Journal ArticleDOI
Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field.
Guillaume Lamoureux,Benoît Roux +1 more
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A polarizable potential function for the hydration of alkali and halide ions is developed on the basis of the recent SWM4-DP water model, which corresponds to an absolute scale in which the intrinsic hydration free energy of the proton is -247 kcal/mol.Abstract:
A polarizable potential function for the hydration of alkali and halide ions is developed on the basis of the recent SWM4-DP water model [Lamoureux, G.; MacKerell, A. D., Jr.; Roux, B. J. Chem. Phys. 2003, 119, 5185]. Induced polarization is incorporated using classical Drude oscillators that are treated as auxiliary dynamical degrees of freedom. The ions are represented as polarizable Lennard-Jones centers, whose parameters are optimized to reproduce the binding energies of gas-phase monohydrates and the hydration free energies in the bulk liquid. Systematic exploration of the parameters shows that the monohydrate binding energies can be consistent with a unique hydration free energy scale if the computed hydration free energies incorporate the contribution from the air/water interfacial electrostatic potential (-540 mV for SWM4-DP). The final model, which can satisfyingly reproduce both gas and bulk-phase properties, corresponds to an absolute scale in which the intrinsic hydration free energy of the proton is -247 kcal/mol.read more
Citations
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Journal ArticleDOI
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
InSuk Joung,Thomas E. Cheatham +1 more
TL;DR: These efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework are described, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models.
Journal ArticleDOI
Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton.
TL;DR: Using the same set of ions that was recently used to develop the SM6 continuum solvation model, SM6 retains its previously determined high accuracy; indeed, in most cases the mean unsigned error improves when it is tested against the more accurate reference data.
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Single-Ion Solvation Free Energies and the Normal Hydrogen Electrode Potential in Methanol, Acetonitrile, and Dimethyl Sulfoxide
TL;DR: In this paper, the relative solvation free energies of ions and ion−solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies, solution-phase reduction potentials and acid dissociation constants.
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Rapid parameterization of small molecules using the Force Field Toolkit.
TL;DR: The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design.
Journal ArticleDOI
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.
TL;DR: The classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs, is reviewed.
References
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Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
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