Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Matsuda, Aya; Mori, Hirotoshi

doi:10.1007/s10953-014-0235-7

Cited by 16 publications

(12 citation statements)

References 41 publications

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“…Thus, there are not experimental studies providing the hydration number nor the average Ra–O(H 2 O) distance of the aqua ion. These shortcomings stimulate the use of theoretical tools to undertake the estimation of physicochemical properties hardly accessible by experiments. , The problem arising from this strategy is to evaluate the degree of confidence of these theoretical results if experimental results are not available for comparison. Two precedent alkaline-earth cations, Sr 2+ and Ba 2+ , are good candidates to be investigated together with Ra 2+ in order to analyze the evolution of properties along the group in a systematic way, starting from a regular increase of the ionic radius.…”

Section: Introductionmentioning

confidence: 99%

Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

et al. 2021

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The physicochemical properties of the three heaviest alkaline-earth cations, Sr 2+ , Ba 2+ , and Ra 2+ in water have been studied by means of classical molecular dynamics (MD) simulations. A specific set of cation–water intermolecular potentials based on ab initio potential energy surfaces has been built on the basis of the hydrated ion concept. The polarizable and flexible model of water MCDHO2 was adopted. The theoretical–experimental comparison of structural, dynamical, energetic, and spectroscopical properties of Sr 2+ and Ba 2+ aqueous solutions is satisfactory, which supports the methodology developed. This good behavior allows a reasonable reliability for the predicted Ra 2+ physicochemical data not experimentally determined yet. Simulated extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge spectroscopy spectra have been computed from the snapshots of the MD simulations and compared with the experimental information available for Sr 2+ and Ba 2+ . For the Ra 2+ case, the Ra L 3 -edge EXAFS spectrum is proposed. Structural and dynamical properties of the aqua ions for the three cations have been obtained and analyzed. Along the [M(H 2 O) n ] m + series, the M–O distance for the first-hydration shell is 2.57, 2.81, and 2.93 Å for Sr 2+ , Ba 2+ , and Ra 2+ , respectively. The hydration number also increases when one is going down along the group: 8.1, 9.4, and 9.8 for Sr 2+ , Ba 2+ , and Ra 2+ , respectively. Whereas [Sr(H 2 O) 8 ] 2+ is a typical aqua ion with a well-defined structure, the Ba 2+ and Ra 2+ hydration provides a picture exhibiting an average between the ennea- and the deca-hydration. These results show a similar chemical behavior of Ba 2+ and Ra 2+ aqueous solutions and support experimental studies on the removal of Ra-226 of aquifers by different techniques, where Ra 2+ is replaced by Ba 2+ . A comparison of the heavy alkaline ions, Rb + and Cs + , with the heavy alkaline-earth ions is made.

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Section: Introductionmentioning

confidence: 99%

Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

et al. 2021

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“…Finally, studies of the structural and energetic trends of “difficult” ions provide key reference points for new developments in computational methodology. Fragment-based and many-body methodologies have shown considerable promise for the simulation of solvated ions. − Recent developments , in near-exact fits to ab initio data also may provide transferable accuracy to large systems. However, the known behavior of n ≤ 4 suggests that considerable collective effects may be at-play in hydrated Cu(I), and a previous study has shown that the many-body decomposition of this system may be qualitatively in error.…”

Section: Introductionmentioning

confidence: 99%

Signatures of Size-Dependent Structural Patterns in Hydrated Copper(I) Clusters, Cu⁺(H₂O)_n=1–10

Herr

Steele

2016

J. Phys. Chem. A

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The isomers of a hydrated Cu(I) ion with n = 1-10 water molecules were investigated by using ab initio quantum chemistry and an automated isomer-search algorithm. The electronic structure and vibrational spectra of the hundreds of resulting isomers were used to analyze the source of the observed bonding patterns. A structural evolution from dominantly two-coordinate structures (n = 1-4) toward a mixture of two- and three-coordinate structures was observed at n = 5-6, where the stability provided by expanded hydrogen-bonding was competitive with the dominantly electrostatic interaction between the water ligand and remaining binding sites of the metal ion. Further hydration (n = 7-10) led to a mixture of three- and four-coordinate structures. The metal ion was found, through spectroscopic signatures, to appreciably perturb the O-H bonds of even third-shell water molecules, which highlighted the ability of this nominally simple ion to partially activate the surrounding water network.

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“…FMO/MD is a promising method to study dynamic properties of complex molecular systems. [55,[92][93][94][95][96][97] In this work, the accuracy of FMO-DFTB/MD has been evaluated for solvated sodium cation, and 100 ps MD simulations have been performed to obtain the radial distribution and coordination number of sodium cation in solution. The obtained coordination number of sodium (6.5) is in reasonable agreement with other studies (5)(6).…”

Section: Discussionmentioning

confidence: 99%

Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

Nishimoto

Fedorov

2017

J Comput Chem

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The three-body fragment molecular orbital (FMO3) method is formulated for density-functional tight-binding (DFTB). The energy, analytic gradient, and Hessian are derived in the gas phase, and the energy and analytic gradient are also derived for polarizable continuum model. The accuracy of FMO3-DFTB is evaluated for five proteins, sodium cation in explicit solvent, and three isomers of polyalanine. It is shown that FMO3-DFTB is considerably more accurate than FMO2-DFTB. Molecular dynamics simulations for sodium cation in water are performed for 100 ps, yielding radial distribution functions and coordination numbers. © 2017 Wiley Periodicals, Inc.

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Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Cited by 16 publications

References 41 publications

Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

Signatures of Size-Dependent Structural Patterns in Hydrated Copper(I) Clusters, Cu⁺(H₂O)_n=1–10

Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

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Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Cited by 16 publications

References 41 publications

Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

Signatures of Size-Dependent Structural Patterns in Hydrated Copper(I) Clusters, Cu+(H2O)n=1–10

Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

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Signatures of Size-Dependent Structural Patterns in Hydrated Copper(I) Clusters, Cu⁺(H₂O)_n=1–10