The generalized Born/volume integral implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area
- PMID: 18307169
- DOI: 10.1002/jcc.20933
The generalized Born/volume integral implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area
Abstract
A new generalized Born model for estimating the free energy of hydration is presented. The new generalized Born/volume integral (GB/VI) estimates the free energy of hydration as a classical electrostatic energy plus a cavitation energy that is not based upon atomic surface area (SA) used in GB/SA hydration models but on a VI London dispersion energy estimated from quantities already calculated in the classical electrostatic energy. The (relatively few) GB/VI model parameters are fitted to experimental data, and parameterizations for two different atomic partial charge models are presented. Comparison of the calculated and experimental free energies of hydration for 560 small molecules (both neutral and charged) shows good agreement (r(2) = 0.94).
(c) 2008 Wiley Periodicals, Inc.
Similar articles
-
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.J Comput Chem. 2002 Apr 15;23(5):517-29. doi: 10.1002/jcc.10045. J Comput Chem. 2002. PMID: 11948578
-
Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.Proteins. 2004 Dec 1;57(4):645-50. doi: 10.1002/prot.20294. Proteins. 2004. PMID: 15481087
-
VBSM: a solvation model based on valence bond theory.J Phys Chem A. 2008 Dec 18;112(50):12761-8. doi: 10.1021/jp711655k. J Phys Chem A. 2008. PMID: 18671376
-
Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.J Phys Chem B. 2009 May 7;113(18):6378-96. doi: 10.1021/jp810292n. J Phys Chem B. 2009. PMID: 19366259
-
Unraveling water's entropic mysteries: a unified view of nonpolar, polar, and ionic hydration.Acc Chem Res. 2008 Aug;41(8):957-67. doi: 10.1021/ar7001478. Acc Chem Res. 2008. PMID: 18710198 Review.
Cited by
-
Molecular insight into isoform specific inhibition of PI3K-α and PKC-η with dietary agents through an ensemble pharmacophore and docking studies.Sci Rep. 2021 Jun 9;11(1):12150. doi: 10.1038/s41598-021-90287-3. Sci Rep. 2021. PMID: 34108504 Free PMC article.
-
Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.J Theor Comput Chem. 2014 May;13(3):1440006. doi: 10.1142/S0219633614400069. J Theor Comput Chem. 2014. PMID: 26236064 Free PMC article.
-
New Pyrazole-Clubbed Pyrimidine or Pyrazoline Hybrids as Anti-Methicillin-Resistant Staphylococcus aureus Agents: Design, Synthesis, In Vitro and In Vivo Evaluation, and Molecular Modeling Simulation.ACS Omega. 2023 Nov 9;8(46):44250-44264. doi: 10.1021/acsomega.3c06936. eCollection 2023 Nov 21. ACS Omega. 2023. PMID: 38027391 Free PMC article.
-
SARS-CoV-2 3CLpro mutations selected in a VSV-based system confer resistance to nirmatrelvir, ensitrelvir, and GC376.Sci Transl Med. 2023 Jan 11;15(678):eabq7360. doi: 10.1126/scitranslmed.abq7360. Epub 2023 Jan 11. Sci Transl Med. 2023. PMID: 36194133 Free PMC article.
-
Online chicken carcass volume estimation using depth imaging and 3-D reconstruction.Poult Sci. 2024 Dec;103(12):104232. doi: 10.1016/j.psj.2024.104232. Epub 2024 Aug 23. Poult Sci. 2024. PMID: 39284266 Free PMC article.
LinkOut - more resources
Full Text Sources
Other Literature Sources
