Density Functional Theory Study of Tetrathiafulvalene and Thianthrene in Acetonitrile:  Structure, Dynamics, and Redox Properties

VandeVondele, Joost; Lynden‐Bell, R. M.; Meijer, Evert Jan; Sprik, Michiel

doi:10.1021/jp054841+

Cited by 42 publications

(74 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is in agreement with our earlier observations of liquid water 5 and liquid acetonitrile 36 at constant volume, where we find surprisingly little effect of the basis on structural and dynamical properties of these liquids. This, however, will not hold if these liquids are allowed to change density, for example, if they are in contact with a 37,38 or calculations of the water vapor-liquid equilibrium, 6,7 where a good description of the diffuse wave function tails remains necessary.…”

Section: A Comparison Between Molecular Dipoles In Gas and Condenssupporting

confidence: 93%

“…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%

See 1 more Smart Citation

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: A Comparison Between Molecular Dipoles In Gas and Condenssupporting

confidence: 93%

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

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

2006

Self Cite

View full text Add to dashboard Cite

Electron-transfer (ET) reactions are among the most fundamental chemical processes and are crucial in a number of important biological processes, such as photosynthesis and cell respiration. [1] Nature and chemists alike have been tuning electron-donor and -acceptor sites or their environments to obtain ET rates and relative donor-acceptor stabilities that are optimized for a particular task. Herein, we report an atomistic theoretical approach based on molecular-dynamics simulations and density functional theory to predict quantitatively the effects of such modifications on the parameters that control ET. This work confirms recent experiments [2] that highlight the role of hydrogen-bonding interactions in ET processes. We have investigated the redox properties of substituted quinones in methanol (MeOH) as a prototypical hydrogen-bonding solvent and in acetonitrile (MeCN) as a solvent with similar dielectric properties but without the specific hydrogen-bonding interactions. In view of their biological importance, it is not surprising that quinones are often employed in electrochemical experiments and that the effects of the solvent and substituents on the redox properties have been well characterized. [3][4][5][6][7][8][9][10] We employed 1,4-benzoquinone (BQ) and 2,3,5,6-tetramethylbenzoquinone (duroquinone, DQ) in this study.A key step in the understanding of ET reactions was the formulation by Marcus [11,12] of the rate of ET (k ET ) as a function of the reaction free energy DG and l, that is, the sum of the inner (l i ) and outer (l o ) sphere reorganization energies [Eq. (1)], in which k is a proportionality constant that depends on the donor and acceptor quantum coupling, T the temperature, and k B the Boltzmann constant. Furthermore, Marcus also derived an approximate expression for l o that provides insight into the nature of the reorganization energy for simple solutes in a homogeneous environment. Based on continuum theory, it provides the nonspecific solvent reorganization energy l s as a function of the effective radii of the donor and the acceptor (r D and r A ), their distance of separation r, the solvent refractive index n D , and the relative permittivity e r [Eq. (2)]. In this work, we obtain estimates for DG and l beyond the continuum approximation by using atomistic simulations.In simulation, the free-energy difference between the oxidized and reduced states of a system can be computed exactly from ensemble averages on the basis of the vertical ionization energy (DE). [13][14][15][16][17][18][19] Such an ensemble average can be computed by using molecular-dynamics (MD) simulations. Herein, we have employed a computationally straightforward, but approximate formula for the free-energy difference DA. This formula can be derived [13][14][15] if the atomistic equivalent of the parabolic functions derived from Marcus theory, which depict the assumed harmonic dependence of the free energy on the vertical energy gap, is introduced as an approximation. This atomistic equivalent is the premise that DE fl...

show abstract

Density Functional Theory Study of Tetrathiafulvalene and Thianthrene in Acetonitrile: Structure, Dynamics, and Redox Properties

Cited by 42 publications

References 75 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

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

Contact Info

Product

Resources

About