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Journal Articles

Development of the ReaxFF methodology for electrolyte-water systems

Fedkin, M. V.*; Shin, Y. K.*; Dasgupta, N.*; Yeon, J.*; Zhang, W.*; van Duin, D.*; Van Duin, A. C. T.*; Mori, Kento*; Fujiwara, Atsushi*; Machida, Masahiko; et al.

Journal of Physical Chemistry A, 123(10), p.2125 - 2141, 2019/03

https://doi.org/10.1021/acs.jpca.8b10453
 Times Cited Count：48 Percentile：95.49(Chemistry, Physical)

no abstracts in English

Journal Articles

First-principles calculation studies on cesium in environmental situations; Hydration structures and adsorption on clay minerals

Machida, Masahiko; Okumura, Masahiko; Nakamura, Hiroki; Sakuramoto, Kazuhiro*

Proceedings of Joint International Conference on Mathematics and Computation, Supercomputing in Nuclear Applications and the Monte Carlo Method (M&C + SNA + MC 2015) (CD-ROM), 12 Pages, 2015/04

In order to clarify physicochemical behaviors of radioactive Cs released into environment from the Fukushima Daiichi Nuclear Power Plants, we study on two issues, i.e., hydration structures of Cs$$^{+}$$ and its adsorption on a specific edge in a clay particle (mica) by employing first principles calculations. In this paper, firstly, we report on hydration structures of Cs$$^{+}$$ by using Born-Oppenheimer first-principles molecular dynamics. Our striking finding in the hydration structures is that Cs$$^{+}$$ has no clear second hydration shell in contrast to any other alkali cations. Secondly, we construct a model of the Frayed Edge Site and confirm that the model actually becomes selective for Cs when expanding the interlayer distance from that of the original crystal structure through the calculation of the ion-exchange energy.

Journal Articles

Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)$$_{2}$$ observed by neutron diffraction measurements

Arai, Shigeki; Chatake, Toshiyuki*; Ohara, Takashi; Kurihara, Kazuo; Tanaka, Ichiro*; Suzuki, Nobuhiro*; Fujimoto, Zui*; Mizuno, Hiroshi*; Niimura, Nobuo

Nucleic Acids Research, 33(9), p.3017 - 3024, 2005/05

https://doi.org/10.1093/nar/gki616
 Times Cited Count：93 Percentile：82.84(Biochemistry & Molecular Biology)

It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the d(CCATTAATGG)$$_{2}$$ duplex. Moreover, the D positions in 27 D$$_{2}$$O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 Å resolution X-ray and 3.0 Å resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in prior X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.

Journal Articles

${it Ab initio}$ molecular dynamics study of polarization effects on ionic hydration in aqueous AlCl$$_{3}$$ solution

Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

Journal of Chemical Physics, 119(23), p.12386 - 12392, 2003/12

https://doi.org/10.1063/1.1627323
 Times Cited Count：43 Percentile：78.79(Chemistry, Physical)

The solvation shell structure and dynamics of Al$$^{3+}$$ and Cl$$^{-}$$ in an aqueous solution of 0.8 M AlCl$$_{3}$$ are studied under ambient conditions by using ${it ab initio}$ molecular dynamics method. The solvation structures obtained from our ${it ab initio}$ simulations are in good agreement with the experimental ones for both Al$$^{3+}$$ and Cl$$^{-}$$. A detailed analysis of intramolecular geometry of hydration waters and dipole moments of the ingredients shows that the polarization has substantial effects on the structures and dynamics of both the cation and anion hydration shells. Implications to the metal hydrolysis of Al$$^{3+}$$ will also be given.

JAEA Reports

Proceedings of the 182nd Basic Science Seminar (The Workshop on Neutron Structural Biology) "New Frontiers of Structural Biology Advanced by Solution Scattering"; February 9-10, 2000, Tokai, Japan

Fujiwara, Satoru

JAERI-Conf 2001-004, 228 Pages, 2001/03

JAERI-Conf-2001-004.pdf:16.25MB

no abstracts in English

Journal Articles

Neutrons expand the field of structural biology

Niimura, Nobuo

Current Opinion in Structural Biology, 9(5), p.602 - 608, 1999/10

https://doi.org/10.1016/S0959-440X(99)00012-3
 Times Cited Count：55 Percentile：50.64(Biochemistry & Molecular Biology)

no abstracts in English

Journal Articles

Hydration of proteins and DNA determined by neutron

Niimura, Nobuo

Hyomen, 37(3), p.50 - 57, 1999/03

no abstracts in English

Oral presentation

Hydration structure of einsteinium by synchrotron radiation based analysis

Yaita, Tsuyoshi; Suzuki, Shinichi; Kobayashi, Toru; Shiwaku, Hideaki; Doi, Reisuke; Yamagami, Hiroshi; Tsukada, Kazuaki; Toyoshima, Atsushi; Asai, Masato

no journal, , 

no abstracts in English

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