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Journal Articles

Structures of liquid and aqueous water isotopologues at ambient temperature from ${it ab initio}$ path integral simulations

Thomsen, B.; Shiga, Motoyuki

Physical Chemistry Chemical Physics, 24(18), p.10851 - 10859, 2022/05

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

Journal Articles

X-ray absorption spectra of aqueous cellobiose; Experiment and theory

Akazawa, Daisuke; Sasaki, Takehiko*; Nagasaka, Masanari*; Shiga, Motoyuki

Journal of Chemical Physics, 156(4), p.044202_1 - 044202_7, 2022/01

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

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 $$^{circ}$$C to 60 $$^{circ}$$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.

Journal Articles

${it Ab initio}$ study of nuclear quantum effects on sub- and supercritical water

Thomsen, B.; Shiga, Motoyuki

Journal of Chemical Physics, 155(19), p.194107_1 - 194107_11, 2021/11

 Times Cited Count:3 Percentile:56.49(Chemistry, Physical)

Journal Articles

Mean force based temperature accelerated sliced sampling; Efficient reconstruction of high dimensional free energy landscapes

Pal, A.*; Pal, S.*; Verma, S.*; Shiga, Motoyuki; Nair, N. N.*

Journal of Computational Chemistry, 42(28), p.1996 - 2003, 2021/10

 Times Cited Count:2 Percentile:52.63(Chemistry, Multidisciplinary)

Temperature-accelerated sliced sampling is a computational method for high-dimensional free energy landscapes. In the conventional method, post-processing of the calculation has been required using the weighted histogram analysis method. In this study, we establish a refined approach without post-processing using the average force. We demonstrated the cases of the two-dimensional and four-dimensional free energy landscapes of alanine dipeptide and tripeptide, where they were computed within an error of about kcal/mol. Vast application of this method is expected for free energy calculations in computational chemistry.

Journal Articles

The Mechanism of sorbitol dehydration in hot acidic solutions

Kondo, Tomomi; Sasaki, Takehiko*; Shiga, Motoyuki

Journal of Computational Chemistry, 42(25), p.1783 - 1791, 2021/09

 Times Cited Count:1 Percentile:31.27(Chemistry, Multidisciplinary)

Sugar alcohol dehydration in hot water is an important reaction that allows for environmentally friendly biomass conversion without the use of organic solvents. Here, we report a free-energy analysis by metadynamics (MTD) simulations based on ab initio and semiempirical electronic structure theory to understand the mechanism of dehydration reactions of sorbitol (SBT) in hot acidic water. It was found that the reaction proceeds via an S$$_{rm N}$$2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected by the acidic species. The free energy barriers of the reaction pathways leading to five-membered ether products are lower than those leading to six-membered ether products.

Journal Articles

Self-learning hybrid Monte Carlo method for isothermal-isobaric ensemble; Application to liquid silica

Kobayashi, Keita; Nagai, Yuki; Itakura, Mitsuhiro; Shiga, Motoyuki

Journal of Chemical Physics, 155(3), p.034106_1 - 034106_9, 2021/07

 Times Cited Count:2 Percentile:33.13(Chemistry, Physical)

no abstracts in English

Journal Articles

Two distinct non-Arrhenius behaviors of hydrogen diffusivities in fcc aluminum, silver, and copper determined by ${it ab initio}$ path integral simulations

Kimizuka, Hajime*; Shiga, Motoyuki

Physical Review Materials (Internet), 5(6), p.065406_1 - 065406_9, 2021/06

 Times Cited Count:3 Percentile:64.73(Materials Science, Multidisciplinary)

Nuclear quantum effects are a non-negligible factor in the dynamic behavior of hydrogen in metals. In this study, we investigated the hydrogen diffusion in the face-centered cubic metals Al, Ag, and Cu using a first-principles integral molecular dynamics simulation that takes into account the nuclear quantum effects. It was found that the temperature dependence of hydrogen diffusion in Ag and Cu is inverted S-shaped, while the temperature dependence of hydrogen diffusion in Al is C-shaped. This difference is due to the fact that the most stable position of hydrogen is the octahedral site in Ag and Cu, while it is the tetrahedral site in Al. Therefore, it is found that the nuclear quantum effects of hydrogen diffusion (zero-point oscillation and tunneling) differ qualitatively depending on metals with different stable sites.

Journal Articles

Nuclear quantum effects on autoionization of water isotopologs studied by ${it ab initio}$ path integral molecular dynamics

Thomsen, B.; Shiga, Motoyuki

Journal of Chemical Physics, 154(8), p.084117_1 - 084117_10, 2021/02

 Times Cited Count:4 Percentile:71(Chemistry, Physical)

In this study we investigate the nuclear quantum effects on the acidity constant of liquid water isotopologues at the ambient condition by ${it ab initio}$ path integral molecular dynamics simulations. This technique not only reproduces the acidity constants of liquid D$$_{2}$$O experimentally measured but also allows for a theoretical prediction of the acidity constants of liquid T$$_{2}$$O, 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.

Journal Articles

Refined metadynamics through canonical sampling using time-invariant bias potential; A Study of polyalcohol dehydration in hot acidic solutions

Kondo, Tomomi; Sasaki, Takehiko*; Ruiz-Barragan, S.*; Ribas-Ari$~n$o, J.*; Shiga, Motoyuki; Ruiz-Barragan, S.*

Journal of Computational Chemistry, 42(3), p.156 - 165, 2021/01

 Times Cited Count:3 Percentile:31.24(Chemistry, Multidisciplinary)

We propose a canonical sampling method to refine metadynamics simulations a posteriori. This approach could be useful particularly when two or more free energy barriers are to be compared among chemical reactions in different or competing conditions. The method was then applied to study the acid dependence of polyalcohol dehydration reactions in high-temperature aqueous solutions. It was found that the reaction proceeds consistently via an S$$_{rm N}$$2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species.

Journal Articles

Quantum-mechanical hydration plays critical role in the stability of firefly oxyluciferin isomers; State-of-the-art calculations of the excited states

Noguchi, Yoshifumi*; Hiyama, Miyabi*; Shiga, Motoyuki; Akiyama, Hidefumi*; Sugino, Osamu*

Journal of Chemical Physics, 153(20), p.201103_1 - 201103_6, 2020/11

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

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.

Journal Articles

Diffusion mechanisms of hydrogen in metals explored via path-integral methods

Kimizuka, Hajime*; Ogata, Shigenobu*; Shiga, Motoyuki

Nihon Butsuri Gakkai-Shi, 75(8), p.484 - 490, 2020/08

Hydrogen is an element having quantum nature, and exhibits a unique diffusion behavior not found in other impurity atoms. In this study, the diffusion behavior of hydrogen isotopes in palladium crystals was predicted at a wide range of temperatures using a first-principles approach that combines the path integral simulation and electronic structure calculation. It was shown that in the high temperature region, the influence of quantum fluctuations becomes apparent as the temperature decreases, causing the suppression of diffusion where the Arrhenius plot bends upward. On the other hand, in the low temperature region, the diffusion barrier decreases due to the manifestation of the quantum tunneling effect, and the Arrhenius plot bents downward. The competition of quantum effects in different temperature regions clearly explains the anomalous isotopic effect of hydrogen diffusion.

Journal Articles

Self-learning hybrid Monte Carlo; A First-principles approach

Nagai, Yuki; Okumura, Masahiko; Kobayashi, Keita*; Shiga, Motoyuki

Physical Review B, 102(4), p.041124_1 - 041124_6, 2020/07

 Times Cited Count:5 Percentile:55.43(Materials Science, Multidisciplinary)

no abstracts in English

Journal Articles

Nuclear quantum effect for hydrogen adsorption on Pt(111)

Yan, L.*; Yamamoto, Yoshiyuki*; Shiga, Motoyuki; Sugino, Osamu*

Physical Review B, 101(16), p.165414_1 - 165414_9, 2020/04

 Times Cited Count:9 Percentile:71.72(Materials Science, Multidisciplinary)

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.

Journal Articles

Unraveling anomalous isotope effect on hydrogen diffusivities in fcc metals from first principles including nuclear quantum effects

Kimizuka, Hajime*; Ogata, Shigenobu*; Shiga, Motoyuki

Physical Review B, 100(2), p.024104_1 - 024104_9, 2019/07

 Times Cited Count:9 Percentile:56.68(Materials Science, Multidisciplinary)

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 ($$^3$$H) diffuses faster than the lighter protium ($$^1$$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.

Journal Articles

Understanding competition of polyalcohol dehydration reactions in hot water

Chang, Y. L.*; Sasaki, Takehiko*; Ribas-Ari$~n$o, J.*; Machida, Masahiko; Shiga, Motoyuki

Journal of Physical Chemistry B, 123(7), p.1662 - 1671, 2019/02

 Times Cited Count:4 Percentile:19.24(Chemistry, Physical)

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 S$$_{rm N}$$2 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.

Journal Articles

Finding free-energy landmarks of chemical reactions

Shiga, Motoyuki; Tuckerman, M. E.*

Journal of Physical Chemistry Letters (Internet), 9(21), p.6207 - 6214, 2018/11

 Times Cited Count:4 Percentile:24.5(Chemistry, Physical)

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.

Journal Articles

Nuclear quantum effects in the direct ionization process of pure helium clusters; Path-integral and ring-polymer molecular dynamics simulations on the diatomics-in-molecule potential energy surfaces

Suzuki, Kento*; Miyazaki, Takaaki*; Takayanagi, Toshiyuki*; Shiga, Motoyuki

Physical Chemistry Chemical Physics, 20(41), p.26489 - 26499, 2018/11

 Times Cited Count:2 Percentile:10.87(Chemistry, Physical)

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.

Journal Articles

Quantum simulation verifies the stability of an 18-coordinated actinium-helium complex

Ozama, Eiki*; Adachi, Sadia*; Takayanagi, Toshiyuki*; Shiga, Motoyuki

Chemistry; A European Journal, 24(48), p.12716 - 12721, 2018/08

 Times Cited Count:5 Percentile:26.85(Chemistry, Multidisciplinary)

The structures of trivalent actinium cation in helium clusters (Ac$$^{3+}$$He$$_n^{}$$) have been studied by quantum path integral molecular dynamics simulations with different cluster sizes, $$n$$ = 18-200. The nuclear quantum effect of helium atoms plays an important role in the vibrational amplitude of the Ac$$^{3+}$$-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$$_{4d}^{}$$ symmetry. The Ac$$^{3+}$$-He$$_{18}^{}$$ 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$$^{3+}$$-He interaction using relativistic ab initio calculations.

Journal Articles

Nuclear quantum effects of light and heavy water studied by all-electron first principles path integral simulations

Machida, Masahiko; Kato, Koichiro*; Shiga, Motoyuki

Journal of Chemical Physics, 148(10), p.102324_1 - 102324_11, 2018/03

AA2017-0553.pdf:4.95MB

 Times Cited Count:15 Percentile:73.92(Chemistry, Physical)

The isotopologs of liquid water, H$$_{2}$$O, D$$_{2}$$O, and T$$_{2}$$O, 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 H$$_{2}$$O and D$$_{2}$$O 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.

Journal Articles

Mechanism of fast lattice diffusion of hydrogen in palladium; Interplay of quantum fluctuations and lattice strain

Kimizuka, Hajime*; Ogata, Shigenobu*; Shiga, Motoyuki

Physical Review B, 97(1), p.014102_1 - 014102_11, 2018/01

AA2017-0587.pdf:0.9MB

 Times Cited Count:16 Percentile:71.39(Materials Science, Multidisciplinary)

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.

176 (Records 1-20 displayed on this page)