Literature DB >> 21495738

Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions.

Maria M Reif1, Philippe H Hünenberger.   

Abstract

The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions (finite or periodic system, system or box size) and treatment of electrostatic interactions (Coulombic, lattice-sum, or cutoff-based) used during these simulations. However, as shown by Kastenholz and Hünenberger [J. Chem. Phys. 124, 224501 (2006)], correction terms can be derived for the effects of: (A) an incorrect solvent polarization around the ion and an incomplete or/and inexact interaction of the ion with the polarized solvent due to the use of an approximate (not strictly Coulombic) electrostatic scheme; (B) the finite-size or artificial periodicity of the simulated system; (C) an improper summation scheme to evaluate the potential at the ion site, and the possible presence of a polarized air-liquid interface or of a constraint of vanishing average electrostatic potential in the simulated system; and (D) an inaccurate dielectric permittivity of the employed solvent model. Comparison with standard experimental data also requires the inclusion of appropriate cavity-formation and standard-state correction terms. In the present study, this correction scheme is extended by: (i) providing simple approximate analytical expressions (empirically-fitted) for the correction terms that were evaluated numerically in the above scheme (continuum-electrostatics calculations); (ii) providing correction terms for derivative thermodynamic single-ion solvation properties (and corresponding partial molar variables in solution), namely, the enthalpy, entropy, isobaric heat capacity, volume, isothermal compressibility, and isobaric expansivity (including appropriate standard-state correction terms). The ability of the correction scheme to produce methodology-independent single-ion solvation free energies based on atomistic simulations is tested in the case of Na(+) hydration, and the nature and magnitude of the correction terms for derivative thermodynamic properties is assessed numerically.

Mesh:

Substances:

Year:  2011        PMID: 21495738     DOI: 10.1063/1.3567020

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  13 in total

1.  Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

Authors:  Gabriel J Rocklin; David L Mobley; Ken A Dill; Philippe H Hünenberger
Journal:  J Chem Phys       Date:  2013-11-14       Impact factor: 3.488

2.  Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments.

Authors:  Anita de Ruiter; Bojan Zagrovic
Journal:  Nucleic Acids Res       Date:  2014-12-30       Impact factor: 16.971

3.  Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.

Authors:  Martin A Olsson; Alfonso T García-Sosa; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2017-09-06       Impact factor: 3.686

4.  Energetics and mechanism of anion permeation across formate-nitrite transporters.

Authors:  Kalina Atkovska; Jochen S Hub
Journal:  Sci Rep       Date:  2017-09-20       Impact factor: 4.379

5.  SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.

Authors:  Martin Amezcua; Léa El Khoury; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2021-01-04       Impact factor: 3.686

6.  Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization.

Authors:  Maria M Reif; Chris Oostenbrink
Journal:  Theor Chem Acc       Date:  2015-01-10       Impact factor: 1.702

7.  Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

Authors:  Maria M Reif; Chris Oostenbrink
Journal:  J Comput Chem       Date:  2013-11-19       Impact factor: 3.376

8.  Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions.

Authors:  Qinghua Liao; Anna Pabis; Birgit Strodel; Shina Caroline Lynn Kamerlin
Journal:  J Phys Chem Lett       Date:  2017-10-23       Impact factor: 6.475

9.  Optimization of Protein-Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method.

Authors:  Alexander D Wade; David J Huggins
Journal:  J Chem Theory Comput       Date:  2019-10-23       Impact factor: 6.006

10.  Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.

Authors:  Maria Lopez-Redondo; Shujie Fan; Akiko Koide; Shohei Koide; Oliver Beckstein; David L Stokes
Journal:  J Gen Physiol       Date:  2021-07-13       Impact factor: 4.086

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.