Akazawa, Daisuke; Sasaki, Takehiko*; Nagasaka, Masanari*; Shiga, Motoyuki
Journal of Chemical Physics, 156(4), p.044202_1 - 044202_7, 2022/01
The hydration structure of cellulose is very important for understanding the hydrolysis of cellulose at the molecular level. In this paper, we report a joint experimental and theoretical study on the X-ray absorption spectroscopy (XAS) of aqueous cellobiose, a disaccharide unit of cellulose. In the experimental part, high resolution measurements of the carbon K-edge XAS spectra were performed. It was found that the peak heights in the spectrum change considerably over the temperature range of 25 C to 60 C, which is a reflection of the number of hydrogen bonds between cellobiose and water. We suggest that this spectral change could be useful information for identifying the hydration of cellulose in various environments.
Thomsen, B.; Shiga, Motoyuki
Journal of Chemical Physics, 155(19), p.194107_1 - 194107_11, 2021/11
Kobayashi, Keita; Nagai, Yuki; Itakura, Mitsuhiro; Shiga, Motoyuki
Journal of Chemical Physics, 155(3), p.034106_1 - 034106_9, 2021/07
no abstracts in English
Thomsen, B.; Shiga, Motoyuki
Journal of Chemical Physics, 154(8), p.084117_1 - 084117_10, 2021/02
In this study we investigate the nuclear quantum effects on the acidity constant of liquid water isotopologues at the ambient condition by path integral molecular dynamics simulations. This technique not only reproduces the acidity constants of liquid DO experimentally measured but also allows for a theoretical prediction of the acidity constants of liquid TO, aqueous HDO and HTO, which are unknown due to its scarcity. The results indicate that the nuclear quantum effects play an indispensable role in the absolute determination of acidity constants.
Noguchi, Yoshifumi*; Hiyama, Miyabi*; Shiga, Motoyuki; Akiyama, Hidefumi*; Sugino, Osamu*
Journal of Chemical Physics, 153(20), p.201103_1 - 201103_6, 2020/11
Stabilizing mechanisms of three isomers of the aqueous oxyluciferin in the first excited state were investigated using first-principles molecular dynamics simulations. Only the phenolate-keto isomer became attracted to the water molecules in its excited state and was stabilized by increasing the number of hydrogen bonds with nearby water molecules. The most stable isomer in the excited state was the phenolate-keto, and the phenolate-enol and phenol-enolate isomers were higher in energy by 0.38 eV and 0.57 eV, respectively, than the phenolate-keto. This was in contrast to the case of ground state in which the phenolate-enol was the most stable isomer.
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.
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
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
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.
Shinozaki, Ayako*; Komatsu, Kazuki*; Kagi, Hiroyuki*; Fujimoto, Chikako*; Machida, Shinichi*; Sano, Asami; Hattori, Takanori
Journal of Chemical Physics, 148(4), p.044507_1 - 044507_8, 2017/01
Pressure-response on the crystal structure of deuterated -glycine was investigated at room temperature, using powder and single-crystal X-ray diffraction, and powder neutron diffraction measurements under high pressure. No phase change was observed up to 8.7 GPa, although anisotropy of the lattice compressibility was found. Neutron diffraction measurements indicated the distance of the intermolecular DO bond along with the -axis increase with compression up to 6.4 GPa. The distance of another DO bond along with the -axis decreased with increasing pressure, and became the shortest intermolecular hydrogen bond above 3 GPa. In contrast, the lengths of the bifurcated N-DO and C-DO hydrogen bonds, which are formed between the layers of the -glycine molecules along the -axis, decreased significantly with increasing pressure. The decrease of the intermolecular distances resulted in the largest compressibility of the -axis, compared to the other two axes. Hirshfeld analysis suggested that the reduction of the void region size, rather than shrinkage of the strong N-DO hydrogen bonds, occurred with compression.
Ogawa, Shuichi*; Tang, J.*; Yoshigoe, Akitaka; Ishizuka, Shinji*; Takakuwa, Yuji*
Journal of Chemical Physics, 145(11), p.114701_1 - 114701_7, 2016/09
Enhancement of SiO/Si(001) interfacial oxidation induced by thermal strain during rapid thermal oxidation was revealed by real time photoelectron spectroscopy using high intensity and high energy-resolution synchrotron radiation. This experimental result indicates the usefulness of the unified Si oxidation reaction model mediated by point defect generation.
Alcaraz, O.*; Trulls, J.*; Tahara, Shuta*; Kawakita, Yukinobu; Takeda, Shinichi*
Journal of Chemical Physics, 145(9), p.094503_1 - 094503_7, 2016/09
Ikeda, Takashi; Boero, M.*
Journal of Chemical Physics, 143(19), p.194510_1 - 194510_7, 2015/11
By resorting to a novel implementation of the first-principles-based van der Waals correction based on maximally localized Wannier functions, we inspect its performance and assess its reliability for aqueous solutions of alkali metal ions. We find that van der Waals interactions, when added to the widely used revPBE gradient corrected functional, influence substantially both structural and dynamical properties of water molecules, with particular emphasis on the hydration shell of the alkali cations. These effects are more evident for strong structure-making and -breaking cationic species. Moreover, self-diffusion coefficients and reorientation correlation times of solvating water molecules change systematically, showing a trend in better agreement with experiments with respect to simulations neglecting the long-range dispersion contributions.
Kido, Kentaro; Kasahara, Kento*; Yokogawa, Daisuke*; Sato, Hirofumi*
Journal of Chemical Physics, 143(1), p.014103_1 - 014103_9, 2015/07
Journal of Chemical Physics, 143(4), p.044506_1 - 044506_9, 2015/07
Shimada, Hiroyuki*; Minami, Hirotake*; Okuizumi, Naoto*; Sakuma, Ichiro*; Ukai, Masatoshi*; Fujii, Kentaro; Yokoya, Akinari; Fukuda, Yoshihiro*; Saito, Yuji
Journal of Chemical Physics, 142(17), p.175102_1 - 175102_9, 2015/05
Honda, Mitsunori; Yanagida, Masatoshi*; Han, L.*; Miyano, Kenjiro*
Journal of Chemical Physics, 141(17), p.174709_1 - 174709_7, 2014/11
Yoshigoe, Akitaka; Teraoka, Yuden; Okada, Ryuta; Yamada, Yoichi*; Sasaki, Masahiro*
Journal of Chemical Physics, 141(17), p.174708_1 - 174708_7, 2014/11
synchrotron radiation photoelectron spectroscopy was performed during the oxidation of the Ge(100)-21 surface induced by a molecular oxygen beam with various incident energies up to 2.2 eV from the initial to saturation coverage of surface oxides. The saturation coverage of oxygen on the clean Ge(100) surface was much lower than one monolayer and the oxidation state of Ge was +2 at most. This indicates that the Ge(100) surface is in strong contrast to Si surfaces. The direct adsorption process can be activated by increasing the translational energy, resulting in an increased population of Ge and a higher final oxygen coverage. Our findings will contribute to the fundamental understanding of oxygen adsorption processes at 300 K from the initial stages to saturated oxidation.