Skip to main content

News about Scitation

In December 2016 Scitation will launch with a new design, enhanced navigation and a much improved user experience.

To ensure a smooth transition, from today, we are temporarily stopping new account registration and single article purchases. If you already have an account you can continue to use the site as normal.

For help or more information please visit our FAQs.

banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.
1. B. Roux and T. Simonson, “Implicit solvent models,” Biophys. Chem. 78, 120 (1999).
2. K. A. Sharp and B. Honig, “Electrostatic interactions in macromolecules: Theory and applications,” Annu. Rev. Biophys. Biophys. Chem. 19, 301332 (1990).
3. M. E. Davis and J. A. McCammon, “Electrostatics in biomolecular structure and dynamics,” Chem. Rev. 90, 509521 (1990).
4. J. Tomasi and M. Persico, “Molecular interactions in solution: An overview of methods based on continuous descriptions of the solvent,” Chem. Rev. 94, 20272094 (1994).
5. J. G. Kirkwood, “Theory of solutions of molecules containing widely separated charges with special application to zwitterions,” J. Chem. Phys. 2, 351 (1934).
6. W. M. Latimer, K. S. Pitzer, and C. M. Slansky, “The free energy of hydration of gaseous ions, and the absolute potential of the normal calomel electrode,” J. Chem. Phys. 7, 108112 (1939).
7. A. A. Kornyshev and G. Sutmann, “Nonlocal dielectric saturation in liquid water,” Phys. Rev. Lett. 79, 34353438 (1997).
8. A. Hildebrandt, R. Blossey, S. Rjasanow, O. Kohlbacher, and H.-P. Lenhof, “Novel formulation of nonlocal electrostatics,” Phys. Rev. Lett. 93, 108104 (2004).
9. R. C. Rizzo, T. Aynechi, D. A. Case, and I. D. Kuntz, “Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial charge models and optimization of nonpolar contributions,” J. Chem. Theory Comput. 2, 128139 (2006).
10. A. Abrashkin, D. Andelman, and H. Orland, “Dipolar Poisson–Boltzmann equation: Ions and dipoles close to charge interfaces,” Phys. Rev. Lett. 99, 077801 (2007).
11. H. Gong and K. F. Freed, “Langevin–Debye model for nonlinear electrostatic screening of solvated ions,” Phys. Rev. Lett. 102, 057603 (2009).
12. Z. Guo, B. Li, J. Dzubiella, L.-T. Cheng, J. A. McCammon, and J. Che, “Evaluation of hydration free energy by level-set variational implicit-solvent model with Coulomb-field approximation,” J. Chem. Theory Comput. 9, 17781787 (2013).
13. S. Zhou, L.-T. Cheng, J. Dzubiella, B. Li, and J. A. McCammon, “Variational implicit solvation with Poisson–Boltzmann theory,” J. Chem. Theory Comput. 10, 14541467 (2014).
14. E. Gallicchio, K. Paris, and R. M. Levy, “The AGBNP2 implicit solvation model,” J. Chem. Theory Comput. 5, 25442564 (2009).
15. A. A. Rashin and B. Honig, “Reevaluation of the Born model of ion hydration,” J. Phys. Chem. 89, 55885593 (1985).
16. H. S. Ashbaugh, “Convergence of molecular and macroscopic continuum descriptions of ion hydration,” J. Phys. Chem. B 104(31), 72357238 (2000).
17. R. M. Lynden-Bell, J. C. Rasaiah, and J. P. Noworyta, “Using simulation to study solvation in water,” Pure Appl. Chem. 73, 17211731 (2001).
18. S. Rajamani, T. Ghosh, and S. Garde, “Size dependent ion hydration, its asymmetry, and convergence to macroscopic behavior,” J. Chem. Phys. 120, 4457 (2004).
19. A. Grossfield, “Dependence of ion hydration on the sign of the ion's charge,” J. Chem. Phys. 122, 024506 (2005).
20. A. Mukhopadhyay, A. T. Fenley, I. S. Tolokh, and A. V. Onufriev, “Charge hydration asymmetry: The basic principle and how to use it to test and improve water models,” J. Phys. Chem. B 116, 97769783 (2012).
21. J. P. Bardhan, P. Jungwirth, and L. Makowski, “Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies,” J. Chem. Phys. 137, 124101 (2012).
22. N. M. Green, “Avidin,” Adv. Prot. Chem. 29, 85133 (1975).
23. G. Hummer, L. R. Pratt, and A. E. García, “Free energy of ionic hydration,” J. Phys. Chem. 100, 12061215 (1996).
24. M. V. Fedorov and A. A. Kornyshev, “Unravelling the solvent response to neutral and charged solutes,” Mol. Phys. 105, 116 (2007).
25. A. Warshel and M. Levitt, “Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme,” J. Mol. Biol. 103, 227249 (1976).
26. C. Azuara, H. Orland, M. Bon, P. Koehl, and M. Delarue, “Incorporating dipolar solvents with variable density in Poisson–Boltzmann electrostatics,” Biophys. J. 95, 55875605 (2008).
27. H. E. Alper and R. M. Levy, “Field strength dependence of dielectric saturation in liquid water,” J. Phys. Chem. 94, 84018403 (1990).
28. E. O. Purisima and T. Sulea, “Restoring charge asymmetry in continuum electrostatic calculations of hydration free energies,” J. Phys. Chem. B 113, 82068209 (2009).
29. A. A. Kornyshev and G. Sutmann, “Nonlocal nonlinear static dielectric response of polar liquids,” J. Electroanal. Chem. 450, 143156 (1998).
30. L. Sandberg and O. Edholm, “Nonlinear response effects in continuum models of the hydration of ions,” J. Chem. Phys. 116, 29362944 (2002).
31. A. K. Jha and K. F. Freed, “Solvation effect on conformations of 1,2:dimethoxyethane: Charge-dependent nonlinear response in implicit solvent models,” J. Chem. Phys. 128, 034501 (2008).
32. H. Gong, G. Hocky, and K. F. Freed, “Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model,” Proc. Natl. Acad. Sci. U.S.A. 105, 1114611151 (2008).
33. L. Hu and G.-W. Wei, “Nonlinear Poisson equation for heterogeneous media,” Biophys. J. 103, 758766 (2012).
34. D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 24052414 (2008).
35. C. R. Corbeil, T. Sulea, and E. O. Purisima, “Rapid prediction of solvation free energy. 2. The first-shell hydration (FiSH) continuum model,” J. Chem. Theory Comput. 6, 16221637 (2010).
36. A. Mukhopadhyay, B. H. Aguilar, I. S. Tolokh, and A. V. Onufriev, “Introducing charge hydration asymmetry into the Generalized Born model,” J. Chem. Theory Comput. 10, 17881794 (2014).
37. J. D. Jackson, Classical Electrodynamics, 3rd ed. (Wiley, 1998).
38. B. Lin, K.-Y. Wong, C. Hu, H. Kokubo, and B. M. Pettitt, “Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions,” J. Phys. Chem. Lett. 2, 16261632 (2011).
39. D. Boda, M. Valiskó, D. Henderson, D. Gillespie, B. Eisenberg, and M. K. Gilson, “Ions and inhibitors in the binding site of HIV protease: Comparison of Monte Carlo simulations and the linearized Poisson–Boltzmann theory,” Biophys. J. 96, 12931306 (2009).
40. I.-L. Chern, J.-G. Liu, and W.-C. Wang, “Accurate evaluation of electrostatics for macromolecules in solution,” Methods Appl. Anal. 10, 309328 (2003).
41. M. Holst, J. A. McCammon, Z. Yu, Y. C. Zhou, and Y. Zhu, “Adaptive finite element modeling techniques for the Poisson–Boltzmann equation,” Commun. Comput. Phys. 11, 179214 (2012).
42. J. P. Bardhan, “Biomolecular electrostatics—I want your solvation (model),” Comput. Sci. Discovery 5, 013001 (2012).
43. F. J. Rizzo, “An integral equation approach to boundary value problems of classical elastostatics,” Q. Appl. Math. 25, 8395 (1967).
44. P. B. Shaw, “Theory of the Poisson Green's-function for discontinuous dielectric media with an application to protein biophysics,” Phys. Rev. A 32(4), 24762487 (1985).
45. A. H. Juffer, E. F. F. Botta, B. A. M. van Keulen, A. van der Ploeg, and H. J. C. Berendsen, “The electric potential of a macromolecule in a solvent: A fundamental approach,” J. Comput. Phys. 97(1), 144171 (1991).
46. J. P. Bardhan, “Numerical solution of boundary-integral equations for molecular electrostatics,” J. Chem. Phys. 130, 094102 (2009).
47. M. D. Altman, J. P. Bardhan, J. K. White, and B. Tidor, “An efficient and accurate surface formulation for biomolecule electrostatics in non-ionic solution,” in Proceedings of the Engineering in Medicine and Biology Conference (EMBC), 2005.
48. S. Miertus, E. Scrocco, and J. Tomasi, “Electrostatic interactions of a solute with a continuum – A direct utilization of ab initio molecular potentials for the prevision of solvent effects,” Chem. Phys. 55(1), 117129 (1981).
49. K. A. Sharp and B. Honig, “Calculating total electrostatic energies with the nonlinear Poisson–Boltzmann equation,” J. Phys. Chem. 94(19), 76847692 (1990).
50. H.-X. Zhou, “Macromolecular electrostatic energy within the nonlinear Poisson–Boltzmann equation,” J. Chem. Phys. 100, 31523162 (1994).
51. J. G. Kirkwood, “On the theory of strong electrolyte solutions,” J. Chem. Phys. 2, 767772 (1934).
52. Yu. I. Kharkats, A. A. Kornyshev, and M. A. Vorotyntsev, “Electrostatic models in the theory of solutions,” J. Chem. Soc. Faraday Trans. 2 72, 361371 (1976).
53. J. P. Bardhan, “Interpreting the Coulomb-field approximation for Generalized-Born electrostatics using boundary-integral equation theory,” J. Chem. Phys. 129, 144105 (2008).
54. E. Harder and B. Roux, “On the origin of the electrostatic potential difference at the liquid-vapor interface,” J. Chem. Phys. 129, 234706 (2008).
55. S. M. Kathmann, I.-F. W. Kuo, C. J. Mundy, and G. K. Schenter, “Understanding the surface potential of water,” J. Phys. Chem. B 115, 43694377 (2011).
56. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, “CHARMM: A program for macromolecular energy, minimization, and dynamics calculations,” J. Comput. Chem. 4, 187217 (1983).
57. M. Nina, D. Beglov, and B. Roux, “Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations,” J. Phys. Chem. B 101, 52395248 (1997).
58. D. Sitkoff, K. A. Sharp, and B. Honig, “Accurate calculation of hydration free energies using macroscopic solvent models,” J. Phys. Chem. B 98, 19781988 (1994).
59. S. Mizzi, R. W. Barber, D. R. Emerson, J. M. Reese, and S. K. Stefanov, “A phenomenological and extended continuum approach for modelling non-equilibrium flows,” Contin. Mech. Thermodyn. 19, 273283 (2007).
60. H. Brenner, “Beyond the no-slip boundary condition,” Phys. Rev. E 84(4), 046309 (2011).
61. J. P. Bardhan and M. G. Knepley, “Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions,” J. Chem. Phys. 135, 124107 (2011).
62. J. C. Maxwell, “On stresses in rarefied gases arising from inequalities of temperature,” Proc. R. Soc. London 27, 304308 (1878).
63. M. von Smolan Smoluchowski, “Über wärmeleitung in verdünnten gasen,” Ann. Phys. 300(1), 101130 (1898).
64. I. L'Heureux and A. D. Fowler, “Dynamical model of oscillatory zoning in plagioclase with nonlinear partition relation,” Geophys. Res. Lett. 23, 1720, doi:10.1029/95GL03327 (1996).
65. P. Macklin and J. Lowengrub, “Evolving interfaces via gradients of geometry-dependent interior Poisson problems: Application to tumor growth,” J. Comput. Phys. 203, 191220 (2005).
66. T.-H. Fan and A. G. Fedorov, “Electrohydrodynamics and surface force analysis in AFM imaging of a charged, deformable biological membrane in a dilute electrolyte solution,” Langmuir 19, 1093010939 (2003).
67. G. Yossifon, I. Frankel, and T. Miloh, “Symmetry breaking in induced-charge electro-osmosis over polarizable spheroids,” Phys. Fluids 19, 068105 (2007).
68. D. Beglov and B. Roux, “Solvation of complex molecules in a polar liquid: An integral equation theory,” J. Chem. Phys. 104(21), 86788689 (1996).
69. J. P. Bardhan, “Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins,” J. Chem. Phys. 135, 104113 (2011).
70. J. P. Bardhan and A. Hildebrandt, “A fast solver for nonlocal electrostatic theory in biomolecular science and engineering,” in Proceedings of the IEEE/ACM Design Automation Conference (DAC), 2011.
71. J. P. Bardhan, “Gradient models in molecular biophysics: Progress, challenges, opportunities,” J. Mech. Behavior Mater. 22, 169184 (2013).
72. See supplementary material at for figures comparing NLBC and MD calculations for the Mobley test set.34 The source code (MATLAB) and surface discretizations for running the nonlinear boundary-condition calculations, data files, parameters, and scripts for preparing and running the MD calculations of titratable residues, as well as source code to generate the figures, are freely and publicly available online at [Supplementary Material]

Data & Media loading...


Article metrics loading...



We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B , 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.


Full text loading...


Access Key

  • FFree Content
  • OAOpen Access Content
  • SSubscribed Content
  • TFree Trial Content
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd