Implicit nonpolar solvent models

被引:208
作者
Tan, Chunhu [1 ]
Tan, Yu-Hong [1 ]
Luo, Ray [1 ]
机构
[1] Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA
关键词
D O I
10.1021/jp073399n
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We have systematically analyzed a new nonpolar solvent model that separates nonpolar solvation free energy into repulsive and attractive components. Our analysis shows that either molecular surfaces or volumes can be used to correlate with repulsive free energies of tested molecules in explicit solvent with correlation coefficients higher than 0.99. In addition, the attractive free energies in explicit solvent can also be reproduced with the new model with a correlation coefficient higher than 0.999. Given each component optimized, the new nonpolar solvent model is found to reproduce monomer nonpolar solvation free energies in explicit solvent very well. However, the overall accuracy of the nonpolar solvation free energies is lower than that of each component. In the more challenging dimer test cases, the agreement of the new model with explicit solvent is less impressive. Nevertheless, it is found that the new model works reasonably well for reproducing the relative nonpolar free energy landscapes near the global minimum of the dimer complexes.
引用
收藏
页码:12263 / 12274
页数:12
相关论文
共 78 条
[21]   Recent advances in the development and application of implicit solvent models in biomolecule simulations [J].
Feig, M ;
Brooks, CL .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2004, 14 (02) :217-224
[22]   EVALUATION OF THE DISPERSION CONTRIBUTION TO THE SOLVATION ENERGY - A SIMPLE COMPUTATIONAL MODEL IN THE CONTINUUM APPROXIMATION [J].
FLORIS, F ;
TOMASI, J .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1989, 10 (05) :616-627
[23]   DISPERSION AND REPULSION CONTRIBUTIONS TO THE SOLVATION ENERGY - REFINEMENTS TO A SIMPLE COMPUTATIONAL MODEL IN THE CONTINUUM APPROXIMATION [J].
FLORIS, FM ;
TOMASI, J ;
AHUIR, JLP .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1991, 12 (07) :784-791
[24]   EVALUATION OF DISPERSION REPULSION CONTRIBUTIONS TO THE SOLVATION ENERGY - CALIBRATION OF THE UNIFORM APPROXIMATION WITH THE AID OF RISM CALCULATIONS [J].
FLORIS, FM ;
TANI, A ;
TOMASI, J .
CHEMICAL PHYSICS, 1993, 169 (01) :11-20
[25]  
Fraczkiewicz R, 1998, J COMPUT CHEM, V19, P319, DOI 10.1002/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.0.CO
[26]  
2-W
[27]   AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling [J].
Gallicchio, E ;
Levy, RM .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (04) :479-499
[28]   The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators [J].
Gallicchio, E ;
Zhang, LY ;
Levy, RM .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2002, 23 (05) :517-529
[29]   Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation [J].
Gallicchio, E ;
Kubo, MM ;
Levy, RM .
JOURNAL OF PHYSICAL CHEMISTRY B, 2000, 104 (26) :6271-6285
[30]   A GAUSSIAN DESCRIPTION OF MOLECULAR SHAPE [J].
GRANT, JA ;
PICKUP, BT .
JOURNAL OF PHYSICAL CHEMISTRY, 1995, 99 (11) :3503-3510