A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

Scherlis, Damián A.; Fattebert, Jean‐Luc; Gygi, François; Cococcioni, Matteo; Marzari, Nicola

doi:10.1063/1.2168456

Cited by 125 publications

(177 citation statements)

References 74 publications

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“…However, this can considerably increase the cost of a simulation, as in the case of large systems in solution where the solvent must fill a correspondingly large volume. Various strategies have been developed for reducing the cost, for example by using implicit solvation methods [38][39][40][41] , however it is frequently desirable to treat explicitly the environmental degrees of freedom. Thanks to the fragment approach, the treatment of solvents and other surrounding molecules can readily be achieved in BigDFT with relatively low cost, as we will demonstrate through the example of the fullerene C 60 in two different environments: when in an aqueous solution and when surrounded by other C 60 molecules.…”

Section: C60mentioning

confidence: 99%

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

Ratcliff

Genovese

Mohr

et al. 2015

The Journal of Chemical Physics

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In a recent paper we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions is optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e. without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.

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Section: C60mentioning

confidence: 99%

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

Ratcliff

Genovese

Mohr

et al. 2015

The Journal of Chemical Physics

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“…To determine the optimal parameters, we separately calculated the minority-spin occupation matrix for either a ferrous or ferric hexa-aqua ion embedded in a dielectric continuum (ǫ=78) [24]. Then, we determine the parameters in the penalty functional so that the occupation matrices of the ferrous or ferric clusters are accurately reproduced once the two are studied in the same unit cell (P I =0.54 eV, f I 0 =0.95 and σ I =0.01 on the ferrous ion and P I =-0.54 eV, f I 0 =0.28 and σ I =0.01 on the ferric ion).…”

mentioning

confidence: 99%

Realistic Quantitative Descriptions of Electron Transfer Reactions: Diabatic Free-Energy Surfaces from First-Principles Molecular Dynamics

2006

Self Cite

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A general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the transfer of an electron at any given ionic configuration (the Marcus energy gap) is accurately assessed within ground-state density-functional theory via a novel penalty functional for oxidation-reduction reactions that appropriately acts on the electronic degrees of freedom alone. The self-interaction error intrinsic to common exchange-correlation functionals is also corrected by the same penalty functional. The diabatic free-energy surfaces are then constructed from umbrella sampling on large ensembles of configurations. As a paradigmatic case study, the self-exchange reaction between ferrous and ferric ions in water is studied in detail.A wide variety of processes and reactions in electrochemistry, molecular electronics, and biochemistry have a common denominator: they involve a diabatic electron transfer process from a donor to an acceptor [1]. These reactions cover processes and applications as diverse as solar-energy conversion in the early steps of photosynthesis, oxidation-reduction reactions between a metallic electrode and solvated ions, and the I-V characteristics of molecular-electronics devices [2]. The key quantities of interest are the reaction rates (or, equivalently, the conductance) and the reaction pathways. Reaction rates, in the general scenario of Marcus theory [3,4,5], have a thermodynamic contribution (the classical Franck-Condon factor, broadly related to the free energy cost of a nuclear fluctuation that makes the donor and the acceptor levels degenerate in energy), and an electronic-structure, tunneling contribution (the LandauZener term, related to the overlap of the initial and final states).We argue in the following that state-of-the-art firstprinciples molecular dynamics calculations, together with several algorithmic and conceptual advances, are able to describe with quantitative accuracy these diabatic processes, while including the realistic description of the complex environment encountered, e.g. in nanoscale devices or at the interface between molecules and metals. Fig. 1 shows schematically an electron-transfer process and the free-energy diabatic surfaces according to the picture that was pioneered by Marcus [3,4,6,7]. In a polar solvent, the electron transfer process is mediated by thermal fluctuations of the solvent molecules. In the reactant state, the transferring electron is trapped at the donor site by solvent polarization; transfer might occur when the electron donor and acceptor sites become degenerate due to the thermal fluctuations of the solvent molecules. To characterize the role of the solvent on the electron-transfer reaction, a reaction coordinate ǫ for a given ionic configuration is introduced, as the energy dif- ference between the product and reactant state at that configuration [8]. This definition of reaction coordinate...

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“…Following the same guidelines, the accuracy of the electrostatic solvation energy [Eq. (30)] with respect to the spatial grid h grid has been investigated and reported in Fig. 6.…”

Section: Solvation Free Energiesmentioning

confidence: 99%

“…Starting from this idea, a cavity can be built up directly from the electronic density, as it has been shown in various publications. 15,29,30 In this second approach, the dielectric function is not explicitly space-dependent, but can be implicitly mapped by means of the electronic charge density.…”

Section: Electronic-structure Computationsmentioning

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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A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

Cited by 125 publications

References 74 publications

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

Realistic Quantitative Descriptions of Electron Transfer Reactions: Diabatic Free-Energy Surfaces from First-Principles Molecular Dynamics

A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

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