Nagai, Yuki; Okumura, Masahiko; Kobayashi, Keita*; Shiga, Motoyuki
Physical Review B, 102(4), p.041124_1 - 041124_6, 2020/07
no abstracts in English
Yan, L.*; Yamamoto, Yoshiyuki*; Shiga, Motoyuki; Sugino, Osamu*
Physical Review B, 101(16), p.165414_1 - 165414_9, 2020/04
Nuclear quantum effect and many-body interaction importantly interplay in the hydrogen on the Pt(111) system under the high coverage conditions of electrochemical interest, as revealed by our ab initio path integral and ring polymer molecular dynamics simulations done at room temperature. At the full monolayer coverage, hydrogen atoms are close-packed either at the atop sites or the fcc sites owing to their strong repulsion and the nearly degenerate nature of the adsorption sites. While at the 2/3 monolayer, they are delocalized over the fcc and hcp sites via the bridge sites because of the hopping. The quantum many-body effect is thus crucially important in determining the coverage dependence and provides a clue for reconciling the long-standing controversy on this system.
Kimizuka, Hajime*; Ogata, Shigenobu*; Shiga, Motoyuki
Physical Review B, 100(2), p.024104_1 - 024104_9, 2019/07
The behavior of H isotopes in crystals is a fundamental and recurrent theme in materials physics. Especially, the information on H diffusion over a wide temperature range provides a critical insight into the quantum mechanical nature of the subject; however, this is not yet fully explored. From state-of-the-art ab initio calculations to treat both electrons and nuclei quantum mechanically, we found that the temperature dependence of H isotope diffusivities in face-centered-cubic (fcc) Pd has an unconventional "reversed S" shape on Arrhenius plots. Such irregular behavior is ascribed to the competition between different nuclear quantum effects with different temperature and mass dependencies, which leads to a peculiar situation, where the heavier tritium (H) diffuses faster than the lighter protium (H) in the limited temperature range of 80 - 400 K. This unveils the mechanism of anomalous crossovers between the normal and reversed isotope effects observed in the experiments at high and low temperatures.
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.
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.
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.
Ozama, Eiki*; Adachi, Sadia*; Takayanagi, Toshiyuki*; Shiga, Motoyuki
Chemistry; A European Journal, 24(48), p.12716 - 12721, 2018/08
The structures of trivalent actinium cation in helium clusters (AcHe) have been studied by quantum path integral molecular dynamics simulations with different cluster sizes, = 18-200. The nuclear quantum effect of helium atoms plays an important role in the vibrational amplitude of the Ac-He complex at low temperatures (1-3 K) where the complex is stable. We found that the coordination number of helium atoms comprising the first solvation shell can be as high as eighteen. In this case, the helium atoms are arranged in D symmetry. The Ac-He complex becomes more rigid as the cluster increases in sizes, implying that it becomes more stable. The simulation results are based on an accurate description of the Ac-He interaction using relativistic ab initio calculations.
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.
Kimizuka, Hajime*; Ogata, Shigenobu*; Shiga, Motoyuki
Physical Review B, 97(1), p.014102_1 - 014102_11, 2018/01
To understand the mechanism of high diffusivity of hydrogen in palladium, we have studied the process of fast diffusion of interstitial H in face-centered cubic Pd, based on a first principles simulation taking account of quantum mechanical nature of both electrons and nuclei under finite strains. The simulated results revealed that the activation barrier for hydrogen migration was drastically increased with decreasing temperature owing to nuclear quantum effects on the octahedral sites. However, under the lattice expansion, nuclear quantum effects became less important since the tetrahedral site is stabilized. This implies that the diffusion mechanism gradually changes from quantum-like to classical-like as the strain is increased.
Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (Internet), 22 Pages, 2018/00
Nuclear quantum effects are important in molecular systems containing light elements such as hydrogen. For example large zero vibration and proton tunneling in hydrogen bonded systems originate from nuclear quantum effects. We herein describe path integral molecular dynamics (PIMD) where nuclear quantum effects are taken into account based on imaginary time path integral theory. PIMD provides numerically exact solutions for quantum statistics of complex molecular systems in thermal equilibrium. Centroid and ring polymer molecular dynamics are extensions to provide approximate quantum dynamics. Combination with ab initio electronic structure calculations enables simulation of the whole entity of many-electron many-nuclei systems.
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.
Ruiz-Barragan, S.*; Ribas Ario, J.*; Shiga, Motoyuki
Physical Chemistry Chemical Physics, 18(47), p.32438 - 32447, 2016/12
The use of high-temperature liquid water (HTW) as a reaction medium is a very promising technology in the field of green chemistry. In order to fully exploit this technology, it is crucial to unravel the reaction mechanisms of the processes carried out in HTW. In this work, the reaction mechanism of 2,5-hexanediol dehydration in HTW has been studied by means of three different ab initio simulations: string method, metadynamics and molecular dynamics in real time. It is found that the whole reaction involving the protonation, bond exchange and the deprotonation occurs in a single step without a stable intermediate. The hydrogen bonded network of surrounding water has a vital role in assisting an efficient proton relay at the beginning and at the end of the reaction. It is confirmed that the reaction is energetically most favorable in the SN2 pathway with an estimated barrier of 36 kcal/mol, which explains the high stereo selectivity and the reaction rate observed in experiment.
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.
Minoshima, Yusuke*; Seki, Yusuke*; Takayanagi, Toshiyuki*; Shiga, Motoyuki
Chemical Physics, 472, p.1 - 8, 2016/06
The dynamical process of electron attachment to a guanine-cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.
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.
Vela, S.*; Deumal, M.*; Shiga, Motoyuki; Novoa, J.*; Ribas-Arino, J.*
Chemical Science, 6(4), p.2371 - 2381, 2015/04
The magnetic properties of molecule-based magnets are commonly rationalized by considering only a single nuclear configuration of the system under study, usually X-ray crystal structure. Here, by means of a computational study in which the results obtained using such a static approach and those obtained by explicitly accounting for thermal fluctuations are compared, we uncover that the serious limitations of the static perspective when dealing with magnetic crystals whose radicals undergo wide-amplitude motions. As a proof of concept, these limitations are illustrated for magnetically bistable 1,3,5-trithia-2,4,6-triazapentalenyl (TTTA) material. The discovery that a single X-ray structure is not adequate enough to interpret the magnetic properties of TTTA is also expected to be decisive in other organic magnets with dominant exchange interactions propagating through labile networks.
Vela, S.*; Mota, F.*; Deumal, M.*; Suizu, Rie*; Shuku, Yoshiaki*; Mizuno, Asato*; Awaga, Kunio*; Shiga, Motoyuki; Novoa, J.*; Ribas-Arino, J.*
Nature Communications (Internet), 5, p.4411_1 - 4411_9, 2014/07
Recent years have witnessed a growing interest in the use of organic radicals as building blocks for bistable materials, i.e. materials that exist in two inter-exchangeable phases under identical thermodynamic conditions. The neutral radical TTTA is a prominent dithiazolyl-based compound because of its spin transition with a hysterisis nature near the room temperature. From ab initio molecular dynamics simulations, it has been evident that this phase transition is driven by the pair exchange dynamics of molecular stacking units accompanied by a significant gain of vibrational entropy.