Updated on 2025/09/01

写真a

 
Tomomi Shimazaki
 
Organization
Graduate School of Nanobioscience Department of Materials System Science Professor
School of Science Department of Science
Title
Professor
Profile

理論・計算・情報化学を用いて『ものづくり』に貢献できることを目指しています。そのために、物理・化学シミュレーションに加え、機械学習のようなデータサイエンス手法の活用についても研究しています。

External link

Degree

  • 博士（工学） ( 2006.3   東京大学 )

Research Interests

  • 情報化学

  • 計算化学

  • 理論化学

Research Areas

  • Nanotechnology/Materials / Fundamental physical chemistry

  • Natural Science / Biophysics, chemical physics and soft matter physics

  • Informatics / Computational science

  • Nanotechnology/Materials / Composite materials and interfaces

  • Nanotechnology/Materials / Energy chemistry

  • Nanotechnology/Materials / Green sustainable chemistry and environmental chemistry

  • Nanotechnology/Materials / Polymer chemistry

  • Nanotechnology/Materials / Structural materials and functional materials

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Papers

  • Metal‐Free Raman Sensing Platforms of Organic Nanowire Arrays Produced by High Energy Charged Particles Reviewed

    Masaki Nobuoka, Shugo Sakaguchi, Yusuke Tsutsui, Akie Taguchi, Makito Takagi, Tomomi Shimazaki, Masanori Tachikawa, Akira Idesaki, Tetsuya Yamaki, Devesh Kumar Avasthi, Merry Gupta, Ramcharan Meena, Ambuj Tripathi, Shu Seki

    Advanced Sensor Research   e00042   2025.6

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    Publishing type：Research paper (scientific journal)   Publisher：Wiley  

    Abstract

    An organic nanowire fabrication technique, i.e., single‐particle‐triggered linear polymerization, which yields nanowires consisting of a wide range of organic molecules with perfectly controlled sizes, is developed via chemical reactions induced by a high‐energy charged particle. A freestanding purely organic nanowire array (ONA) structure is fabricated to maximize the surface area with the designed surface affinity for analyte molecules. The ONA is demonstrated as an effective sensing platform for Raman spectroscopy with a high enough sensitivity against a series of analytes including rhodamine, crystal violet, methylene blue, neutral red, methyl orange, as well as oligopeptides. The designed electron transfer reactions between the analytes and nanowires provide Raman signal enhancement factors of up to 10<sup>8</sup> with the detection limit of the analytes as 10<sup>−9</sup> M for the rhodamine, indicating the viability of these ONAs as a novel class of metal‐free Raman sensing probes.

    DOI： 10.1002/adsr.202500042

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  • Rolling two-dimensional covalent organic framework (COF) sheets into one-dimensional electronic and proton-conductive nanotubes Reviewed

    Zhuowei Li, Rajendra Prasad Paitandi, Yusuke Tsutsui, Wakana Matsuda, Masaki Nobuoka, Bin Chen, Samrat Ghosh, Takayuki Tanaka, Masayuki Suda, Tong Zhu, Hiroshi Kageyama, Yoshihiro Miyake, Hiroshi Shinokubo, Makito Takagi, Tomomi Shimazaki, Masanori Tachikawa, Katsuaki Suzuki, Hironori Kaji, Yasunobu Ando, Takahiro Ezaki, Shu Seki

    Proceedings of the National Academy of Sciences   122 ( 16 )   e2424314122   2025.4

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    Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

    Mimicking the interconvertible carbon allotropes of 2-dimensional (2D) graphene and 1-dimensional (1D) carbon nanotubes (CNTs), herein we report the in situ transformation of 2D π-conjugated covalent organic frameworks (COFs) sheet into 1D nanotubular structures via self-assembly the sheets at solvent interfaces. The facile “roll-sheets” self-assembly resulted in coaxial nanotubes with uniform cross-sectional diameter, which was realized for diazapyrene-based COFs but not for the corresponding pyrene COF, although both possess similar chemical structures. Upon replacing the carbon atoms at 2,7-positions of pyrene with nitrogen, contrasting optical and electronic properties were realized, reflecting the rolled structure of the conjugated 2D sheets. The nanotubes exhibited concerted electronic- and proton-conducting nature with stable conducting pathways at ambient conditions. The nitrogen centers act simultaneously as the site for charge carrier doping and proton acceptors, as evidenced by the high photo- and electrical conductivity, as well as the record proton conductivity (σ = 1.98 S cm <sup>−1</sup> ) results. The present diazapyrene-based 1D nanotubular COF serves as a unique materials platform with electronic conduction in the wall and proton conduction in the core, respectively.

    DOI： 10.1073/pnas.2424314122

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  • A theoretical study of the molecular passivation of p-/n-type defects on tin- and germanium-mixed perovskite surfaces using Lewis base/acid Reviewed

    Emi Kino, Makito Takagi, Takumi Naito, Masanori Tachikawa, Koichi Yamashita, Tomomi Shimazaki

    Physical Chemistry Chemical Physics   27 ( 14 )   7429 - 7439   2025.4

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    Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    Lewis base can effectively remove the p-type deep defect levels from Sn and Ge mixed perovskite surface, through interacting with the defect site and donating an electron pair toward the defect state.

    DOI： 10.1039/d4cp03817g

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  • Development of Hessian calculation using the combined plane wave and localized basis sets method and its application to adsorption of a water molecule on Pt(111) surface Reviewed

    Hiroki Sakagami, Makito Takagi, Takayoshi Ishimoto, Tomomi Shimazaki, Masanori Tachikawa

    Molecular Catalysis   572   114791 - 114791   2025.2

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.mcat.2024.114791

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  • Density functional theory predictions of properties of bioactive molecules based on guided neural network approach using semi-empirical quantum chemistry Reviewed

    Tomomi Shimazaki, Masanori Tachikawa

    Chemical Physics Letters   861   141830 - 141830   2025.2

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.cplett.2024.141830

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  • Inclusion of Gold Ion in Tiara-Like Nickel Hexanuclear Nanoclusters Reviewed

    Kana Takemae, Shiho Tomihari, Takumi Naitou, Makito Takagi, Tomomi Shimazaki, Tokuhisa Kawawaki, Masanori Tachikawa, Yuichi Negishi

    Nanoscale   3721 - 3727   2025

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    Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    Tiara-like metal nanoclusters (TNCs) composed of group 10 transition metals and thiolates can easily change their number of polymerization and include various molecules and metal ions as guests within their...

    DOI： 10.1039/d4nr04579c

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  • A theoretical study on muoniated N-heterocyclic carbenes using path integral molecular dynamics Reviewed

    Satoshi Orikono, Kazuaki Kuwahata, Tomomi Shimazaki, Masanori Tachikawa

    The Journal of Chemical Physics   161 ( 18 )   184305   2024.11

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    Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

    Several N-heterocyclic carbenes (NHCs) are experimentally observed upon the addition of muonium (Mu), and the hyperfine coupling constants (HFCCs) of muon are measured. Theoretical investigation of Mu has been challenging due to significant quantum effects. Herein, we performed an ab initio path integral molecular dynamics (PIMD) simulation, which accurately considers multi-dimensional quantum effects, to theoretically investigate muoniated 1,3-dihydro-2H-imidazole-2-ylidene (Mu-IY). Our findings indicate that quantum effects have two contradictory contributions: the quantum effect of bond vibrations increases the HFCC values, whereas that of out-of-plane angular vibrations decreases the HFCC values. Moreover, we show that the HFCC values of other NHCs can be predicted without the PIMD simulations by applying the structural changes caused by the quantum effect derived from the PIMD simulations of Mu-IY.

    DOI： 10.1063/5.0234050

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  • One-dimensional C60 Arrays in Noncovalent Benzidine Networks Reviewed

    Takatsugu Wakahara, Chika Hirata, Dorra Mahdaoui, Kazuko Fujii, Yoshitaka Matsushita, Osamu Ito, Makito Takagi, Tomomi Shimazaki, Masanori Tachikawa, Shinjiro Yagyu, Yubin Liu, Yoshiyuki Nakajima, Takuro Nagai, Kazuhito Tsukagoshi

    Carbon   119838 - 119838   2024.11

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.carbon.2024.119838

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  • Metal single-atom interaction with graphitic C3N4 surface based on density functional theory calculations and linear regression analysis Reviewed

    Adie Tri Hanindriyo, Makito Takagi, Yuto Tanaka, Tokuhisa Kawawaki, Yuichi Negishi, Tomomi Shimazaki, Masanori Tachikawa

    Chemical Physics   112478 - 112478   2024.10

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.chemphys.2024.112478

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  • Ultrafine Spatial Modulation of Diazapyrene-Based Two-Dimensional Conjugated Covalent Organic Frameworks Reviewed

    Zhuowei Li, Takahiro Tsuneyuki, Rajendra Prasad Paitandi, Takumi Nakazato, Masahiro Odawara, Yusuke Tsutsui, Takayuki Tanaka, Yoshihiro Miyake, Hiroshi Shinokubo, Makito Takagi, Tomomi Shimazaki, Masanori Tachikawa, Katsuaki Suzuki, Hironori Kaji, Samrat Ghosh, Shu Seki

    Journal of the American Chemical Society   23497 - 23507   2024.8

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/jacs.4c07091

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  • Theoretical study of short-range exchange interaction based on semiconductor dielectric function model toward time-dependent dielectric density functional theory. Reviewed International journal

    Tomomi Shimazaki, Masanori Tachikawa

    The Journal of chemical physics   161 ( 1 )   014107   2024.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    This study explores various models of semiconductor dielectric functions, with a specific emphasis on the large wavenumber spectrum and the derivation of the screened exchange interaction. Particularly, we discuss the short-range effect of the screened exchange potential. Our investigation reveals that the short-range effect originating from the high wavenumber spectrum is contingent upon the dielectric constant of the targeted system. To incorporate dielectric-dependent behaviors concerning the short-range aspect into the dielectric density functional theory (DFT) framework, we utilize the local Slater term and the Yukawa-type term, adjusting the ratio between these terms based on the dielectric constant. Additionally, we demonstrate the efficacy of the time-dependent dielectric DFT method in accurately characterizing the electronic structure of excited states in dyes and functional molecules. Several theoretical approaches have incorporated parameters dependent on the system to elucidate short-range exchange interactions. Our theoretical analysis and discussions will be useful for those studies.

    DOI： 10.1063/5.0207751

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  • Theoretical Study on Rate-Determining Reactions for Constructing Self-Assembling Molecular Cages Controlled by Distorted Ditopic Ligands Reviewed

    Yu Ichinose, Osamu Kobayashi, Tomomi Shimazaki, Shuichi Hiraoka, Masanori Tachikawa

    The Journal of Physical Chemistry C   128 ( 25 )   10643 - 10649   2024.6

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jpcc.4c01525

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  • Theoretical and machine learning models for reaction-barrier predictions: acrylate and methacrylate radical reactions Reviewed

    Makito Takagi, Tomomi Shimazaki, Osamu Kobayashi, Takayoshi Ishimoto, Masanori Tachikawa

    Physical Chemistry Chemical Physics   1772 - 1777   2024

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    Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    The radical reaction of acrylate (ACR) and/or methacrylate (MA) is necessary for producing synthetic acrylic polymers. However, this synthesis requires sophisticated and precise control of employed radical reactions. As a...

    DOI： 10.1039/d4cp04656k

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  • Analysis of the structural H/D isotope effect with an excess proton/deuteron in light/heavy water solvent using path integral molecular dynamics simulations Reviewed

    Kazuki Tatenuma, Makito Takagi, Tomomi Shimazaki, Masanori Tachikawa

    Bulletin of the Chemical Society of Japan   97 ( 1 )   uoad009   2024

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    Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

    Abstract

    We analyzed the difference in the structural H/D isotope effect between an excess proton in light water (H-body) and an excess deuteron in heavy water (D-body), including the nuclear quantum effect, using path integral molecular dynamics simulations. We found that the second peak of the H-body is shorter than that of the D-body in the radial distribution function of O*–O, where O* is the oxygen atom of the H3O+/D3O+ fragment. The main reason for this would be the difference in the ratio of the Zundel structure with the sp3-like configuration, where the Zundel structure in the H-body (14.0%) is greater than that in the D-body (12.0%). We also found rare occurrences of double H3O+/D3O+ configurations, mainly including Zundel–Zundel-like structures such as H7O3+/D7O3+ and H9O4+/D9O4+. The ratios of such configurations appearing in our simulations are 0.89% and 0.20% for the H-body and the D-body, respectively.

    DOI： 10.1093/bulcsj/uoad009

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    Other Link： https://academic.oup.com/bcsj/article-pdf/97/1/uoad009/56616043/uoad009.pdf

  • Time-dependent dielectric density functional theory predictions for excited-state molecular properties using neural networks guided by lower-level quantum chemistry Reviewed

    Tomomi Shimazaki, Masanori Tachikawa

    Chemical Physics Letters   829   140744 - 140744   2023.10

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.cplett.2023.140744

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  • Theoretical Study of the Molecular Passivation Effect of Lewis Base/Acid on Lead-Free Tin Perovskite Surface Defects Reviewed

    Takumi Naito, Makito Takagi, Masanori Tachikawa, Koichi Yamashita, Tomomi Shimazaki

    The Journal of Physical Chemistry Letters   14   6695 - 6701   2023.7

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jpclett.3c01450

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  • Theoretical Analysis of Hydrogen-Bonded Structures of the Enhanced Green Fluorescent Protein with Multi-Component Density Functional Theory Reviewed

    Mio Takakuwa, Yukiumi Kita, Tomomi Shimazaki, Yusuke Kanematsu, Takayoshi Ishimoto, Motoyasu Adachi, Masanori Tachikawa

    Bulletin of the Chemical Society of Japan   96 ( 7 )   711 - 716   2023.7

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    Publishing type：Research paper (scientific journal)   Publisher：The Chemical Society of Japan  

    DOI： 10.1246/bcsj.20230085

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  • Computational analysis of H/D isotope effect on adsorption of water and its dissociated species on Pt(111) surface Reviewed

    Kazuma Nasu, Hiroki Sakagami, Yusuke Kanematsu, David S. Rivera Rocabado, Tomomi Shimazaki, Masanori Tachikawa, Takayoshi Ishimoto

    AIP Advances   13 ( 6 )   065305   2023.6

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    Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

    To understand the mechanism of the H–D exchange reaction for synthesizing various deuterium-labeled molecules on heterogeneous metal catalysts as a first step, we analyzed the effects of H/D isotopes on the adsorption of H2O/D2O and their dissociated OH/OD and H/D species on the Pt(111) surface. We applied the combined plane-wave and localized basis set method developed by us to directly treat the electronic structures of the surface and the localized adsorbed region and the nuclear quantum effect of H and D. The results showed that the adsorption energies for the D-compounds on the Pt surface were larger than those for the H-compounds. This is in keeping with the experimental observations. The difference in the distance between the adsorbates and the Pt surface induced by the H/D isotope effect depends on the bonding characteristics. While the distance between D2O and the Pt surface was longer than that in the H2O case, the distance between the D atom and the Pt surface was shorter than that for the H atom. This is the first report on the geometrical differences between H and D based on a systematic analysis of water and its dissociated species.

    DOI： 10.1063/5.0151660

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  • Stability and bonding nature of positronic lithium molecular dianion. Reviewed International journal

    Shumpei Ito, Daisuke Yoshida, Yukiumi Kita, Tomomi Shimazaki, Masanori Tachikawa

    The Journal of Chemical Physics   158 ( 20 )   204303   2023.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    We studied the stability of a system consisting of a positron (e+) and two lithium anions, [Li-; e+; Li-], using first-principles quantum Monte Carlo calculations combined with the multi-component molecular orbital method. While diatomic lithium molecular dianions Li22- are unstable, we found that its positronic complex can form a bound state with respect to the lowest energy decay into the dissociation channel Li2- and a positronium (Ps). The [Li-; e+; Li-] system has the minimum energy at the internuclear distance of ∼3 Å, which is close to the equilibrium internuclear distance of Li2-. At the minimum energy structure both an excess electron and a positron are delocalized as orbiting around the Li2- molecular anion core. A dominant feature of such a positron bonding structure is described as the Ps fraction bound to Li2-, unlike the covalent positron bonding scheme for the electronically isovalent [H-; e+; H-] complex.

    DOI： 10.1063/5.0150246

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  • Metal Single‐Atom Cocatalyst on Carbon Nitride for the Photocatalytic Hydrogen Evolution Reaction: Effects of Metal Species Reviewed

    Yuki Akinaga, Tokuhisa Kawawaki, Hinano Kameko, Yuki Yamazaki, Kenji Yamazaki, Yuhi Nakayasu, Kosaku Kato, Yuto Tanaka, Adie Tri Hanindriyo, Makito Takagi, Tomomi Shimazaki, Masanori Tachikawa, Akira Yamakata, Yuichi Negishi

    Advanced Functional Materials   33   2303321   2023.5

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    Publishing type：Research paper (scientific journal)   Publisher：Wiley  

    DOI： 10.1002/adfm.202303321

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  • Improved activity for the oxygen evolution reaction using a tiara-like thiolate-protected nickel nanocluster Reviewed

    Sota Funaki, Tokuhisa Kawawaki, Tomoshige Okada, Kana Takemae, Sakiat Hossain, Yoshiki Niihori, Takumi Naitou, Makito Takagi, Tomomi Shimazaki, Soichi Kikkawa, Seiji Yamazoe, Masanori Tachikawa, Yuichi Negishi

    Nanoscale   15 ( 11 )   5201 - 5208   2023

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    Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    This study demonstrated that nickel-nanocluster catalysts exhibit 2.3 times higher electrocatalytic oxygen evolution reaction activity compared with nickel-oxide catalysts prepared using a general impregnation method on carbon black.

    DOI： 10.1039/D2NR06952K

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  • Molecular Dynamics Study on the Structure–Property Relationship of Self-Assembled Gear-Shaped Amphiphile Molecules with/without Methyl Groups Reviewed International journal

    Moe Murata, Takuya Koide, Osamu Kobayashi, Shuichi Hiraoka, Tomomi Shimazaki, Masanori Tachikawa

    The Journal of Physical Chemistry B   127 ( 1 )   328 - 334   2023

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    Gaining insight into the encapsulation mechanism is important for controlling the encapsulation rate toward the self-assembly of gear-shaped amphiphile molecules (GSAs). To this aim, we conducted molecular dynamics (MD) simulations for three different hexameric nanocubes (1612+, 2612+, and 3612+) of GSAs (12+, 22+, and 32+, respectively) to elucidate the quantitative structure-property relationship between the stability of the nanocubes and the rate of encapsulation of a guest molecule. The 12+, 22+, and 32+ monomers differ from each other in the number of methyl groups, having three, zero, and two methyl groups, respectively. The 3612+ hexamer has methyl groups only on the equatorial region. In the cases of the simulations of 1612+ and 3612+, the cubic structures are maintained due to a tight triple-π stacking around the equator region. Meanwhile, 2612+ deforms easily due to the occurrence of a large fluctuation. These results indicate that the methyl groups on the equator are crucial to stabilize the nanocubes. The encapsulation of an iodide ion as a guest molecule is revealed to occur through the pole region via a gap that is easily formed in the nanocubes without methyl groups on the poles. Our study clearly suggests that self-assembled nanocubes can be designed to attain a specific stability and encapsulation efficiency simultaneously.

    DOI： 10.1021/acs.jpcb.2c07444

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  • Development of anharmonic vibrational structure theory using backflow transformation Reviewed

    Kiriko Ishii, Tomomi Shimazaki, Masanori Tachikawa, Yukiumi Kita

    Chemical Physics Letters   787   139263 - 139263   2022

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.cplett.2021.139263

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  • Decomposition analysis on the excitation behaviors of thiazolothiazole (TTz)-based dyes <i>via</i> the time-dependent dielectric density functional theory approach Reviewed International journal

    Takumi Naito, Yukiumi Kita, Tomomi Shimazaki, Masanori Tachikawa

    RSC Advances   12 ( 53 )   34685 - 34693   2022

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    Decomposition analysis shows that the solvent reorientation effect causes solvatofluorochromism of TTz dyes.

    DOI： 10.1039/d2ra06454e

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  • Theoretical investigations of positron affinities and their structure-dependent properties of carbon dioxide clusters (CO<sub>2</sub>)<sub><i>n</i></sub> (<i>n</i> = 1–5) Reviewed

    Miku Furushima, Makito Takagi, Daisuke Yoshida, Yukiumi Kita, Tomomi Shimazaki, Masanori Tachikawa

    Physical Chemistry Chemical Physics   25 ( 1 )   625 - 632   2022

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    Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    Clusters of CO<sub>2</sub> can have positron binding states. Besides, they have various kinds of binding origins depending on the nuclear configurations.

    DOI： 10.1039/d2cp03788b

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  • A comprehensive theoretical study of positron binding and annihilation properties of hydrogen bonded binary molecular clusters Reviewed International journal

    Daisuke Yoshida, Yukiumi Kita, Tomomi Shimazaki, Masanori Tachikawa

    Physical Chemistry Chemical Physics   24 ( 43 )   26898 - 26907   2022

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    Small hydrogen inorganic molecules such as water have no positron binding ability. We revealed that their hydrogen bonded binary molecular clusters exhibit greater positron affinities due to the increased dipole moments and polarization effect.

    DOI： 10.1039/d2cp03813g

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  • Theoretical study of the effect of nonlocal short-range exchange on calculations of molecular excitation energies in the dielectric screened-exchange method Reviewed

    Tomomi Shimazaki, Masanori Tachikawa

    Chemical Physics Letters   802   139740 - 139740   2022

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.cplett.2022.139740

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  • Fullerene C70/porphyrin hybrid nanoarchitectures: single-cocrystal nanoribbons with ambipolar charge transport properties Reviewed International journal

    Takatsugu Wakahara, Kahori Nagaoka, Chika Hirata, Kun'ichi Miyazawa, Kazuko Fujii, Yoshitaka Matsushita, Osamu Ito, Makito Takagi, Tomomi Shimazaki, Masanori Tachikawa, Yoshiki Wada, Shinjiro Yagyu, Yubin Liu, Yoshiyuki Nakajima, Kazuhito Tsukagoshi

    RSC Advances   12 ( 30 )   19548 - 19553   2022

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    The one-dimensional porphyrin chains in the cocrystal play a very important role in the hole transport properties of C<sub>70</sub>/porphyrin nanoribbons.

    DOI： 10.1039/d2ra02669d

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  • Collaborative Approach between Explainable Artificial Intelligence and Simplified Chemical Interactions to Explore Active Ligands for Cyclin-Dependent Kinase 2 Reviewed

    Tomomi Shimazaki, Masanori Tachikawa

    ACS Omega   7 ( 12 )   10372 - 10381   2022

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acsomega.1c06976

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  • Theoretical Study of the Isotope and Homologue Effects on Nuclear Magnetic Shielding in Water and Hydrogen Sulfide Molecules Reviewed

    Kiriko Ishii, Tomomi Shimazaki, Masanori Tachikawa, Yukiumi Kita

    Chemistry Letters   51 ( 3 )   342 - 344   2022

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Chemical Society of Japan  

    DOI： 10.1246/cl.210760

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  • Hydrogen/Deuterium Transfer from Anisole to Methoxy Radicals: A Theoretical Study of a Deuterium-Labeled Drug Model Reviewed International journal

    Yuka Kimura, Yusuke Kanematsu, Hiroki Sakagami, David S. Rivera Rocabado, Tomomi Shimazaki, Masanori Tachikawa, Takayoshi Ishimoto

    The Journal of Physical Chemistry A   126 ( 1 )   155 - 163   2022

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    Recently, deuterium-labeled drugs, such as deutetrabenazine, have attracted considerable attention. Consequently, understanding the reaction mechanisms of deuterium-labeled drugs is crucial, both fundamentally and for real applications. To understand the mechanisms of H- and D-transfer reactions, in this study, we used deuterated anisole as a deutetrabenazine model and computationally considered the nuclear quantum effects of protons, deuterons, and electrons. We demonstrated that geometrical differences exist in the partially and fully deuterated methoxy groups and hydrogen-bonded structures of intermediates and transition states due to the H/D isotope effect. The observed geometrical features and electronic structures are ascribable to the different nuclear quantum effects of protons and deuterons. Primary and secondary kinetic isotope effects (KIEs) were calculated for H- and D-transfer reactions from deuterated and undeuterated anisole, with the calculated primary KIEs in good agreement with the corresponding experimental data. These results reveal that the nuclear quantum effects of protons and deuterons need to be considered when analyzing the reaction mechanisms of H- and D-transfer reactions and that a theoretical approach that directly includes nuclear quantum effects is a powerful tool for the analysis of H/D isotope effects in H- and D-transfer reactions.

    DOI： 10.1021/acs.jpca.1c08514

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  • Positron Binding and Annihilation Properties of Amino Acid Systems Reviewed International journal

    Maya Ozaki, Daisuke Yoshida, Yukiumi Kita, Tomomi Shimazaki, Masanori Tachikawa

    ACS Omega   6 ( 44 )   29449 - 29458   2021

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    Despite the fact that the positron annihilation has been used in biomedical applications, the detailed mechanism of the positron annihilation on biological molecules remains poorly understood so far. In this work, we investigated the positron binding and positron annihilation properties for both global minimum and hydrogen-bonded structures of 20 amino acid molecules using the multicomponent molecular orbital method. By regression analysis, we confirmed that positron affinity can increase with an increase of the permanent dipole moment of the parent amino acids as reported in previous studies, while the annihilation rate linearly increases with respect to the square root of positron affinity. By the one-particle property analyses for probabilities of electron-positron contacts, we found that delocalization characteristics of both electrons and positrons play key roles to enhance the positron annihilation rate arising from both the valence electrons in σ- and π-type molecular orbitals from 2p atomic orbitals but not from the highest occupied molecular orbital electrons, particularly for comparatively weakly bound positronic amino acid systems.

    DOI： 10.1021/acsomega.1c03409

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  • A theoretical study on solvatofluorochromic asymmetric thiazolothiazole (TTz) dyes using dielectric-dependent density functional theory Reviewed

    Tomomi Shimazaki, Masanori Tachikawa

    Physical Chemistry Chemical Physics   23 ( 37 )   21078 - 21086   2021

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1039/d1cp02047a

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  • Theoretical investigation of the enhancement of positron affinity by the vibration and dimerization of non-polar carbon disulfide Reviewed International journal

    Miku Furushima, Daisuke Yoshida, Yukiumi Kita, Tomomi Shimazaki, Masanori Tachikawa

    Physical Chemistry Chemical Physics   23 ( 38 )   21512 - 21520   2021

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1039/d1cp02808a

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  • Role of OH Termination in Mitigating Friction of Diamond-like Carbon under High Load: A Joint Simulation and Experimental Study Reviewed

    Yang Wang, Kentaro Hayashi, Yusuke Ootani, Shandan Bai, Tomomi Shimazaki, Yuji Higuchi, Nobuki Ozawa, Koshi Adachi, Maria-Isabel De Barros Bouchet, Jean Michel Martin, Momoji Kubo

    Langmuir   37 ( 20 )   6292 - 6300   2021

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    DOI： 10.1021/acs.langmuir.1c00727

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  • Terahertz Spectroscopy for Characterization of Hydrogen Bonding and Cross-linked Structure Dynamics in Polyurethane Reviewed

    Hiromichi Hoshina, Yuichi Saito, Takumi Furuhashi, Tomomi Shimazaki, Manabu Sawada, Yasunori Hioki, Chiko Otani

    Journal of Infrared Millimeter and Terahertz waves   41 ( 3 )   265 - 275   2020

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    DOI： 10.1007/s10762-019-00667-0

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  • PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties Reviewed

    Maho Nakata, Tomomi Shimazaki, Masatomo Hashimoto, Toshiyuki Maeda

    Journal of Chemical Information and Modeling   60 ( 12 )   5891 - 5899   2020

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jcim.0c00740

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  • Theoretical study on mesoscopic-size impurity effects in the charge separation process of organic photocells Reviewed

    Tomomi Shimazaki, Motomichi Tashiro, Takahito Nakajima

    Physical Chemistry Chemical Physics   20 ( 21 )   14846 - 14854   2018

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    DOI： 10.1039/c7cp08125a

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  • A theoretical study on hot charge-transfer states and dimensional effects of organic photocells based on an ideal diode model Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Physical Chemistry Chemical Physics   19 ( 19 )   12517 - 12526   2017

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    DOI： 10.1039/c7cp01455d

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  • PubChemQC Project: A Large-Scale First-Principles Electronic Structure Database for Data-Driven Chemistry Reviewed

    Maho Nakata, Tomomi Shimazaki

    Journal of Chemical Information and Modeling   57 ( 6 )   1300 - 1308   2017

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    DOI： 10.1021/acs.jcim.7b00083

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  • Group molecular orbital approach to solve the Huzinaga subsystem self-consistent-field equations Reviewed

    Tomomi Shimazaki, Kazuo Kitaura, Dmitri G. Fedorov, Takahito Nakajima

    Journal of Chemical Physics   146 ( 8 )   2017

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    DOI： 10.1063/1.4976646

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  • Theoretical study on the cooperative exciton dissociation process based on dimensional and hot charge-transfer state effects in an organic photocell Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Journal of Chemical Physics   144 ( 23 )   2016.6

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    DOI： 10.1063/1.4953905

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  • Gaussian-based range-separation approach on Hartree-Fock exchange interaction and second-order perturbation theory Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Chemical Physics Letters   647   132 - 138   2016

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    DOI： 10.1016/j.cplett.2015.12.069

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  • Application of the dielectric-dependent screened exchange potential approach to organic photocell materials Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Physical Chemistry Chemical Physics   18 ( 39 )   27554 - 27563   2016

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    DOI： 10.1039/c6cp04863c

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  • Theoretical study of a screened Hartree-Fock exchange potential using position-dependent atomic dielectric constants Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Journal of Chemical Physics   142 ( 7 )   2015.2

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    DOI： 10.1063/1.4908061

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  • Developing a high-performance quantum chemistry program with a dynamic scripting language Reviewed

    Tomomi Shimazaki, Masatomo Hashimoto, Toshiyuki Maeda

    Proceedings of the 3rd International Workshop on Software Engineering for High Performance Computing in Computational Science and Engineering - SE-HPCCSE '15   2015

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    Publishing type：Research paper (international conference proceedings)   Publisher：ACM Press  

    DOI： 10.1145/2830168.2830170

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  • Theoretical study of exciton dissociation through hot states at donor-acceptor interface in organic photocell Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Physical Chemistry Chemical Physics   17 ( 19 )   12538 - 12544   2015

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1039/c5cp00740b

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  • Gaussian-based cutoff scheme on Hartree-Fock exchange term of dielectric-dependent potential Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Chemical Physics Letters   634   83 - 87   2015

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    DOI： 10.1016/j.cplett.2015.06.001

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  • Communication: Different behavior of Young's modulus and fracture strength of CeO2: Density functional theory calculations Reviewed

    Ryota Sakanoi, Tomomi Shimazaki, Jingxiang Xu, Yuji Higuchi, Nobuki Ozawa, Kazuhisa Sato, Toshiyuki Hashida, Momoji Kubo

    Journal of Chemical Physics   140 ( 12 )   2014.3

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    DOI： 10.1063/1.4869515

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  • Dielectric-dependent screened Hartree-Fock exchange potential and Slater-formula with Coulomb-hole interaction for energy band structure calculations Reviewed

    Tomomi Shimazaki, Takahito Nakajima

    Journal of Chemical Physics   141 ( 11 )   2014

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    DOI： 10.1063/1.4895623

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  • Density functional theory analysis of methanation reaction of CO2 on Ru nanoparticle supported on TiO2 (101) Reviewed

    Satoshi Akamaru, Tomomi Shimazaki, Momoji Kubo, Takayuki Abe

    Applied Catalysis A-General   470   405 - 411   2014

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    DOI： 10.1016/j.apcata.2013.11.016

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  • Range-Separation Density-Fitting Band Structure Calculation with Gaussian Auxiliary Function Reviewed

    Tomomi Shimazaki, Taichi Kosugi, Takahito Nakajima

    Journal of Physical Society of Japan   83 ( 5 )   2014

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    DOI： 10.7566/JPSJ.83.054702

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  • Controlling Formation of Single-Molecule Junctions by Electrochemical Reduction of Diazonium Terminal Groups Reviewed

    Thomas Hines, Ismael Diez-Perez, Hisao Nakamura, Tomomi Shimazaki, Yoshihiro Asai, Nongjian Tao

    Journal of American Chemical Society   135 ( 9 )   3319 - 3322   2013

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    DOI： 10.1021/ja3106434

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  • Efficient density functional theory calculations with weak hydrogen quantum effect: Electron density analysis Reviewed

    Tomomi Shimazaki, Momoji Kubo

    Chemical Physics Letters   525-26   134 - 139   2012

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    DOI： 10.1016/j.cplett.2011.12.059

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  • Fate of methanol molecule sandwiched between hydrogen-terminated diamond-like carbon films by tribochemical reactions: tight-binding quantum chemical molecular dynamics study Reviewed

    Kentaro Hayashi, Seiichiro Sato, Shandan Bai, Yuji Higuchi, Nobuki Ozawa, Tomomi Shimazaki, Koshi Adachi, Jean-Michel Martin, Momoji Kubo

    Faraday Discussions   156   137 - 146   2012

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1039/c2fd00125j

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  • Density functional theory study on quasi-three-dimensional oxidized platinum surface: phase transition between alpha-PtO2-like and beta-PtO2-like structures Reviewed

    Tomomi Shimazaki, Toshiya Suzuki, Momoji Kubo

    THEORETICAL CHEMISTRY ACCOUNTS   130 ( 4-6 )   1031 - 1038   2011.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s00214-011-1012-y

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  • Tribochemical Reaction Dynamics Simulation of Hydrogen on a Diamond-like Carbon Surface Based on Tight-Binding Quantum Chemical Molecular Dynamics Reviewed

    Kentaro Hayashi, Kotoe Tezuka, Nobuki Ozawa, Tomomi Shimazaki, Koshi Adachi, Momoji Kubo

    JOURNAL OF PHYSICAL CHEMISTRY C   115 ( 46 )   22981 - 22986   2011.11

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    DOI： 10.1021/jp207065n

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  • Analytical energy gradient of Gaussian and Fourier transform (GFT) method for periodic condensed systems Reviewed

    Tomomi Shimazaki, Momoji Kubo

    CHEMICAL PHYSICS LETTERS   503 ( 4-6 )   316 - 321   2011.2

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    DOI： 10.1016/j.cplett.2010.12.089

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  • Communication: The reason why +c ZnO surface is less stable than -c ZnO surface: First-principles calculation Reviewed

    Seitaro Ito, Tomomi Shimazaki, Momoji Kubo, Hideomi Koinuma, Masatomo Sumiya

    Journal of Chemical Physics   135 ( 24 )   2011

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1063/1.3675680

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  • Energy band structure calculations based on screened Hartree-Fock exchange method: Si, AlP, AlAs, GaP, and GaAs Reviewed

    Tomomi Shimazaki, Yoshihiro Asai

    JOURNAL OF CHEMICAL PHYSICS   132 ( 22 )   2010.6

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    DOI： 10.1063/1.3431293

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  • On the Brillouin-Zone Integrations in Second-Order Many-Body Perturbation Calculations for Extended Systems of One-Dimensional Periodicity Reviewed

    Tomomi Shimazaki, So Hirata

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   109 ( 13 )   2953 - 2959   2009.11

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    DOI： 10.1002/qua.22176

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  • A Theoretical Study of Molecular Conduction. V. NEGF-Based MP2 Approach Reviewed

    Tomomi Shimazaki, Koichi Yamashita

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   109 ( 9 )   1834 - 1840   2009.8

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    DOI： 10.1002/qua.21994

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  • Fast second-order many-body perturbation method for extended systems Reviewed

    So Hirata, Tomomi Shimazaki

    PHYSICAL REVIEW B   80 ( 8 )   2009.8

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    DOI： 10.1103/PhysRevB.80.085118

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  • First principles band structure calculations based on self-consistent screened Hartree-Fock exchange potential Reviewed

    Tomomi Shimazaki, Yoshihiro Asai

    JOURNAL OF CHEMICAL PHYSICS   130 ( 16 )   2009.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1063/1.3119259

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  • Chemical Synthesis and Properties of 5-Taurinomethyluridine and 5-Taurinomethyl-2-thiouridine Reviewed

    Toshihiko Ogata, Tomomi Shimazaki, Tadashi Umemoto, Shinya Kurata, Takashi Ohtsuki, Tsutomu Suzuki, Takeshi Wada

    JOURNAL OF ORGANIC CHEMISTRY   74 ( 6 )   2585 - 2588   2009.3

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    DOI： 10.1021/jo802697r

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  • Electronic Structure Calculations under Periodic Boundary Conditions Based on the Gaussian and Fourier Transform (GFT) Method Reviewed

    Tomomi Shimazaki, Yoshihiro Asai

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION   5 ( 1 )   136 - 143   2009.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/ct800329m

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  • Band structure calculations based on screened Fock exchange method Reviewed

    Tomomi Shimazaki, Yoshihiro Asai

    CHEMICAL PHYSICS LETTERS   466 ( 1-3 )   91 - 94   2008.11

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    DOI： 10.1016/j.cplett.2008.10.012

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  • Modified uridines with c5-methylene substituents at the first position of the tRNA anticodon stabilize U center dot G wobble pairing during decoding Reviewed

    Shinya Kurata, Albert Weixlbaumer, Takashi Ohtsuki, Tomomi Shimazaki, Takeshi Wada, Yohei Kirino, Kazuyuki Takai, Kimitsuna Watanabe, V. Ramakrishnan, Tsutomu Suzuki

    JOURNAL OF BIOLOGICAL CHEMISTRY   283 ( 27 )   18801 - 18811   2008.7

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    DOI： 10.1074/jbc.M800233200

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  • Theoretical study of the lineshape of inelastic electron tunneling spectroscopy Reviewed

    Tomomi Shimazaki, Yoshihiro Asai

    PHYSICAL REVIEW B   77 ( 11 )   2008.3

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    DOI： 10.1103/PhysRevB.77.115428

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  • Bias voltage dependence on the vibronic electric current Reviewed

    Tomomi Shimazaki, Yoshihiro Asai

    PHYSICAL REVIEW B   77 ( 7 )   2008.2

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    DOI： 10.1103/PhysRevB.77.075110

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  • A theoretical study of molecular conduction: IV. A three-terminal molecular device Reviewed

    Tomomi Shimazaki, Koichi Yamashita

    NANOTECHNOLOGY   18 ( 42 )   2007.10

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    DOI： 10.1088/0957-4484/18/42/424012

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  • A theoretical study of molecular conduction. III. A nonequilibrium-Green’s-function-based Hartree-Fock approach Reviewed

    Tomomi Shimazaki, Yongqiang Xue, Mark A. Ratner, Koichi Yamashita

    The Journal of Chemical Physics   124 ( 11 )   114708 - 114708   2006.3

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    Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

    DOI： 10.1063/1.2177652

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  • Theoretical study of molecular conduction: I. Effective Green's function based on perturbation theory Reviewed

    Tomomi Shimazaki, Koichi Yamashita

    International Journal of Quantum Chemistry   106 ( 4 )   803 - 813   2006

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    Publishing type：Research paper (scientific journal)   Publisher：Wiley  

    DOI： 10.1002/qua.20819

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  • A theoretical study of molecular conduction. II. A Hartree-Fock approach to transmission probability Reviewed

    Tomomi Shimazaki, Hitoshi Maruyama, Yoshihiro Asai, Koichi Yamashita

    The Journal of Chemical Physics   123 ( 16 )   164111 - 164111   2005.10

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    DOI： 10.1063/1.2074127

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  • Theoretical Rate Constants of Super-Exchange Hole Transfer and Thermally Induced Hopping in DNA Reviewed

    Tomomi Shimazaki, Yoshihiro Asai, Koichi Yamashita

    The Journal of Physical Chemistry B   109 ( 3 )   1295 - 1303   2005.1

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/jp047456d

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Research Projects

  • Understanding deuterated medicine and its design guideline via in silico techniques

    Grant number：25H00428  2025.4 - 2030.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (S)

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    Grant amount：\203450000 （ Direct Cost: \156500000 、 Indirect Cost：\46950000 ）

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  • 燃料電池触媒層の物質輸送機構解明に向けた、マルチスケール計算技術構築とその活用

    2023 - 2025

    文部科学省、スーパーコンピュータ「富岳」成果創出加速プログラム

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  • Giant CISS物質: 界面陽電子・電子の全運動量制御

    2023

    科学技術振興機構（JST）  戦略的創造研究推進事業CREST

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    Authorship：Collaborating Investigator(s) (not designated on Grant-in-Aid) 

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  • 第一原理計算およびデバイス・モデルによる非フラーレン・アクセプター材料の機能 解明

    2022.4 - 2024.3

    日本学術振興会 科学研究費助成事業  基盤研究(C) 

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  • 鉛フリー・アロイ化錫ペロブスカイト・タンデム太陽電池の国際共同研究開発

    2021 - 2024

    産業技術総合開発機構(NEDO) 

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    Authorship：Coinvestigator(s) 

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  • 第一原理計算に基づいた有機薄膜太陽電池の励起子拡散プロセス改善

    Grant number：18K05051  2018.4 - 2021.3

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    島崎 智実

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    Grant amount：\4290000 （ Direct Cost: \3300000 、 Indirect Cost：\990000 ）

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  • First principles simulation study on dissociation process between electron and hole in organic photocell

    Grant number：15K05403  2015.4 - 2018.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    Shimazaki Tomomi

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    Grant amount：\4550000 （ Direct Cost: \3500000 、 Indirect Cost：\1050000 ）

    Organic devices based on blends of conjugated polymers and fullerene derivative have been gathering much attention as promising photovoltaic applications, because of their low production costs, thin and light structures, flexibilities, designs, and so on. However, the power conversion efficiency of organic photocells still remains low compared with inorganic devices. In order to improve their performance, we need to more deeply investigate the mechanism to generate electric currents from photons. For that purpose, we studied the theoretical method to calculate the charge separation process with the hot CT state effect. We integrate the CT state mechanism into the diode model, and calculate several device properties of organic photocell device, such as short circuit current, open circuit voltage, and power conversion efficiency. Our study showed that the hot CT state gives strong influences on the device performance.

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  • Development of large-scale first-principles quantum chemistry method with quantum hydrogen effect

    Grant number：24550005  2012.4 - 2015.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    TOMOMI Shimazaki

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    Grant amount：\5070000 （ Direct Cost: \3900000 、 Indirect Cost：\1170000 ）

    We developed an efficient theoretical methodology that takes into account the weak nuclear quantum effect of hydrogen. In our methodology the differences between the weak hydrogen (nuclear) quantum effect and the Born-Oppenheimer approximation are described by a short-range Coulomb-like one electron potential. In this study, we focused on density functional theory (DFT) with the weak hydrogen quantum effect, and show that there is no strong DFT-functional dependence of the weak hydrogen quantum effect. In addition, we show an electron density analysis to investigate complex calculation results from different DFT functionals considering the hydrogen quantum effect.

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  • ab-initio法に基づいたBS触媒活性に関する理論研究

    2011.4 - 2012.3

    富山大学、富山大学水素同位体科学研究センター  一般共同研究A 

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    Authorship：Principal investigator 

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  • 第一原理分子動力学法に基づくトライボ反応シミュレータの開発と自動車用潤滑剤の設計

    Grant number：22360065  2010 - 2012

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    久保 百司, 島崎 智実

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    Grant amount：\12350000 （ Direct Cost: \9500000 、 Indirect Cost：\2850000 ）

    近年、省エネルギー対策、地球温暖化対策に対する強い要請から、摩擦・摩耗・潤滑、いわゆるトライボロジーに関する社会的要求が厳しさを増している。具体的に自動車業界では、エンジン出力エネルギーの約30%が摩擦に消費されていることから、エンジンオイル用フリクション低減剤、摩耗防止剤の高性能化によるエンジン摺動部の低摩擦化・高耐摩耗性化の実現が社会的に急務の課題となっている。特に上記課題には迅速な対応が求められることから、実験研究に加え、理論的添加剤設計手法の確立が望まれている。そこで本研究では、経験的なパラメータを使用せずに電子状態計算を行うことが可能な第一原理計算手法に基づき、トライボ反応ダイナミクスを解明することが可能なトライボ反応シミュレータの開発を目的とした。また、近年の実験研究により、摩擦下における電子放出、いわゆるエキソエレクトロン現象がトライボケミカル反応に大きな影響を与えることが知られている。そこで本研究ではエキソエレクトロン現象を解明可能な第一原理分子動力学シミュレータの開発をも目的とした。
    初年度は、当研究室で開発済みのGaussian & Fourier Transform(GFT)法に基づく第一原理分子動力学計算プログラムに対して、摩擦プロセスのシミュレーションが可能な機能を追加することで、第一原理分子動力学法に基づくトライボ反応シミュレータを開発した。具体的には、2枚の基板で挟まれた潤滑膜に対して、片方の基板のみをスライドさせることで、摩擦プロセスにおける化学反応シミュレーションを可能とした。さらに、開発プログラムを活用することで、ダイヤモンドライクカーボンの摩擦プロセスにおける電子状態ダイナミクスを解明することに成功した。その結果、ダイヤモンドライクカーボンを水素終端することで、低摩擦を実現できることを明らかにした。

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  • First-principles molecular dynamics study based on Gaussian & Fourier Transform (GFT)

    Grant number：21850002  2009 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Research Activity start-up  Grant-in-Aid for Research Activity start-up

    SHIMAZAKI Tomomi

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    Grant amount：\1911000 （ Direct Cost: \1470000 、 Indirect Cost：\441000 ）

    In this research project, we expand the Gaussian & Fourier transform (GFT) methodology, which has been developed by the project representative, in order to execute first-principles molecular dynamics simulations, and we performed a condensed-system molecular dynamics simulation. Here, we derived an analytical expression for the GFT gradient, and implemented the theory into our simulation program based on the parallel coding techniques of OpenMP and MPI methods for cluster-type super-computers. We examine a bulk water model under the ambient conditions, and show the importance of the quantum effect on hydrogen atoms in the condensed-system through the simulation result. In addition to this, we reconsider the density functional theory (DFT) in the framework of the GFT method, and propose the screened Hartree-Fock exchange potential method. The screened Hartree-Fock exchange method can give the better electronic structure description compared with the local density approximation (LDA) and the generalized gradient approximation (GGA), and proposed an novel physical and chemical interpretation for the hybrid-DFT method which will be useful for the DFT community.

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