ways to treat solvation computationally explicit and implicit. Microsolvation, explicit solvation, places solvent molecules around the solute... 

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]. 

Sulfite addition in water can be treated but here it seems necessary to use nine explicit waters solvating the C-O- in the initial product of sulfite addition in order to avoid breakdown of the adduct. Clearly it would be better to include a large number of waters in every case but the cost of the optimizations goes up as the number of waters increases. From a practical perspective it is better to allow a bit of empiricism to find the number of waters needed to reliably give a good result. This reaction is still under investigation as we seek to find a general way to carry out structure optimizations with reaction intermediates that have a lifetime in solution but are unstable in the gas phase unless explicitly solvated. 

Thiolate addition is a simple reaction and once we had realized the necessity of including explicit solvation was straightforward this work will be reported shortly. 

Joung, I. S., and Cheatham, T. E. Ill (2008). Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B 112, 9020-9041. 

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