Poisson–Boltzmann Implicit Solvation Models

Cai, Qiong; Wang, Jun; Hsieh, Meng-Juei; Xiang, Yu‐Tao; Luo, Ray

doi:10.1016/b978-0-444-59440-2.00006-5

Cited by 20 publications

(19 citation statements)

References 130 publications

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“… 19 − 21 The PB theory is a well-established continuum description of electrostatic interactions of biomolecules in an aqueous solvent. 32 − 42 To couple the PB theory into VISM, here we develop robust numerical methods to solve the PB equation with arbitrarily shaped dielectric boundaries and to calculate the effective dielectric boundary force (DBF) that is the electrostatic part of total force as the negative variation of the VISM functional with respect to the location change of dielectric boundary. 39 , 43 − 47 The concept of DBF only arises in the variational approach to implicit solvation.…”

Section: Introductionmentioning

confidence: 99%

Variational Implicit Solvation with Poisson–Boltzmann Theory

Zhou

Cheng

Dzubiella

et al. 2014

J. Chem. Theory Comput.

105

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We incorporate the Poisson–Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also apply our VISM-PB theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host–guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host–guest system. We finally discuss several issues for further improvement of VISM.

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Section: Introductionmentioning

confidence: 99%

Variational Implicit Solvation with Poisson–Boltzmann Theory

Zhou

Cheng

Dzubiella

et al. 2014

J. Chem. Theory Comput.

105

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“…Since most particles in biomolecular simulations are to represent water molecules solvating the target biomolecules, an implicit treatment of water molecules allows greatly increased simulation efficiency. Indeed, implicit solvation offers a unique opportunity for more efficient simulations without the loss of atomic-level resolution for biomolecules [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid

Xiao

Luo

2017

The Journal of Chemical Physics

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We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

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“…In such a model, one first determines a dielectric boundary that separates a charged molecular region from the solvent region, with the dielectric coefficients of these regions close to 1 and 80, respectively, and then applies the a) H. Sun, J. Wen, and Y. Zhao contributed equally to this work. b) Electronic mail: hus003@ucsd.edu c) Electronic mail: wen.jiayi.thomas@gmail.com d) Electronic mail: yxzhao@email.gwu.edu e) Electronic mail: bli@math.ucsd.edu f) Electronic mail: jmccammon@ucsd.edu Poisson-Boltzmann (PB) theory [13][14][15][16][17][18][19][20][21][22][23][24] or the generalized Born (GB) model 25,26 to calculate the electrostatic free energy.…”

Section: Introductionmentioning

confidence: 99%

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

Sun

Wen

Zhao³

et al. 2015

The Journal of Chemical Physics

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Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. C 2015 AIP Publishing LLC. [http://dx

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Poisson–Boltzmann Implicit Solvation Models

Cited by 20 publications

References 130 publications

Variational Implicit Solvation with Poisson–Boltzmann Theory

Variational Implicit Solvation with Poisson–Boltzmann Theory

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

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