Bom model

This fomuila does not include the charge-dipole interaction between reactants A and B. The correlation between measured rate constants in different solvents and their dielectric parameters in general is of a similar quality as illustrated for neutral reactants. This is not, however, due to the approximate nature of the Bom model itself which, in spite of its simplicity, leads to remarkably accurate values of ion solvation energies, if the ionic radii can be reliably estimated [15],... 

Rashin A A and B Honig 1985. Reevaluation of the Bom Model of Ion Hydration. Journal of Physici Chemistry 89 5588-5593. 

The simplest reaction field model is a spherical cavity, where only the net charge and dipole moment of the molecule are taken into account, and cavity/dispersion effects are neglected. For a net charge in a cavity of radius a, the difference in energy between vacuum and a medium with a dielectric constant of e is given by the Bom model. ... 

Totrov, M. Accurate and efficient generalized Bom model based on solvent accessibility derivation and application for logP octanol/water prediction and flexible peptide docking, f Comput. Chem. 2004, 25, 609-619. 

Im W, Lee MS, Brooks CL III (2003) Generalized Bom model with a simple smoothing function. J Comput Chem 24 1691-1702. 

This result implies that AA should be a quadratic function of the ionic charge. This is exactly what is predicted by the Bom model, in which the ion is a spherical particle of radius a and the solvent is represented as a dielectric continuum characterized by a dielectric constant e [1]... 

Modeling of n (e) can be motivated by a simple thermodynamic model for this electrostatic contribution. The Bom model [34] for the hydration free energy of a spherical ion of radius Ra with a charge qa at its center is... 

X. Xou, Y. Sun, and I. Kuntz, Inclusion of solvation in ligand binding free energy calculations using the generalized-Bom model, J. Am. Chem. Soc. 121 8033 (1999). 

In the generalized Bom model, the solvent polarization energy, Gpoi, is approximated by the following equation... 

The incorporation of the generalized Bom model into free energy calculation methods using FEP/TI and A-dynamics was carried out by Banba and Brooks.81 They define the electrostatic solvation energy for the hybrid system as follows... 

D. Bashford and D. A. Case, Generalized Bom models of macromolecular solvation... 

The use of electrostatic potentials, defined in the context of DFT, for the calculation of ion solvation energies has been reviewed. It has been shown that physically meaningful ionic radii may be obtained from this methodology. In spite of the fact that the electrostatic potentials for cations and anions display a quite different functional dependence with the radial variable, we have shown that it is still possible in both cases to build up a procedure consistent with the Bom model of ion solvation. 

Various components of the interactions are calculated using different formalisms. In fact, the shape and size of the cavity are defined differently in various versions of the continuum models. It is generally accepted that the cavity shape should reproduce that of the molecule. The simplest cavity is spherical or ellipsoidal. Computations are simpler and faster when simple molecular shapes are used. In Bom model, with simplest spherical reaction held, the free energy of difference between vacuum and a medium with a dielectric constant is given as [16]... 

The generalized Bom model (GBM) can be regarded as a special case of the preceding procedures the reaction field is expressed in terms of a multi-center monopole representation of the solute molecule, using the Bom formula, Eq. (32).l3 ,6, 3 "5 The centers are the atomic nuclei. The results are quite sensitive to the method used to calculate the atomic charges Cramer and Truhlar, who have applied the GBM approach extensively13,16,107 use their Class IV charges for this purpose.16,107,116 Various techniques have been utilized to determine the radii.16,95,101,107... 

Kang, X. S., Shafer, R. H., and Kuntz, I. D. 2004. Calculation of Ligand-nucleic Acid Binding Free Energies with the Generalized-Bom Model in dock . Biopolymers, 73, 192. 

Generalized Bom models do not suffer from the multiple cavity problem, which is a particular advantage of that methodology. However, initial studies have suggested that... 

To support the user, step-by-step guiding dialogs are implemented in the database. As long as the site-specific BOM has not been modified by the user, all data entries are marked to be estimates since they are only derived from the default BOM. To accommodate process improvements that are expected over time, the BOM modeling can be further detailed to include time-dependent changes. 

Liu, H. Y., and Zou, X. (2006). Electrostatics of ligand binding Parametrization of the generalized Bom model and comparison with the Poisson-Boltzmann approach. J. Phys. Chem. B 110, 9304-9313. 

Bashford D, Case DA (2000) Generalized Bom Models of Macromolecular Solvation Effects Annu. Rev. Phys. Chem. 51 129-152... 

Jayaram B, Fine R, Sharp K, Honig B (1989) Free energy calculations of ion hydration, an analysis of the Bom model in terms of microscopic simulations. J. Phys. Chem. 93 4320-4327... 

Grycuk TJ (2003) Deficiency of the Coulomb-field approximation in the generalized Bom model, An improved formula for Bom radii evaluation. Chem. Phys. 119 4817... 

Wojciechowski M, Lesyng B (2004) Generalized Bom Model, Analysis, Refinement and Applications to Proteins, J. Phys. Chem. B 108 18368-18376... 

The slope of the AU/Ar curve for the ion pair around Tq is a measure of the restoring force for small displacements from the equilibrium position. The greater the slope, the higher the modulus, and the stiffer the material. As demonstrated in Example 10.6, the Bom model is, at best, only semiquantitative. One reason for this is that ions are treated as point charges and ion polarizabUity (Table 2.3) is not accounted for. 

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