From Solvent Fluctuations to Quantitative Redox Properties of Quinones in Methanol and Acetonitrile

VandeVondele, Joost; Sulpizi, Marialore; Sprik, Michiel

doi:10.1002/anie.200503581

Cited by 31 publications

(57 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The condition number in the condensed phase is reported for a number of systems, all molecular liquids simulated using periodic boundary conditions as described in more detail in previous work, 5,36,40 in Table V. The BSSE as estimated with the counterpoise correction 41 is reported in Table VI for a number of hydrogen bonded dimers.…”

Section: Condition Number and Basis Set Superposition Errormentioning

confidence: 99%

Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases

VandeVondele

Hutter

2007

The Journal of Chemical Physics

Self Cite

3,322

2,672

View full text Add to dashboard Cite

(2007). Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases. The Journal of Chemical Physics, 127 (11) Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases AbstractWe present a library of Gaussian basis sets that has been specifically optimized to perform accurate molecular calculations based on density functional theory. It targets a wide range of chemical environments, including the gas phase, interfaces, and the condensed phase. These generally contracted basis sets, which include diffuse primitives, are obtained minimizing a linear combination of the total energy and the condition number of the overlap matrix for a set of molecules with respect to the exponents and contraction coefficients of the full basis. Typically, for a given accuracy in the total energy, significantly fewer basis functions are needed in this scheme than in the usual split valence scheme, leading to a speedup for systems where the computational cost is dominated by diagonalization. More importantly, binding energies of hydrogen bonded complexes are of similar quality as the ones obtained with augmented basis sets, i.e., have a small (down to 0.2 kcal/mol) basis set superposition error, and the monomers have dipoles within 0.1 D of the basis set limit. However, contrary to typical augmented basis sets, there are no near linear dependencies in the basis, so that the overlap matrix is always well conditioned, also, in the condensed phase. The basis can therefore be used in first principles molecular dynamics simulations and is well suited for linear scaling calculations. We present a library of Gaussian basis sets that has been specifically optimized to perform accurate molecular calculations based on density functional theory. It targets a wide range of chemical environments, including the gas phase, interfaces, and the condensed phase. These generally contracted basis sets, which include diffuse primitives, are obtained minimizing a linear combination of the total energy and the condition number of the overlap matrix for a set of molecules with respect to the exponents and contraction coefficients of the full basis. Typically, for a given accuracy in the total energy, significantly fewer basis functions are needed in this scheme than in the usual split valence scheme, leading to a speedup for systems where the computational cost is dominated by diagonalization. More importantly, binding energies of hydrogen bonded complexes are of similar quality as the ones obtained with augmented basis sets, i.e., have a small ͑down to 0.2 kcal/ mol͒ basis set superposition error, and the monomers have dipoles within 0.1 D of the basis set limit. However, contrary to typical augmented basis sets, there are no near linear dependencies in the basis, so that the overlap matrix is always well conditioned, also, in the condensed phase. The basis can therefore be used in first principles molecular dynamics simulations and is well suited for linear scaling calculations. Gaus...

show abstract

Section: Condition Number and Basis Set Superposition Errormentioning

confidence: 99%

Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases

VandeVondele

Hutter

2007

The Journal of Chemical Physics

Self Cite

3,322

2,672

View full text Add to dashboard Cite

show abstract

“…These are: i) the organosulphur compounds tetrathiafulvalenene (TTF) and thianthrene (TH) in acetonitrile (ACN) solution, [10] ii) model quinones, benzoquinone (BQ) and duroquinone (DQ) in two different solvents, ACN and methanol (MeOH), [12] iii) two natural varieties of the iron-sulfur protein rubredoxin in aqueous solution. [15] Three variants of the same three-step recipe have been employed.…”

Section: Resultsmentioning

confidence: 99%

“…[23] for a complete technical review of the method, and refs. [10,12,15] for specific computational details for each of the selected applications. The unifying theme for the simulations that we have selected for this paper is that all DFT calculations have been performed using the freely available simulation package CP2K/Quickstep.…”

Section: Atomistic Theory Of Electron Transfermentioning

confidence: 99%

“…differences in redox potentials), and the rate of electron transfer between them are of particular interest, as they reflect directly what is thermodynamically and kinetically feasible. In this paper, we will summarize some of our previous work [3][4][5][6][7][8][9][10][11][12][13][14][15] aimed at computing these quantities directly from doi: 10.2533/chimia.2007.155 k ET …”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Electron Transfer Properties from Atomistic Simulations and Density Functional Theory

VandeVondele

Sulpizi²,

Sprik³

2007

Chimia

Self Cite

View full text Add to dashboard Cite

Marcus theory of electron transfer is the quintessential example of a successful theory in physical chemistry. In this paper, we describe the theoretical approach we have adopted to compute key parameters in Marcus theory. In our method, based on molecular dynamics simulations and density functional theory, the redox center and its environment are treated at the same level of theory. Such a detailed atomistic model describes specific solvent-solute interactions, such as hydrogen bonding, explicitly. The quantum chemical nature of our computations enables us to study the effect of chemical modifications of the redox centers and deals accurately with the electronic polarization of the environment. Based on results of previous work, we will illustrate that quantitative agreement with experiment can be obtained for differences in redox potentials and solvent reorganization energies for systems ranging from small organic compounds to proteins in solution. Keywords: Density functional theory · Electron transfer · Marcus theory · Molecular dynamicsatomistic models using density functional Theory (DFT). The quantum chemical nature of DFT allows the effects of chemical modifications of the redox centers to be studied without a need for prior knowledge or empirical parameterization. This can thus make our method truly predictive. A key feature of ET reactions, or redox reactions in general, is the crucial role played by the environment. Indeed, oxidation (reduction) potentials are the condensed phase equivalents of ionization potentials (electron affinities) in the gas phase, and these quantities can differ significantly. Our atomistic models explicitly include the environment ( e.g. solvent and/or protein) so that not only dielectric properties but also specific interactions, such as hydrogen bonding or conformational changes are taken explicitly into account. Furthermore, the environment is far from being a static spectator. Its fluctuations bring donor and acceptor sites in an energy resonant state, triggering ET, and its ability to relax after ET influences significantly the energetics. In order to probe these fluctuations and relaxations in our computational setup, molecular dynamics is employed to generate a sufficiently large number of representative configurations of solute and solvent.A major step in the understanding of ET reactions was the formulation by Marcus [16,17] of the rate of electron transfer (k ET ) as a simple function of the reaction free energy ( Δ G), the solvent reorganization energy ( λ ) and a proportionality constant ( κ ) depending on the quantum coupling between donor and acceptor states.The fruitful concept that underlies this formula is the assumed harmonic nature of the free energy surface with respect to the reaction coordinate of electron transfer. This restricts the validity of this formula to the range of systems that fall in the linear response regime, which might thus exclude systems that undergo significant changes in conformation or solvation upon electron transfer. Ulti...

show abstract

“…This introduces significant flexibility, allowing for bond rearrangement (difficult with empirical force fields that generally assume a prescribed bonding topology), 8 electron transfer, 9 and transitions between electronic states. 10,11 The most straightforward AIMD approach is the Born-Oppenheimer scheme (BOMD).…”

Section: Introductionmentioning

confidence: 99%

Multiple time step integrators in ab initio molecular dynamics

Luehr

Markland

Martı́nez

2014

The Journal of Chemical Physics

View full text Add to dashboard Cite

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we show that such a timescale separation is possible using two different schemes: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

show abstract

From Solvent Fluctuations to Quantitative Redox Properties of Quinones in Methanol and Acetonitrile

Cited by 31 publications

References 33 publications

Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases

Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases

Electron Transfer Properties from Atomistic Simulations and Density Functional Theory

Multiple time step integrators in ab initio molecular dynamics

Contact Info

Product

Resources

About