Direct Modeling of EXAFS Spectra from Molecular Dynamics Simulations

Palmer, Bruce; Pfund, David M.; Fulton, John L.

doi:10.1021/jp960160q

Cited by 134 publications

(168 citation statements)

References 21 publications

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“…36,37 As input to this procedure, an ensemble of Zn 2+ ͑H 2 O͒ n clusters was generated from every 60 fs of the simulation in which the 100 nearest atoms to the zinc atom were extracted subject to periodic boundary conditions. Each cluster of the ensemble was then used as input into the FEFF8 electron multiple scattering code 38 to generate the EXAFS fine structure factor ͑E͒ for the zinc ion and then averaged over the ensemble to determine ͑E͒.…”

Section: Md-exafs and Experimental Exafsmentioning

confidence: 99%

“…45,54,[56][57][58][59] However, we also compared the x-ray scattering calculated from the simulated structures directly to the observed EXAFS spectra. 36 This type of analysis has recently been used to compare AIMD simulations of UO 2 2+ + 64H 2 O ͑UO 2 2+ + 122H 2 O͒ to EXAFS measurements with remarkable success. 60 In Fig.…”

Section: B Comparison Of Simulations With Exafs Datamentioning

confidence: 99%

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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

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103

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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.

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Section: Md-exafs and Experimental Exafsmentioning

confidence: 99%

Section: B Comparison Of Simulations With Exafs Datamentioning

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

Self Cite

103

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“…14 and 16͒, are required to shed light on this point, as already shown in the XAS study of other single ions. 27,28,[51][52][53][54][55] Related to these XANES computations, a further point to be investigated is the analysis of the efficiency of the FMS approach when the asymmetric structures, resulting from the fluxional behavior of the aquaion and its close environment, were considered to provide an average spectrum. The efficiency of alternative methods, such as finite-difference method, 56 should be explored.…”

Section: Figmentioning

confidence: 99%

“…We believe that the spectroscopical peculiarities associated to the double channel appearing in the ionization pro- cess of the Cu͑II͒ hydrate in water provide a fairly good background to further XAS molecular-dynamics combined studies. 27,28,[51][52][53][54][55] Thus, the microscopic representation of the dynamics of this hydration would allow the computation of simulated EXAFS and XANES spectra from a statistically significant set of structures, and then to extract additional conclusions about the relative importance of the different structures contributing to the XAS spectra, the doublechannel spectroscopic peculiarity being simultaneously considered.…”

Section: Figmentioning

confidence: 99%

The hydration of Cu2+: Can the Jahn-Teller effect be detected in liquid solution?

Chaboy

Muñoz‐Páez

Merkling

et al. 2006

The Journal of Chemical Physics

114

125

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The long elusive structure of Cu͑II͒ hydrate in aqueous solutions, classically described as a Jahn-Teller distorted octahedron and recently proposed to be a fivefold coordination structure ͓Pasquarello et al., Science 291, 856 ͑2001͔͒, has been probed with x-ray-absorption spectroscopy by performing a combined theoretical and experimental analysis. Two absorption channels were needed to obtain a proper reproduction of the x-ray-absorption near-edge structure ͑XANES͒ region spectrum, as already observed in other Cu͑II͒ complexes ͓Chaboy et al., Phys. Rev. B 71, 134208 ͑2005͔͒. The extended x-ray-absorption fine-structure ͑EXAFS͒ spectrum was analyzed as well within this approach. Quite good reproductions of both XANES and EXAFS spectra were attained for several distorted and undistorted structures previously proposed. Nevertheless, there is not a clearly preferred structure among those including four-, five-, and sixfold coordinated Cu͑II͒ ions. Taking into account our results, as well as many more from several other authors using different techniques, the picture of a distorted octahedron for the Cu͑II͒ hexahydrate in aqueous solution, paradigm of the Jahn-Teller effect, is no longer supported. In solution a dynamical view where the different structures exchange among themselves is the picture that better suits the results presented here.

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“…The interplay of XAS spectroscopy with quantum mechanics and numerical simulations has shown to be as an appropriate strategy to get insight into structural information on ionic aqueous solutions, [18][19][20][21][22][23][24][25][26][27] and will be explored for the case of a non-aqueous solution.…”

Section: 17mentioning

confidence: 99%

The solvation of bromide anion in acetonitrile: a structural study based on the combination of theoretical calculations and X-ray absorption spectroscopy

Ayala

Martı́nez

Pappalardo

et al. 2006

Molecular Simulation

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Direct Modeling of EXAFS Spectra from Molecular Dynamics Simulations

Cited by 134 publications

References 21 publications

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

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

The hydration of Cu2+: Can the Jahn-Teller effect be detected in liquid solution?

The solvation of bromide anion in acetonitrile: a structural study based on the combination of theoretical calculations and X-ray absorption spectroscopy

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