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Journal Articles

Understanding water-mediated DNA damage production by molecular dynamics calculation of solvent accessibility

Yonetani, Yoshiteru*; Nakagawa, Hiroshi

Chemical Physics Letters, 749, p.137441_1 - 137441_5, 2020/06

 Times Cited Count:0 Percentile:100(Chemistry, Physical)

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.

Journal Articles

Quantum chemical calculations for the norbadione A complexes with Cs$$^+$$, K$$^+$$, and Na$$^+$$ in gas and aqueous phases

Suno, Hiroya; Machida, Masahiko

Chemical Physics Letters, 730, p.26 - 31, 2019/09

 Times Cited Count:0 Percentile:100(Chemistry, Physical)

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 $textit{et al.}$, 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.

Journal Articles

A Screened automated structural search with semiempirical methods

Ota, Yukihiro; Ruiz-Barragan, S.*; Machida, Masahiko; Shiga, Motoyuki

Chemical Physics Letters, 648, p.119 - 123, 2016/03

 Times Cited Count:2 Percentile:89.03(Chemistry, Physical)

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.

Journal Articles

On the hierarchical parallelization of ${{it ab initio}}$ simulations

Ruiz-Barragan, S.*; Ishimura, Kazuya*; Shiga, Motoyuki

Chemical Physics Letters, 646, p.130 - 135, 2016/02

 Times Cited Count:6 Percentile:68.58(Chemistry, Physical)

A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ${{it ab initio}}$ 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.

Journal Articles

Semiclassical dynamics of electron attachment to guanine-cytosine base pair

Honda, Tomohiro*; Minoshima, Yusuke*; Yokoi, Yuki*; Takayanagi, Toshiyuki*; Shiga, Motoyuki

Chemical Physics Letters, 625, p.174 - 178, 2015/04

 Times Cited Count:3 Percentile:84.09(Chemistry, Physical)

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.

Journal Articles

Structure of ultra-thin silicon film on HOPG studied by polarization-dependence of X-ray absorption fine structure

Baba, Yuji; Shimoyama, Iwao; Hirao, Norie; Sekiguchi, Tetsuhiro

Chemical Physics Letters, 594, p.64 - 68, 2014/02

 Times Cited Count:2 Percentile:91.14(Chemistry, Physical)

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 $$pi$$$$^{*}$$ and $$sigma$$$$^{*}$$ 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.

Journal Articles

Structural changes of nucleic acid base in aqueous solution as observed in X-ray absorption near edge structure (XANES)

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

 Times Cited Count:6 Percentile:70.38(Chemistry, Physical)

Journal Articles

Terahertz absorption spectroscopy of protein-containing reverse micellar solution

Murakami, Hiroshi; Toyota, Yuji*; Nishi, Takaki*; Nashima, Shigeki*

Chemical Physics Letters, 519-520, p.105 - 109, 2012/01

 Times Cited Count:14 Percentile:45.73(Chemistry, Physical)

no abstracts in English

Journal Articles

Ferromagnetic interlayer coupling in C$$_{60}$$-Co compound/Ni bilayer structure

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

 Times Cited Count:5 Percentile:80.4(Chemistry, Physical)

X-ray magnetic circular dichroism (XMCD) spectroscopy was employed to investigate the electronic and magnetic structures of the bilayers of a C$$_{60}$$-Co compound and Ni. A few -several nm thick C$$_{60}$$-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$$_{60}$$-Co compound within 3 nm from the interface is ferromagnetically coupled with Ni due to the indirect exchange interaction mediated by C$$_{60}$$, probably relevant to the interlayer charge transfer.

Journal Articles

${it Ab initio}$ LC-DFT study of graphene, multilayer graphenes and graphite

Avramov, P.; Sakai, Seiji; Entani, Shiro; Matsumoto, Yoshihiro; Naramoto, Hiroshi*

Chemical Physics Letters, 508(1-3), p.86 - 89, 2011/05

 Times Cited Count:19 Percentile:36.88(Chemistry, Physical)

Journal Articles

Low-linear energy transfer radiolysis of liquid water at elevated temperatures up to 350$$^{circ}$$C; Monte-Carlo simulations

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

 Times Cited Count:36 Percentile:16.27(Chemistry, Physical)

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 $$g$$-values of the various radiolytic products with recently re-assessed experimental data up to 350$$^{circ}$$C. The inclusion in our simulations of the abrupt drop in the rate constant for the self-reaction of hydrated electron above 150$$^{circ}$$C 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$$_{2}$$ above 200$$^{circ}$$C was also briefly discussed.

Journal Articles

Theoretical study on the mechanism of double proton transfer in porphycene by path-integral molecular dynamics simulations

Yoshikawa, Takehiro*; Sugawara, Shuichi*; Takayanagi, Toshiyuki*; Shiga, Motoyuki; Tachikawa, Masanori*

Chemical Physics Letters, 496(1-3), p.14 - 19, 2010/08

 Times Cited Count:24 Percentile:30.81(Chemistry, Physical)

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.

Journal Articles

X-ray absorption spectra of nucleotides (AMP, GMP, and CMP) in liquid water solutions near the nitrogen K-edge

Ukai, Masatoshi*; Yokoya, Akinari; Fujii, Kentaro; Saito, Yuji

Chemical Physics Letters, 495(1-3), p.90 - 95, 2010/07

 Times Cited Count:9 Percentile:66.65(Chemistry, Physical)

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$$rightarrow$$$$pi$$* 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.

Journal Articles

Vibration-selective coherent anti-Stokes Raman scattering with linearly chirped white-light pulses

Kasajima, Tatsuya; Yokoyama, Keiichi; Matsuoka, Leo; Yokoyama, Atsushi

Chemical Physics Letters, 485(1-3), p.45 - 48, 2010/01

 Times Cited Count:1 Percentile:96.44(Chemistry, Physical)

Journal Articles

Path-integral molecular dynamics simulations for water anion clusters (H$$_2$$O)$$_5^-$$ and (D$$_2$$O)$$_5^-$$

Takayanagi, Toshiyuki*; Yoshikawa, Takehiro*; Motegi, Haruki*; Shiga, Motoyuki

Chemical Physics Letters, 482(4-6), p.195 - 200, 2009/12

 Times Cited Count:8 Percentile:70.71(Chemistry, Physical)

Path-integral molecular dynamics simulations have been performed for water anion clusters,(H$$_2$$O)$$_5^-$$ and (D$$_2$$O)$$_5^-$$, 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 (H$$_2$$O)$$_5^-$$ cluster are slightly larger than those in (D$$_2$$O)$$_5^-$$. The distribution of the vertical detachment energies for (H$$_2$$O)$$_5^-$$ also show a broader feature than that for (D$$_2$$O)$$_5^-$$. The present simulations thus demonstrate the importance of nuclear quantum effects in water anion clusters.

Journal Articles

Age-momentum correlation measurements of positron annihilation in water; Possibility of quantum beats on ortho-positronium reactions

Hirade, Tetsuya

Chemical Physics Letters, 480(1-3), p.132 - 135, 2009/09

 Times Cited Count:4 Percentile:86.24(Chemistry, Physical)

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 $$gamma$$-ray energy distribution observed using AMOC measurements did successfully reveal quantum beats in water. The results supported the two-state model of water structure.

Journal Articles

Photoelectron-photoion coincidence momentum imaging for dissociative ionization of ethanol in intense laser fields

Hosaka, Koichi; Itakura, Ryuji; Yokoyama, Keiichi; Yamanouchi, Kaoru*; Yokoyama, Atsushi

Chemical Physics Letters, 475(1-3), p.19 - 23, 2009/06

 Times Cited Count:10 Percentile:63.45(Chemistry, Physical)

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.

Journal Articles

X-ray absorption spectroscopy and magnetic circular dichroism in codeposited C$$_{60}$$-Co films with giant tunnel magnetoresistance

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

 Times Cited Count:17 Percentile:43.59(Chemistry, Physical)

Electronic and spin states of the codeposited C$$_{60}$$-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$$_{60}$$-Co compound generated in the C$$_{60}$$-Co films shows the clear MCD signal attributed to the spin-polarized Co 3d states hybridized with C$$_{60}$$ $$pi$$ orbitals. The magnetic response of these Co 3d-derived states agrees well with temperature dependence of the observed MR ratios of the granular C$$_{60}$$-Co films. This suggests the incorporation of the spin-polarized Co 3d-derived states of the C$$_{60}$$-Co compound into the observed TMR effect.

Journal Articles

Determination of the time-dependent OH-yield by using a fluorescent probe; Application to heavy ion irradiation

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

 Times Cited Count:30 Percentile:23.42(Chemistry, Physical)

This paper reports a sensitive method using HPLC-fluorescence detection of $$^{bullet}$$OH in liquid water under high-energy heavy-ion irradiation. The coumarin-3-carboxylic-acid (3CCA) molecule was selected for probing $$^{bullet}$$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 2$$times$$10$$^{-9}$$ mol/J for 4.8-GeV-$$^{12}$$C$$^{6+}$$ of and 20-GeV-$$^{40}$$Ar$$^{18+}$$ in the ns time-range. They decrease with the linear energy transfer from 2.8$$times$$10$$^{-7}$$ to 1.3$$times$$10$$^{-7}$$ mol/J ($$^{12}$$C$$^{6+}$$ of 11 eV/nm) and 1.5$$times$$10$$^{-7}$$ to 0.9$$times$$10$$^{-7}$$ mol/J ($$^{40}$$Ar$$^{18+}$$ of 90 eV/nm) which is in agreement with the literature data.

Journal Articles

Intense laser-induced decomposition of mass-selected 2-, 3-, and 4-methylaniline cations

Itakura, Ryuji; Tanaka, Takatsugu*; Kuwata, Mikinori*; Suzuki, Hideaki*; Yamanouchi, Kaoru*

Chemical Physics Letters, 462(1-3), p.27 - 30, 2008/09

 Times Cited Count:2 Percentile:93.93(Chemistry, Physical)

Photodecomposition processes of 2-, 3-, and 4-methylaniline cations induced by a moderately intense ($$sim$$ 10$$^{11}$$ W/cm$$^{2}$$) visible nanosecond laser field and an intense ($$sim$$ 10$$^{15}$$ W/cm$$^{2}$$) UV femtosecond laser field are investigated using a tandem mass spectrometer. Highly unsaturated fragment cations such as C$$_{6}$$H$$_{2}$$$$^{+}$$, C$$_{6}$$H$$_{3}$$$$^{+}$$ are dominantly produced by the nanosecond laser, while less unsaturated smaller fragment cations such as C$$_{3}$$H$$_{3}$$$$^{+}$$, C$$_{4}$$H$$_{4}$$$$^{+}$$, C$$_{5}$$H$$_{5}$$$$^{+}$$ are produced mainly by the femtosecond laser.

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