Solvent-excluded surfaces

Solvent-excluded surfaces correlate with the molecular or Connolly surfaces (there is some confusion in the literature). The definition simply proceeds from another point of view. In this c ase, one assumes to be inside a molecaile and examines how the molecule secs the surrounding solvent molecules. The surface where the probe sphere does not intersect the molecular volume is determined. Thus, the SES embodies the solvent-excluded volume, which is the sum of the van der Waals volume and the interstitial (re-entrant) volume (Figures 2-119. 2-120). 

J. L. Pascual-Ahuir, E. Silla and I. Tunon, GEPOL An improved description of molecular surfaces, m. A new algorithm for the computation of a solvent-excluding surface, J. Comput. Chem., 15 (1994) 1127-1138. 

This equation provides a way to estimate the molecular cavity volume for any system but the shape of the cavity has also to be defined. Constant coordinate cavities such as the sphere or the ellipsoid are obviously not appropriate for most systems and they have been almost definitively abandoned in favor of molecular-shaped cavities. The majority of current continuum methods, and MPE as well, use van der Waals-type molecular surfaces. Atomic radii are in general larger than standard Bondi radii so that the obtained surface is close to the so-called solvent-excluding surface [64,65], Consistent with the expression for the volume given above, the order of magnitude of atomic radii should be... 

Ssa is not appropriate for the calculation of Gei. For this quantity, it is convenient to resort to the solvent excluding surface Sse defined as the surface limiting the portion of space not accessible to the solvent molecules. This cavity may be defined in terms of fhs, supplemented by an obstruction function /0(,s (Pomelli and Tomasi, 1995), such as ... 

An immediate consequence of our models is that the surfaces generated are free of troublesome geometric singularities that commonly occur in conventional solvent-accessible and solvent-excluded surfaces [146, 147] and impact computational stability of methods (see Fig. 12.2 for a smooth surface profile). Addition, without using ad hoc molecular surfaces, both our solvation models and the models of Dzubiella et al. significantly reduce the number of free parameters that users must "fit" or adjust in applications to real-world systems [136]. Our recent work shows that physical parameters i.e., pressure and surface tension, obtained from experimental data can be directly employed in our DG-based solvation models to achieve an accurate prediction of solvation energy [135]. 

Figure 2.1.5. Molecular Surface models, (a) van der Waals Surface (b) Accessible Surface and (c) Solvent Excluding Surface.

Figure 2.1.6. Variation of the area of the Solvent Accessible Surface and Solvent Excluding Surface of a methane dimer as a function of the intermolecular distance.

Figure 2.1.7. The Solvent Excluding Surface of a particular solute is the envelope of the volume excluded to the solvent considered as a whole sphere that represents its charge density.

There are no intrinsic reasons in the model to keep a spherical shape for the cavity or to only extend the model to other regular cavities, such as the ellipsoids considered by Onsager. Efforts to keep a spherical shape for the cavity may lead to absurd results see, for example, the remarks expressed by Luzkhov and War-shel [12] about its use for ion pairs. The most convenient shape is based on the van der Waals envelope of the molecule, modified by factors related to the finite size of the solvent molecules the solvent excluding surface may be a first acceptable description. Today models adopt cavities with these irregular shapes. 

CSM = continuum solvation model COSMO = conductorlike screening model COSMO-RS = generalization of COSMO to real solvents QC = quantum chemical PCM = polarizable continuum model SAS = solvent accessible surface SES = solvent excluding surface NPPA = average number of segments per full atom vdW = van der Waals, VWN = Vosko-Wilk-Nusair functional (see Density Functional Theory Applications to Transition Metal Problems). 

The solvent-excluded volume is the volume of space that the probe is excluded from. This volume is bounded by the molecular surface. There is some terminology confusion here, because some authors define the solvent-excluded volume to be the surface contained within the accessible surface. Additionally, the molecular surface is sometimes called the solvent-accessible surface, the solvent-excluded surface, or the solvent-excluding surface. 

A modification of the molecular surface has been proposed because the molecular surface as defined above is capable of intersecting itself (see Figure 4 of Molecular Surface and Volume). This modification is called the solvent excluded surface and is the envelope of the region from which all parts of the spherical solvent molecules are excluded. In effect, the self-intersecting portions of the molecular surface (if any) are removed. The application of this surface to the hydrophobic interaction between two methane molecules leads to results which agree well with the contact, the barrier, and the infinite separation free energies from molecular dynamics calculations. ... 

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