1
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Sakakibara M, Nakamuro T, Nakamura E. Kinetic Exploration of Nanoscale Polymorphs through Interface Energy Adjustment. ACS NANO 2024; 18:22325-22333. [PMID: 39117583 DOI: 10.1021/acsnano.4c06618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Traditionally, the study of crystal polymorphism has relied on thermodynamics and measurements averaged over time and the crystal's constituents. This work introduces a kinetic approach to phase identification─millisecond cinematographic electron microscopic imaging of the dynamics of phase transitions of crystals of a few nm in diameter. We demonstrate a remarkable impact of the interface energy on the relative stability of the nanocrystal's polymorphs, enabling in situ manipulation of phase transitions through size increase or decrease. Starting with the B1 NaI polymorph at 298 K, we identified the previously unknown B2 polymorph of a 1 s lifetime upon sublimation of the crystal. From the CsCl liquid phase, we produced the B1 phase, previously described only at 749 K.
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Affiliation(s)
- Masaya Sakakibara
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, 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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Liu D, Fu J, Elishav O, Sakakibara M, Yamanouchi K, Hirshberg B, Nakamuro T, Nakamura E. Melting entropy of crystals determined by electron-beam-induced configurational disordering. Science 2024; 384:1212-1219. [PMID: 38815089 DOI: 10.1126/science.adk3620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
Upon melting, the molecules in a crystal explore numerous configurations, reflecting an increase in disorder. The molar entropy of disorder can be defined by Boltzmann's formula ΔSd = Rln(Wd), where Wd is the increase in the number of microscopic states, so far inaccessible experimentally. We found that the Arrhenius frequency factor A of the electron diffraction signal decay provides Wd through an experimental equation A = AINTWd, where AINT is an inelastic scattering cross section. The method connects Clausius and Boltzmann experimentally and supplements the Clausius approach, being applicable to a femtogram quantity of thermally unstable and biomolecular crystals. The data also showed that crystal disordering and crystallization of melt are reciprocal, both governed by the entropy change but manifesting in opposite directions.
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Affiliation(s)
- Dongxin Liu
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jiarui Fu
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Oren Elishav
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Masaya Sakakibara
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kaoru Yamanouchi
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Barak Hirshberg
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - 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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3
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Onoe J, Noda Y, Wang Q, Harano K, Nakaya M, Nakayama T. Structures, fundamental properties, and potential applications of low-dimensional C 60 polymers and other nanocarbons: a review. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2024; 25:2346068. [PMID: 38774495 PMCID: PMC11107862 DOI: 10.1080/14686996.2024.2346068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 05/24/2024]
Abstract
Since carbon (C) atom has a variety of chemical bonds via hybridization between s and p atomic orbitals, it is well known that there are robust carbon materials. In particular, discovery of C60 has been an epoch making to cultivate nanocarbon fields. Since then, nanocarbon materials such as nanotube and graphene have been reported. It is interesting to note that C60 is soluble and volatile unlike nanotube and graphene. This indicates that C60 film is easy to be produced on any kinds of substrates, which is advantage for device fabrication. In particular, electron-/photo-induced C60 polymerization finally results in formation of one-dimensional (1D) metallic peanut-shaped and 2D dumbbell-shaped semiconducting C60 polymers, respectively. This enables us to control the physicochemical properties of C60 films using electron-/photo-lithography techniques. In this review, we focused on the structures, fundamental properties, and potential applications of the low-dimensional C60 polymers and other nanocarbons such as C60 peapods, wavy-structured graphene, and penta-nanotubes with topological defects. We hope this review will provide new insights for producing new novel nanocarbon materials and inspire broad readers to cultivate new further research in carbon materials.
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Affiliation(s)
- Jun Onoe
- Department of Energy Science and Engineering, Nagoya University, Nagoya, Japan
| | - Yusuke Noda
- Department of Information and Communication Engineering, Okayama Prefectural University, Soja, Japan
| | - Qian Wang
- School of Materials Science and Engineering/Center for Applied Physics and Technology, Peking University, Beijing, China
| | - Koji Harano
- Center for Basic Research on Materials, and Division of International Collaborations and Public Relations, National Institute for Materials Science (NIMS), Tsukuba, Japan
| | - Masato Nakaya
- Department of Energy Science and Engineering, Nagoya University, Nagoya, Japan
| | - Tomonobu Nakayama
- Center for Basic Research on Materials, and Division of International Collaborations and Public Relations, National Institute for Materials Science (NIMS), Tsukuba, Japan
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4
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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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5
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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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6
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Cardillo-Zallo I, Biskupek J, Bloodworth S, Marsden ES, Fay MW, Ramasse QM, Rance GA, Stoppiello CT, Cull WJ, Weare BL, Whitby RJ, Kaiser U, Brown PD, Khlobystov AN. Atomic-Scale Time-Resolved Imaging of Krypton Dimers, Chains and Transition to a One-Dimensional Gas. ACS NANO 2024; 18:2958-2971. [PMID: 38251654 PMCID: PMC10832048 DOI: 10.1021/acsnano.3c07853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Single-atom dynamics of noble-gas elements have been investigated using time-resolved transmission electron microscopy (TEM), with direct observation providing for a deeper understanding of chemical bonding, reactivity, and states of matter at the nanoscale. We report on a nanoscale system consisting of endohedral fullerenes encapsulated within single-walled carbon nanotubes ((Kr@C60)@SWCNT), capable of the delivery and release of krypton atoms on-demand, via coalescence of host fullerene cages under the action of the electron beam (in situ) or heat (ex situ). The state and dynamics of Kr atoms were investigated by energy dispersive X-ray spectroscopy (EDS), electron energy loss spectroscopy (EELS), and X-ray photoelectron spectroscopy (XPS). Kr atom positions were measured precisely using aberration-corrected high-resolution TEM (AC-HRTEM), aberration-corrected scanning TEM (AC-STEM), and single-atom spectroscopic imaging (STEM-EELS). The electron beam drove the formation of 2Kr@C120 capsules, in which van der Waals Kr2 and transient covalent [Kr2]+ bonding states were identified. Thermal coalescence led to the formation of longer coalesced nested nanotubes containing more loosely bound Krn chains (n = 3-6). In some instances, delocalization of Kr atomic positions was confirmed by STEM analysis as the transition to a one-dimensional (1D) gas, as Kr atoms were constrained to only one degree of translational freedom within long, well-annealed, nested nanotubes. Such nested nanotube structures were investigated by Raman spectroscopy. This material represents a highly compressed and dimensionally constrained 1D gas stable under ambient conditions. Direct atomic-scale imaging has revealed elusive bonding states and a previously unseen 1D gaseous state of matter of this noble gas element, demonstrating TEM to be a powerful tool in the discovery of chemistry at the single-atom level.
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Affiliation(s)
- Ian Cardillo-Zallo
- School
of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Johannes Biskupek
- Electron
Microscopy Group of Materials Science, Central Facility for Electron
Microscopy, Ulm University, Ulm 89081, Germany
| | - Sally Bloodworth
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Elizabeth S. Marsden
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Michael W. Fay
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham NG7 2QL, United
Kingdom
| | - Quentin M. Ramasse
- SuperSTEM
Laboratory, SciTech Daresbury Campus, Daresbury WA4 4AD, United Kingdom
- School of
Chemical and Process Engineering and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Graham A. Rance
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham NG7 2QL, United
Kingdom
| | - Craig T. Stoppiello
- Centre
for Microscopy and Microanalysis, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - William J. Cull
- School
of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Benjamin L. Weare
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham NG7 2QL, United
Kingdom
| | - Richard J. Whitby
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Ute Kaiser
- Electron
Microscopy Group of Materials Science, Central Facility for Electron
Microscopy, Ulm University, Ulm 89081, Germany
| | - Paul D. Brown
- Department
of Mechanical, Materials & Manufacturing Engineering, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Andrei N. Khlobystov
- School
of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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7
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Abella L, Novell-Leruth G, Ricart JM, Poblet JM, Rodríguez-Fortea A. Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations. Beilstein J Org Chem 2024; 20:92-100. [PMID: 38264452 PMCID: PMC10804564 DOI: 10.3762/bjoc.20.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
Fullerene dimerization inside a peapod is analyzed at DFT level by characterizing the stationary points and deriving the energy profile of the initial and reversible process named phase 1. We find that the barriers for the radical cation mechanism are significantly lower than those found for the neutral pathway. The peapod is mainly providing one-dimensional confinement for the reaction to take place in a more efficient way. Car-Parrinello metadynamics simulations provide hints on structures for the initial steps of the irreversible phase 2 where bond formation and breaking lead to important structural reorganizations within the coalescence process.
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Affiliation(s)
- Laura Abella
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Gerard Novell-Leruth
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo 1, 43007 Tarragona, Spain
- Hydrogen and Power-to-X Department, Iberian Center for Research in Energy Storage (CIIAE), FUNDECYT-PCTEx, Polytechnic School of Caceres Building, Office CIIAE-C7, Av. Universidad s/n, 10003 Cáceres, Spain
| | - Josep M Ricart
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Josep M Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Antonio Rodríguez-Fortea
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo 1, 43007 Tarragona, Spain
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8
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Hashikawa Y, Okamoto S, Murata Y. Synthesis of inter-[60]fullerene conjugates with inherent chirality. Nat Commun 2024; 15:514. [PMID: 38225251 PMCID: PMC10789730 DOI: 10.1038/s41467-024-44834-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
Coalescence of [60]fullerenes potentially produces hypothetical nanocarbon assemblies with non-naturally occurring topologies. Since the discovery of [60]fullerene in 1985, coalesced [60]fullerene oligomers have only been observed as transient species by transmission electron microscopy during an oligomerization process under a high electron acceleration voltage. Herein, we showcase the rational synthesis of covalent assemblies consisting of inherently chiral open-[60]fullerenes. The crystallographic analyses unveiled double-caged structures of non-conjugated and conjugated inter-[60]fullerene hybrids, in which the two [60]fullerene cages are bounds to each other through a covalent linkage. The former one further assembles via a heterochiral recognition so that four carbon cages are arranged in a tetrahedral manner both in solution and solid state. Reflecting radially-conjugated double π-surface nature, the inter-[60]fullerene conjugate exhibits strong electronic communication in its reduced states, intense absorption behavior, and chiroptical activity with a dissymmetry factor of 0.21 (at 674 nm) which breaks the record for known chiral organic molecules.
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Affiliation(s)
- Yoshifumi Hashikawa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.
| | - Shu Okamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yasujiro Murata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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9
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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: 7] [Impact Index Per Article: 7.0] [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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10
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Fung KLY, Skowron ST, Hayter R, Mason SE, Weare BL, Besley NA, Ramasse QM, Allen CS, Khlobystov AN. Direct measurement of single-molecule dynamics and reaction kinetics in confinement using time-resolved transmission electron microscopy. Phys Chem Chem Phys 2023; 25:9092-9103. [PMID: 36920796 DOI: 10.1039/d2cp05183d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
We report experimental methodologies utilising transmission electron microscopy (TEM) as an imaging tool for reaction kinetics at the single molecule level, in direct space and with spatiotemporal continuity. Using reactions of perchlorocoronene (PCC) in nanotubes of different diameters and at different temperatures, we found a period of molecular movement to precede the intermolecular addition of PCC, with a stronger dependence of the reaction rate on the nanotube diameter, controlling the local environments around molecules, than on the reaction temperature (-175, 23 or 400 °C). Once initiated, polymerisation of PCC follows zero-order reaction kinetics with the observed reaction cross section σobs of 1.13 × 10-9 nm2 (11.3 ± 0.6 barn), determined directly from time-resolved TEM image series acquired with a rate of 100 frames per second. Polymerisation was shown to proceed from a single point, with molecules reacting sequentially, as in a domino effect, due to the strict conformational requirement of the Diels-Alder cycloaddition creating the bottleneck for the reaction. The reaction mechanism was corroborated by correlating structures of reaction intermediates observed in TEM images, with molecular weights measured by using mass spectrometry (MS) when the same reaction was triggered by UV irradiation. The approaches developed in this study bring the imaging of chemical reactions at the single-molecule level closer to traditional concepts of chemistry.
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Affiliation(s)
- Kayleigh L Y Fung
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Stephen T Skowron
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Ruth Hayter
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Stephen E Mason
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Benjamin L Weare
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Nicholas A Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Quentin M Ramasse
- SuperSTEM Laboratory, SciTech Daresbury Campus, Keckwick Lane, Daresbury WA4 4AD, UK.,School of Chemical and Process Engineering and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Christopher S Allen
- Electron Physical Sciences Imaging Centre, Diamond Light Source Ltd., Oxfordshire OX11 0DE, UK.,Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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11
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Abstract
The two natural allotropes of carbon, diamond and graphite, are extended networks of sp3-hybridized and sp2-hybridized atoms, respectively1. By mixing different hybridizations and geometries of carbon, one could conceptually construct countless synthetic allotropes. Here we introduce graphullerene, a two-dimensional crystalline polymer of C60 that bridges the gulf between molecular and extended carbon materials. Its constituent fullerene subunits arrange hexagonally in a covalently interconnected molecular sheet. We report charge-neutral, purely carbon-based macroscopic crystals that are large enough to be mechanically exfoliated to produce molecularly thin flakes with clean interfaces-a critical requirement for the creation of heterostructures and optoelectronic devices2. The synthesis entails growing single crystals of layered polymeric (Mg4C60)∞ by chemical vapour transport and subsequently removing the magnesium with dilute acid. We explore the thermal conductivity of this material and find it to be much higher than that of molecular C60, which is a consequence of the in-plane covalent bonding. Furthermore, imaging few-layer graphullerene flakes using transmission electron microscopy and near-field nano-photoluminescence spectroscopy reveals the existence of moiré-like superlattices3. More broadly, the synthesis of extended carbon structures by polymerization of molecular precursors charts a clear path to the systematic design of materials for the construction of two-dimensional heterostructures with tunable optoelectronic properties.
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12
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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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13
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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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14
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Dynamic hetero-metallic bondings visualized by sequential atom imaging. Nat Commun 2022; 13:2968. [PMID: 35624108 PMCID: PMC9142510 DOI: 10.1038/s41467-022-30533-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
Traditionally, chemistry has been developed to obtain thermodynamically stable and isolable compounds such as molecules and solids by chemical reactions. However, recent developments in computational chemistry have placed increased importance on studying the dynamic assembly and disassembly of atoms and molecules formed in situ. This study directly visualizes the formation and dissociation dynamics of labile dimers and trimers at atomic resolution with elemental identification. The video recordings of many homo- and hetero-metallic dimers are carried out by combining scanning transmission electron microscopy (STEM) with elemental identification based on the Z-contrast principle. Even short-lived molecules with low probability of existence such as AuAg, AgCu, and AuAgCu are directly visualized as a result of identifying moving atoms at low electron doses. The dynamic assembly and disassembly of atoms and molecules is challenging to characterize in real time, with atomic resolution and elemental identification. Here, the authors report direct observation of more than twenty homo and hetero-metallic compounds, including labile Ag-Cu dimers and Au-Ag-Cu trimers.
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15
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Ionization and electron excitation of C 60 in a carbon nanotube: A variable temperature/voltage transmission electron microscopic study. Proc Natl Acad Sci U S A 2022; 119:e2200290119. [PMID: 35377799 PMCID: PMC9169795 DOI: 10.1073/pnas.2200290119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The destruction of specimen molecules by an electron beam (e-beam) is either beneficial, as in mass spectrometry capitalizing on ion formation, or deleterious, as in electron microscopy. In the latter application, the e-beam not only produces the specimen image, but also causes information loss upon prolonged irradiation. However, the atomistic mechanism of such loss has been unclear. Performing single-molecule kinetic analysis of C60 dimerization in a carbon nanotube (CNT) under variable-temperature/voltage conditions, we identified three reactive species—that is, radical cation, singlet, and triplet excited states—reacting competitively as the voltage and the properties of the CNT were changed. The key enabler was in situ continuous recording of the whole reaction process, suggesting an upcoming new era of “cinematic chemistry.” There is increasing attention to chemical applications of transmission electron microscopy, which is often plagued by radiation damage. The damage in organic matter predominantly occurs via radiolysis. Although radiolysis is highly important, previous studies on radiolysis have largely been descriptive and qualitative, lacking in such fundamental information as the product structure, the influence of the energy of the electrons, and the reaction kinetics. We need a chemically well-defined system to obtain such data and have chosen as a model a variable-temperature and variable-voltage (VT/VV) study of the [2 + 2] dimerization of a van der Waals dimer [60]fullerene (C60) to C120 in a carbon nanotube (CNT), as studied for several hundred individual reaction events at atomic resolution. We report here the identification of five reaction pathways that serve as mechanistic models of radiolysis damage. Two of them occur via a radical cation of the specimen generated by specimen ionization, and three involve singlet or triplet excited states of the specimen, as initiated by electron excitation of the CNT, followed by energy transfer to the specimen. The [2 + 2] product was identified by measuring the distance between the two C60 moieties, and the mechanisms were distinguished by the pre-exponential factor and the Arrhenius activation energy—the standard protocol of chemical kinetic studies. The results illustrate the importance of VT/VV kinetic analysis in the studies of radiation damage and show that chemical ionization and electron excitation are inseparable, but different, mechanisms of radiation damage, which has so far been classified loosely under the single term “ionization.”
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16
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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: 10] [Impact Index Per Article: 5.0] [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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17
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Fung KLY, Skowron ST, Allen CS, Khlobystov AN. Counting molecules in nano test tubes: a method for determining the activation parameters of thermally driven reactions through direct imaging. Chem Commun (Camb) 2021; 57:10628-10631. [PMID: 34580683 DOI: 10.1039/d1cc03827c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A methodology for measuring activation parameters of a thermally driven chemical reaction by direct imaging and counting reactant molecules has been developed. The method combines the use of single walled carbon nanotubes (SWNTs) as a nano test tube, transmission electron microscopy (TEM) as an imaging tool, and a heating protocol that decouples the effect of the electron beam from the thermal activation. Polycyclic aromatic perchlorocoronene molecules are stable within SWNTs at room temperature, allowing imaging of individual molecules before and after each heating cycle between 500-600 °C. Polymerisation reaction rates can be determined at different temperatures simply by counting the number of molecules, resulting in an enthalpy of activation of 104 kJ mol-1 and very large entropic contributions to the Gibbs free energy of activation. This experimental methodology provides a link between reactions at the single-molecule level and macroscopic chemical kinetics parameters, through filming the chemical reaction in direct space.
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Affiliation(s)
- Kayleigh L Y Fung
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Stephen T Skowron
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Christopher S Allen
- Electron Physical Sciences Imaging Centre, Diamond Light Source Ltd., Oxfordshire OX11 0DE, UK.,Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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18
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Lungerich D, Hoelzel H, Harano K, Jux N, Amsharov KY, Nakamura E. A Singular Molecule-to-Molecule Transformation on Video: The Bottom-Up Synthesis of Fullerene C 60 from Truxene Derivative C 60H 30. ACS NANO 2021; 15:12804-12814. [PMID: 34018713 DOI: 10.1021/acsnano.1c02222] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Singular reaction events of small molecules and their dynamics remain a hardly understood territory in chemical sciences since spectroscopy relies on ensemble-averaged data, and microscopic scanning probe techniques show snapshots of frozen scenes. Herein, we report on continuous high-resolution transmission electron microscopic video imaging of the electron-beam-induced bottom-up synthesis of fullerene C60 through cyclodehydrogenation of tailor-made truxene derivative 1 (C60H30), which was deposited on graphene as substrate. During the reaction, C60H30 transformed in a multistep process to fullerene C60. Hereby, the precursor, metastable intermediates, and the product were identified by correlations with electron dose-corrected molecular simulations and single-molecule statistical analysis, which were substantiated with extensive density functional theory calculations. Our observations revealed that the initial cyclodehydrogenation pathway leads to thermodynamically favored intermediates through seemingly classical organic reaction mechanisms. However, dynamic interactions of the intermediates with the substrate render graphene as a non-innocent participant in the dehydrogenation process, which leads to a deviation from the classical reaction pathway. Our precise visual comprehension of the dynamic transformation implies that the outcome of electron-beam-initiated reactions can be controlled with careful molecular precursor design, which is important for the development and design of materials by electron beam lithography.
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Affiliation(s)
- Dominik Lungerich
- 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
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Helen Hoelzel
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University Erlangen-Nuernberg (FAU), Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Koji Harano
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Norbert Jux
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University Erlangen-Nuernberg (FAU), Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Konstantin Yu Amsharov
- Department of Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle, Germany
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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19
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Takada K, Morita M, Imaoka T, Kakinuma J, Albrecht K, Yamamoto K. Metal atom-guided conformational analysis of single polynuclear coordination molecules. SCIENCE ADVANCES 2021; 7:7/32/eabd9887. [PMID: 34362728 PMCID: PMC8346213 DOI: 10.1126/sciadv.abd9887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Microscopic observation of single molecules is a rapidly expanding field in chemistry and differs from conventional characterization techniques that require a large number of molecules. One of such form of single-molecule microscopy is high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), which is especially suitable for coordination compounds because of its atomic number-dependent contrast. However, to date, single-molecule observations using HAADF-STEM has limited to simple planar molecules. In the present study, we demonstrate a direct structural investigation of nonplanar dendronized polynuclear Ir complexes with subnanometer resolution using Ir as an atomic label. Decreasing the electron dose to the dendrimer complexes is critical for the single-molecule observation. A comparison with simulated STEM images of conformational isomers is performed to determine the most plausible conformation. Our results enlarge the potential of electron microscopic observation to realize structural analysis of coordination macromolecules, which has been impossible with conventional methods.
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Affiliation(s)
- Kenji Takada
- JST ERATO, Yamamoto Atom Hybrid Project, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Mari Morita
- JST ERATO, Yamamoto Atom Hybrid Project, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Takane Imaoka
- JST ERATO, Yamamoto Atom Hybrid Project, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan.
- Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Junko Kakinuma
- JST ERATO, Yamamoto Atom Hybrid Project, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Ken Albrecht
- JST ERATO, Yamamoto Atom Hybrid Project, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan.
- Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Kimihisa Yamamoto
- JST ERATO, Yamamoto Atom Hybrid Project, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan.
- Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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20
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Jordan JW, Fung KLY, Skowron ST, Allen CS, Biskupek J, Newton GN, Kaiser U, Khlobystov AN. Single-molecule imaging and kinetic analysis of intermolecular polyoxometalate reactions. Chem Sci 2021; 12:7377-7387. [PMID: 34163827 PMCID: PMC8171355 DOI: 10.1039/d1sc01874d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
We induce and study reactions of polyoxometalate (POM) molecules, [PW12O40]3- (Keggin) and [P2W18O62]6- (Wells-Dawson), at the single-molecule level. Several identical carbon nanotubes aligned side by side within a bundle provided a platform for spatiotemporally resolved imaging of ca. 100 molecules encapsulated within the nanotubes by transmission electron microscopy (TEM). Due to the entrapment of POM molecules their proximity to one another is effectively controlled, limiting molecular motion in two dimensions but leaving the third dimension available for intermolecular reactions between pairs of neighbouring molecules. By coupling the information gained from high resolution structural and kinetics experiments via the variation of key imaging parameters in the TEM, we shed light on the reaction mechanism. The dissociation of W-O bonds, a key initial step of POM reactions, is revealed to be reversible by the kinetic analysis, followed by an irreversible bonding of POM molecules to their nearest neighbours, leading to a continuous tungsten oxide nanowire, which subsequently transforms into amorphous tungsten-rich clusters due to progressive loss of oxygen atoms. The overall intermolecular reaction can therefore be described as a step-wise reductive polycondensation of POM molecules, via an intermediate state of an oxide nanowire. Kinetic analysis enabled by controlled variation of the electron flux in TEM revealed the reaction to be highly flux-dependent, which leads to reaction rates too fast to follow under the standard TEM imaging conditions. Although this presents a challenge for traditional structural characterisation of POM molecules, we harness this effect by controlling the conditions around the molecules and tuning the imaging parameters in TEM, which combined with theoretical modelling and image simulation, can shed light on the atomistic mechanisms of the reactions of POMs. This approach, based on the direct space and real time chemical reaction analysis by TEM, adds a new method to the arsenal of single-molecule kinetics techniques.
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Affiliation(s)
- Jack W Jordan
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Kayleigh L Y Fung
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Stephen T Skowron
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Christopher S Allen
- Electron Physical Science Imaging Center, Diamond Light Source Ltd. Didcot OX11 0DE UK
- Department of Materials, University of Oxford Oxford OX1 3HP UK
| | - Johannes Biskupek
- Electron Microscopy Group of Materials Science, Ulm University 89081 Ulm Germany
| | - Graham N Newton
- GSK Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham Nottingham NG7 2TU UK
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Ulm University 89081 Ulm Germany
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
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21
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Hanayama H, Yamada J, Tomotsuka I, Harano K, Nakamura E. Rim Binding of Cyclodextrins in Size-Sensitive Guest Recognition. J Am Chem Soc 2021; 143:5786-5792. [PMID: 33826331 DOI: 10.1021/jacs.1c00651] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyclodextrins (CDs) are doughnut-shaped cyclic oligosaccharides having a cavity and two rims. Inclusion binding in the cavity has long served as a classic model of molecular recognition, and rim binding has been neglected. We found that CDs recognize guests by size-sensitive binding using the two rims in addition to the cavity, using single-molecule electron microscopy and a library of graphitic cones as a solid-state substrate for complexation. For example, with its cavity and rim binding ability combined, γ-CD can recognize a guest of radius between 4 and 9 Å with a size-recognition precision of better than 1 Å, as shown by structural analysis of thousands of individual specimens and statistical analysis of the data thereof. A 2.5 ms resolution electron microscopic video provided direct evidence of the process of size recognition. The data suggest the occurrence of the rim binding mode for guests larger than the size of the CD cavity and illustrate a unique application of dynamic molecular electron microscopy for deciphering the spatiotemporal details of supramolecular events.
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Affiliation(s)
- Hiroki Hanayama
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junya Yamada
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Issei Tomotsuka
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - 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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22
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Kratish Y, Nakamuro T, Liu Y, Li J, Tomotsuka I, Harano K, Nakamura E, Marks TJ. Synthesis and Characterization of a Well-Defined Carbon Nanohorn-Supported Molybdenum Dioxo Catalyst by SMART-EM Imaging. Surface Structure at the Atomic Level. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200299] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yosi Kratish
- Department of Chemistry and the Institute for Catalysis in Energy Processes (ICEP), Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
| | - Takayuki Nakamuro
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yiqi Liu
- Department of Chemistry and the Institute for Catalysis in Energy Processes (ICEP), Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
| | - Jiaqi Li
- Department of Chemistry and the Institute for Catalysis in Energy Processes (ICEP), Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
| | - Issei Tomotsuka
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - Koji Harano
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tobin J. Marks
- Department of Chemistry and the Institute for Catalysis in Energy Processes (ICEP), Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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23
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Harano K. Self-Assembly Mechanism in Nucleation Processes of Molecular Crystalline Materials. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200333] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Koji Harano
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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24
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Nakamuro T, Sakakibara M, Nada H, Harano K, Nakamura E. Capturing the Moment of Emergence of Crystal Nucleus from Disorder. J Am Chem Soc 2021; 143:1763-1767. [PMID: 33475359 DOI: 10.1021/jacs.0c12100] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Crystallization is the process of atoms or molecules forming an organized solid via nucleation and growth. Being intrinsically stochastic, the research at an atomistic level has been a huge experimental challenge. We report herein in situ detection of a crystal nucleus forming during nucleation/growth of a NaCl nanocrystal, as video recorded in the interior of a vibrating conical carbon nanotube at 20-40 ms frame-1 with localization precision of <0.1 nm. We saw NaCl units assembled to form a cluster fluctuating between featureless and semiordered states, which suddenly formed a crystal. Subsequent crystal growth at 298 K and shrinkage at 473 K took place also in a stochastic manner. Productive contributions of the graphitic surface and its mechanical vibration have been experimentally indicated.
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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
| | - Masaya Sakakibara
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki Nada
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
| | - 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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25
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Kamei K, Shimizu T, Harano K, Nakamura E. Aryl Radical Addition to Curvatures of Carbon Nanohorns for Single-Molecule-Level Molecular Imaging. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200232] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ko Kamei
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiki Shimizu
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - 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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26
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Shimizu T, Lungerich D, Stuckner J, Murayama M, Harano K, Nakamura E. Real-Time Video Imaging of Mechanical Motions of a Single Molecular Shuttle with Sub-Millisecond Sub-Angstrom Precision. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200134] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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
| | - Joshua Stuckner
- Materials Science and Engineering Department, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mitsuhiro Murayama
- Materials Science and Engineering Department, Virginia Tech, Blacksburg, VA 24061, USA
- Reactor Materials and Mechanical Design Group, Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
- Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - 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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27
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Stuckner J, Shimizu T, Harano K, Nakamura E, Murayama M. Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:667-675. [PMID: 32684204 DOI: 10.1017/s1431927620001750] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Time-resolved imaging of molecules and materials made of light elements is an emerging field of transmission electron microscopy (TEM), and the recent development of direct electron detection cameras, capable of taking as many as 1,600 fps, has potentially broadened the scope of the time-resolved TEM imaging in chemistry and nanotechnology. However, such a high frame rate reduces electron dose per frame, lowers the signal-to-noise ratio (SNR), and renders the molecular images practically invisible. Here, we examined image noise reduction to take the best advantage of fast cameras and concluded that the Chambolle total variation denoising algorithm is the method of choice, as illustrated for imaging of a molecule in the 1D hollow space of a carbon nanotube with ~1 ms time resolution. Through the systematic comparison of the performance of multiple denoising algorithms, we found that the Chambolle algorithm improves the SNR by more than an order of magnitude when applied to TEM images taken at a low electron dose as required for imaging at around 1,000 fps. Open-source code and a standalone application to apply Chambolle denoising to TEM images and video frames are available for download.
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Affiliation(s)
- Joshua Stuckner
- Material Science and Engineering Department, Virginia Polytechnic Institute and State University, 109A Surge, 400 Stanger Street, Blacksburg, VA24060, USA
| | - Toshiki Shimizu
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-0033, Japan
| | - Koji Harano
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-0033, Japan
| | - Mitsuhiro Murayama
- Material Science and Engineering Department, Virginia Polytechnic Institute and State University, 109A Surge, 400 Stanger Street, Blacksburg, VA24060, USA
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28
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A Conversion Dynamics of (C
60
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Dimer Fullerenes to a Fused Dimer Cage in Carbon Nanopeapods: Tight‐Binding Molecular Dynamics Simulation. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Atomistic structures and dynamics of prenucleation clusters in MOF-2 and MOF-5 syntheses. Nat Commun 2019; 10:3608. [PMID: 31444338 PMCID: PMC6707309 DOI: 10.1038/s41467-019-11564-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/17/2019] [Indexed: 11/22/2022] Open
Abstract
Chemical reactions in solution almost always take place via a series of minute intermediates that are often in rapid equilibrium with each other, and hence hardly characterizable at the level of atomistic molecular structures. We found that single-molecule atomic-resolution real-time electron microscopic (SMART-EM) video imaging provides a unique methodology for capturing and analyzing the minute reaction intermediates, as illustrated here for single prenucleation clusters (PNCs) in the reaction mixture of metal–organic frameworks (MOFs). Specifically, we found two different types of PNCs are involved in the formation of MOF-2 and MOF-5 from a mixture of zinc nitrate and benzene dicarboxylates at 95 °C and 120 °C, respectively. SMART-EM identified a small amount of 1-nm-sized cube and cube-like PNCs in the MOF-5 synthesis, but not in the MOF-2 synthesis. In the latter, we instead found only linear and square PNCs, suggesting that the MOF-2/-5 bifurcation takes place at the PNC stage. Numerous techniques have been used to study the crystallization process of metal-organic frameworks, but little is known about their prenucleation clusters. Here the authors use single-molecule atomic-resolution real-time electron microscopic video imaging to identify prenucleation clusters in the synthesis of MOF-2 and MOF-5.
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Imaoka T, Toyonaga T, Morita M, Haruta N, Yamamoto K. Isomerizations of a Pt 4 cluster revealed by spatiotemporal microscopic analysis. Chem Commun (Camb) 2019; 55:4753-4756. [PMID: 30897188 DOI: 10.1039/c9cc00530g] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We now report the first direct observation of the fluxional nature in which the four-atomic platinum cluster (Pt4) randomly walks through several isomers. Time-lapse analysis by a Cs-corrected transmission electron microscope allowed us to acquire the atomic coordinates at a sub-angstrom space resolution and 0.2 s time resolution for each cluster isomer. The analysis revealed that the isomerization follows a simple first-order kinetic model.
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Affiliation(s)
- Takane Imaoka
- Laboratory for Chemistry and Life Science (CLS), Institute of Innovative Research (IIR), Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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NAKAMURA E, HARANO K. Chemical kinetics study through observation of individual reaction events with atomic-resolution electron microscopy. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2018; 94:428-440. [PMID: 30541968 PMCID: PMC6374138 DOI: 10.2183/pjab.94.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/11/2018] [Indexed: 06/01/2023]
Abstract
Single-molecule atomic-resolution real-time electron microscopic movie imaging is an emerging new tool for obtaining dynamic structural information on molecules and molecular assemblies. This method provides a hitherto inaccessible possibility to in situ observe the time evolution of chemical events at various temperatures from the beginning till the end, as demonstrated for the kinetics study of [2 + 2] cycloaddition of [60]fullerene molecules, which was found to occur via an excited state or via radical cation depending on the temperature. One unique feature of this methodology is that, by observing directly the reaction events, one can obtain information on the frequency of events unperturbed by molecular diffusion. With the obtained experimental data set, we provided the first experimental proof of what the quantum mechanical transition state theory predicted, in that isolated molecules behave as if all their accessible states were occupied in a random order. We also found that, under the 1-D reaction conditions, molecular-level information on a few hundred molecules suffices to deduce statistically meaningful kinetics data that match with those obtained by bulk experiments.
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Affiliation(s)
- Eiichi NAKAMURA
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Koji HARANO
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
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