First‐principles molecular dynamics simulations in a continuum solvent

Fattebert, Jean‐Luc; Gygi, François

doi:10.1002/qua.10548

Cited by 136 publications

(192 citation statements)

References 35 publications

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“…We also ignore repulsion between solvent molecules and thus ignore the layering in the double layer. 60 Here, in contrast to other studies where the dielectric function is explicitly dependent on either the electric field ε(E) 61 or the electronic density of solutes 26 or metal electrodes ε(ρ) 49,50 causing dielectric saturation in regions of high electric field or electronic density, we use a spatially dependent dielectric function ε( r). As has been demonstrated, 62 a smooth "step-like" function ε(z) which decays from its bulk value to the high frequency limit in the vicinity of the electrode (at sufficiently high surface electron density σ) can accurately reproduce a response consistent with Booth's ansatz for ε(E).…”

Section: E3440mentioning

confidence: 99%

Improving Continuum Models to Define Practical Limits for Molecular Models of Electrified Interfaces

Baskin

2017

J. Electrochem. Soc.

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We develop a continuum theory of electrolyte solutions in contact with a metal electrode, based on a generalized free energy functional, and use it to explore the structure of the electric double layer at different electrochemical conditions. The model captures the effects of specific adsorption of ions and solvent polarization, and can be applied on the same footing to cases with non-zero faradaic current, beyond the classical double-layer regime. These advances permit the prediction of peculiar character in the ion profiles at electrode potentials near the redox level, exploration of the electrochemical stability of the interface, and differentiation between the mechanisms of electron and ion transport and associated time scales. The developed methodology enables us to selfconsistently determine the fundamental limits for a microscopic description of biased interfaces, in terms characteristic sizes and time scales of relevant processes, within atomistic and ab initio molecular dynamics simulations. As the efficiency of electrochemical conversion is dictated by the energetics of elementary charge transfer reactions occurring at the electrode/electrolyte interface, the formulation of methods of control over these reactions has become the pivotal goal of fundamental material science for advanced energy storage systems. The ultimate goal of theoretical electrochemistry then is to explore the energetics of the relevant processes from an atomistic perspective by means of ab initio molecular dynamics (AIMD) where ionic and electronic components of the system are described explicitly and are constrained by various realistic conditions, such as the external bias, the temperature and the electrolyte concentration. However, despite more than a decade of efforts this goal is still far from being fulfilled.There are several interconnected fundamental problems to resolve before an atomistic approach could be routinely used to describe electrochemistry, if only at the level of a half-cell (i.e., a single electrodeelectrolyte interface). First, there are at least three distinct regimes of performance of the electrochemical interface and each of these is characterized by different sets of the time and space scales: a) the classical electric double layer (EDL) regime when no charge transfer is assumed, b) the regime of an electrode at equilibrium with the electrolyte (open circuit conditions, (OCP)) when only an exchange current in a form of mutually compensating fluxes of charged particles is possible, and c) the "true" electrochemical regime with a non-zero net faradaic current. As long as the goal of atomistic simulations is to reach a state when one would observe the actual electrochemical reactions driven by the bias, the computational electrode potential scanning protocol should carry the system through a set of (quasi-)equilibrium points at which the atomistic structure is consistent with the targeted external conditions. The key requirement for such simulations is thus thermodynamic stability of the interface that encom...

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Section: E3440mentioning

confidence: 99%

Improving Continuum Models to Define Practical Limits for Molecular Models of Electrified Interfaces

Baskin

2017

J. Electrochem. Soc.

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“…Dziedzic et al In contrast, the recent model proposed by Fattebert and Gygi [5,6], and later developed by Scherlis et al [7] (henceforth called the FGS model), utilizes a dielectric cavity constructed directly from the electronic density of the solute, which greatly reduces the number of parameters involved.…”

Section: -P1mentioning

confidence: 99%

Minimal parameter implicit solvent model for ab initio electronic-structure calculations

Dziedzic¹,

Helal²,

Skylaris³

et al. 2011

EPL

140

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We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersionrepulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.

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“…Performances of the implemented PCG procedure are also higher than multigrid approaches to solve the GPe, where a number of iterations between 17 and 25 are needed to reach an accuracy of ∼10 −8 . 16 For the sake of completeness, the preconditioned steepest descent scheme (Algorithm 2 with β k = 0) has been tested with the preconditioner described by Eq. (11).…”

Section: Numerical Resultsmentioning

confidence: 99%

A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

Fisicaro

Genovese²,

Andreussi

et al. 2016

The Journal of Chemical Physics

102

152

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The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes. C 2016 AIP Publishing LLC. [http://dx

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First‐principles molecular dynamics simulations in a continuum solvent

Cited by 136 publications

References 35 publications

Improving Continuum Models to Define Practical Limits for Molecular Models of Electrified Interfaces

Improving Continuum Models to Define Practical Limits for Molecular Models of Electrified Interfaces

Minimal parameter implicit solvent model for ab initio electronic-structure calculations

A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

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