Software introduction "PIMD"

Shiga, Motoyuki; Thomsen, B.; Nagai, Yuki

Ansanburu, 25(4), p.303 - 310, 2023/10

The parallel molecular simulation software "PIMD" will be presented. The use of PIMD will be explained through specific examples such as water structure by ab initio path integral molecular dynamics, quantum diffusion of hydrogen in metal by ring polymer molecular dynamics, machine learning potential generation and phonon properties of superconductors, and polyalcohol dehydration reaction by metadynamics.

Path integral Brownian chain molecular dynamics; A Simple approximation of quantum vibrational dynamics

Shiga, Motoyuki

Journal of Computational Chemistry, 43(27), p.1864 - 1879, 2022/10

https://doi.org/10.1002/jcc.26989

A new approximate method for quantum vibrational dynamics (Brownian chain molecular dynamics: BCMD) based on the path integral method is proposed. Conventional methods such as centroid molecular dynamics and ring polymer dynamics cannot correctly calculate quantum vibration spectra under low temperature conditions. Thus, I introduce an over-damped Langevin equation for the non-centroid degrees of freedom of atoms to suppress unphysical resonances and vibrational rotational couplings, which are the source of the problem. I verify this approximation through applications to infrared absorption spectra of light and heavy water. I also demonstrate the feasibility of ab initio BCMD simulations by the combination with electronic structure theory.

Structures of liquid and aqueous water isotopologues at ambient temperature from path integral simulations

Thomsen, B.; Shiga, Motoyuki

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

https://doi.org/10.1039/D2CP00499B

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

https://doi.org/10.1063/5.0071857

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

https://doi.org/10.1002/jcc.26710

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 S2 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.

Two distinct non-Arrhenius behaviors of hydrogen diffusivities in fcc aluminum, silver, and copper determined by path integral simulations

Kimizuka, Hajime*; Shiga, Motoyuki

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

https://doi.org/10.1103/PhysRevMaterials.5.065406

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.

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-Ario, J.*; Shiga, Motoyuki; Ruiz-Barragan, S.*

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

https://doi.org/10.1002/jcc.26443

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 S2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species.

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

https://doi.org/10.11316/butsuri.75.8_484

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.

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

https://doi.org/10.1103/PhysRevB.101.165414

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.

Understanding competition of polyalcohol dehydration reactions in hot water

Chang, Y. L.*; Sasaki, Takehiko*; Ribas-Ario, J.*; Machida, Masahiko; Shiga, Motoyuki

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

https://doi.org/10.1021/acs.jpcb.8b11615

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.