Response to “Comment on ‘<i>Ab initio</i> molecular dynamics calculation of ion hydration free energies’  [J. Chem. Phys. <b>133</b>, 047103 (2010)]”

Rempe, Susan B.; Leung, Kevin

doi:10.1063/1.3456167

Cited by 9 publications

(9 citation statements)

References 17 publications

(20 reference statements)

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“…A similar QCT analysis for Li + (aq) arrives at a value of −121.1 kcal/mol for μ Li + (ex) (see the Supporting Information). Then the QCT prediction for the neutral combination, μ F – (ex) + μ Li + (ex) = −227.5 kcal/mol, is in fair agreement with experimental tabulations, which range between −229 and −232 kcal/mol. ,,, Issues of a surface potential are not involved in this comparison. , …”

Section: Resultssupporting

confidence: 63%

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F^–) Anion Hydration

et al. 2018

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Accurate predictions of the hydration free energy for anions typically have been more challenging than for cations. Hydrogen bond donation to the anion in hydrated clusters such as F(H 2 O) n − can lead to delicate structures. Consequently, the energy landscape contains many local minima, even for small clusters, and these minima present a challenge for computational optimization. Utilization of cluster experimental results for the free energies of gas phase clusters shows that, even though anharmonic effects are interesting, they need not be troublesome magnitudes for careful applications of quasi-chemical theory to ion hydration. Energy-optimized cluster structures for anions can leave the central ion highly exposed and application of implicit solvation models to these structures can incur more serious errors than for metal cations. Utilizing cluster structures sampled from ab initio molecular dynamics simulations substantially fixes those issues.

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Section: Resultssupporting

confidence: 63%

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F^–) Anion Hydration

et al. 2018

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“…33), which underlies the form of the correction term adopted in the present study. Interestingly, a similar debate is arising at present, in the quantum-mechanical community [137][138][139][140][141][142][143][144] (see also Refs. 145 and 146 at the classical level), the same issues being discussed anew, and the same conclusions being progressively reached.…”

Section: Discussionmentioning

confidence: 82%

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

Rocklin¹,

Mobley²,

Dill³

et al. 2013

The Journal of Chemical Physics

222

368

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The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

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“…As mentioned above, the too negative values of the calculated ion-pair hydration enthalpies and aqueous partial molar entropies are probably due at least in part to the use of an implicit-polarization model for the ion–solvent interactions. The application of explicitly polarizable models , or even of quantum-mechanical models (e.g., Car–Parrinello ,− or quantum-mechanics molecular mechanics − ) would probably enable a more accurate representation of the enthalpy–entropy partitioning. Note in this respect that the present work considers relatively large monovalent ions, for which the electronic polarization of the solvent and the partially covalent character of ion–solvent interactions are expected to have limited effects.…”

Section: Discussionmentioning

confidence: 99%

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations

Dahlgren

Reif

Hünenberger

et al. 2012

J. Chem. Theory Comput.

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The raw ionic solvation free energies calculated on the basis of atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [Kastenholz, M. A.; Hünenberger, P. H. J. Chem. Phys.2006, 124, 224501 and Reif, M. M.; Hünenberger, P. H. J. Chem. Phys.2011, 134, 144104], the application of an appropriate correction scheme allows for a conversion of the methodology-dependent raw data into methodology-independent results. In this work, methodology-independent derivative thermodynamic hydration and aqueous partial molar properties are calculated for the Na(+) and Cl(-) ions at P° = 1 bar and T(-) = 298.15 K, based on the SPC water model and on ion-solvent Lennard-Jones interaction coefficients previously reoptimized against experimental hydration free energies. The hydration parameters considered are the hydration free energy and enthalpy. The aqueous partial molar parameters considered are the partial molar entropy, volume, heat capacity, volume-compressibility, and volume-expansivity. Two alternative calculation methods are employed to access these properties. Method I relies on the difference in average volume and energy between two aqueous systems involving the same number of water molecules, either in the absence or in the presence of the ion, along with variations of these differences corresponding to finite pressure or/and temperature changes. Method II relies on the calculation of the hydration free energy of the ion, along with variations of this free energy corresponding to finite pressure or/and temperature changes. Both methods are used considering two distinct variants in the application of the correction scheme. In variant A, the raw values from the simulations are corrected after the application of finite difference in pressure or/and temperature, based on correction terms specifically designed for derivative parameters at P° and T(-). In variant B, these raw values are corrected prior to differentiation, based on corresponding correction terms appropriate for the different simulation pressures P and temperatures T. The results corresponding to the different calculation schemes show that, except for the hydration free energy itself, accurate methodological independence and quantitative agreement with even the most reliable experimental parameters (ion-pair properties) are not yet reached. Nevertheless, approximate internal consistency and qualitative agreement with experimental results can be achieved, but only when an appropriate correction scheme is applied, along with a careful consideration of standard-state issues. In this sense, the main merit of the present study is to set a clear framework for these types of calculations and to point toward directions for future improvements, with the ultimate goal of reaching a consistent and quantitative description of single-ion hydration thermodynamics in molecular dynamics simulations.

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Response to “Comment on ‘Ab initio molecular dynamics calculation of ion hydration free energies’ [J. Chem. Phys. 133, 047103 (2010)]”

Abstract: Re-examining the tetraphenyl-arsonium/tetraphenyl-borate (TATB) hypothesis for single-ion solvation free

Cited by 9 publications

References 17 publications

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F^–) Anion Hydration

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F^–) Anion Hydration

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

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations

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Response to “Comment on ‘Ab initio molecular dynamics calculation of ion hydration free energies’ [J. Chem. Phys. 133, 047103 (2010)]”

Abstract: Re-examining the tetraphenyl-arsonium/tetraphenyl-borate (TATB) hypothesis for single-ion solvation free

Cited by 9 publications

References 17 publications

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F–) Anion Hydration

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F–) Anion Hydration

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

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations

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Product

Resources

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Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F^–) Anion Hydration

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F^–) Anion Hydration