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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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Park J, Lee S, Jafter OF, Cheon J, Lungerich D. Electron beam-induced demetallation of Fe, Co, Ni, Cu, Zn, Pd, and Pt metalloporphyrins: insights in e-beam chemistry and metal cluster formations. Phys Chem Chem Phys 2024; 26:8051-8061. [PMID: 38314818 DOI: 10.1039/d3cp05848d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Electron beams are versatile tools for nanoscale fabrication processes, however, the underlying e-beam chemistry remains in its infancy. Through operando transmission electron microscopy investigations, we elucidate a redox-driven cargo release of individual metal atoms triggered by electron beams. The chosen organic delivery molecule, tetraphenylporphyrin (TPP), proves highly versatile, forming complexes with nearly all metals from the periodic table and being easily processed in solution. A comprehensive cinematographic analysis of the dynamics of single metal atoms confirms the nearly instantaneous ejection of complexed metal atoms under an 80 kV electron beam, underscoring the system's broad versatility. Providing mechanistic insights, we employ density functional theory to support the proposed reductive demetallation pathway facilitated by secondary electrons, contributing novel perspectives to electron beam-mediated chemical reaction mechanisms. Lastly, our findings demonstrate that all seven metals investigated form nanoclusters once ejected from TPP, highlighting the method's potential for studying and developing sustainable single-atom and nanocluster catalysts.
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Affiliation(s)
- Jongseong Park
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
| | - Sol Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Orein Francis Jafter
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Dominik Lungerich
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
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3
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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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4
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Wang Y, Zhao R, Ackermann L. Electrochemical Syntheses of Polycyclic Aromatic Hydrocarbons (PAHs). ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300760. [PMID: 36965124 DOI: 10.1002/adma.202300760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) have surfaced as increasingly viable components in optoelectronics and material sciences. The development of highly efficient and atom-economic tools to prepare PAHs under exceedingly mild conditions constitutes a long-term goal. Traditional syntheses of PAHs have largely relied on multistep approaches or the conventional Scholl reaction. However, Scholl reactions are largely inefficient with electron-deficient substrates, require stoichiometric chemical oxidants, and typically occur in the presence of strong acid. In sharp contrast, electrochemistry has gained considerable momentum during the past decade as an alternative for the facile and straightforward PAHs assembly, generally via electro-oxidative dehydrogenative annulation, releasing molecular hydrogen as the sole stoichiometric byproduct by the hydrogen evolution reaction. This review provides an overview on the recent and significant advances in the field of electrochemical syntheses of various PAHs until January 2023.
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Affiliation(s)
- Yulei Wang
- Institut für Organische und Biomolekulare Chemie and Wöhler Research Institute for Sustainable Chemistry (WISCh), Georg-August-Universität Göttingen, Tammanstraße 2, 37077, Göttingen, Germany
| | - Rong Zhao
- Institut für Organische und Biomolekulare Chemie and Wöhler Research Institute for Sustainable Chemistry (WISCh), Georg-August-Universität Göttingen, Tammanstraße 2, 37077, Göttingen, Germany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare Chemie and Wöhler Research Institute for Sustainable Chemistry (WISCh), Georg-August-Universität Göttingen, Tammanstraße 2, 37077, Göttingen, Germany
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Paukov M, Kramberger C, Begichev I, Kharlamova M, Burdanova M. Functionalized Fullerenes and Their Applications in Electrochemistry, Solar Cells, and Nanoelectronics. MATERIALS (BASEL, SWITZERLAND) 2023; 16:1276. [PMID: 36770286 PMCID: PMC9919315 DOI: 10.3390/ma16031276] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/09/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Carbon-based nanomaterials have rapidly advanced over the last few decades. Fullerenes, carbon nanotubes, graphene and its derivatives, graphene oxide, nanodiamonds, and carbon-based quantum dots have been developed and intensively studied. Among them, fullerenes have attracted increasing research attention due to their unique chemical and physical properties, which have great potential in a wide range of applications. In this article, we offer a comprehensive review of recent progress in the synthesis and the chemical and physical properties of fullerenes and related composites. The review begins with the introduction of various methods for the synthesis of functionalized fullerenes. A discussion then follows on their chemical and physical properties. Thereafter, various intriguing applications, such as using carbon nanotubes as nanoreactors for fullerene chemical reactions, are highlighted. Finally, this review concludes with a summary of future research, major challenges to be met, and possible solutions.
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Affiliation(s)
- Maksim Paukov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 9 Institutsky Lane, 141700 Dolgoprudny, Russia
| | - Christian Kramberger
- Faculty of Physics, University of Vienna, Strudlhofgasse 4, 1090 Vienna, Austria
| | - Ilia Begichev
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 9 Institutsky Lane, 141700 Dolgoprudny, Russia
- Center for Photonics and Quantum Materials, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Marianna Kharlamova
- Centre for Advanced Material Application (CEMEA), Slovak Academy of Sciences, Dúbravská cesta 5807/9, 854 11 Bratislava, Slovakia
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9-BC-2, 1060 Vienna, Austria
- Laboratory of Nanobiotechnologies, Moscow Institute of Physics and Technology, Institutskii Pereulok 9, 141700 Dolgoprudny, Russia
| | - Maria Burdanova
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 9 Institutsky Lane, 141700 Dolgoprudny, Russia
- Institute of Solid State Physics, Russian Academy of Sciences, 142432 Chernogolovka, Russia
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Excited state modulation of C70 dimerization in a carbon nanotube under a variable electron acceleration voltage. Micron 2022; 160:103316. [DOI: 10.1016/j.micron.2022.103316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 11/20/2022]
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7
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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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Gu Y, Qiu Z, Müllen K. Nanographenes and Graphene Nanoribbons as Multitalents of Present and Future Materials Science. J Am Chem Soc 2022; 144:11499-11524. [PMID: 35671225 PMCID: PMC9264366 DOI: 10.1021/jacs.2c02491] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
As cut-outs from a graphene sheet, nanographenes (NGs) and graphene nanoribbons (GNRs) are ideal cases with which to connect the world of molecules with that of bulk carbon materials. While various top-down approaches have been developed to produce such nanostructures in high yields, in the present perspective, precision structural control is emphasized for the length, width, and edge structures of NGs and GNRs achieved by modern solution and on-surface syntheses. Their structural possibilities have been further extended from "flatland" to the three-dimensional world, where chirality and handedness are the jewels in the crown. In addition to properties exhibited at the molecular level, self-assembly and thin-film structures cannot be neglected, which emphasizes the importance of processing techniques. With the rich toolkit of chemistry in hand, NGs and GNRs can be endowed with versatile properties and functions ranging from stimulated emission to spintronics and from bioimaging to energy storage, thus demonstrating their multitalents in present and future materials science.
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Affiliation(s)
- Yanwei Gu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Zijie Qiu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Shenzhen
Institute of Aggregate Science and Technology, School of Science and
Engineering, The Chinese University of Hong
Kong, Shenzhen 518172, China
| | - Klaus Müllen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
for Physical Chemistry , Johannes Gutenberg
University Mainz, Duesbergweg
10-14, 55128 Mainz, Germany
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9
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Shimizu T, Lungerich D, Harano K, Nakamura E. Time-Resolved Imaging of Stochastic Cascade Reactions over a Submillisecond to Second Time Range at the Angstrom Level. J Am Chem Soc 2022; 144:9797-9805. [PMID: 35609254 DOI: 10.1021/jacs.2c02297] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Many chemical reactions, such as multistep catalytic cycles, are cascade reactions in which a series of transient intermediates appear and disappear stochastically over an extended period. The mechanisms of such reactions are challenging to study, even in ultrafast pump-probe experiments. The dimerization of a van der Waals dimer of [60]fullerene producing a short carbon nanotube is a typical cascade reaction and is probably the most frequently studied in carbon materials chemistry. As many as 23 intermediates were predicted by theory, but only the first stable one has been verified experimentally. With the aid of fast electron microscopy, we obtained cinematographic recordings of individual molecules at a maximum frame rate of 1600 frames per second. Using Chambolle total variation algorithm processing and automated cross-correlation image matching analysis, we report on the identification of several metastable intermediates by their shape and size. Although the reaction events occurred stochastically, varying the lifetime of each intermediate accordingly, the average lifetime for each intermediate structure could be obtained from statistical analysis of many cinematographic images for the cascade reaction. Among the shortest-living intermediates, we detected one that lasted less than 3 ms in three independent cascade reactions. We anticipate that the rapid technological development of microscopy and image processing will soon initiate an era of cinematographic studies of chemical reactions and cinematic chemistry.
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Affiliation(s)
- Toshiki Shimizu
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dominik Lungerich
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Center for Nanomedicine (CNM), Institute for Basic Science (IBS), IBS Hall, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea.,Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, South Korea
| | - 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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Atomic-number ( Z)-correlated atomic sizes for deciphering electron microscopic molecular images. Proc Natl Acad Sci U S A 2022; 119:e2114432119. [PMID: 35349339 PMCID: PMC9168473 DOI: 10.1073/pnas.2114432119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Atomic resolution transmission electron microscopy (TEM) has opened up a new era of molecular science by providing atomic video images of dynamic motions of single organic and inorganic molecules. However, the images often look different from the images of molecular models, because these models are designed to visualize the electronic properties of the molecule instead of nuclear electrostatic potentials that are felt by the e-beam in TEM imaging. Here, we propose a molecular model that reproduces TEM images using atomic radii correlated to atomic number (Z). The model serves to provide a priori a useful idea of how a single molecule, molecular assemblies, and thin crystals of organic or inorganic materials look in TEM. With the advent of atomic resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of cinematic molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. We found a good correlation between the atomic number (Z) and the atomic size seen in TEM images when we consider shot noise in digital images. We propose Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. Two parameter sets were developed for TEM images recorded under high-noise (ZCHN) and low-noise (ZCLN) conditions. The molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research.
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