Hydration shell model

The Langevin model has been employed extensively in the literature for various numerical and physical reasons. For example, the Langevin framework has been used to eliminate explicit representation of water molecules [22], treat droplet surface effects [23, 24], represent hydration shell models in large systems [25, 26, 27], or enhance sampling [28, 29, 30]. See Pastor s comprehensive review [22]. 

Y. K. Kang, K. D. Gibson, G. Nemethy, and H. A. Scheraga, J. Phys. Chem., 92, 4739 (1988). Free Energies of Hydration of Solute Molecules. 4. Revised Treatment of the Hydration Shell Model. 

Solvation effects are an important aspect of conformational studies involving biologically important molecules. CAMSEQ/M utilizes a modified hydration shell model to account for these environmental effects (3,9,11,15). Several simulated solvent environments may be calculated. These include aqueous, 1-octanol... 

Free Energies of Hydration of Solute Molecules. 3. Application of the Hydration Shell Model to Charged Organic Molecules. 

Fig. 3.16. Hydration shell model (according to Modes et al, 1979a). Hydration of N-methyl-acetamide is shown. iV-Methylacetamide is represented by its cross section. The heavy line delineates the van der Waals contour the thin line surrounding the molecule indicates the boundary of the hydration shell. Two specifically bound water molecules and W2 are shown. Water molecules contained within the boundary contribute to specific and to nonspecific hydration (see text).

Taking into account the hydration shell of the NA and the possibility of the water content changing we are forced to consider the water -I- nucleic acid as an open system. In the present study a phenomenological model taking into account the interdependence of hydration and the NA conformation transition processes is offered. In accordance with the algorithm described above we consider two types of the basic processes in the system and thus two time intervals the water adsorption and the conformational transitions of the NA, times of the conformational transitions being much more greater... 

One of the most thoroughly investigated examples of polymeric biomolecules in regard to the stabilization of ordered structures by hydration are the DNAs. Only shortly after establishing the double-helix model by Watson and Crick 1953 it became clear, that the hydration shell of DNA plays an important role in stabilizing the native conformation. The data obtained by the authors working in this field up until 1977 are reviewed by Hopfinger155>. 

A fourth solvent structural effect refers to the average properties of solvent molecules near the solute. These solvent molecules may have different bond lengths, bond angles, dipole moments, and polarizabilities than do bulk solvent molecules. For example, Wahlqvist [132] found a decrease in the magnitude of the dipole moment of water molecules near a hydrophobic wall from 2.8 D (in their model) to 2.55 D, and van Belle et al. [29] found a drop from 2.8 D to 2.6 D for first-hydration-shell water molecules around a methane molecule. 

We summarize this section by emphasizing that we have identified a host of effects, and we have seen that they are mainly short-range effects that are primarily associated with the first solvation shell. A reasonable way to model these effects quantitatively is to assume they are proportional to the number of solvent molecules in the first hydration shell with environment-dependent proportionality constants. 

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... 

Figure 7. A schematic representation of the microscopic model for the metal/electrolyte solution interface. Shown from top to bottom are an ion that is contact adsorbed with partial loss of its hydration shell, an ion whose hydration shell partially consists of first layer of water molecules, and an ion that is not contact adsorbed.

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