Faculty of Science and Technology, Department of Applied Physics and Physico-Informatics 基礎理工学専攻 (Yagami)


Associate Professor

Related Websites


Tomoko K. Shimizu

External Links

Career 【 Display / hide

  • 2007.07

    RIKEN, Surface Chemistry Laboraboty, Associate Researcher

  • 2009.04

    RIKEN, Surface Chemistry Laboraboty, Special Postdoctoral Researcher

  • 2010.04

    RIKEN, Surface and Interface Science Laboraboty, Special Postdoctoral Researcher

  • 2012.04

    RIKEN, Surface and Interface Science Laboraboty, ASI Researcher

  • 2013.04

    National Institute for Materials Science, Atomic Force Probe Group, Nano Characterization Unit, Advanced Key Technologies Division, Senior Researcher

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Academic Background 【 Display / hide

  • 1998.04

    Keio University, Faculty of Science and Technology, Department of Applied Physics and Physico-Informatics

    University, Graduated

  • 2002.08

    University of California, Berkeley, College of Engineering, Department of Materials Science and Engineering

    United States, Graduate School, Completed, Master's course

  • 2004.08

    University of California, Berkeley, College of Engineering, Department of Materials Science and Engineering

    United States, Graduate School, Completed, Doctoral course

Academic Degrees 【 Display / hide

  • 学士(工学), Keio University, 2002.03

  • M. Sci., University of California, Berkeley, 2004.05

  • Ph.D., University of California, Berkeley, Coursework, 2007.05

    Water Adsorption on Ruthenium (0001) Studied by Scanning Tunneling Microscopy


Research Areas 【 Display / hide

  • Nanotechnology/Materials / Nanometer-scale chemistry

  • Nanotechnology/Materials / Nanostructural physics

  • Nanotechnology/Materials / Thin film/surface and interfacial physical properties

  • Nanotechnology/Materials / Fundamental physical chemistry

Research Keywords 【 Display / hide

  • Atomic Force Microscopy

  • Functional organic thin films

  • Surface Science

  • Scanning Tunneling Microscopy

  • Scanning Probe Microscopy


Books 【 Display / hide

  • エンジニアのための物理化学

    川合眞紀, 宗像利明, 清水 智子, 東京化学同人, 2010

Papers 【 Display / hide

  • Stability and formation process of hydrogen-bonded organic porous thin films: A molecular dynamics study

    Kazuma Matsui, Hiroshi Watanabe, Tomoko K. Shimizu

    AIP Advances (American Institute of Physics)  12 ( 10 ) 105109  2022.10

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

     View Summary

    Molecular dynamics simulation using the reactive force field was performed to investigate the stability and formation mechanisms of organic porous thin films made of 1,3,5-tris(4-carboxyphenyl) benzene (BTB) molecules fabricated at the air/water interface. A single-layer honeycomb structure is found to be unstable, whereas thicker films are stable, which is consistent with experimental findings. The slight corrugation of the existing film produces local charge variation that attracts isolated molecules via the Coulomb interaction. When the isolated molecule approaches the film, a hydrogen bond is formed, and then the molecule adjusts the adsorption configuration by itself to maximize both horizontal and vertical intermolecular interactions. The key to the initial hydrogen bond formation is suggested to be the density of the molecules provided in the system as well as the spontaneous alignment of the BTB molecules to the solution/water interface. Our study showed that the BTB film is stable, and the molecules are self-assembled without external forces in the quasi-two-dimensional system. These results suggest that the dominant factor for the film formation at the air/water interface is interactions among BTB molecules and confinement to the two-dimensional space.

  • Evidence of One-Dimensional Channels in Hydrogen-Bonded Organic Porous Thin Films Fabricated at the Air/Liquid Interface

    Kanae Yamanami, Yuto Fujita, Kazuma Matsui, Ryu Asari, Tomoko Kusawake, Tomoko K. Shimizu

    Langmuir (American Chemical Society)  38 ( 5 ) 1910 - 1914 2022.02

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted,  ISSN  07437463

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    Visualization of periodically aligned pores in organic frameworks is a key to the understanding of their structural control. Comparing to monolayer-thick self-assembled molecular networks, real-space nanoscale characterization of thicker films, especially obtaining information on the stacking manner of molecules is challenging. Here, we report an atomic force microscopy study of hydrogen-bonded thin films fabricated at the air/liquid interface. The presence of one-dimensional channels is evidenced by resolving honeycomb structures over the films with the thickness variation of more than several nanometers. We also demonstrate that the film thickness can be controlled by the ratio of mixed solvent rather than the surface pressure during the fabrication at the air/liquid interface.

  • Effect of Molecule-Substrate Interactions on the Adsorption of meso-Dibenzoporphycene Tautomers Studied by Scanning Probe Microscopy and First-Principles Calculations

    Tomoko K. Shimizu, C. Romero-Muñiz, O. Stetsovych, J. Carracedo-Cosme, M. Ellner, P. Pou , K. Oohora, T. Hayashi, R. Perez, O. Custance

    Journal of Physical Chemistry C (American Chemical Society)  124 ( 49 ) 26759 - 26768 2020.12

    Research paper (scientific journal), Joint Work, Lead author, Accepted,  ISSN  19327447

     View Summary

    meso-Dibenzoporphycene molecules adsorbed on the Ag(111) surface and on 2-monolayer-thick NaCl films were studied using submolecular resolution atomic force microscopy (AFM), scanning tunneling microscopy (STM), and first-principles calculations to clarify their stability and tautomerization behavior. We have found that the bonding of the molecules with the surface is determined by the interplay of different contributions, including the interaction of the π-aromatic orbitals of the benzene rings and the metal-coordination bond of the lone-pair electrons of the imine nitrogen atoms with the metal atoms (Ag, Na) on each substrate. The strength of the latter ultimately governs the molecular adsorption configuration and determines the nature and energy barriers for tautomerization. On Ag(111), the interaction of the imine nitrogen atoms with the Ag atoms deforms the macrocycle of porphycene, leading to a distinct AFM contrast that allows a clear identification of the molecule in its cis tautomeric form. In contrast, on NaCl films, the weaker interaction with the Na atoms leads to a flatter geometry and very similar adsorption configurations for the cis- and trans-forms, which cannot be distinguished in AFM experiments. Although weak, the dominant role of this local N-Na interaction, compared to the essentially nondirectional dispersive interactions, results in a new type of tautomerization process. In this case, the transfer of hydrogen atoms within the porphycene cavity is accompanied by a significant displacement of the whole molecule to a new site to reach a new minimum energy adsorption configuration. Our theoretical calculations indicate that this lateral translation, rather than the intramolecular H transfer, dominates the activation energy on NaCl. This novel tautomerization behavior, which we have identified on a rather inert ionic surface, might also be present on other weakly interacting substrates.

  • Aromatic Azide Transformation on the Ag(111) Surface Studied by Scanning Probe Microscopy

    Ivo Stary, Jack Hellerstedt, Aleš Cahlík, Oleksander Stetsovych, Martin Švec, Tomoko K. Shimizu, Pingo Mutombo, Jiří Klívar, Irena G. Stará, Pavel Jelínek

    Angewandte Chemie International Edition (Wiley)  58 ( 8 ) 2266 - 2271 2019.01

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  14337851

     View Summary

    © 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Chemical transformation of 9-azidophenanthrene on the Ag(111) surface was studied by nc-AFM in UHV. High-resolution imaging supported by first-principle calculations revealed the structure of the final products that originated from a common and elusive 9-phenanthryl nitrenoid intermediate chemisorbed on the Ag(111) surface. A formal nitrene insertion into the C−H bond along with its dimerisation and hydrogenation were identified as main reaction channels. Thus, the ability of aryl azides to form covalent σ- and π-bonds between their transformation products on a solid surface was demonstrated at a single-molecule level.

  • Energy-level alignment of a single molecule on ultrathin insulating film

    Miyabi Imai-Imada, Hiroshi Imada, Kuniyuki Miwa, Jeahoon Jung, Tomoko K. Shimizu, Maki Kawai, and Yousoo Kim

    Physical Review B (Physical Review B)  98 ( 20 ) 201403 2018.11

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  24699950

     View Summary

    Elucidation of the energy-level alignment mechanism at a molecule/insulator/metal interface is a key to understanding the molecular and interfacial phenomena. Herein, we provide a detailed investigation into the electronic structures of a free-base phthalocyanine on NaCl films of various thicknesses using scanning tunneling microscopy/spectroscopy (STM/STS). The energy of the ionization and the affinity levels of the molecule were deduced from the STS spectra, and we determined their dependence on the NaCl-film thickness, which can be explained based on three effects: a voltage drop within the NaCl films, the degree of electric-field screening around the molecule, and a variation in the work function of the substrates. We further found that the energy levels relative to the vacuum level are independent of the work function of the substrate, and that the size of the energy gap increases with the thickness. Our results suggest that it is possible to predict the energy levels at the interfaces based on the energy levels of the molecules in a gas phase, the work function of the substrate, and the thickness of the insulating films.

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Papers, etc., Registered in KOARA 【 Display / hide

Reviews, Commentaries, etc. 【 Display / hide

  • 慶應義塾大学理工学部 物理情報工学科 清水研究室(研究紹介)


    応用物理学会薄膜表面分科会ニュースレター No.176   45 - 47 2021.09

    Single Work

  • 高解像度走査型プローブ顕微鏡による炭素材料の評価

    Tomoko K. Shimizu

    Tanso 285   204 - 209 2018.12

    Article, review, commentary, editorial, etc. (scientific journal), Single Work, Lead author, Corresponding author

  • 分子の内部構造を見る原子間力顕微鏡技術

    清水智子, Oscar Custance

    表面科学 37 ( 7 ) 320 - 325 2016.07

    Article, review, commentary, editorial, etc. (scientific journal), Joint Work

  • 第2部 計測テクノロジー最前線 第1章 原子一つにせまるテクノロジー 2 原子間の力をはかる -AFM-

    清水智子, クスタンセ オスカル

    NIMS調査分析室レポート 材料イノベーションを加速する先進計測テクノロジーの現状と動向-物質・材料研究のための先端計測テクノロジー (物質・材料研究機構)     42 - 51 2016.01

    Article, review, commentary, editorial, etc. (bulletin of university, research institution), Joint Work

  • フォトクロミック分子を金属表面に乗せると?

    清水 智子

    日本化学会研究会「低次元系光機能材料研究会」ニュースレター 10   6 - 8 2016.01

    Article, review, commentary, editorial, etc. (scientific journal), Single Work, Lead author, Corresponding author

Presentations 【 Display / hide

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Research Projects of Competitive Funds, etc. 【 Display / hide

  • 磁鉄鉱単結晶およびナノ粒子表面へのガス吸着状態の観察と検証


    公益財団法人東京応化科学技術振興財団, 第35回研究助成, Other, Principal investigator

  • 単分子表面分光手法を用いた塵表面における反応素過程の分子レベル解明


    科学研究費補助金, 学術変革領域研究(A), Research grant, Coinvestigator(s)

  • 走査型プローブ顕微鏡によるカーボンブラック表面の可視化


    慶應義塾先端科学技術研究センター, 2020 年度指定研究プロジェクト産学連携支援(単年度), Joint research, Principal investigator

  • プラズモン効果による単分子フォトクロミック反応の実現検証


    MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Principal investigator

  • 機能性ナノ材料の評価に向けたマルチスケール走査型プローブ顕微鏡の開発


    公益財団法人 高橋産業経済研究財団, Other, Principal investigator

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Awards 【 Display / hide

  • 平成30年度科学技術分野の文部科学大臣表彰若手科学者賞

    2018.04, 文部科学省


Courses Taught 【 Display / hide











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Memberships in Academic Societies 【 Display / hide

  • The Japan Society of Applied Physics, 

  • 日本表面真空学会, 

  • 日本化学会, 

  • 日本物理学会, 

  • 日本表面科学会, 


Committee Experiences 【 Display / hide

  • 2022.04

    日本表面真空学会関東支部役員, 公益社団法人 日本表面真空学会関東支部

  • 2022.02

    Program Committee of The 14th International Symposium on Atomic Level Characterizations for New Materials and Devices (ALC’22), The 14th International Symposium on Atomic Level Characterizations for New Materials and Devices (ALC’22)

  • 2021.04

    応用物理学会薄膜・表面物理分科会常任幹事, 応用物理学会薄膜・表面物理分科会

  • 2021.03

    Program Committee of The 13th International Symposium on Atomic Level Characterizations for New Materials and Devices (ALC’21), The 13th International Symposium on Atomic Level Characterizations for New Materials and Devices (ALC’21)

  • 2020.04

    日本学術振興会 ナノプローブテクノロジー第167委員会委員, 日本学術振興会 ナノプローブテクノロジー第167委員会

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