Toigawa, Tomohiro; Peterman, D. R.*; Meeker, D. S.*; Grimes, T. S.*; Zalupski, P. R.*; Mezyk, S. P.*; Cook, A. R.*; Yamashita, Shinichi*; Kumagai, Yuta; Matsumura, Tatsuro; et al.
Physical Chemistry Chemical Physics, 23(2), p.1343 - 1351, 2021/01
The candidate An(III)/Ln(III) separation ligand hexa--octylnitrilo-triacetamide (HONTA) was irradiated under envisioned SELECT (Solvent Extraction from Liquid waste using Extractants of CHON-type for Transmutation) process conditions using a solvent test loop in conjunction with cobalt-60 gamma irradiation. We demonstrate that HONTA undergoes exponential decay with increasing gamma dose to produce a range of degradation products which have been identified and quantified by HPLC-ESI-MS/MS techniques. The combination of HONTA destruction and degradation product ingrowth, particularly dioctylamine, negatively impacts the extraction and back-extraction of both americium and europium ions. The loss of HONTA was attributed to its reaction with the solvent (-dodecane) radical cation of (HONTA + R) = (7.61 0.82) 10 M s obtained by pulse radiolysis techniques. However, when this ligand is bound to either americium or europium ions, the observed -dodecane radical cation kinetics increase by over an order of magnitude. This large reactivity increase to additional reaction pathways occurring upon metal-ion binding. Lastly nanosecond time-resolved measurements showed that both direct and indirect HONTA radiolysis yielded the short-lived (100 ns) HONTA radical cation as well as a longer-lived (s) HONTA triplet excited state. These HONTA species are important precursors to the suite of HONTA degradation products observed.
Akahama, Yuichi*; Miyakawa, Masashi*; Taniguchi, Takashi*; Sano, Asami; Machida, Shinichi*; Hattori, Takanori
Journal of Chemical Physics, 153(1), p.014704_1 - 014704_5, 2020/07
The structure refinement of black phosphorus was performed at pressures of up to 3.2 GPa at room temperature by powder neutron diffraction techniques. The bond lengths and bond angles between the phosphorus atoms at pressures were precisely determined and confirmed to be consistent with those of the previous single crystal X-ray analysis [Brown and Randqvist, Acta Cryst. 19, 684 (1965)]. Although lattice parameters exhibited an anisotropic compressibility, the covalent P1-P2 and P1-P3 bond lengths were almost independent of pressure and only the P3-P1-P2 bond angle was reduced significantly. On the basis of our results, the significant discrepancy in the bond length reported by Cartz et al. [J. Chem. Phys. 71, 1718 (1979)] has been solved. Our structural data will contribute to the elucidation of the Dirac semimetal state of black phosphorus under high pressure.
Yonetani, Yoshiteru*; Nakagawa, Hiroshi
Chemical Physics Letters, 749, p.137441_1 - 137441_5, 2020/06
We calculated solvent accessibility of DNA backbone hydrogen sites, H1'-H5' by using molecular dynamics simulation of DNA. The result of accessibility is well correlated with the site-dependent reactivity with OH radicals experimentally reported, indicating that the different DNA-radical reactivity is mainly caused by the difference in the solvent accessibility of each hydrogen site. Compared with the previous calculation with solvent-accessible surface area, the present MD-based counting of molecular access provided a slightly improved result, which suggests importance of more realistic molecular components such as electrostatic interactions and DNA conformational fluctuation.
Yamakawa, Koichiro; Nasu, Hirokazu*; Suzuki, Natsumi*; Shimizu, Genki*; Arakawa, Ichiro*
Journal of Chemical Physics, 152(17), p.174310_1 - 174310_13, 2020/05
We have established an apparatus for terahertz and mid-infrared spectroscopy in an ultrahigh vacuum and have measured absorption spectra of DO clusters trapped in solid Ar. To assign terahertz absorption peaks due to the DO dimer, trimer, and tetramer, the dependence of the spectrum on the annealing temperature and DO dilution was analyzed. The assignment was also examined by ab initio calculations with use of the ONIOM method, where flexibility of surrounding Ar atoms was systematically incorporated. We identified all of the intermolecular fundamentals of the dimer and those with significant intensities of the trimer and tetramer, whose structural symmetries were revealed to be broken down. After isolating the DO clusters in solid Ar, we sublimated only Ar atoms to leave behind matrix-sublimation ice, which was found to be amorphous- or crystal-like depending on the formation conditions: the dilution and sublimation-temperature. Since the crystallinity got higher with raising the dilution and sublimation-temperature, the diffusion of the DO monomer on the surface of sublimating solid Ar was found to be crucial to the crystallization of the sublimation ice.
Okazaki, Hiroyuki*; Kakitani, Kenta*; Kimata, Tetsuya*; Idesaki, Akira*; Koshikawa, Hiroshi*; Matsumura, Daiju; Yamamoto, Shunya*; Yamaki, Tetsuya*
Journal of Chemical Physics, 152(12), p.124708_1 - 124708_5, 2020/03
Suno, Hiroya; Machida, Masahiko
Chemical Physics Letters, 730, p.26 - 31, 2019/09
We perform quantum chemical calculations for the Cs, K, and Na complexes of norbadione A (NBA), a pigment molecule in mushrooms known to accumulate Cs. A numerical two-step approach, by Ota , is employed to examine its alkali-metal-cation complexation selectivity in aqueous solutions. Applying it to the neutral, di- and tetra-deprotonated NBAs, we confirm that the complexation selectivity on Cs emerges only in high pHs, in which the di-protonated NBA dominates, in agreement with experimental results. This is the first demonstration of the approach for a biological molecule whose selectivity is known to be anomalous.
Akutsu, Kazuhiro*; Cagnes, M.*; Tamura, Kazuhisa; Kanaya, Toshiji*; Darwish, T. A.*
Physical Chemistry Chemical Physics, 21(32), p.17512 - 17516, 2019/08
We combined the deuterium labeling and neutron reflectivity techniques to determine the fine structure of the electric double layer structure in an imidazolium ionic liquid (IL). For this, a simple and large scale deuteration method for imidazolium ILs was developed, where the deuteration level can be systematically controlled.
Kusaka, Ryoji; Watanabe, Masayuki
Physical Chemistry Chemical Physics, 20(47), p.29588 - 29590, 2018/12
Mechanistic understanding of solvent extraction of uranyl ions (UO) by tributyl phosphate (TBP) will help improve the technology for the treatment and disposal of spent nuclear fuels. So far, it has been believed that uranyl ions in the aqueous phase are adsorbed to a TBP-enriched organic/aqueous interface, form complexes with TBP at the interface, and are extracted into the organic phase. Here we show that uranyl-TBP complex formation does not take place at the interface using vibrational sum frequency generation (VSFG) spectroscopy and propose an alternative extraction mechanism that uranyl nitrate, UO(NO), passes through the interface and forms the uranyl-TBP complex, UO(NO)(TBP), in the organic phase.
Suzuki, Kento*; Miyazaki, Takaaki*; Takayanagi, Toshiyuki*; Shiga, Motoyuki
Physical Chemistry Chemical Physics, 20(41), p.26489 - 26499, 2018/11
The direct photoionization of pure helium clusters and its subsequent short-time process have been studied by path integral molecular dynamics (PIMD) and ring-polymer molecular dynamics (RPMD) simulations. The PIMD simulations reproduced the experimental ionization spectra with a broad and asymmetric nature, which can be ascribed to the inhomogeneity of the energy levels of He atoms. From the RPMD simulations, it is found that the ionized helium cluster in the highly excited state brings about fast electronic state relaxation via nonadiabatic charge transfer and subsequently slow structural relaxation.
Yoshida, Koji*; Inoue, Takuya*; Torigoe, Motokatsu*; Yamada, Takeshi*; Shibata, Kaoru; Yamaguchi, Toshio*
Journal of Chemical Physics, 149(12), p.124502_1 - 124502_10, 2018/09
Differential scanning calorimetry, X-ray diffraction, and quasi-elastic neutron scattering (QENS) measurements of aqueous glycine solutions confined in mesoporous silica (MCM-41) were performed at different glycine concentrations, pH, and loading ratio (= mass of glycine solution / mass of dry MCM-41) in the temperature range from 305 to 180 K to discuss the confinement effect on the thermal behavior, the structure, and the dynamic properties of the solutions.
Nemoto, Fumiya*; Kofu, Maiko; Nagao, Michihiro*; Oishi, Kazuki*; Takata, Shinichi; Suzuki, Junichi*; Yamada, Takeshi*; Shibata, Kaoru; Ueki, Takeshi*; Kitazawa, Yuzo*; et al.
Journal of Chemical Physics, 149(5), p.054502_1 - 054502_11, 2018/08
Ishii, Yusuke*; Komatsu, Kazuki*; Nakano, Satoshi*; Machida, Shinichi*; Hattori, Takanori; Sano, Asami; Kagi, Hiroyuki*
Physical Chemistry Chemical Physics, 20(24), p.16650 - 16656, 2018/06
The structure of an aluminum layered hydroxide, boehmite (-AlOOH), as a function of pressure was studied by using synchrotron X-ray and neutron diffraction. Peak broadening and subsequent splitting, which are only found for hkl (h 0) peaks in the X-ray diffraction patterns above 25 GPa, are explained by stacking disorder accompanied with a continuously increasing displacement of the AlO octahedral layer along a-axis. This finding could be the first experimental result for the pressure-induced stacking disorder driven by the continuous layer displacement. The magnitude of the layer displacement was estimated from the X-ray scattering profile calculation based on the stacking disordered structure model. Hydrogen bond geometries of boehmite, obtained by structure refinements on the observed neutron diffraction patterns for deuterated sample up to 10 GPa, show linearly approaching O-D covalent and DO hydrogen bond distances and they could merge below 26 GPa. The pressure-induced stacking disorder would make the electrostatic potential of hydrogen bonds asymmetric, yielding less chance for the proton-tunnelling.
Machida, Masahiko; Kato, Koichiro*; Shiga, Motoyuki
Journal of Chemical Physics, 148(10), p.102324_1 - 102324_11, 2018/03
The isotopologs of liquid water, HO, DO, and TO, are studied systematically by first principles PIMD simulations, in which the whole entity of the electrons and nuclei are treated quantum mechanically. The simulation results are in reasonable agreement with available experimental data on isotope effects, in particular, on the peak shift in the radial distributions of HO and DO and the shift in the evaporation energies. It is found that, due to differences in nuclear quantum effects, the H atoms in the OH bonds more easily access the dissociative region up to the hydrogen bond center than the D (T) atoms in the OD (OT) bonds. The accuracy and limitation in the use of the current density-functional-theory-based first principles PIMD simulations are also discussed. It is argued that the inclusion of the dispersion correction or relevant improvements in the density functionals are required for the quantitative estimation of isotope effects.
Yoshioka, Satoru*; Tsuruta, Konosuke*; Yamamoto, Tomokazu*; Yasuda, Kazuhiro*; Matsumura, Sho*; Ishikawa, Norito; Kobayashi, Eiichi*
Physical Chemistry Chemical Physics, 20(7), p.4962 - 4969, 2018/02
Cationic disorder in the MgAlO spinel induced by swift heavy ions was investigated using the X-ray absorption near edge structure. With changes in the irradiation fluences of 200 MeV Xe ions, the Mg K-edge and Al K-edge spectra were synchronously changed. The calculated spectra based on density function theory indicate that the change in the experimental spectra was due to cationic disorder between Mg in tetrahedral sites and Al in octahedral sites. These results suggest a high inversion degree to an extent that the completely random configuration is achieved in MgAlO induced by the high density electronic excitation under swift heavy ion irradiation.
Kai, Takeshi; Yokoya, Akinari*; Ukai, Masatoshi*; Fujii, Kentaro*; Toigawa, Tomohiro; Watanabe, Ritsuko*
Physical Chemistry Chemical Physics, 20(4), p.2838 - 2844, 2018/01
It is thought that complex DNA damage which induces in radiation biological effects is formed at radiation track end. Thus, the earliest stage of water radiolysis at the electron track end was studied to predict DNA damage. These results indicate that DNA damage sites comprising multiple nucleobase lesions with a single strand breaks can therefore be formed by multiple collisions of the electrons within three base pairs (3bp) of a DNA strand. This multiple damage site cannot be processed by base excision repair enzymes. However, pre-hydrated electrons can also be produced resulting in an additional base lesion more than 3bp away from the multi-damage site. This clustered damage site may be finally converted into a double strand break (DSB) when base excision enzymes process the additional base lesions. These DSBs include another base lesion(s) at their termini that escape from the base excision process and which may result in biological effects such as mutation in surviving cells.
Kusaka, Ryoji; Watanabe, Masayuki
Physical Chemistry Chemical Physics, 20(4), p.2809 - 2813, 2018/01
Solvent extraction plays an integral part in the separation and purification of metals. Because extractants generally used as complexing agents for metal extractions, such as di-(2-ethylhexyl)phosphoric acid (HDEHP) for lanthanide extractions, are amphiphilic, they come to the organic/water interface, and the interface plays a crucial role as the site of the formation of metal complexes and subsequent transfer reaction to an organic phase. Despite the importance of the interface for solvent extractions, however, molecular-level structure of the interface is unclear because of experimental difficulty. Here we studied structure of a trivalent europium (Eu) complex with HDEHP formed at HDEHP monolayer/water interface by heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectroscopy. The study on the HDEHP/water interface enables us to investigate the structure of the interfacial Eu complex by excluding the migration of Eu into an organic phase after the complex formation at the interface. The interface-selective vibrational Im spectra observed by HD-VSFG of HDEHP/Eu(NO) aqueous solution interface in the 2800-3500 cm region indicate that Eu at the HDEHP/water interface is bonded by HDEHP from the air side and by water molecules from the water side. To the best of our knowledge, such metal complex structures have not been identified in the organic or water solutions.
Sassi, M.*; Okumura, Masahiko; Machida, Masahiko; Rosso, K. M.*
Physical Chemistry Chemical Physics, 19(39), p.27007 - 27014, 2017/10
no abstracts in English
Kurosaki, Yuzuru*; Yokoyama, Keiichi
Chemical Physics, 493, p.183 - 193, 2017/08
Electric field of laser pulses which gives maximum selectivity in the isotope-selective rovibrational excitation of lithium chloride molecules is calculated. Applying the optimal control theory, we calculate optimal electric field to produce mixture of LiCl-35 (=0, =0) and LiCl-37 (=1, =1) from molecular ensemble of LiCl-35 (=0, =0) and LiCl-37 (=0, =0). As a result, it is found that electric field which permit rotational excitations only gives high yield in the selective excitation compared to the electric field which permit both rotational and vibrational excitations.
Seki, Yusuke*; Takayanagi, Toshiyuki*; Shiga, Motoyuki
Physical Chemistry Chemical Physics, 19(21), p.13798 - 13806, 2017/06
Ring-polymer molecular dynamics (RPMD) simulations have been performed to understand the photoexcitation dynamics of the Ag atom embedded in a low-temperature cluster consisting of 500 helium atoms, after the electronic excitation of the Ag atom. Along the RPMD trajectory the time evolution of the electronic wavefunction within the spin-orbit P manifold is calculated, whereby the time-dependent Schrdinger equation and the RPMD equation of motion are coupled, la Ehrenfest mean field approach. It is found from the simulations that the Ag atom is mostly ejected from the helium cluster with the average time of 100 ps after photoexcitation. The average velocity of the ejected Ag atom is estimated to be 60-70 m/s. These results are qualitatively in line with previous experimental findings.
Hiyama, Miyabi*; Shiga, Motoyuki; Koga, Nobuaki*; Sugino, Osamu*; Akiyama, Hidefumi*; Noguchi, Yoshifumi*
Physical Chemistry Chemical Physics, 19(15), p.10028 - 10035, 2017/04
In this study, the effect of hydration on the absorption spectra of oxyluciferin anion isomers in an aqueous solution is investigated for elucidating the influence of characteristic hydration structures. Using a canonical ensemble of hydration structures obtained from first-principles molecular dynamics simulations, the instantaneous absorption spectra of keto-, enol-, and enolate-type aqueous oxyluciferin anions at room temperature are computed from a collection of QM/MM calculations using an explicit solvent. It is demonstrated that the calculations reproduce experimental results concerning spectral shifts and broadening, for which traditional methods based on quantum chemistry and the Franck-Condon approximation fail because of the molecular vibrations of oxyluciferin anions and dynamical fluctuations of their hydration structures.