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.
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.
Ota, Yukihiro; Ruiz-Barragan, S.*; Machida, Masahiko; Shiga, Motoyuki
Chemical Physics Letters, 648, p.119 - 123, 2016/03
We developed an interface program between a program suite for an automated search of chemical reaction pathways, GRRM, and a program package of semiempirical methods, MOPAC. A two-step structural search is proposed as an application of this interface program. A screening test is first performed by semiempirical calculations. Subsequently, a reoptimization procedure is done by ab initio or density functional calculations. We apply this approach to ion adsorption on cellulose. The computational efficiency is also shown for a GRRM search. The interface program is suitable for the structural search of large molecular systems for which semiempirical methods are applicable.
Ruiz-Barragan, S.*; Ishimura, Kazuya*; Shiga, Motoyuki
Chemical Physics Letters, 646, p.130 - 135, 2016/02
A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.
Honda, Tomohiro*; Minoshima, Yusuke*; Yokoi, Yuki*; Takayanagi, Toshiyuki*; Shiga, Motoyuki
Chemical Physics Letters, 625, p.174 - 178, 2015/04
Electron attachment dynamics to the guanine-cytosine (G-C) base pair in the gas phase isstudied using DFT and molecular dynamics. The potential energy surface of the G-C anion isconstructed with the empirical-valence-bond method using force-field information obtained from long-range corrected DFT calculations. Ring-polymer molecular dynamics simulations predict that theinitial dipole-bound anion readily converts into the valence-bound anion within 0.1 ps and proton-transfer occurs subsequently within 10 ps. The same process was found in classical simulations, buton a much slower time scale. This result suggests that nuclear quantum effects are important inunderstanding DNA damage by low-energy electrons.
Baba, Yuji; Shimoyama, Iwao; Hirao, Norie; Sekiguchi, Tetsuhiro
Chemical Physics Letters, 594, p.64 - 68, 2014/02
Structures of mono-layered silicon on a highly oriented pyrolytic graphite (HOPG) have been investigated by X-ray photoelectron spectroscopy and X-ray absorption near edge structure (XANES). For the Si K-edge XANES spectrum of the 0.15 mono-layered film, two distinct peaks were observed, which were assigned to the resonant excitations from the Si 1s into the valence unoccupied orbitals with and characters. On the basis of the polarization dependences of the peak intensities, it was concluded that a part of the Si film lies flat on the HOPG surface, which supports the existence of two-dimensional graphene-like structure in mono-layered silicon.
Shimada, Hiroyuki*; Fukao, Taishi*; Minami, Hirotake*; Ukai, Masatoshi*; Fujii, Kentaro; Yokoya, Akinari; Fukuda, Yoshihiro*; Saito, Yuji
Chemical Physics Letters, 591, p.137 - 141, 2014/01
Murakami, Hiroshi; Toyota, Yuji*; Nishi, Takaki*; Nashima, Shigeki*
Chemical Physics Letters, 519-520, p.105 - 109, 2012/01
no abstracts in English
Matsumoto, Yoshihiro; Sakai, Seiji; Entani, Shiro; Takagi, Yasumasa*; Nakagawa, Takeshi*; Naramoto, Hiroshi*; Avramov, P.; Yokoyama, Toshihiko*
Chemical Physics Letters, 511(1-3), p.68 - 72, 2011/07
X-ray magnetic circular dichroism (XMCD) spectroscopy was employed to investigate the electronic and magnetic structures of the bilayers of a C-Co compound and Ni. A few -several nm thick C-Co compound layers on the Ni(111) surface are found to show intense XMCD signals attributed to the localized Co d-spins only with the remanent magnetization of Ni layer. It is suggested that the region of the C-Co compound within 3 nm from the interface is ferromagnetically coupled with Ni due to the indirect exchange interaction mediated by C, probably relevant to the interlayer charge transfer.
Avramov, P.; Sakai, Seiji; Entani, Shiro; Matsumoto, Yoshihiro; Naramoto, Hiroshi*
Chemical Physics Letters, 508(1-3), p.86 - 89, 2011/05
Sanguanmith, S.*; Muroya, Yusa*; Meesungnoen, J.*; Lin, M.; Katsumura, Yosuke*; Mirsaleh Kohan, L.*; Guzonas, D. A.*; Stuart, C. R.*; Jay-Gerin, J.-P.*
Chemical Physics Letters, 508(4-6), p.224 - 230, 2011/05
Our Monte-Carlo modeling of the high-temperature radiolysis of water by low-LET radiation was re-examined in an attempt to reconcile our computed -values of the various radiolytic products with recently re-assessed experimental data up to 350C. The inclusion in our simulations of the abrupt drop in the rate constant for the self-reaction of hydrated electron above 150C led us to re-evaluate the temperature dependence of certain parameters intervening in the physicochemical stage of the radiolysis. A very good agreement was found between model and experiment. The importance of the reaction of H atoms with water in the unexplained yield of H above 200C was also briefly discussed.
Yoshikawa, Takehiro*; Sugawara, Shuichi*; Takayanagi, Toshiyuki*; Shiga, Motoyuki; Tachikawa, Masanori*
Chemical Physics Letters, 496(1-3), p.14 - 19, 2010/08
Full-dimensional path-integral molecular dynamics simulations were performed to determine whether the double proton transfer tautomerization of porphycene is a concerted or a stepwise process. It was found that double proton transfer occurs dominantly through the concerted pathway via the second-order saddle point structure and that contribution of the stepwise mechanism increases with a temperature increase. Nuclear quantum effects play essential roles in determining the proton transfer mechanism.
Ukai, Masatoshi*; Yokoya, Akinari; Fujii, Kentaro; Saito, Yuji
Chemical Physics Letters, 495(1-3), p.90 - 95, 2010/07
The X-ray absorption of nucleotides (adenosine-5'-monophosphate, guanosine-5'-monophosophate, and cytidine-5'-monophosophate) are measured in both water solutions and thin solid films at X-ray energies near the nitrogen K-edge in the "water-window" region. Each spectrum corresponds to the selective excitation of a nucleobase site in a nucleotide, and thus has features similar to the spectrum of the corresponding nucleobase. An additional new peak in the energy region of the nitrogen 1s* resonance is observed for each nucleotide. No significant difference between the water solutions and thin solid films is found, which might be attributable to the hydrophobic properties of a nucleobase in a nucleotide.
Kasajima, Tatsuya; Yokoyama, Keiichi; Matsuoka, Leo; Yokoyama, Atsushi
Chemical Physics Letters, 485(1-3), p.45 - 48, 2010/01
Takayanagi, Toshiyuki*; Yoshikawa, Takehiro*; Motegi, Haruki*; Shiga, Motoyuki
Chemical Physics Letters, 482(4-6), p.195 - 200, 2009/12
Path-integral molecular dynamics simulations have been performed for water anion clusters,(HO) and (DO), on the basis of a semiempirical one-electron pseudopotential polarization model. Due to larger zero-point vibrational amplitudes for H atoms than that of D atoms, hydrogen-bond lengths in the (HO) cluster are slightly larger than those in (DO). The distribution of the vertical detachment energies for (HO) also show a broader feature than that for (DO). The present simulations thus demonstrate the importance of nuclear quantum effects in water anion clusters.
Chemical Physics Letters, 480(1-3), p.132 - 135, 2009/09
Quantum beats were detected in the reaction of electron-spin-correlated pairs of ortho-positronium and hydroxyl radical. Singlet ortho-positronium and hydroxyl radical pairs were generated in positron radiolysis of water molecules. The singlet-triplet transition caused via the hyperfine coupling of every radical affects the rate of the radical reaction, and then affects the rate of the competing reaction, the spin conversion reaction between ortho-positronium and hydroxyl radical. Spin conversion of ortho-positronium can possibly be detected using positron annihilation age-momentum correlation (AMOC) measurements, and time resolved annihilation -ray energy distribution observed using AMOC measurements did successfully reveal quantum beats in water. The results supported the two-state model of water structure.
Hosaka, Koichi; Itakura, Ryuji; Yokoyama, Keiichi; Yamanouchi, Kaoru*; Yokoyama, Atsushi
Chemical Physics Letters, 475(1-3), p.19 - 23, 2009/06
In intense laser fields, molecules are decomposed into fragments through a number of competing dissociative ionization pathways. We investigate the dissociative ionization dynamics of ethanol in intense laser fields with photoelectron-photoion coincidence momentum imaging. The channel-specific photoelectron spectra reveal the electronic states prepared just after ionization, depending both on the decomposition pathways and on the temporal profile of laser pulses.
Matsumoto, Yoshihiro; Sakai, Seiji; Takagi, Yasumasa*; Nakagawa, Takeshi*; Yokoyama, Toshihiko*; Shimada, Toshihiro*; Mitani, Seiji*; Naramoto, Hiroshi*; Maeda, Yoshihito
Chemical Physics Letters, 470(4-6), p.244 - 248, 2009/03
Electronic and spin states of the codeposited C-Co films with large tunnel magnetoresistance (TMR) effect were investigated with the X-ray absorption and magnetic circular dichroism (MCD) spectroscopies. It is revealed that a C-Co compound generated in the C-Co films shows the clear MCD signal attributed to the spin-polarized Co 3d states hybridized with C orbitals. The magnetic response of these Co 3d-derived states agrees well with temperature dependence of the observed MR ratios of the granular C-Co films. This suggests the incorporation of the spin-polarized Co 3d-derived states of the C-Co compound into the observed TMR effect.
Baldacchino, G.*; Maeyama, Takuya*; Yamashita, Shinichi; Taguchi, Mitsumasa; Kimura, Atsushi; Katsumura, Yosuke; Murakami, Takeshi*
Chemical Physics Letters, 468(4-6), p.275 - 279, 2009/01
This paper reports a sensitive method using HPLC-fluorescence detection of OH in liquid water under high-energy heavy-ion irradiation. The coumarin-3-carboxylic-acid (3CCA) molecule was selected for probing OH and providing the fluorescent 7-hydroxy-coumarin-3-carboxylic-acid (7OH-3CCA). Since the concentration limit achievable is better than 1 nM, the radiolytic yields were determined with a sensitivity of 210 mol/J for 4.8-GeV-C of and 20-GeV-Ar in the ns time-range. They decrease with the linear energy transfer from 2.810 to 1.310 mol/J (C of 11 eV/nm) and 1.510 to 0.910 mol/J (Ar of 90 eV/nm) which is in agreement with the literature data.
Itakura, Ryuji; Tanaka, Takatsugu*; Kuwata, Mikinori*; Suzuki, Hideaki*; Yamanouchi, Kaoru*
Chemical Physics Letters, 462(1-3), p.27 - 30, 2008/09
Photodecomposition processes of 2-, 3-, and 4-methylaniline cations induced by a moderately intense ( 10 W/cm) visible nanosecond laser field and an intense ( 10 W/cm) UV femtosecond laser field are investigated using a tandem mass spectrometer. Highly unsaturated fragment cations such as CH, CH are dominantly produced by the nanosecond laser, while less unsaturated smaller fragment cations such as CH, CH, CH are produced mainly by the femtosecond laser.