Continuum polarizable force field within the Poisson-Boltzmann framework.
We have developed and tested a complete set of nonbonded parameters for a continuum polarizable force field. Our analysis shows that the new continuum polarizable model is consistent with B3LYP/cc-pVTZ in modeling electronic response upon variation of dielectric environment. Comparison with experiment also shows that the new continuum polarizable model is reasonable, with accuracy similar to that of B3LYP/cc-pVTZ in reproduction of dipole moments of selected organic molecules in the gas phase. We have further tested the validity to interchange the Amber van der Waals parameters between the explicit and continuum polarizable force fields with a series of dimers. It can be found that the continuum polarizable model agrees well with MP2/cc-pVTZ, with deviations in dimer binding energies less than 0.9 kcal/mol in the aqueous dielectric environment. Finally, we have optimized atomic cavity radii with respect to experimental solvation free energies of 177 training molecules. To validate the optimized cavity radii, we have tested these parameters against 176 test molecules. It is found that the optimized Poisson-Boltzmann atomic cavity radii transfer well from the training set to the test set, with an overall root-mean-square deviation of 1.30 kcal/mol, an unsigned average error of 1.07 kcal/mol, and a correlation coefficient of 92% for all 353 molecules in both the training and test sets. Given the development documented here, the next natural step is the construction of a full protein/nucleic acid force field within the new continuum polarization framework.
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.
Yu-Hong
YH
Tan
Chunhu
C
Tan
Junmei
J
Wang
Ray
R
Luo
D002138:Calibration; D003198:Computer Simulation; D019281:Dimerization; D005740:Gases / Q000737:chemistry; D008956:Models, Chemical; D012995:Solubility; D013816:Thermodynamics
D005740:Gases