Generalized Born/surface area method

GAPT (generalized atomic polar tensor) a charge calculation method GB/SA (generalized Born/surface area) method for computing solvation effects... 

Molecular Mechanics Poisson-Boltzmann or Generalized Born Surface Area Methods... 

The generalized Born/surface area (GB/SA) model is a combination of the Born and SASA models. This method has been effective in describing the solvation of biomolecular molecules. It is incorporated in the MacroModel software package. 

GB/S A Generalized-Born/Surface-Area. A method for simulating solvation implicitly, developed by W.C. Still s group at Columbia University. The solute-solvent electrostatic polarization is computed using the Generalized-Born equation. Nonpolar solvation effects such as solvent-solvent cavity formation and solute-solvent van der Waals interactions are computed using atomic solvation parameters, which are based on the solvent accessible surface area. Both water and chloroform solvation can be emulated. 

Using partial atomic charges in eq. (14.59) is often called the generalized Bom model, which has been used especially in connection with force field methods in the Generalized Born/Surface Area (GB/SA) model. In this case, the Coulomb interaction between the partial charges (eq. (2.20)) is combined with the Bom formula by means of a function fy depending on the intemuclear distance and Born radii for each of the two atoms,and aj. 

The change in free energy for the transfer of a solute from an aqueous to an organic solvent can be computed using a continuum solvation model (the generalized Born/surface area, GB/SA) or a quantum mechanical model such as SMI, SM2, SMS,. . . , etc., where SM denotes solvation model. These methods are less CPU intensive than the molecular dynamics or Monte Carlo approaches described below. 

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. 

Although, generally speaking, these expectations are borne out by experiments in a qualitative manner, significant quantitative discrepancies are observed. Apparently, caution should be exercised when interpreting the adsorption data in terms of external and internal surface areas, as will be evident from the following discussion of the methods and their limitations according to experimental data in the Uterature. 

The hrst step in theoretical predictions of pathway branching are electronic structure ab initio) calculations to define at least the lowest Born-Oppenheimer electronic potential energy surface for a system. For a system of N atoms, the PES has (iN — 6) dimensions, and is denoted V Ri,R2, - , RiN-6)- At a minimum, the energy, geometry, and vibrational frequencies of stationary points (i.e., asymptotes, wells, and saddle points where dV/dRi = 0) of the potential surface must be calculated. For the statistical methods described in Section IV.B, information on other areas of the potential are generally not needed. However, it must be stressed that failure to locate relevant stationary points may lead to omission of valid pathways. For this reason, as wide a search as practicable must be made through configuration space to ensure that the PES is sufficiently complete. Furthermore, a search only of stationary points will not treat pathways that avoid transition states. 

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