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The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
Abstract
Atomic Born radii (α) are used in the generalized Born (GB) equation to calculate approximations to the electrical polarization component ( G pol ) of solvation free energy. We present here a simple analytical formula for calculating Born radii rapidly and with useful accuracy. The new function is based on an atomic pairwise r ij -4 treatment and contains several empirically determined parameters that were established by optimization against a data set of >10 000 accurate Born radii computed numerically using the Poisson equation on a diverse group of organic molecules, molecular complexes, oligopeptides, and a small protein. Coupling this new Born radius calculation with the previously described GB/SA solvation treatment provides a fully analytical solvation model that is computationally efficient in comparison with traditional molecular solvent models and also affords first and second derivatives. Tests with the GB/SA model and Born radii calculated with our new analytical function and with the accurate but more time-consuming Poisson−Boltzmann methods indicate that comparable free energies of solventlike dielectric polarization can be obtained using either method and that the resulting GB/SA solvation free energies compare well with the experimental results on small molecules in water.
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Cites
Hermann, R. B. (1972) · The Journal of Physical Chemistry · doi:10.1021/j100663a023 · Cited by 700
Cited by
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Guedes, I. A., Pereira, F. S. S., & Dardenne, L. E. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.01089 · Cited by 331
A model binding site for testing scoring functions in molecular docking.
Wei, B. Q., Baase, W. A., Weaver, L. H., Matthews, B. W., & Shoichet, B. K. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00777-5 · Cited by 237
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Water Formation on Pt and Pt‐based Alloys: A Theoretical Description of a Catalytic Reaction
Jacob, T., & Goddard, W. A. (2006) · ChemPhysChem · doi:10.1002/cphc.200500613 · Cited by 115
Yang, Y., Lightstone, F. C., & Wong, S. E. (2013) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2013.749853 · Cited by 65
Eildal, J. N. N., Hultqvist, G., Balle, T., Stuhr-Hansen, N., Padrah, S., Gianni, S., Strømgaard, K., & Jemth, P. (2013) · Journal of the American Chemical Society · doi:10.1021/ja402875h · Cited by 61
Elder, L. H., & Onufriev, A. V. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c02263 · Cited by 2
Metadata
- Authors
- Qiu, D., Shenkin, P. S., Hollinger, F. P., & Still, W. C.
- Venue
- The Journal of Physical Chemistry A
- Publisher
- American Chemical Society (ACS)
- Published
- 1997-04-01
- Volume
- 101
- Issue
- 16
- Pages
- 3005-3014
- ISSN
- 1089-5639 (ISSN-L)
- 1520-5215
- OpenAlex
- W2064747164
- Cited by
- 962
- References
- 1
- FWCI
- 12.28
- Type
- journal article
- Language
- en
- Open access
- closed
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