Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

Bardhan, Jaydeep P.; Knepley, Matthew G.

doi:10.1063/1.4897324

Cited by 27 publications

(103 citation statements)

References 76 publications

(99 reference statements)

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“…This could indicate that charge-sign hydration asymmetry is more significant in protic solvents, and furthermore it may be dependent on R s . We recently developed a semi-empirical nonlinear SLIC that captures charge-sign asymmetry [42,43]. Similar to our work here, that SLIC replaced a normal-field-dependent 'radius perturbation' with a perturbation in the boundary condition.…”

Section: Discussionmentioning

confidence: 87%

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface

2016

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In this paper, we extend the familiar continuum electrostatic model to incorporate finite-size effects in the solvation layer, by perturbing the usual macroscopic interface condition. The perturbation is based on the mean spherical approximation (MSA), to derive a multiscale solvation-layer interface condition (SLIC/MSA). We show that SLIC/MSA reproduces MSA predictions for Born ions in a variety of polar solvents, including water as well as other protic and aprotic solvents. Importantly, the SLIC/MSA model predicts not only solvation free energies accurately but also solvation entropies, which standard continuum electrostatic models fail to predict. The SLIC/MSA model depends only on the normal electric field at the dielectric boundary, similar to our recent development of a SLIC model for charge-sign hydration asymmetry, and the reformulation of the MSA as an effective boundary condition enables its straightforward application to complex molecules such as proteins, whereas traditionally it is primarily a bulk theory. This work also opens the possibility for other electrolyte models to be incorporated into fast implicit-solvent models of biomolecular electrostatics.

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Section: Discussionmentioning

confidence: 87%

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface

2016

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“…A hierarchy of approximations, many of which are essentially unavoidable, separates the PB (and the GB) from the more fundamental explicit solvent representation, and from reality . These approximations result in notable limitations of the pure GB or PB frameworks, such as their inability to account for many prominent explicit solvent effects, including charge hydration asymmetry and other water multipole effects, water ‘bridges,’ electrostriction and dielectric saturation . Also, accurate estimates of total solvation energies, and especially their differences in conformational transitions, need accurate nonpolar estimates of the nonpolar contribution .…”

Section: Implicit Solvent Modelsmentioning

confidence: 99%

Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

171

225

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Modern simulation and modeling approaches to investigation of biomolecular structure and function rely heavily on a variety of methods—water models—to approximate the influence of solvent. We give a brief overview of several distinct classes of available water models, with the emphasis on the conceptual basis at each level of approximation. The main focus is on classes of models most widely used in atomistic simulations, including popular implicit and explicit solvent models. Among the latter, nonpolarizable N‐point models are covered in most detail, including some recent methodological advances and nuances. Notes on practical availability and usage in biomolecular simulations are included. Atomistic simulations that were hardly possible only a short while ago have revealed significant problems that can be traced to deficiencies of most commonly used N‐point water models. Recently developed models of this class approximate experimental properties of liquid water much closer than before, and show promise in practical biomolecular simulations. Obstacles to wider adoption of these more accurate water models, both technical and conceptual, are discussed. It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed. The review is concluded with a discussion on how force‐field development efforts can benefit from better solvent models, and vice versa. WIREs Comput Mol Sci 2018, 8:e1347. doi: 10.1002/wcms.1347 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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“…One remedy then is to reparameterize all the solute–water LJ parameters. Another is to consider solute–solvent interfacial conditions for the Poisson or PB treatment . A second theoretical issue is the estimate of entropy.…”

Section: Discussionmentioning

confidence: 99%

“…Another is to consider solute-solvent interfacial conditions for the Poisson or PB treatment. [83] A second theoretical issue is the estimate of entropy. This is completely missing in our current theory.…”

Section: Discussionmentioning

confidence: 99%

LS-VISM: A software package for analysis of biomolecular solvation

et al. 2015

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We introduce a software package for the analysis of biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit-solvent model (VISM). The input of the package includes the atomic data of biomolecules under consideration and the macroscopic parameters such as solute-solvent surface tension, bulk solvent density and ionic concentrations, and the dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute-solvent interfaces that are obtained by minimizing the VISM solvation free-energy functional among all possible solute-solvent interfaces enclosing the solute atoms. We review the VISM with various descriptions of electrostatics. We also review our numerical methods that consist mainly of the level-set method for relaxing the VISM free-energy functional and a compact coupling interface method for the dielectric Poisson–Boltzmann equation. Such numerical methods and algorithms constitute the central modules of the software package. We detail the structure of the package, format of input and output files, work flow of the codes, and the post-processing of output data. Our demo application to a host-guest system illustrates how to use the package to perform solvation analysis for biomolecules, including ligand-receptor binding systems. The package is simple and flexible with respect to minimum adjustable parameters and a wide range of applications. Future extensions of the package use can include the efficient identification of ligand binding pockets on protein surfaces.

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Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

Cited by 27 publications

References 76 publications

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface

Water models for biomolecular simulations

LS-VISM: A software package for analysis of biomolecular solvation

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