Solute solvent-accessible surface area

The solvent accessible surface area (SASA) method is built around the assumption that the greatest amount of interaction with the solvent is in the area very close to the solute molecule. This is accounted for by determining a surface area for each atom or group of atoms that is in contact with the solvent. The free energy of solvation AG° is then computed by... 

AGg (X) can be removed by assuming that it is equivalent to the polar contribution to the free energy of solution of solute X in a nonpolar hydrocarbon solvent, such as squalane. A second reason for using a reference hydrocarbon solvent is to correct, at least partially, for the fact that the hardcore van der Haals volume is a poor estimate of the size of the cavity and its accessible surface for solvent interactions for aromatic and cyclic solutes. The solvent accessible surface area would logically be the preferred parameter for the cavity term but is very difficult to calculate while the van der Haals volume is readily accessible. With the above approximations the solvent interaction term for... 

Non-electrostatic terms, comprising the solvent-solvent cavity term and solute-solvent van der Waals term, may be linearly related to solvent-accessible surface area (SA)... 

Our extension of the LIE approach to calculate free energies of hydration (AGhyd) incorporated a third term proportional to the solute s solvent-accessible surface area (SASA), as an index for cavity formation within the solvent.19,27 The latter term is needed for cases with positive AGhyd such as alkanes and additional improvement occurred when both a and P were allowed to vary. Equation 8 gives the corresponding LIE/SA equation for... 

Kaznessis et al. [24] used Monte Carlo simulations on a data set of 85 molecules collected from various sources, to calculate physically significant descriptors such as solvent accessible surface area (SASA), solute dipole, number of hydrogen-bond acceptors (HBAC) and donors (HBDN), molecular volume (MVOL), and the hydrophilic, hydrophobic, and amphiphilic components of SASA and related them with BBB permeability using the MLR method. After removing nine strong outliers, the following relationship was developed (Eq. 37) ... 

Kaznessis et al. [24] Solvent accessible surface area, hydrogen-bonding, solute dipole, molecular volume, etc. 

The summation is over solute atoms, a are empirical constants (parameters) specific to atom types and S are solvent-accessible surface areas. 

The nonpolar (or hydrophobic) component, AGnp may be decomposed into a surface component, which is proportional to the solvent accessible surface area (SASA) of the solute and the component representing the solute-solvent non-electrostatic interactions,57... 

The choice of exactly what surface area to calculate is, however, not entirely unambiguous. Although one might consider constructing a surface from standard atomic van der Waals radii, the more typical approach is to use the so-called solvent-accessible surface area (SASA)." 23,125 solvent-accessible surface is defined as that generated by the center of a spherical solvent molecule rolling on the van der Waals surface of the solute. A moment s reflection shows that this is the same as the exposed surface obtained by placing spheres at each of the atomic centers, where each sphere has a radius equal to the van der Waals radius of the atom plus the radius of a solvent molecule. For water, which is reasonably well approximated as a spherical solvent, the radius is usually taken as 1.4... 

The most expensive part of a simulation of a system with explicit solvent is the computation of the long-range interactions because this scales as Consequently, a model that represents the solvent properties implicitly will considerably reduce the number of degrees of freedom of the system and thus also the computational cost. A variety of implicit water models has been developed for molecular simulations [56-60]. Explicit solvent can be replaced by a dipole-lattice model representation [60] or a continuum Poisson-Boltzmann approach [61], or less accurately, by a generalised Bom (GB) method [62] or semi-empirical model based on solvent accessible surface area [59]. Thermodynamic properties can often be well represented by such models, but dynamic properties suffer from the implicit representation. The molecular nature of the first hydration shell is important for some systems, and consequently, mixed models have been proposed, in which the solute is immersed in an explicit solvent sphere or shell surrounded by an implicit solvent continuum. A boundary potential is added that takes into account the influence of the van der Waals and the electrostatic interactions [63-67]. 

The most rigorous dielectric continuum methods employ numerical solutions to the Poisson-Boltzmann equation [55]. As these methods are computationally quite expensive, in particular in connection with calculations of derivatives, much work has been concentrated on the development of computationally less expensive approximate continuum models of sufficient accuracy. One of the most widely used of these is the Generalized Born Solvent Accessible Surface Area (GB/SA) model developed by Still and coworkers [56,57]. The model is implemented in the MacroModel program [17,28] and parameterized for water and chloroform. It may be used in conjunction with the force fields available in MacroModel, e.g., AMBER, MM2, MM3, MMFF, OPTS. It should be noted that the original parameterization of the GB/SA model is based on the OPLS force field. 

Dielectric continuum models such as the Generalized Born Solvent Accessible Surface Area (GB/SA) model are, in conjunction with force fields, excellent tools for fast and reliable calculations of hydration energies and solvent effects on, e.g., conformational equilibria and ligand-receptor interactions. The performance for neutral solutes is very good, whereas calculations on ionic compounds are currently more problematic. A solution to these problems most probably requires force fields that include polarization effects. For optimal accuracy of calculations using a dielectric continuum model, it is a clear advantage if the model is parameterized for the particular force field used. 

---