Differential geometry (DG) based solvation models have shown their great success in solvation analysis by avoiding the use of ad hoc surface definitions, coupling the polar and nonpolar free energies, and generating solvent-solute boundary in a physically self-consistent fashion. Parameter optimization is a key factor for their accuracy, predictive ability of solvation free energies, and other applications. Recently, a series of efforts have been made to improve the parameterization of these new implicit solvent models. In thiswork, we aim at studying the role of dispersion attraction in the parameterization of our DG based solvation models. To this end, we first investigate the necessity of van derWaals (vdW) dispersion interactions in the model and then carry out systematic parameterization for the model in the absence of electrostatic interactions. In particular, we explore how the changes in Lennard-Jones (L-J) potential expression, its decomposition scheme, and choices of some fixed parameter values affect the optimal values of other parameters as well as the overall modeling error. Our study on nonpolar solvation analysis offers insights into the parameterization of nonpolar components for the full DG based models by eliminating uncertainties from the electrostatic polar component. Therefore, it can be regarded as a step towards better parameterization for the full DG based model.
@article{bwmeta1.element.doi-10_1515_mlbmb-2015-0012,
author = {Zhan Chen},
title = {Role of Dispersion Attraction in Differential Geometry Based Nonpolar Solvation Models},
journal = {Molecular Based Mathematical Biology},
volume = {3},
year = {2015},
language = {en},
url = {http://dml.mathdoc.fr/item/bwmeta1.element.doi-10_1515_mlbmb-2015-0012}
}
Zhan Chen. Role of Dispersion Attraction in Differential Geometry Based Nonpolar Solvation Models. Molecular Based Mathematical Biology, Tome 3 (2015) . http://gdmltest.u-ga.fr/item/bwmeta1.element.doi-10_1515_mlbmb-2015-0012/
[1] E. L. Ratkova, G. N. Chuev, V. P. Sergiievskyi, and M. V. Fedorov. An accurate prediction of hydration free energies by combination of molecular integral equations theory with structural descriptors. J. Phys. Chem. B, 114(37):12068–2079, 2010. [Crossref]
[2] D. S. Palmer, V. P. Sergiievskyi, F. Jensen, and M. V. Fedorov. Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model. J. Chem. Phys., 133(044104), 2010.
[3] B. Husowitz and V. Talanquer. Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: A density functional approach. The Journal of Chemical Physics, 126(5):054508, 2007. [WoS][Crossref]
[4] M. R. Reddy, U. C. Singh, and M. D. Erion. Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies. Journal of Computational Chemistry, 28(2):491–4, 2007. [Crossref][WoS]
[5] Aleksandr V. Marenich, Christopher J. Cramer, and Donald G. Truhlar. Perspective on foundations of solvation modeling: The electrostatic contribution to the free energy of solvation. Journal of Chemical Theory and Computation, 4(6):877–887, 2008. [WoS]
[6] S. C. L. Kamerlin, M. Haranczyk, and A. Warshel. Progress in ab initio qm/mm free-energy simulations of electrostatic energies in proteins: Accelerated qm/mm studies of pk(a), redox reactions and solvation free energies. Journal of Phys. Chem. B, 113:1253–1272, 2009.
[7] B. Roux and T. Simonson. Implicit solvent models. Biophysical Chemistry, 78(1-2):1–20, 1999. [Crossref]
[8] A.Warshel and A. Papazyan. Electrostatic effects inmacromolecules: fundamental concepts and practical modeling. Current Opinion in Structural Biology, 8(2):211–7, 1998. [Crossref]
[9] T. Simonson. Macromolecular electrostatics: continuum models and their growing pains. Current Opinion in Structural Biology, 11(2):243–252, 2001. [Crossref]
[10] K. A. Sharp and B. Honig. Electrostatic interactions in macromolecules - theory and applications. Annual Review of Biophysics and Biophysical Chemistry, 19:301–332, 1990. [Crossref]
[11] J. W. Ponder and D. A. Case. Force fields for protein simulations. Advances in Protein Chemistry, 66:27–85, 2003.
[12] N. A. Baker. Biomolecular applications of Poisson-Boltzmann methods. In K. B. Lipkowitz, R. Larter, and T. R. Cundari, editors, Reviews in Computational Chemistry, volume 21. John Wiley and Sons, Hoboken, NJ, 2005. [WoS]
[13] N. A. Baker, D. Bashford, and D. A. Case. Implicit solvent electrostatics in biomolecular simulation. In B. Leimkuhler, C. Chipot, R. Elber, A. Laaksonen, A. Mark, T. Schlick, C. Schutte, and R. Skeel, editors, New Algorithms for Macromolecular Simulation. Springer, 2006.
[14] M. E. Davis and J. A. McCammon. Electrostatics in biomolecular structure and dynamics. Chemical Reviews, 94:509–21, 1990. [Crossref]
[15] B. Honig and A. Nicholls. Classical electrostatics in biology and chemistry. Science, 268(5214):1144–9, 1995.
[16] R. Jinnouchi and A. B. Anderson. Electronic structure calculations of liquid-solid interfaces: Combination of density functional theory and modified Poisson-Boltzmann theory. PHYSICAL REVIEW B, 77(245417), 2008. [Crossref]
[17] N. A. Baker. Poisson-Boltzmann methods for biomolecular electrostatics. Methods in Enzymology, 383:94–118, 2004.
[18] M. Feig and C. L. Brooks III. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol., 14:217 – 224, 2004. [Crossref]
[19] N. A. Baker. Improving implicit solvent simulations: a Poisson-centric view. Current Opinion in Structural Biology, 15(2):137– 43, 2005. [Crossref]
[20] F. Dong, B.Olsen, and N. A. Baker. Computational methods for biomolecular electrostatics. Methods in Cell Biology, 84:843– 70, 2008. [Crossref][WoS]
[21] B. Lee and F. M. Richards. The interpretation of protein structures: estimation of static accessibility. J Mol Biol, 55(3):379– 400, 1971. [Crossref]
[22] F. M. Richards. Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering, 6(1):151– 176, 1977. [Crossref]
[23] M. L. Connolly. Analytical molecular surface calculation. Journal of Applied Crystallography, 16(5):548–558, 1983. [Crossref]
[24] F. Dong, M. Vijaykumar, and H. X. Zhou. Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophysical Journal, 85(1):49–60, 2003. [Crossref]
[25] F. Dong and H. X. Zhou. Electrostatic contribution to the binding stability of protein-protein complexes. Proteins, 65(1):87– 102, 2006. [Crossref]
[26] M. Nina, W. Im, and B. Roux. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophysical Chemistry, 78(1-2):89–96, 1999. [Crossref]
[27] J. M. J. Swanson, J. Mongan, and J. A. McCammon. Limitations of atom-centered dielectric functions in implicit solvent models. Journal of Physical Chemistry B, 109(31):14769–72, 2005. [Crossref]
[28] G. W. Wei. Differential geometry based multiscale models. Bulletin of Mathematical Biology, 72:1562 – 1622, 2010. [WoS] | Zbl 1198.92001
[29] Z. Chen, N. A. Baker, and G. W. Wei. Differential geometry based solvation models I: Eulerian formulation. J. Comput. Phys., 229:8231–8258, 2010. | Zbl 1229.92030
[30] Z. Chen, N. A. Baker, and G.W. Wei. Differential geometry based solvation models II: Lagrangian formulation. J.Math. Biol., 63:1139–1200, 2010. | Zbl 1284.92025
[31] Z. Chen and G.W. Wei. Differential geometry based solvation models III: Quantumformulation. J. Chem. Phys., 135:1941108, 2011. [WoS]
[32] Zhan Chen, Shan Zhao, Jaehun Chun, Dennis G Thomas, Nathan A Baker, Peter W Bates, and GW Wei. Variational approach for nonpolar solvation analysis. The Journal of chemical physics, 137(8):084101, 2012. [WoS]
[33] J. Dzubiella, J. M. J. Swanson, and J. A. McCammon. Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Physical Review Letters, 96:087802, 2006.
[34] L. T. Cheng, Joachim Dzubiella, Andrew J. McCammon, and B. Li. Application of the level-set method to the implicit solvation of nonpolar molecules. Journal of Chemical Physics, 127(8), 2007. [Crossref][WoS]
[35] Dennis G Thomas, Jaehun Chun, Zhan Chen, Guowei Wei, and Nathan A Baker. Parameterization of a geometric flow implicit solvation model. Journal of computational chemistry, 34(8):687–695, 2013. [WoS]
[36] Michael D Daily, Jaehun Chun, Alejandro Heredia-Langner, Guowei Wei, and Nathan A Baker. Origin of parameter degeneracy andmolecular shape relationships in geometric-flowcalculations of solvation free energies. The Journal of chemical physics, 139(20):204108, 2013.
[37] G. W. Wang, B. Wei. Parameter optimization in differential geometry based solvation models. Cornell University Library, page arXiv:1508.00642, 2015.
[38] R. M. Levy, L. Y. Zhang, E. Gallicchio, and A. K. Felts. On the nonpolar hydration free energy of proteins: surface area and continuumsolvent models for the solute-solvent interaction energy. Journal of theAmerican Chemical Society, 125(31):9523– 9530, 2003.
[39] J. A. Wagoner and N. A. Baker. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proceedings of the National Academy of Sciences of the United States of America, 103(22):8331–6, 2006. [WoS]
[40] W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J Am Chem Soc, 118:11225–11236, 1996.
[41] S. Cabani, P. Gianni, V Mollica, and L Lepori. Group Contributions to the Thermodynamic Properties of Non-Ionic Organic Solutes in Dilute Aqueous Solution. Journal of Solution Chemistry, 10(8):563–595, 1981.
[42] E. Gallicchio, M. M. Kubo, and R. M. Levy. Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation. Journal of Physical Chemistry B, 104(26):6271–85, 2000. [Crossref]