Luo, P.*; Zhai, Y.*; Leao, J. B.*; Kofu, Maiko; Nakajima, Kenji; Faraone, A.*; Zhang, Y.*
Journal of Physical Chemistry Letters (Internet), 12(1), p.392 - 398, 2021/01
Using neutron spin-echo spectroscopy, we studied the microscopic structural relaxation of a prototypical network ionic liquid ZnCl at the structure factor primary peak and prepeak. The results show that the relaxation at the primary peak is faster than the prepeak and that the activation energy is % higher. A stretched exponential relaxation is observed even at temperatures well-above the melting point . Surprisingly, the stretching exponent shows a rapid increase upon cooling, especially at the primary peak, where it changes from a stretched exponential to a simple exponential on approaching the . These results suggest that the appearance of glassy dynamics typical of the supercooled state even in the equilibrium liquid state of ZnCl as well as the difference of activation energy at the two investigated length scales are related to the formation of a network structure on cooling.
Gonzalz, M. A.*; Borodin, O.*; Kofu, Maiko; Shibata, Kaoru; Yamada, Takeshi*; Yamamuro, Osamu*; Xu, K.*; Price, D. L.*; Saboungi, M.-L.*
Journal of Physical Chemistry Letters (Internet), 11(17), p.7279 - 7284, 2020/09
Itoi, Hiroyuki*; Ninomiya, Takeru*; Hasegawa, Hideyuki*; Maki, Shintaro*; Sakakibara, Akihiro*; Suzuki, Ryutaro*; Kasai, Yuto*; Iwata, Hiroyuki*; Matsumura, Daiju; Owada, Mao*; et al.
Journal of Physical Chemistry C, 124(28), p.15205 - 15215, 2020/07
Fujiwara, Satoru*; Matsuo, Tatsuhito*; Sugimoto, Yasunobu*; Shibata, Kaoru
Journal of Physical Chemistry Letters (Internet), 10(23), p.7505 - 7509, 2019/12
Characterization of the dynamics of disordered polypeptide chains is required to elucidate the behavior of intrinsically disordered proteins and proteins under non-native states related to the folding process. Here we develop a method using quasielastic neutron scattering, combined with small-angle X-ray scattering and dynamic light scattering, to evaluate segmental motions of proteins as well as diffusion of the entire molecules and local side-chain motions. We apply this method to RNase A under the unfolded and molten-globule (MG) states. The diffusion coefficients arising from the segmental motions are evaluated and found to be different between the unfolded and MG states. The values obtained here are consistent with those obtained using the fluorescence-based techniques. These results demonstrate not only feasibility of this method but also usefulness to characterize the behavior of proteins under various disordered states.
Kumagai, Yuta; Fidalgo, A. B.*; Jonsson, M.*
Journal of Physical Chemistry C, 123(15), p.9919 - 9925, 2019/04
Radiation-induced oxidative dissolution of uranium dioxide (UO) is one of the most important chemical processes of U driven by redox reactions. We have examined the effect of UO stoichiometry on the oxidative dissolution of UO induced by hydrogen peroxide (HO) and -ray irradiation. By comparing the reaction kinetics of HO between stoichiometric UO and hyper-stoichiometric UO, we observed a significant difference in reaction speed and U dissolution kinetics. The stoichiometric UO reacted with HO much faster than the hyper-stoichiometric UO. The U dissolution from UO was initially much lower than that from UO, but gradually increased as the oxidation by HO proceeded. The -ray irradiation induced the U dissolution that is analogous to the kinetics by the exposure to a low concentration (0.2 mM) of HO. The exposure to higher HO concentrations caused lower U dissolution and resulted in deviation from the U dissolution behavior by -ray irradiation.
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
no abstracts in English
Chang, Y. L.*; Sasaki, Takehiko*; Ribas-Ario, J.*; Machida, Masahiko; Shiga, Motoyuki
Journal of Physical Chemistry B, 123(7), p.1662 - 1671, 2019/02
Dehydration of biomass-derived polyalcohols has recently drawn attention in green chemistry as a prototype of selective reactions controllable in hot water or hot carbonated water, without any use of organic solvents or metal catalysts. Here, we report a free-energy analysis based on first-principles metadynamics and blue-moon ensemble simulations to understand the mechanism of competing intramolecular dehydration reactions of 1,2,5-pentanetriol in hot acidic water. The simulations consistently predict that the most dominant mechanism is the proton-assisted S2 process, where the protonation of the hydroxyl group by water and the C-O bond breaking and formation occur in a single step. The detailed mechanism found from the simulations shows how the reaction paths are selective in hot water and why the reaction rates are accelerated in acidic environments, thus giving a clear explanation of experimental findings for a broad class of competing dehydration processes of polyalcohols.
Saeki, Morihisa*; Matsumura, Daiju; Yomogida, Takumi; Taguchi, Tomitsugu*; Tsuji, Takuya; Saito, Hiroyuki*; Oba, Hironori*
Journal of Physical Chemistry C, 123(1), p.817 - 824, 2019/01
Reaction kinetics of laser-induced particle formation in an aqueous solution of PdCl was investigated by transmission electron microscope (TEM) and dispersive X-ray absorption fine structure (DXAFS). The Pd particle was generated by irradiation of nanosecond pulsed 266-nm laser. The TEM observation showed dependence of the particle size on the laser fluence and promotion of the particle growth by irradiation of high-fluence laser. The DXAFS data give us the Pd concentration. Temporal changes of the Pd concentration analyzed based on Finke-Watzky two step mechanism. The analysis elucidates that the laser photon contributes to the reduction of the PdCl ion by the one-photon process and to the autocatalytic growth of the Pd particles by the multi-photon process.
Okubo, Takahiro*; Okamoto, Takuya*; Kawamura, Katsuyuki*; Gugan, R.*; Deguchi, Kenzo*; Oki, Shinobu*; Shimizu, Tadashi*; Tachi, Yukio; Iwadate, Yasuhiko*
Journal of Physical Chemistry A, 122(48), p.9326 - 9337, 2018/12
The structures of Cs adsorption on montmorillonite were investigated by the nuclear magnetic resonance (NMR) spectroscopy. The NMR spectra of Cs adsorbed on montmorillonite samples were measured under different Cs contents and relative humidity levels. NMR parameters were evaluated by the first principle calculations in order to identify the relationship between adsorbed Cs structures and NMR parameters. The comparisons between experimental and theoretical NMR spectra revealed that Cs is preferentially adsorbed at sites near Al for low Cs substituted montmorillonites, and that non-hydrated Cs present in partially Cs substituted samples, even after being hydrated under high relative humidity.
Shiga, Motoyuki; Tuckerman, M. E.*
Journal of Physical Chemistry Letters (Internet), 9(21), p.6207 - 6214, 2018/11
Predicting reaction pathways is one of the most important goals in theoretical and computational chemistry. In this paper, we propose a novel approach to search for free-energy landmarks, i.e., minima and the saddle points, of chemical reactions in an automated manner using a combination of steepest descent and gentlest ascent methods. As demonstrations, we present applications to the ring-opening reaction of benzocyclobutene and an SN2 reaction in aqueous solution.
Ota, Atsuyuki*; Tanaka, Kazuya; Tsuno, Hiroshi*
Journal of Physical Chemistry A, 122(41), p.8152 - 8161, 2018/10
We investigated the application of L-edge XANES spectra to the local structural analysis of lanthanoids in aqueous solution, iron hydroxide, manganese dioxide, and calcium carbonate. For each lanthanoid, the full width at half maximum (FWHM) values of lanthanoid compounds roughly decreased with increasing coordination numbers. However, they did not strictly reflect the local coordination sphere of the lanthanoid complex, but were rather sensitive to their chemical forms. The relationship between the magnitude of the FWHM values was determined by the crystal field splitting or degeneracy of 5d orbitals. The systematic variation of FWHM can be explained by the ligand strength of the ligand molecules (-HO, -O, -OH, -CO, -Cl, and -O) that cause the crystal field splitting. Therefore, the FWHM values of L-edge XANES of lanthanoid compounds may be more useful in speciation analysis rather than structural analysis such as EXAFS.
Taminato, So*; Hirayama, Masaaki*; Suzuki, Kota*; Kim, K.-S.*; Tamura, Kazuhisa; Kanno, Ryoji*
Journal of Physical Chemistry C, 122(29), p.16607 - 16612, 2018/07
Lithium-rich layered rocksalt oxides are promising cathode materials for lithium-ion batteries. We investigate the effects of surface modification by amorphous LiPO on the structures and electrochemical reactions in the surface region of an epitaxial LiRuO(010) film electrode. Structural characterization using SXRD, HAXPES, and NR shows that surface modification by LiPO resulted in the partial substitution of P for Li in the surface region of LiRuO. The modified (010) surface exhibits better rate capability at 20 C compared to the unmodified surface. surface XRD confirmed that highly reversible structural changes occurred at the modified surface during lithium (de)intercalation. These results demonstrate that this surface modification stabilizes the crystal structure in the surface region, and it can improve the rate capability of lithium-rich layered rocksalt oxide cathodes.
Mu, J.*; Motokawa, Ryuhei; Akutsu, Kazuhiro*; Nishitsuji, Shotaro*; Masters, A. J.*
Journal of Physical Chemistry B, 122(4), p.1439 - 1452, 2018/02
Kumagai, Yuta; Kimura, Atsushi*; Taguchi, Mitsumasa*; Watanabe, Masayuki
Journal of Physical Chemistry C, 121(34), p.18525 - 18533, 2017/08
H production by irradiation of zeolite-water mixtures was studied, to investigate effect of zeolites in the reaction process for H. Four different types of zeolites were examined comparatively under anoxic and under aerated conditions. High production yields of H were observed for the zeolites of high Al contents at low water fraction and under anoxic condition, compared to zeolites having lower Al contents. A comparison of the H yields in connection with chemical analysis of the zeolites suggests that extraframework Al species in the zeolites are involved in a reaction pathway for H. Meanwhile, under aerated condition and at high mixing ratio of water, the difference in H yield among the zeolites was suppressed and the yields of H were lower than those under anoxic condition probably due to HO produced by water radiolysis. The comparable H yields suggest another reaction pathway for H which is less dependent on the structure and composition of the zeolites.
Itoi, Hiroyuki*; Nishihara, Hirotomo*; Kobayashi, Shunsuke*; Ittisanronnachai, S.*; Ishii, Takafumi*; Berenguer, R.*; Ito, Masashi*; Matsumura, Daiju; Kyotani, Takashi*
Journal of Physical Chemistry C, 121(14), p.7892 - 7902, 2017/04
Wang, Y.*; Wang, L.*; Zheng, H.*; Li, K.*; Andrzejewski, M.*; Hattori, Takanori; Sano, Asami; Katrusiak, A.*; Meng, Y.*; Liao, F.*; et al.
Journal of Physical Chemistry C, 120(51), p.29510 - 29519, 2016/12
Pressure-induced polymerization (PIP) of aromatic molecules can generate saturated carbon nanostructures. As a strongly interacted - stacking unit, the CH-CF adduct is widely applied in supramolecular chemistry, and it provides a good preorganization for the PIP. Here we investigated the structural variation of CH-CF cocrystal and the subsequent PIP process under high pressure. Four new molecular-complex phases V, VI, VII, and VIII have been identified and characterized by the in situ Raman, IR, synchrotron X-ray, and neutron diffraction. The phase V is different from the phases observed at low temperature, which has a tilted column structure. Phases VI and VII have a structure similar to phase V. Phase VIII polymerizes irreversibly upon compression above 25 GPa without any catalyst, producing sp(CH/F) materials. The - interaction is still dominant below 0.5 GPa but is most likely to be overstepped under further compression, which is important for discussing the supramolecular phase transition and the polymerization process.
Sekine, Yurina; Endo, Hitoshi*; Iwase, Hiroki*; Takeda, Shigeo*; Mukai, Sadaatsu*; Fukazawa, Hiroshi; Littrell, K. C.*; Sasaki, Yoshihiro*; Akiyoshi, Kazunari*
Journal of Physical Chemistry B, 120(46), p.11996 - 12002, 2016/11
The detailed structure of a nanogel formed by self-association of cholesterol-bearing pullulans (CHP) was determined by contrast variation small-angle neutron scattering. The decomposition of scattering intensities into partial scattering functions of each CHP nanogel component, i.e., pullulan, cholesterol, and the cross-term between the pullulan and the cholesterol allows us to investigate the internal structure of the nanogel. The effective spherical radius of the skeleton formed by pullulan chains was found to be about 8.1 nm. In the CHP nanogel, there are about 19 cross-linking points where a cross-linking point is formed by aggregation of trimer cholesterol molecules with the spatially inhomogeneous distribution of the mass fractal dimension of 2.6. The average radius of the partial chains can also be determined to be 1.7 nm. As the result, the complex structure of the nanogels is coherently revealed at the nanoscopical level.
Kai, Takeshi; Yokoya, Akinari*; Ukai, Masatoshi*; Fujii, Kentaro*; Watanabe, Ritsuko*
Journal of Physical Chemistry A, 120(42), p.8228 - 8233, 2016/10
Low energy secondary electrons produced by an ionizing radiation in a living cell may involve in formation of complexed DNA damage. We performed theoretical study for numerical calculation of dynamic behavior of the electrons to imply a formation of radiation damage to DNA. The decelerating electrons are gradually attracted to their parent cations by the Coulombic force within hundreds of fs, and about 12.6 % of electrons are finally distributed within 2 nm from the cations. The collision fraction of the ionization and excitation within 1 nm from the cation was estimated to be about 40 %. From those analyses, we suggested a process of DNA damage that the secondary electrons may cause highly localized lesions around a cation in DNA molecule through additional dissociative electron transfer as well as the ionization or the excitation if the electrons are ejected from DNA. The localized damage may involve ultimately in biological effects such as cell death or mutation induction.
Noguchi, Yoshifumi*; Hiyama, Miyabi*; Shiga, Motoyuki; Sugino, Osamu*; Akiyama, Hidefumi*
Journal of Physical Chemistry B, 120(34), p.8776 - 8783, 2016/09
We investigated the stability of oxyluciferin anions (keto, enol, and enolate isomers) in aqueous solution at room temperature by performing a nanosecond time scale first-principles molecular dynamics simulation. In contrast to all previous quantum chemistry calculations, which suggested the keto-type to be the most stable, we show that the enol-type is slightly more stable than the keto-type, in agreement with some recent experimental studies. The simulation highlights the remarkable hydrophobicity of the keto-type by the cavity formed at the oxyluciferin-water interface as well as a reduction in hydrophobicity with the number of hydrating water molecules. It is therefore predicted that the isomeric form in a hydrated cluster is size-dependent.
Tamura, Kazuhisa; Nishihata, Yasuo
Journal of Physical Chemistry C, 120(29), p.15691 - 15697, 2016/07
The behavior of halide ions on the Au(111) electrode surface in two ionic liquids (ILs) was investigated by monitoring the structure of the electrode surface. The potential dependences of the X-ray diffraction intensity, which originate from the Au(111)-(11) structure and the surface normal structure, were measured simultaneously with cyclic voltammograms. The results revealed that halide ions are co-adsorbed with IL molecules on the electrode surface and increase the mobility of surface atoms. This suggests that the interaction between halide ions and surface Au atoms is weaker than that between IL molecules and surface Au atoms; that is, the surface properties are mainly governed by adsorbed IL molecules. Furthermore, a comparison of the two ILs revealed that the effect of halide ions on the structure of the Au(111) electrode surface depends on the strength of the interaction between IL molecules and surface Au atoms.