Characterization of dynamics and reactivities of solvated ions by<i>ab initio</i>simulations

Hofer, Thomas S.; Tran, Hung Thuan; Schwenk, Christian F.; Rode, Bernd M.

doi:10.1002/jcc.10374

Cited by 270 publications

(415 citation statements)

References 27 publications

Supporting

Mentioning

389

Contrasting

Order By: Relevance

“…32 In addition angular radial distribution functions (ARD) were computed. The vibrational power spectrum was computed via Fourier transformation of the velocity auto-correlation function (VACF) (eqn (1)).…”

Section: Evaluation Methodsmentioning

confidence: 99%

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

Wiedemair

Weiss²,

Rode

2014

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

A single sodium chloride molecule in aqueous solution was simulated by the ab initio quantum mechanical charge field-molecular dynamics (QMCF-MD) approach. During a series of simulations the solvated molecule (CIP), dissociated solvated ions and -most noticeably -a solvent separated ion pair (SSIP) were observed and the structural and dynamical characteristics of these systems were investigated. In addition to a detailed structural analysis of the observed species, vibrational spectra and charge distributions were calculated to elucidate the mechanism of the NaCl dissociation.

show abstract

Section: Evaluation Methodsmentioning

confidence: 99%

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

Wiedemair

Weiss²,

Rode

2014

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The height of the RDF at this minimum is comparable at the QM/MM and MM levels, namely, 0.12-0.17 (Na + ) and 0.32-0.36 (K + ). The exchange dynamics was further quantified by calculating the mean residence times (MRTs) τ of the water molecules in the first hydration shell and the associated rate coefficients R. This was done by monitoring exchange events, 272 with a cutoff set to the position of the first minimum in the RDF. The MRT is the average time a water molecule remains in the first shell, allowing a maximum excursion time of 0.5 ps to the second shell.…”

Section: B Hydration Structure and Dynamicsmentioning

confidence: 99%

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

Hofer

Hünenberger

2018

The Journal of Chemical Physics

Self Cite

104

View full text Add to dashboard Cite

The absolute intrinsic hydration free energy G • H + ,wat of the proton, the surface electric potential jump χ • wat upon entering bulk water, and the absolute redox potential V • H + ,wat of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na + ) and potassium (K + ) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potentialsummation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for G • H + ,wat , χ • wat , and V • H + ,wat , reported with statistical errors based on a confidence interval of 99%. The values obtained from the independent Na + and K + simulations are in excellent agreement. In particular, the difference between the two hydration free energies, which is not an elusive quantity, is 73.9 ± 5.4 kJ mol 1 (K + minus Na + ), to be compared with the experimental value of 71.7 ± 2.8 kJ mol 1 . The calculated values of G • H + ,wat , χ • wat , and V • H + ,wat ( 1096.7 ± 6.1 kJ mol 1 , 0.10 ± 0.10 V, and 4.32 ± 0.06 V, respectively, averaging over the two ions) are also in remarkable agreement with the values recommended by Reif and Hünenberger based on a thorough analysis of the experimental literature ( 1100 ± 5 kJ mol 1 , 0.13 ± 0.10 V, and 4.28 ± 0.13 V, respectively). The QM/MM MD simulations are also shown to provide an accurate description of the hydration structure, dynamics, and energetics. Published by AIP Publishing.

show abstract

“…However, a significant number of exchanges between the second and third shells are seen in both the AIMD and AIMD/MM simulations. To quantify these exchanges, the mean residence times ͑MRTs͒, the number of exchanges per 10 ps, and the sustainability of water molecules in the second shell were calculated using the direct method procedure suggested by Hofer et al 68 ͑Table IV͒. The MRT is calculated by…”

Section: E Hydration Shell Particle Exchangementioning

confidence: 99%

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Cauët

Bogatko

Weare

et al. 2010

The Journal of Chemical Physics

102

View full text Add to dashboard Cite

Results of ab initio molecular dynamics ͑AIMD͒ simulations ͑density functional theory+ PBE96͒ of the dynamics of waters in the hydration shells surrounding the Zn 2+ ion ͑T Ϸ 300 K, Ϸ 1 gm/ cm 3 ͒ are compared to simulations using a combined quantum and classical molecular dynamics ͓AIMD/molecular mechanical ͑MM͔͒ approach. Both classes of simulations were performed with 64 solvating water molecules ͑ϳ15 ps͒ and used the same methods in the electronic structure calculation ͑plane-wave basis set, time steps, effective mass, etc.͒. In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical ͑QM͒ region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure ͑EXAFS͒ spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is ͑maximally located at 2.13-2.15 Å versus 2.072 Å EXAFS experiment͒. The widths of the peak of the simulated EXAFS spectra agree well with the data ͑8.4 Å 2 versus 8.9 Å 2 in experiment͒. Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d 10 electronic structure of the valence shell of the Zn 2+ ion is retained. The simulations show substantial and complex charge relocation on both the Zn 2+ ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D ͑3.3 D AIMD/MM͒ versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell ͑2.8 D͒. No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations ͑256 waters͒ there is a significant reduction in the second shell to bulk exchanges.

show abstract

Characterization of dynamics and reactivities of solvated ions byab initiosimulations

Cited by 270 publications

References 27 publications

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Contact Info

Product

Resources

About