Solvent-Excluded Surface SES

The surfaces of large molecules such as proteins cannot be represented effectively with the methods described above (e.g., SAS), However, in order to represent these surfaces, less calculation-intensive, harmonic approximation methods with SES approaches can be used [1S5]. 

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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). 

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 simplest shape for the cavity would be a sphere or possibly an ellipsoid. However, for accurate values of solvation energy more realistic shapes are required. The PCM model (MiertuS et al. [68], Cammi and Tomasi [80]) uses a particular shape of cavity, the solvent excluding (SE) surface (Pomelli and Tomasi [81]), shown in Figure 7.2. 

As described above VWS and SAS are easily defined as sets of spheres centred on atoms. This definition, however, does not apply to SES in this case in fact, the pair of surfaces delimiting the boundary between the excluded volume and the solvent cannot be defined using spheres. There are several algorithms which translate the abstract definition of the SES into a complex solid composed of simple geometrical objects from which the surface can be easily tessellated. 

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