1
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Harano K, Nakamuro T, Nakamura E. Cinematographic study of stochastic chemical events at atomic resolution. Microscopy (Oxf) 2024; 73:101-116. [PMID: 37864546 DOI: 10.1093/jmicro/dfad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/07/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023] Open
Abstract
The advent of single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM) has created a new field of 'cinematic chemistry,' allowing for the cinematographic recording of dynamic behaviors of organic and inorganic molecules and their assembly. However, the limited electron dose per frame of video images presents a major challenge in SMART-EM. Recent advances in direct electron counting cameras and techniques to enhance image quality through the implementation of a denoising algorithm have enabled the tracking of stochastic molecular motions and chemical reactions with sub-millisecond temporal resolution and sub-angstrom localization precision. This review showcases the development of dynamic molecular imaging using the SMART-EM technique, highlighting insights into nanomechanical behavior during molecular shuttle motion, pathways of multistep chemical reactions, and elucidation of crystallization processes at the atomic level.
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Affiliation(s)
- Koji Harano
- Center for Basic Research on Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Takayuki Nakamuro
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Ariga K. 2D Materials Nanoarchitectonics for 3D Structures/Functions. MATERIALS (BASEL, SWITZERLAND) 2024; 17:936. [PMID: 38399187 PMCID: PMC10890396 DOI: 10.3390/ma17040936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
It has become clear that superior material functions are derived from precisely controlled nanostructures. This has been greatly accelerated by the development of nanotechnology. The next step is to assemble materials with knowledge of their nano-level structures. This task is assigned to the post-nanotechnology concept of nanoarchitectonics. However, nanoarchitectonics, which creates intricate three-dimensional functional structures, is not always easy. Two-dimensional nanoarchitectonics based on reactions and arrangements at the surface may be an easier target to tackle. A better methodology would be to define a two-dimensional structure and then develop it into a three-dimensional structure and function. According to these backgrounds, this review paper is organized as follows. The introduction is followed by a summary of the three issues; (i) 2D to 3D dynamic structure control: liquid crystal commanded by the surface, (ii) 2D to 3D rational construction: a metal-organic framework (MOF) and a covalent organic framework (COF); (iii) 2D to 3D functional amplification: cells regulated by the surface. In addition, this review summarizes the important aspects of the ultimate three-dimensional nanoarchitectonics as a perspective. The goal of this paper is to establish an integrated concept of functional material creation by reconsidering various reported cases from the viewpoint of nanoarchitectonics, where nanoarchitectonics can be regarded as a method for everything in materials science.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
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3
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Ariga K. Materials Nanoarchitectonics at Dynamic Interfaces: Structure Formation and Functional Manipulation. MATERIALS (BASEL, SWITZERLAND) 2024; 17:271. [PMID: 38204123 PMCID: PMC10780059 DOI: 10.3390/ma17010271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
The next step in nanotechnology is to establish a methodology to assemble new functional materials based on the knowledge of nanotechnology. This task is undertaken by nanoarchitectonics. In nanoarchitectonics, we architect functional material systems from nanounits such as atoms, molecules, and nanomaterials. In terms of the hierarchy of the structure and the harmonization of the function, the material created by nanoarchitectonics has similar characteristics to the organization of the functional structure in biosystems. Looking at actual biofunctional systems, dynamic properties and interfacial environments are key. In other words, nanoarchitectonics at dynamic interfaces is important for the production of bio-like highly functional materials systems. In this review paper, nanoarchitectonics at dynamic interfaces will be discussed, looking at recent typical examples. In particular, the basic topics of "molecular manipulation, arrangement, and assembly" and "material production" will be discussed in the first two sections. Then, in the following section, "fullerene assembly: from zero-dimensional unit to advanced materials", we will discuss how various functional structures can be created from the very basic nanounit, the fullerene. The above examples demonstrate the versatile possibilities of architectonics at dynamic interfaces. In the last section, these tendencies will be summarized, and future directions will be discussed.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
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4
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Otsuka C, Takahashi S, Isobe A, Saito T, Aizawa T, Tsuchida R, Yamashita S, Harano K, Hanayama H, Shimizu N, Takagi H, Haruki R, Liu L, Hollamby MJ, Ohkubo T, Yagai S. Supramolecular Polymer Polymorphism: Spontaneous Helix-Helicoid Transition through Dislocation of Hydrogen-Bonded π-Rosettes. J Am Chem Soc 2023; 145:22563-22576. [PMID: 37796243 DOI: 10.1021/jacs.3c07556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Polymorphism, a phenomenon whereby disparate self-assembled products can be formed from identical molecules, has incited interest in the field of supramolecular polymers. Conventionally, the monomers that constitute supramolecular polymers are engineered to facilitate one-dimensional aggregation and, consequently, their polymorphism surfaces primarily when the states of assembly differ significantly. This engenders polymorphs of divergent dimensionalities such as one- and two-dimensional aggregates. Notwithstanding, realizing supramolecular polymer polymorphism, wherein polymorphs maintain one-dimensional aggregation, persists as a daunting challenge. In this work, we expound upon the manifestation of two supramolecular polymer polymorphs formed from a large discotic supramolecular monomer (rosette), which consists of six hydrogen-bonded molecules with an extended π-conjugated core. These polymorphs are generated in mixtures of chloroform and methylcyclohexane, attributable to distinctly different disc stacking arrangements. The face-to-face (minimal displacement) and offset (large displacement) stacking arrangements can be predicated on their distinctive photophysical properties. The face-to-face stacking results in a twisted helix structure. Conversely, the offset stacking induces inherent curvature in the supramolecular fiber, thereby culminating in a hollow helical coil (helicoid). While both polymorphs exhibit bistability in nonpolar solvent compositions, the face-to-face stacking attains stability purely in a kinetic sense within a polar solvent composition and undergoes conversion into offset stacking through a dislocation of stacked rosettes. This occurs without the dissociation and nucleation of monomers, leading to unprecedented helicoidal folding of supramolecular polymers. Our findings augment our understanding of supramolecular polymer polymorphism, but they also highlight a distinctive method for achieving helicoidal folding in supramolecular polymers.
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Affiliation(s)
- Chie Otsuka
- Division of Advanced Science and Engineering, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Sho Takahashi
- Division of Advanced Science and Engineering, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Atsushi Isobe
- Division of Advanced Science and Engineering, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Takuho Saito
- Division of Advanced Science and Engineering, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Takumi Aizawa
- Division of Advanced Science and Engineering, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Ryoma Tsuchida
- Division of Advanced Science and Engineering, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Shuhei Yamashita
- Division of Advanced Science and Engineering, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Koji Harano
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba 305-0044, Japan
| | - Hiroki Hanayama
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University, Chiba 263-8522, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
| | - Hideaki Takagi
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
| | - Rie Haruki
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
| | - Luzhi Liu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, China
| | - Martin J Hollamby
- Department of Chemistry, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST55BG, U.K
| | - Takahiro Ohkubo
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University, Chiba 263-8522, Japan
| | - Shiki Yagai
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University, Chiba 263-8522, Japan
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba 263-8522, Japan
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5
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Hoelzel H, Lee S, Amsharov KY, Jux N, Harano K, Nakamura E, Lungerich D. Time-resolved imaging and analysis of the electron beam-induced formation of an open-cage metallo-azafullerene. Nat Chem 2023; 15:1444-1451. [PMID: 37386284 DOI: 10.1038/s41557-023-01261-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 05/26/2023] [Indexed: 07/01/2023]
Abstract
The visualization of single-molecule reactions provides crucial insights into chemical processes, and the ability to do so has grown with the advances in high-resolution transmission electron microscopy. There is currently a limited mechanistic understanding of chemical reactions under the electron beam. However, such reactions may enable synthetic methodologies that cannot be accessed by traditional organic chemistry methods. Here we demonstrate the synthetic use of the electron beam, by in-depth single-molecule, atomic-resolution, time-resolved transmission electron microscopy studies, in inducing the formation of a doubly holed fullerene-porphyrin cage structure from a well-defined benzoporphyrin precursor deposited on graphene. Through real-time imaging, we analyse the hybrid's ability to host up to two Pb atoms, and subsequently probe the dynamics of the Pb-Pb binding motif in this exotic metallo-organic cage structure. Through simulation, we conclude that the secondary electrons, which accumulate in the periphery of the irradiated area, can also initiate chemical reactions. Consequently, designing advanced carbon nanostructures by electron-beam lithography will depend on the understanding and limitations of molecular radiation chemistry.
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Affiliation(s)
- Helen Hoelzel
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg (FAU), Erlangen, Germany
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Sol Lee
- Center for NanoMedicine, Institute for Basic Science (IBS), Seodaemun-gu, Seoul, South Korea
| | | | - Norbert Jux
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg (FAU), Erlangen, Germany
| | - Koji Harano
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Dominik Lungerich
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Center for NanoMedicine, Institute for Basic Science (IBS), Seodaemun-gu, Seoul, South Korea.
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, South Korea.
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6
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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7
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Chevalier OJGL, Nakamuro T, Sato W, Miyashita S, Chiba T, Kido J, Shang R, Nakamura E. Precision Synthesis and Atomistic Analysis of Deep-Blue Cubic Quantum Dots Made via Self-Organization. J Am Chem Soc 2022; 144:21146-21156. [DOI: 10.1021/jacs.2c08227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Takayuki Nakamuro
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Wataru Sato
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoru Miyashita
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Chiba
- Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Junji Kido
- Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Rui Shang
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Nakamuro T, Kamei K, Sun K, Bode JW, Harano K, Nakamura E. Time-Resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ions. J Am Chem Soc 2022; 144:13612-13622. [PMID: 35857028 DOI: 10.1021/jacs.2c03949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca2+-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level. We studied the ability of DP molecule to aggregate by itself in water, the effects of Ca2+ ions to promote the aggregation, and the connectivity of the DP molecules in the oligomers by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in homogeneous aqueous solution. The dimer remains as the major species, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer in its cyclic form is the largest oligomer observed, while the trimer forms in its linear form. The study has shown that the DP molecule has an intrinsic property of forming tetramers in water, which is enhanced by the presence of calcium ions. Such experimental structural information will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording for the study of self-organization processes.
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Affiliation(s)
- Takayuki Nakamuro
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Kamei
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keyi Sun
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich 8093, Switzerland
| | - Koji Harano
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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9
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Fu S, Jin E, Hanayama H, Zheng W, Zhang H, Di Virgilio L, Addicoat MA, Mezger M, Narita A, Bonn M, Müllen K, Wang HI. Outstanding Charge Mobility by Band Transport in Two-Dimensional Semiconducting Covalent Organic Frameworks. J Am Chem Soc 2022; 144:7489-7496. [PMID: 35420808 PMCID: PMC9052747 DOI: 10.1021/jacs.2c02408] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Two-dimensional covalent
organic frameworks (2D COFs) represent
a family of crystalline porous polymers with a long-range order and
well-defined open nanochannels that hold great promise for electronics,
catalysis, sensing, and energy storage. To date, the development of
highly conductive 2D COFs has remained challenging due to the finite
π-conjugation along the 2D lattice and charge localization at
grain boundaries. Furthermore, the charge transport mechanism within
the crystalline framework remains elusive. Here, time- and frequency-resolved
terahertz spectroscopy reveals intrinsically Drude-type band transport
of charge carriers in semiconducting 2D COF thin films condensed by
1,3,5-tris(4-aminophenyl)benzene (TPB) and 1,3,5-triformylbenzene
(TFB). The TPB–TFB COF thin films demonstrate high photoconductivity
with a long charge scattering time exceeding 70 fs at room temperature
which resembles crystalline inorganic materials. This corresponds
to a record charge carrier mobility of 165 ± 10 cm2 V–1 s–1, vastly outperforming
that of the state-of-the-art conductive COFs. These results reveal
TPB–TFB COF thin films as promising candidates for organic
electronics and catalysis and provide insights into the rational design
of highly crystalline porous materials for efficient and long-range
charge transport.
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Affiliation(s)
- Shuai Fu
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
| | - Enquan Jin
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany.,State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry and International Center of Future Science, Jilin University, Changchun 130012, P.R. China
| | - Hiroki Hanayama
- Organic and Carbon Nanomaterials Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Wenhao Zheng
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
| | - Heng Zhang
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
| | - Lucia Di Virgilio
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
| | - Matthew A Addicoat
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, U.K
| | - Markus Mezger
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
| | - Akimitsu Narita
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany.,Organic and Carbon Nanomaterials Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
| | - Klaus Müllen
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany.,Institute of Physical Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, Mainz 55128, Germany
| | - Hai I Wang
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
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