Generalized born

In order to solve die Poisson equation for an arbitrary cavity, recourse to numerical methods is required. An altemative approach that has seen considerable development involves computing die polarization free energy using an approximation to the Poisson equation that can be solved analytically, and diis is the Generalized Bom (GB) approach. As its name implies, the GB method extends the Born Eq. (11.12) to polyatomic molecules. The fundamental equation of the GB method expresses the polarization energy as 

Y has units of inverse length, i.e., it is an effective Coulomb integral. In order for the GB equation to be an accurate approximation to the PB equation, a suitable functional form for 

Y must be chosen. A very good functional form is given by 

the steps in a GB calculation to determine the polarization free energy given a particular molecular geometry are essentially  

Assign atomic radii to all atoms for purposes of defining the cavity. 

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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. 

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

Using a set of (partial) atomic charges is often called the generalized Born model. It can be noted that the Born model predicts equal solvation for positive and negative ions of the same size, which is not the observed behaviour in solvents like H2O. 

Totrov [31] developed a model to estimate electrostatic solvation transfer energy AGd" in Eq. (1) based on the Generalized Born approximation, which considers the electrostatic contribution to the free energy of solvation as ... 

Considering the success of fragment methods, which apply additive models for log P predichon, one can assume that addihve approaches may also sahsfactory work for MLP. Indeed, similar to the Generalized Born model, one can consider fragments of molecules as centers of some potenhal functions and use an empirically defined distance function ) to calculate the MLP value by ... 

Another advantage of PB based pKa calculations is that effects of electrolytes are readily accounted for in the PB equation. The Coulombic contribution in conjunction with salt dependence to the abnormally depressed pAVs of histidine in staphylococcal nuclease has been experimentally tested [56], Recently, the methodology used in the PB calculations (Eqs. 10-11 and 10-12) has been combined with the generalized Born (GB) implicit solvent model [94] to offer pKa predictions at a reduced computational cost [52],... 

Chen J, Im W, Brooks CL III (2006) Balancing solvation and intramolecular interactions Toward a consistent generalized Born force field. J Am Chem Soc 128 3728-3736. 

Lee S, Feig M, Salsbury FR Jr, Brooks CL III (2003) New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem 24 1348-1356. 

Mongan J, Case DA, McCammon JA (2004) Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem 25 2038-2048. 

Srinivasan J, Trevathan MW, Beroza P, Case DA (1999) Application of a pairwise generalized Born model to proteins and nucleic acids Inclusion of salt effects. Theor ChemAcc 101 426-434. 

Kikuchi, O., T. Matsuoka, H. Sawahata, and O. Takahashi. 1994. Ab Initio Molecular Orbital Calculations Including Solvent Effects by Generalized Born Formula. Conformation of Zwitterionic Forms of Glycine, Alanine and Serine in Water. J. Mol. Struct. (Theochem) 305, 79-87. 

Ghosh, A. Rapp, C.S. Friesner, R.A., Generalized Born model based on a surface area formulation, J. Phys. Chem. B 1998,102, 10983-10990... 

Incorporation of Continuum Solvent Models Using a Generalized Born Approach... 

RR is similar to PCR in that the independent variables are transformed to their principal components (PCs). However, while PCR utilizes only a subset of the PCs, RR retains them all but downweighs them based on their eigenvalues. With PLS, a subset of the PCs is also used, but the PCs are selected by considering both the independent and dependent variables. Statistical theory suggests that RR is the best of the three methods, and this has been generally borne out in multiple comparative studies [30,36-38]. Thus, some of our published studies report RR results only. 

From the above, it would be expected that, except for metal-metal contacts, charging can be very sensitive to the method of contacting and to the surface condition (or state of contamination) of the material. This is, in general, borne out by the seeming contradiction of available data, which are based on widely different methods of contacting and degrees of cleanliness. 

Catti M. (1981). A generalized Born-Mayer parametrization of the lattice energy in orthorhombic ionic crystals. Acta Cryst., A37 72-76. 

Michel, J., Taylor, R.D., Essex, J.W. Efficient generalized born models for Monte Carlo simulations. J. Chem. Theory Comput. 2006, 2, 732-9. 

Ulmschneider, J.P., Ulmschneider, M.B., Di Nola, A. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Protein. Struct. Funct. Genet. 2007, 69, 297-308. 

Bashford, D. and Case, D. A. 2000. Generalized Born Models of Macromolecular Solvation Effects Annu. Rev. Phys. Chem., 51, 129. 

A problem of molecular-shaped SCRF models is the absence of an analytical solution for the reaction field. One line of development was the search for an approximate expression for the dielectric interaction energy of a solute in a molecular-shaped cavity, without the need for explicit calculation of the solvent polarization. These models were summarized as generalized Born (GB) approximations [22,30]. The most popular of these models... 

In the Generalized Born model [2-5], the solvent is described in a extremely simplified way and there is no mutual polarization between solute and solvent. The Onsager model [6] allows for solute-solvent polarization, but the description of the cavity and of the solvent is still very crude. 

O. Takahashi, H. Sawahata, Y. Ogawa and O. Kikuchi, Incorporation of solvent effects into ab initio molecular orbital calculations by the generalized Born formula. Formulation, parameterization, and applications, J. Mol. Struct. (THEOCHEM), 393 (1997) 141-150. 

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