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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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2
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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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3
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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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4
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5
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Kashin AS, Degtyareva ES, Eremin DB, Ananikov VP. Exploring the performance of nanostructured reagents with organic-group-defined morphology in cross-coupling reaction. Nat Commun 2018; 9:2936. [PMID: 30050139 PMCID: PMC6062554 DOI: 10.1038/s41467-018-05350-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 06/24/2018] [Indexed: 11/09/2022] Open
Abstract
The great impact of the nanoscale organization of reactive species on their performance in chemical transformations creates the possibility of fine-tuning of reaction parameters by modulating the nano-level properties. This methodology is extensively applied for the catalysts development whereas nanostructured reactants represent the practically unexplored area. Here we report the palladium- and copper-catalyzed cross-coupling reaction involving nano-structured nickel thiolate particles as reagents. On the basis of experimental findings we propose the cooperative effect of nano-level and molecular-level properties on their reactivity. The high degree of ordering, small particles size, and electron donating properties of the substituents favor the product formation. Reactant particles evolution in the reaction is visualized directly by dynamic liquid-phase electron microscopy including recording of video movies. Mechanism of the reaction in liquid phase is established using on-line mass spectrometry measurements. Together the findings provide new opportunities for organic chemical transformations design and for mechanistic studies.
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Affiliation(s)
- Alexey S Kashin
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia, 119991
| | - Evgeniya S Degtyareva
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia, 119991
| | - Dmitry B Eremin
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia, 119991
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia, 119991.
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6
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Chamorro R, de Juan-Fernández L, Nieto-Ortega B, Mayoral MJ, Casado S, Ruiz-González L, Pérez EM, González-Rodríguez D. Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings. Chem Sci 2018; 9:4176-4184. [PMID: 29780548 PMCID: PMC5941269 DOI: 10.1039/c8sc00843d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/04/2018] [Indexed: 01/30/2023] Open
Abstract
Due to their outstanding electronic and mechanical properties, single-walled carbon nanotubes (SWCNTs) are promising nanomaterials for the future generation of optoelectronic devices and composites. However, their scarce solubility limits their application in many technologies that demand solution-processing of high-purity SWCNT samples. Although some non-covalent functionalization approaches have demonstrated their utility in extracting SWCNTs into different media, many of them produce short-lived dispersions or ultimately suffer from contamination by the dispersing agent. Here, we introduce an unprecedented strategy that relies on a cooperative clamping process. When mixing (6,5)SWCNTs with a dinucleoside monomer that is able to self-assemble in nanorings via Watson-Crick base-pairing, a synergistic relationship is established. On one hand, the H-bonded rings are able to associate intimately with SWCNTs by embracing the tube sidewalls, which allows for an efficient SWCNT debundling and for the production of long-lasting SWCNT dispersions of high optical quality along a broad concentration range. On the other, nanoring stability is enhanced in the presence of SWCNTs, which are suitable guests for the ring cavity and contribute to the establishment of multiple cooperative noncovalent interactions. The inhibition of these reversible interactions, by just adding, for instance, a competing solvent for hydrogen-bonding, proved to be a simple and effective method to recover the pristine nanomaterial with no trace of the dispersing agent.
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Affiliation(s)
- Raquel Chamorro
- Organic Chemistry Department , Universidad Autónoma de Madrid , 28049 Madrid , Spain .
| | | | - Belén Nieto-Ortega
- IMDEA Nanociencia , c/Faraday 9, Campus de Cantoblanco , 28049 , Madrid , Spain .
| | - Maria J Mayoral
- Organic Chemistry Department , Universidad Autónoma de Madrid , 28049 Madrid , Spain .
| | - Santiago Casado
- IMDEA Nanociencia , c/Faraday 9, Campus de Cantoblanco , 28049 , Madrid , Spain .
| | - Luisa Ruiz-González
- Inorganic Chemistry Department , Universidad Complutense de Madrid , 28040 , Madrid , Spain
| | - Emilio M Pérez
- IMDEA Nanociencia , c/Faraday 9, Campus de Cantoblanco , 28049 , Madrid , Spain .
| | - David González-Rodríguez
- Organic Chemistry Department , Universidad Autónoma de Madrid , 28049 Madrid , Spain .
- Institute for Advanced Research in Chemical Sciences (IAdChem) , Universidad Autónoma de Madrid , 28049 Madrid , Spain
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7
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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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8
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Okada S, Kowashi S, Schweighauser L, Yamanouchi K, Harano K, Nakamura E. Direct Microscopic Analysis of Individual C 60 Dimerization Events: Kinetics and Mechanisms. J Am Chem Soc 2017; 139:18281-18287. [PMID: 29172523 DOI: 10.1021/jacs.7b09776] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Modern transition state theory states that the statistical behavior of a chemical reaction is the sum of individual chemical events that occur randomly. Statistical analysis of each event for individual molecules in a three-dimensional space however is practically impossible. We report here that kinetics and mechanisms of chemical reactions can be investigated by using a one-dimensional system where reaction events can be observed in situ and counted one by one using variable-temperature (VT) atomic-resolution transmission electron microscopy (TEM). We thereby provide direct proof that the ensemble behavior of random events conforms to the Rice-Ramsperger-Kassel-Marcus theory, as illustrated for [2 + 2] cycloaddition of C60 molecules in carbon nanotubes (CNTs). This method gives kinetic and structural information for different types of reactions occurring simultaneously in the microscopic view field, suggesting that the VT-TEM opens a new dimension of chemical kinetics research on molecules and their assemblies in their excited and ionized states. The study carried out at 393-493 K showed that pristine CNT primarily acts as a singlet sensitizer of the cycloaddition reaction that takes place with an activation energy of 33.5 ± 6.8 kJ/mol. On the other hand, CNT suffers electron damage of the conjugated system at 103-203 K and promotes a reactive radical cation path that takes place with an activation energy of only 1.9 ± 0.7 kJ/mol. The pre-exponential factor of the Arrhenius plot gave us further mechanistic insights.
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Affiliation(s)
- Satoshi Okada
- Department of Chemistry, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satori Kowashi
- Department of Chemistry, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Luca Schweighauser
- 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
| | - Koji Harano
- Department of Chemistry, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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9
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Schweighauser L, Harano K, Nakamura E. Experimental study on interconversion between cubic MOF-5 and square MOF-2 arrays. INORG CHEM COMMUN 2017. [DOI: 10.1016/j.inoche.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Affiliation(s)
- Emilio M. Pérez
- IMDEA Nanociencia; Ciudad Universitaria de Cantoblanco; Faraday 9 28049 Madrid Spain
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11
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Nakamura E. Atomic-Resolution Transmission Electron Microscopic Movies for Study of Organic Molecules, Assemblies, and Reactions: The First 10 Years of Development. Acc Chem Res 2017; 50:1281-1292. [PMID: 28481074 DOI: 10.1021/acs.accounts.7b00076] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A molecule is a quantum mechanical entity. "Watching motions and reactions of a molecule with our eyes" has therefore been a dream of chemists for a century. This dream has come true with the aid of the movies of atomic-resolution transmission electron microscopic (AR-TEM) molecular images through real-time observation of dynamic motions of single organic molecules (denoted hereafter as single-molecule atomic-resolution real-time (SMART) TEM imaging). Since 2007, we have reported movies of a variety of single organic molecules, organometallic molecules, and their assemblies, which are rotating, stretching, and reacting. Like movies in the theater, the atomic-resolution molecular movies provide us information on the 3-D structures of the molecules and also their time evolution. The success of the SMART-TEM imaging crucially depends on the development of "chemical fishhooks" with which fish (organic molecules) in solution can be captured on a single-walled carbon nanotube (CNT, serving as a "fishing rod"). The captured molecules are connected to a slowly vibrating CNT, and their motions are displayed on a monitor in real time. A "fishing line" connecting the fish and the rod may be a σ-bond, a van der Waals force, or other weak connections. Here, the molecule/CNT system behaves as a coupled oscillator, where the low-frequency anisotropic vibration of the CNT is transmitted to the molecules via the weak chemical connections that act as an energy filter. Interpretation of the observed motions of the molecules at atomic resolution needs us to consider the quantum mechanical nature of electrons as well as bond rotation, letting us deviate from the conventional statistical world of chemistry. What new horizons can we explore? We have so far carried out conformational studies of individual molecules, assigning anti or gauche conformations to each C-C bond in conformers that we saw. We can also determine the structures of van der Waals assemblies of organic molecules, thereby providing mechanistic insights into crystal formation-phenomena of general significance in science, engineering, and our daily life. Whereas many of the single organic molecules in a vacuum seen by SMART-TEM are sufficiently long-lived for detailed studies, molecules with low ionization potentials (<6 eV) were found to undergo chemical reactions, for example, [60]fullerene and organometallic compounds possibly via a hole catalysis mechanism, where a radical cation of CNT generated under electron irradiation catalyzes the transformation via an electron transfer mechanism. Common organic molecules whose ionization potentials are much higher (>8 eV) than that of CNT (5 eV) remain stable for a time long enough for observation at 60-120 kV acceleration voltage, as they are not oxidized by the CNT radical cation. Alternatively, the reaction may have taken place via an excited state of a molecule produced by energy transfer from CNT possessing excess energy provided by the electron beam. SMART-TEM imaging is a simple approach to the study of the structures and reactions of molecules and their assemblies and will serve as a gateway to the research and education of the science connecting the quantum mechanical world and the real world.
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Affiliation(s)
- Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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12
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Sosso G, Chen J, Cox SJ, Fitzner M, Pedevilla P, Zen A, Michaelides A. Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations. Chem Rev 2016; 116:7078-116. [PMID: 27228560 PMCID: PMC4919765 DOI: 10.1021/acs.chemrev.5b00744] [Citation(s) in RCA: 389] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 11/28/2022]
Abstract
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.
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Affiliation(s)
- Gabriele
C. Sosso
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Ji Chen
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | | | - Martin Fitzner
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Philipp Pedevilla
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Andrea Zen
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Angelos Michaelides
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
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13
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Majorovits E, Angert I, Kaiser U, Schröder RR. Benefits and Limitations of Low-kV Macromolecular Imaging of Frozen-Hydrated Biological Samples. Biophys J 2016; 110:776-84. [PMID: 26910420 DOI: 10.1016/j.bpj.2016.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
Object contrast is one of the most important parameters of macromolecular imaging. Low-voltage transmission electron microscopy has shown an increased atom contrast for carbon materials, indicating that amplitude contrast contributions increase at a higher rate than phase contrast and inelastic scattering. Here, we studied image contrast using ice-embedded tobacco mosaic virus particles as test samples at 20-80 keV electron energy. The particles showed the expected increase in contrast for lower energies, but at the same time the 2.3-nm-resolution measure decayed more rapidly. We found a pronounced signal loss below 60 keV, and therefore we conclude that increased inelastic scattering counteracts increased amplitude contrast. This model also implies that as long as the amplitude contrast does not increase with resolution, beam damage and multiple scattering will always win over increased contrast at the lowest energies. Therefore, we cannot expect that low-energy imaging of conventionally prepared samples would provide better data than state-of-the-art 200-300 keV imaging.
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Affiliation(s)
| | | | | | - Rasmus R Schröder
- Centre for Advanced Materials, Universität Heidelberg, Heidelberg, Germany; Cryo Electron Microscopy, CellNetworks, BioQuant, Universitätsklinikum Heidelberg, Heidelberg, Germany.
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14
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Molecular interactions on single-walled carbon nanotubes revealed by high-resolution transmission microscopy. Nat Commun 2015; 6:7732. [PMID: 26173983 PMCID: PMC4518305 DOI: 10.1038/ncomms8732] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/05/2015] [Indexed: 02/02/2023] Open
Abstract
The close solid-state structure–property relationships of organic π−aromatic molecules have attracted interest due to their implications for the design of organic functional materials. In particular, a dimeric structure, that is, a unit consisting of two molecules, is required for precisely evaluating intermolecular interactions. Here, we show that the sidewall of a single-walled carbon nanotube (SWNT) represents a unique molecular dimer platform that can be directly visualized using high-resolution transmission electron microscopy. Pyrene is chosen as the π−aromatic molecule; its dimer is covalently linked to the SWNT sidewalls by aryl addition. Reflecting the orientation and separation of the two molecules, the pyrene dimer on the SWNT exhibits characteristic optical and photophysical properties. The methodology discussed here—form and probe molecular dimers—is highly promising for the creation of unique models and provides indispensable and fundamental information regarding molecular interactions. Probing local molecular properties is crucial for the rational designs of functional organic materials. Here, Umeyama et al. prepare a dimeric structure of a model π-aromatic compound on the sidewall of a carbon nanotube to be visualized by transmission electron microscopy at a single-molecule level.
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15
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Schröder RR. Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography. Arch Biochem Biophys 2015; 581:25-38. [PMID: 26032338 DOI: 10.1016/j.abb.2015.05.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/08/2015] [Accepted: 05/21/2015] [Indexed: 02/03/2023]
Abstract
Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy.(1) While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation - often developed in other fields of electron microscopy - may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.
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Affiliation(s)
- Rasmus R Schröder
- Cryo Electron Microscopy, CellNetwork, BioQuant, Universitätsklinikum Heidelberg, Universität Heidelberg, Germany.
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16
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Gorgoll RM, Yücelen E, Kumamoto A, Shibata N, Harano K, Nakamura E. Electron Microscopic Observation of Selective Excitation of Conformational Change of a Single Organic Molecule. J Am Chem Soc 2015; 137:3474-7. [DOI: 10.1021/jacs.5b00511] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ricardo M. Gorgoll
- Department
of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Emrah Yücelen
- FEI
Company, Europe NanoPort, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Akihito Kumamoto
- Institute
of Engineering Innovation, Graduate School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naoya Shibata
- Institute
of Engineering Innovation, Graduate School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8656, 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
- CREST, JST, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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17
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Abstract
Pyrene serves as a recognition motif to template the synthesis of mechanically interlocked derivatives of SWNTs.
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Affiliation(s)
| | - Emilio M. Pérez
- IMDEA Nanociencia
- Ciudad Universitaria de Cantoblanco
- Madrid
- Spain
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18
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Chamberlain TW, Lebedeva MA, Abuajwa W, Suyetin M, Lewis W, Bichoutskaia E, Schröder M, Khlobystov AN. Switching intermolecular interactions by confinement in carbon nanotubes. Chem Commun (Camb) 2015; 51:648-51. [DOI: 10.1039/c4cc08029g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Carbon nanotube encapsulation offers a mechanism to trap kinetically rather than thermodynamically favoured supramolecular arrays.
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Affiliation(s)
- T. W. Chamberlain
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
| | - M. A. Lebedeva
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
| | - W. Abuajwa
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
| | - M. Suyetin
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
| | - W. Lewis
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
| | - E. Bichoutskaia
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
| | - M. Schröder
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
| | - A. N. Khlobystov
- School of Chemistry
- The University of Nottingham
- University Park
- Nottingham
- UK
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19
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Harano K, Okada S, Furukawa S, Tanaka H, Nakamura E. Formation of a polycrystalline film of donor material on PEDOT:PSS buffer induced by crystal nucleation. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/polb.23493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Koji Harano
- Department of Chemistry; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Satoshi Okada
- Department of Chemistry; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Shunsuke Furukawa
- Department of Chemistry; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hideyuki Tanaka
- 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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20
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de Juan A, Pouillon Y, Ruiz-González L, Torres-Pardo A, Casado S, Martín N, Rubio Á, Pérez EM. Mechanically Interlocked Single-Wall Carbon Nanotubes. Angew Chem Int Ed Engl 2014; 53:5394-400. [DOI: 10.1002/anie.201402258] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 11/07/2022]
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21
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de Juan A, Pouillon Y, Ruiz-González L, Torres-Pardo A, Casado S, Martín N, Rubio Á, Pérez EM. Mechanically Interlocked Single-Wall Carbon Nanotubes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Cabana L, Ballesteros B, Batista E, Magén C, Arenal R, Oró-Solé J, Rurali R, Tobias G. Synthesis of PbI(2) single-layered inorganic nanotubes encapsulated within carbon nanotubes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:2016-2021. [PMID: 24339133 DOI: 10.1002/adma.201305169] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Indexed: 06/03/2023]
Abstract
The template assisted growth of single-layered inorganic nanotubes is reported. Single-crystalline lead iodide single-layered nanotubes have been prepared using the inner cavities of carbon nanotubes as hosting templates. The diameter of the resulting inorganic nanotubes is merely dependent on the diameter of the host. This facile method is highly versatile opening up new horizons in the preparation of single-layered nanostructures.
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Affiliation(s)
- Laura Cabana
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193, Bellaterra, Barcelona, Spain
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23
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He J, Yan L, Liu G, Ma Z, Luo S, He S, Guo Q, Lan J, Wu D. Synthesis of Water-Soluble Cyclen-Functionalised Fullerene C 60 Derivatives. JOURNAL OF CHEMICAL RESEARCH 2014. [DOI: 10.3184/174751914x13945582435462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The fullerene family has interesting photophysical, electrochemical and mechanical properties with applications in organic solar cells, nanotechnology, superconductivity, chemosensors and biomedicine. Water-soluble cyclen-functionalised fullerene derivatives cyclen-C60-1 and bis(cyclen)-C60-2 have been synthesised. The whole synthetic routes are simple and the total yields are relatively high.
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Affiliation(s)
- Jiaheng He
- Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900, P.R. China
| | - Lipeng Yan
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P.R. China
| | - Guoping Liu
- Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900, P.R. China
| | - Zongping Ma
- Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900, P.R. China
| | - Shunzhong Luo
- Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900, P.R. China
| | - Songhua He
- Institute of Media and Communic ation, Shenzhen Polytechnic, Shenzhen 518055, P.R. China
| | - Qiang Guo
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P.R. China
| | - Jingbo Lan
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P.R. China
| | - Di Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P.R. China
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24
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Harano K, Takenaga S, Okada S, Niimi Y, Yoshikai N, Isobe H, Suenaga K, Kataura H, Koshino M, Nakamura E. Conformational analysis of single perfluoroalkyl chains by single-molecule real-time transmission electron microscopic imaging. J Am Chem Soc 2013; 136:466-73. [PMID: 24341551 DOI: 10.1021/ja411235x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Whereas a statistical average of molecular ensembles has been the conventional source of information on molecular structures, atomic resolution movies of single organic molecules obtained by single-molecule real-time transmission electron microscopy have recently emerged as a new tool to study the time evolution of the structures of individual molecules. The present work describes a proof-of-principle study of the determination of the conformation of each C-C bond in single perfluoroalkyl fullerene molecules encapsulated in a single-walled carbon nanotube (CNT) as well as those attached to the outer surface of a carbon nanohorn (CNH). Analysis of 82 individual molecules in CNTs under a 120 kV electron beam indicated that 6% of the CF2-CF2 bonds and about 20% of the CH2-CH2 bonds in the corresponding hydrocarbon analogue are in the gauche conformation. This comparison qualitatively matches the known conformational data based on time- and molecular-average as determined for ensembles. The transmission electron microscopy images also showed that the molecules entered the CNTs predominantly in one orientation. The molecules attached on a CNH surface moved more freely and exhibited more diverse conformation than those in a CNT, suggesting the potential applicability of this method for the determination of the dynamic shape of flexible molecules and of detailed conformations. We observed little sign of any decomposition of the specimen molecules, at least up to 10(7) e·nm(-2) (electrons/nm(2)) at 120 kV acceleration voltage. Decomposition of CNHs under irradiation with a 300 kV electron beam was suppressed by cooling to 77 K, suggesting that the decomposition is a chemical process. Several lines of evidence suggest that the graphitic substrate and the attached molecules are very cold.
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Affiliation(s)
- Koji Harano
- Department of Chemistry, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
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25
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Affiliation(s)
- Markus Heyde
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
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26
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Huang PY, Kurasch S, Alden JS, Shekhawat A, Alemi AA, McEuen PL, Sethna JP, Kaiser U, Muller DA. Imaging Atomic Rearrangements in Two-Dimensional Silica Glass: Watching Silica's Dance. Science 2013; 342:224-7. [DOI: 10.1126/science.1242248] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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27
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Harano K, Narita A, Nakamura E. Photocrosslinking of Fullerene Vesicles that Prevents Phase Transition and Decreases Water Permeation. CHEM LETT 2013. [DOI: 10.1246/cl.130505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Harano
- Department of Chemistry, The University of Tokyo
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28
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de Juan A, Pérez EM. Getting tubed: mechanical bond in endohedral derivatives of carbon nanotubes? NANOSCALE 2013; 5:7141-8. [PMID: 23759875 DOI: 10.1039/c3nr01683h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We present a brief overview of some of the most prominent examples of encapsulation of molecules inside carbon nanotubes. We then relate them to mechanically interlocked molecules, and in particular rotaxanes, by examining the most prominent features of the mechanical bond (topology, dynamic properties, and stability) and comparing them to those of endohedral derivatives of nanotubes. Our analysis shows that there is a surprisingly clear link between these two apparently disparate species.
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Affiliation(s)
- Alberto de Juan
- IMDEA Nanoscience, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
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29
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Yabu H, Kanahara M, Shimomura M, Arita T, Harano K, Nakamura E, Higuchi T, Jinnai H. Polymer Janus particles containing block-copolymer stabilized magnetic nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2013; 5:3262-3266. [PMID: 23480421 DOI: 10.1021/am4003149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this report, we show a simple route to fabricate Janus particles having magnetic nanoparticles inside them, which can respond and rotate along to magnetic fields. By solvent evaporation from the tetrahydrofran solution of polymer stabilized γ-Fe2O3 nanoparticles, polystyrene (PS), and polyisoprene containing water, aqueous dispersion of Janus microparticles were successfully prepared, and the γ-Fe2O3 nanoparticles were selectively introduced into the PS phase. We demonstrate rotation and accumulation of Janus particles by using a neodymium magnet.
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Affiliation(s)
- Hiroshi Yabu
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1, Katahira, Sendai, Japan.
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30
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Harano K, Minami K, Noiri E, Okamoto K, Nakamura E. Protein-coated nanocapsules via multilevel surface modification. Controlled preparation and microscopic analysis at nanometer resolution. Chem Commun (Camb) 2013; 49:3525-7. [DOI: 10.1039/c3cc40752g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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