X-ray absorption spectroscopy and molecular dynamics studies of hydration in aqueous solutions

Kuzmin, Alexei; Obst, Stefan; Purans, J.

doi:10.1088/0953-8984/9/46/004

Cited by 65 publications

(73 citation statements)

References 41 publications

(90 reference statements)

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“…2͒, predict 14 water molecules in the second shell region ͑3.5-4.7 Å͒ and nearly within the large range of values obtained from the analysis of the x-ray data, 45-50 7.6-13.2 waters. This number also agrees well with the results from several prior MD and QM/MM simulations 40,44,[51][52][53][54][55] and within the range of values of the conventional MD simulations. However, compared to these prior simulations our second shell maximum is found to be 5%-10% smaller.…”

Section: A the Hydration Shell Structuresupporting

confidence: 90%

“…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.…”

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

101

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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: A the Hydration Shell Structuresupporting

confidence: 90%

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

101

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“…Mistakenly identifying a Mn signal for an O signal causes several inconsistencies in the EXAFS results. First, while it is difficult or impossible to detect a second hydration sphere in aqueous Zn samples with EXAFS spectroscopy due to long bond lengths, large degree of disorder in the bonds, and weak scattering power of O atoms, other techniques have measured or predicted the Zn-O interatomic distance produced by the second hydration shell to be 4.20-4.39 Å (Kuzmin et al, 1997). This range of values is not in agreement with second shell Zn-O interatomic distances of 3.46-3.50 Å .…”

Section: Discussionmentioning

confidence: 99%

Zinc sorption to biogenic hexagonal-birnessite particles within a hydrated bacterial biofilm

Toner

Manceau

Webb

et al. 2006

Geochimica et Cosmochimica Acta

178

152

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“…MD simulations have been used in the past to investigate hydrated systems (Wallen et aL 1998;Kuzmin et al 1997;D'Angelo et al 1996;D'Angelo et aL 1994), but in most cases the analysis has been limited to single scattering paths. In this study, we use the MD simulation to generate a cumulant expansion in the manner of McCarthy et al (1997), allowing all MS paths to be taken into account.…”

Section: Introductionmentioning

confidence: 99%

XAFS Debye–Waller factors in aqueous Cr+3 from molecular dynamics

Campbell¹,

Rehr²,

Schenter³

et al. 1999

J Synchrotron Radiat

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Controversy exists on whether the second hydration shell of the aqueous chromium +3 cation is observable by XAFS. The problem is aggravated by strong first shell multiple scattering contributions competing with the second hydration shell signal. By finding ab initio values for nearly all free parameters in the theory, we greatly reduce the number of parameters to be fit, thus allowing an unambiguous resolution of this controversy. Quantum chemistry calculations yielded a parameterized force field model which was used in classical molecular dynamics simulations to calculate all the multiple scattering Debye-Waller factors. The self-consistent FEFF8 code fixes Eo to within 1 eV. The predicted spectrum is in good agreement with experiment. Fitted distances for the first and second hydration shell are 2.0008 + 0.0068/~ and 3.914 4-0.096/~, respectively. The second shell is shown to be responsible for about 1/3 of the XAFS Fourier transformed signal at the position of the second shell.

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X-ray absorption spectroscopy and molecular dynamics studies of hydration in aqueous solutions

Cited by 65 publications

References 41 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

Zinc sorption to biogenic hexagonal-birnessite particles within a hydrated bacterial biofilm

XAFS Debye–Waller factors in aqueous Cr+3 from molecular dynamics

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