1
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Andrusenko I, Gemmi M. 3D electron diffraction for structure determination of small-molecule nanocrystals: A possible breakthrough for the pharmaceutical industry. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1810. [PMID: 35595285 PMCID: PMC9539612 DOI: 10.1002/wnan.1810] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Abstract
Nanomedicine is among the most fascinating areas of research. Most of the newly discovered pharmaceutical polymorphs, as well as many new synthesized or isolated natural products, appear only in form of nanocrystals. The development of techniques that allow investigating the atomic structure of nanocrystalline materials is therefore one of the most important frontiers of crystallography. Some unique features of electrons, like their non-neutral charge and their strong interaction with matter, make this radiation suitable for imaging and detecting individual atoms, molecules, or nanoscale objects down to sub-angstrom resolution. In the recent years the development of three-dimensional (3D) electron diffraction (3D ED) has shown that electron diffraction can be successfully used to solve the crystal structure of nanocrystals and most of its limiting factors like dynamical scattering or limited completeness can be easily overcome. This article is a review of the state of the art of this method with a specific focus on how it can be applied to beam sensitive samples like small-molecule organic nanocrystals. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Iryna Andrusenko
- Center for Materials Interfaces, Electron CrystallographyIstituto Italiano di TecnologiaPontedera
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron CrystallographyIstituto Italiano di TecnologiaPontedera
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2
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Ning S, Xu W, Ma Y, Loh L, Pennycook TJ, Zhou W, Zhang F, Bosman M, Pennycook SJ, He Q, Loh ND. Accurate and Robust Calibration of the Uniform Affine Transformation Between Scan-Camera Coordinates for Atom-Resolved In-Focus 4D-STEM Datasets. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-11. [PMID: 35260221 DOI: 10.1017/s1431927622000320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge of the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.
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Affiliation(s)
- Shoucong Ning
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore117557, Singapore
| | - Wenhui Xu
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen518055, China
- Harbin Institute of Technology, Harbin150001, China
| | - Yinhang Ma
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Leyi Loh
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | | | - Wu Zhou
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Fucai Zhang
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen518055, China
| | - Michel Bosman
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | - Stephen J Pennycook
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Qian He
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | - N Duane Loh
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore117557, Singapore
- Department of Physics, National University of Singapore, Singapore117551, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore117557, Singapore
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3
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Samperisi L, Zou X, Huang Z. Three-Dimensional Electron Diffraction: A Powerful Structural Characterization Technique for Crystal Engineering. CrystEngComm 2022. [DOI: 10.1039/d2ce00051b] [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
Understanding crystal structures and behaviors is crucial for constructing and engineering crystalline materials with various properties and functions. Recent advancement in three-dimensional electron diffraction (3D ED) and its application on...
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4
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Gruene T, Mugnaioli E. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Chem Rev 2021; 121:11823-11834. [PMID: 34533919 PMCID: PMC8517952 DOI: 10.1021/acs.chemrev.1c00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 01/26/2023]
Abstract
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.
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Affiliation(s)
- Tim Gruene
- University
of Vienna, Faculty of Chemistry,
Department of Inorganic Chemistry, AT-1090 Vienna, Austria
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, IT-56127 Pisa, Italy
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5
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Paton KA, Veale MC, Mu X, Allen CS, Maneuski D, Kübel C, O'Shea V, Kirkland AI, McGrouther D. Quantifying the performance of a hybrid pixel detector with GaAs:Cr sensor for transmission electron microscopy. Ultramicroscopy 2021; 227:113298. [PMID: 34051540 DOI: 10.1016/j.ultramic.2021.113298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/01/2021] [Accepted: 04/24/2021] [Indexed: 10/21/2022]
Abstract
Hybrid pixel detectors (HPDs) have been shown to be highly effective for diffraction-based and time-resolved studies in transmission electron microscopy, but their performance is limited by the fact that high-energy electrons scatter over long distances in their thick Si sensors. An advantage of HPDs compared to monolithic active pixel sensors is that their sensors do not need to be fabricated from Si. We have compared the performance of the Medipix3 HPD with a Si sensor and a GaAs:Cr sensor using primary electrons in the energy range of 60-300 keV. We describe the measurement and calculation of the detectors' modulation transfer function (MTF) and detective quantum efficiency (DQE), which show that the performance of the GaAs:Cr device is markedly superior to that of the Si device for high-energy electrons.
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Affiliation(s)
- Kirsty A Paton
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK.
| | - Matthew C Veale
- UKRI Science & Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Xiaoke Mu
- Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christopher S Allen
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK; electron Physical Sciences Imaging Centre (ePSIC), Diamond Lightsource Ltd., Didcot, OX11 0DE, UK
| | - Dzmitry Maneuski
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK
| | - Christian Kübel
- Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany; Department of Materials and Earth Science, Technische Universität Darmstadt and Karlsruhe Institute of Technology, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Val O'Shea
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK
| | - Angus I Kirkland
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK; electron Physical Sciences Imaging Centre (ePSIC), Diamond Lightsource Ltd., Didcot, OX11 0DE, UK
| | - Damien McGrouther
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, G12 8QQ, UK
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6
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Takaba K, Maki-Yonekura S, Inoue S, Hasegawa T, Yonekura K. Protein and Organic-Molecular Crystallography With 300kV Electrons on a Direct Electron Detector. Front Mol Biosci 2021; 7:612226. [PMID: 33469549 PMCID: PMC7814344 DOI: 10.3389/fmolb.2020.612226] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
Electron 3D crystallography can reveal the atomic structure from undersized crystals of various samples owing to the strong scattering power of electrons. Here, a direct electron detector DE64 was tested for small and thin crystals of protein and an organic molecule using a JEOL CRYO ARM 300 electron microscope. The microscope is equipped with a cold-field emission gun operated at an accelerating voltage of 300 kV, quad condenser lenses for parallel illumination, an in-column energy filter, and a stable rotational goniometer stage. Rotational diffraction data were collected in an unsupervised manner from crystals of a heme-binding enzyme catalase and a representative organic semiconductor material Ph-BTBT-C10. The structures were determined by molecular replacement for catalase and by the direct method for Ph-BTBT-C10. The analyses demonstrate that the system works well for electron 3D crystallography of these molecules with less damaging, a smaller point spread, and less noise than using the conventional scintillator-coupled camera.
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Affiliation(s)
- Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan
| | | | - Satoru Inoue
- Department of Applied Physics, The University of Tokyo, Tokyo, Japan
| | - Tatsuo Hasegawa
- Department of Applied Physics, The University of Tokyo, Tokyo, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan.,Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, Sayo, Japan.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
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7
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Abstract
Structural elucidation of small macromolecules such as peptides has recently been facilitated by a growing number of technological advances to existing crystallographic methods. The emergence of electron micro-diffraction (MicroED) of protein nanocrystals under cryogenic conditions has enabled the interrogation of crystalline peptide assemblies only hundreds of nanometers thick. Collection of atomic or near-atomic resolution data by these methods has permitted the ab initio determination of structures of various amyloid-forming peptides, including segments derived from prions and ice-nucleating proteins. This chapter focuses on the process of ab initio structural determination from nano-scale peptide assemblies and other similar molecules.
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Affiliation(s)
- Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Ambarneil Saha
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry, Chemistry & Biochemistry, and Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
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8
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Abstract
Microcrystal Electron Diffraction (MicroED) enables structure determination of very small crystals that are much too small to be of use for other conventional diffraction techniques. MicroED has been used to determine the structures of many proteins and small organic molecules, and the technique can be performed on most standard cryo-TEM instruments equipped with high-speed detectors capable of collecting electron diffraction data. Here, we present protocols for MicroED sample preparation and data collection for protein microcrystals.
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Affiliation(s)
- Guanhong Bu
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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9
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Sub-pixel electron detection using a convolutional neural network. Ultramicroscopy 2020; 218:113091. [DOI: 10.1016/j.ultramic.2020.113091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/28/2020] [Accepted: 08/02/2020] [Indexed: 11/23/2022]
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10
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Mugnaioli E, Lanza AE, Bortolozzi G, Righi L, Merlini M, Cappello V, Marini L, Athanassiou A, Gemmi M. Electron Diffraction on Flash-Frozen Cowlesite Reveals the Structure of the First Two-Dimensional Natural Zeolite. ACS CENTRAL SCIENCE 2020; 6:1578-1586. [PMID: 32999933 PMCID: PMC7517411 DOI: 10.1021/acscentsci.9b01100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Indexed: 05/24/2023]
Abstract
Cowlesite, ideally Ca6Al12Si18O60·36H2O, is to date the only natural zeolite whose structure could not be determined by X-ray methods. In this paper, we present the ab initio structure determination of this mineral obtained by three-dimensional (3D) electron diffraction data collected from single-crystal domains of a few hundreds of nanometers. The structure of cowlesite consists of an alternation of rigid zeolitic layers and low-density interlayers supported by water and cations. This makes cowlesite the only two-dimensional (2D) zeolite known in nature. When cowlesite gets in contact with a transmission electron microscope vacuum, a phase transition to a conventional 3D zeolite framework occurs in few seconds. The original cowlesite structure could be preserved only by adopting a cryo-plunging sample preparation protocol usually employed for macromolecular samples. Such a protocol allows the investigation by 3D electron diffraction of very hydrated and very beam-sensitive inorganic materials, which were previously considered intractable by transmission electron microscopy crystallographic methods.
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Affiliation(s)
- Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Arianna E. Lanza
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Giorgio Bortolozzi
- Associazione
Micromineralogica Italiana (AMI), via Gioconda 3, 26100 Cremona, Italy
| | - Lara Righi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43124, Italy
- IMEM-CNR, Parco Area
delle Scienze 37/A, 43123 Parma, Italy
| | - Marco Merlini
- Dipartimento
di Scienze della Terra, Università
degli Studi di Milano, Via Botticelli 23, 20133 Milano, Italy
| | - Valentina Cappello
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Lara Marini
- Smart Materials, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | | | - Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
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11
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Nord M, Webster RWH, Paton KA, McVitie S, McGrouther D, MacLaren I, Paterson GW. Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:653-666. [PMID: 32627727 DOI: 10.1017/s1431927620001713] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The use of fast pixelated detectors and direct electron detection technology is revolutionizing many aspects of scanning transmission electron microscopy (STEM). The widespread adoption of these new technologies is impeded by the technical challenges associated with them. These include issues related to hardware control, and the acquisition, real-time processing and visualization, and storage of data from such detectors. We discuss these problems and present software solutions for them, with a view to making the benefits of new detectors in the context of STEM more accessible. Throughout, we provide examples of the application of the technologies presented, using data from a Medipix3 direct electron detector. Most of our software are available under an open source licence, permitting transparency of the implemented algorithms, and allowing the community to freely use and further improve upon them.
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Affiliation(s)
- Magnus Nord
- SUPA, School of Physics and Astronomy, University of Glasgow, GlasgowG12 8QQ, UK
- EMAT, Department of Physics, University of Antwerp, Antwerp2000, Belgium
| | - Robert W H Webster
- SUPA, School of Physics and Astronomy, University of Glasgow, GlasgowG12 8QQ, UK
| | - Kirsty A Paton
- SUPA, School of Physics and Astronomy, University of Glasgow, GlasgowG12 8QQ, UK
| | - Stephen McVitie
- SUPA, School of Physics and Astronomy, University of Glasgow, GlasgowG12 8QQ, UK
| | - Damien McGrouther
- SUPA, School of Physics and Astronomy, University of Glasgow, GlasgowG12 8QQ, UK
| | - Ian MacLaren
- SUPA, School of Physics and Astronomy, University of Glasgow, GlasgowG12 8QQ, UK
| | - Gary W Paterson
- SUPA, School of Physics and Astronomy, University of Glasgow, GlasgowG12 8QQ, UK
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12
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Nannenga BL. MicroED methodology and development. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014304. [PMID: 32071929 PMCID: PMC7018523 DOI: 10.1063/1.5128226] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Microcrystal electron diffraction, or MicroED, is a method that is capable of determining structure from very small and thin 3D crystals using a transmission electron microscope. MicroED has been successfully used on microcrystalline samples, including proteins, peptides, and small organic molecules, in many cases to very high resolutions. In this work, the MicroED workflow will be briefly described and areas of future method development will be highlighted. These areas include improvements in sample preparation, data collection, and structure determination.
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Affiliation(s)
- Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
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13
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Allen AJ. Recent trends in crystallography - a current IUCr journals perspective. IUCRJ 2019; 6:984-987. [PMID: 31709052 PMCID: PMC6830219 DOI: 10.1107/s2052252519014507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This Editorial considers the impact of recent work published in IUCrJ and other IUCr journals, as well as the relationship between IUCrJ and the other journals, in terms of where the most cited recent papers are used.
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Affiliation(s)
- Andrew J. Allen
- Materials Measurement Science Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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14
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Naydenova K, McMullan G, Peet MJ, Lee Y, Edwards PC, Chen S, Leahy E, Scotcher S, Henderson R, Russo CJ. CryoEM at 100 keV: a demonstration and prospects. IUCRJ 2019; 6:1086-1098. [PMID: 31709064 PMCID: PMC6830209 DOI: 10.1107/s2052252519012612] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/10/2019] [Indexed: 05/23/2023]
Abstract
100 kV is investigated as the operating voltage for single-particle electron cryomicroscopy (cryoEM). Reducing the electron energy from the current standard of 300 or 200 keV offers both cost savings and potentially improved imaging. The latter follows from recent measurements of radiation damage to biological specimens by high-energy electrons, which show that at lower energies there is an increased amount of information available per unit damage. For frozen hydrated specimens around 300 Å in thickness, the predicted optimal electron energy for imaging is 100 keV. Currently available electron cryomicroscopes in the 100-120 keV range are not optimized for cryoEM as they lack both the spatially coherent illumination needed for the high defocus used in cryoEM and imaging detectors optimized for 100 keV electrons. To demonstrate the potential of imaging at 100 kV, the voltage of a standard, commercial 200 kV field-emission gun (FEG) microscope was reduced to 100 kV and a side-entry cryoholder was used. As high-efficiency, large-area cameras are not currently available for 100 keV electrons, a commercial hybrid pixel camera designed for X-ray detection was attached to the camera chamber and was used for low-dose data collection. Using this configuration, five single-particle specimens were imaged: hepatitis B virus capsid, bacterial 70S ribosome, catalase, DNA protection during starvation protein and haemoglobin, ranging in size from 4.5 MDa to 64 kDa with corresponding diameters from 320 to 72 Å. These five data sets were used to reconstruct 3D structures with resolutions between 8.4 and 3.4 Å. Based on this work, the practical advantages and current technological limitations to single-particle cryoEM at 100 keV are considered. These results are also discussed in the context of future microscope development towards the goal of rapid, simple and widely available structure determination of any purified biological specimen.
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Affiliation(s)
- K. Naydenova
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - G. McMullan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - M. J. Peet
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - Y. Lee
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - P. C. Edwards
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - S. Chen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - E. Leahy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - S. Scotcher
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - R. Henderson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - C. J. Russo
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
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15
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Hattne J, Martynowycz MW, Penczek PA, Gonen T. MicroED with the Falcon III direct electron detector. IUCRJ 2019; 6:921-926. [PMID: 31576224 PMCID: PMC6760445 DOI: 10.1107/s2052252519010583] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/25/2019] [Indexed: 05/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Pawel A. Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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16
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Gemmi M, Mugnaioli E, Gorelik TE, Kolb U, Palatinus L, Boullay P, Hovmöller S, Abrahams JP. 3D Electron Diffraction: The Nanocrystallography Revolution. ACS CENTRAL SCIENCE 2019; 5:1315-1329. [PMID: 31482114 PMCID: PMC6716134 DOI: 10.1021/acscentsci.9b00394] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Indexed: 05/20/2023]
Abstract
Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.
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Affiliation(s)
- Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Tatiana E. Gorelik
- University
of Ulm, Central Facility for Electron Microscopy, Electron Microscopy
Group of Materials Science (EMMS), Albert Einstein Allee 11, 89081 Ulm, Germany
| | - Ute Kolb
- Institut
für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
- Institut
für Angewandte Geowissenschaften, Technische Universität Darmstadt, Schnittspahnstraße 9, 64287 Darmstadt, Germany
| | - Lukas Palatinus
- Department
of Structure Analysis, Institute of Physics
of the CAS, Na Slovance 2, 182 21 Prague 8, Czechia
| | - Philippe Boullay
- CRISMAT,
Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Cedex Caen, France
| | - Sven Hovmöller
- Inorganic
and Structural Chemistry, Department of Materials and Environmental
Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Jan Pieter Abrahams
- Center
for Cellular Imaging and NanoAnalytics (C−CINA), Biozentrum, Basel University, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Department
of Biology and Chemistry, Paul Scherrer
Institut (PSI), CH-5232 Villigen PSI, Switzerland
- Leiden
Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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17
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Data-driven challenges and opportunities in crystallography. Emerg Top Life Sci 2019; 3:423-432. [PMID: 33523208 PMCID: PMC7289006 DOI: 10.1042/etls20180177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/13/2019] [Accepted: 06/24/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Structural biology is in the midst of a revolution fueled by faster and more powerful instruments capable of delivering orders of magnitude more data than their predecessors. This increased pace in data gathering introduces new experimental and computational challenges, frustrating real-time processing and interpretation of data and requiring long-term solutions for data archival and retrieval. This combination of challenges and opportunities is driving the exploration of new areas of structural biology, including studies of macromolecular dynamics and the investigation of molecular ensembles in search of a better understanding of conformational landscapes. The next generation of instruments promises to yield even greater data rates, requiring a concerted effort by institutions, centers and individuals to extract meaning from every bit and make data accessible to the community at large, facilitating data mining efforts by individuals or groups as analysis tools improve.
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18
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Mugnaioli E, Gorelik TE. Structure analysis of materials at the order–disorder borderline using three-dimensional electron diffraction. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2019; 75:550-563. [DOI: 10.1107/s2052520619007339] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/20/2019] [Indexed: 11/10/2022]
Abstract
Diffuse scattering, observed as intensity distribution between the Bragg peaks, is associated with deviations from the average crystal structure, generally referred to as disorder. In many cases crystal defects are seen as unwanted perturbations of the periodic structure and therefore they are often ignored. Yet, when it comes to the structure analysis of nano-volumes, what electron crystallography is designed for, the significance of defects increases. Twinning and polytypic sequences are other perturbations from ideal crystal structure that are also commonly observed in nanocrystals. Here we present an overview of defect types and review some of the most prominent studies published on the analysis of defective nanocrystalline structures by means of three-dimensional electron diffraction.
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19
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Gemmi M, Lanza AE. 3D electron diffraction techniques. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:495-504. [PMID: 32830707 DOI: 10.1107/s2052520619007510] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/23/2019] [Indexed: 06/11/2023]
Abstract
3D electron diffraction is an emerging technique for the structural analysis of nanocrystals. The challenges that 3D electron diffraction has to face for providing reliable data for structure solution and the different ways of overcoming these challenges are described. The route from zone axis patterns towards 3D electron diffraction techniques such as precession-assisted electron diffraction tomography, rotation electron diffraction and continuous rotation is also discussed. Finally, the advantages of the new hybrid detectors with high sensitivity and fast readout are demonstrated with a proof of concept experiment of continuous rotation electron diffraction on a natrolite nanocrystal.
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Affiliation(s)
- Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, 56127, Italy
| | - Arianna E Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, 56127, Italy
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20
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Heidler J, Pantelic R, Wennmacher JTC, Zaubitzer C, Fecteau-Lefebvre A, Goldie KN, Müller E, Holstein JJ, van Genderen E, De Carlo S, Gruene T. Design guidelines for an electron diffractometer for structural chemistry and structural biology. Acta Crystallogr D Struct Biol 2019; 75:458-466. [PMID: 31063148 PMCID: PMC6503764 DOI: 10.1107/s2059798319003942] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/22/2019] [Indexed: 11/11/2022] Open
Abstract
3D electron diffraction has reached a stage where the structures of chemical compounds can be solved productively. Instrumentation is lagging behind this development, and to date dedicated electron diffractometers for data collection based on the rotation method do not exist. Current studies use transmission electron microscopes as a workaround. These are optimized for imaging, which is not optimal for diffraction studies. The beam intensity is very high, it is difficult to create parallel beam illumination and the detectors used for imaging are of only limited use for diffraction studies. In this work, the combination of an EIGER hybrid pixel detector with a transmission electron microscope to construct a productive electron diffractometer is described. The construction not only refers to the combination of hardware but also to the calibration of the system, so that it provides rapid access to the experimental parameters that are necessary for processing diffraction data. Until fully integrated electron diffractometers become available, this describes a setup for productive and efficient operation in chemical crystallography.
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Affiliation(s)
- Jonas Heidler
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | | | - Christian Zaubitzer
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics, University Basel, 4058 Basel, Switzerland
| | | | - Julian J Holstein
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto Hahn Strasse 6, 44227 Dortmund, Germany
| | | | | | - Tim Gruene
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
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21
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Clabbers MTB, Gruene T, van Genderen E, Abrahams JP. Reducing dynamical electron scattering reveals hydrogen atoms. Acta Crystallogr A Found Adv 2019; 75:82-93. [PMID: 30575586 PMCID: PMC6302931 DOI: 10.1107/s2053273318013918] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/02/2018] [Indexed: 11/26/2022] Open
Abstract
Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.
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Affiliation(s)
- Max T. B. Clabbers
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Tim Gruene
- Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland
| | | | - Jan Pieter Abrahams
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland
- Leiden Institute of Biology, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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22
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Pennycook TJ, Martinez GT, Nellist PD, Meyer JC. High dose efficiency atomic resolution imaging via electron ptychography. Ultramicroscopy 2019; 196:131-135. [PMID: 30366318 DOI: 10.1016/j.ultramic.2018.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/09/2018] [Accepted: 10/17/2018] [Indexed: 10/28/2022]
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23
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Gruene T, Wennmacher JTC, Zaubitzer C, Holstein JJ, Heidler J, Fecteau‐Lefebvre A, De Carlo S, Müller E, Goldie KN, Regeni I, Li T, Santiso‐Quinones G, Steinfeld G, Handschin S, van Genderen E, van Bokhoven JA, Clever GH, Pantelic R. Rapid Structure Determination of Microcrystalline Molecular Compounds Using Electron Diffraction. Angew Chem Int Ed Engl 2018; 57:16313-16317. [PMID: 30325568 PMCID: PMC6468266 DOI: 10.1002/anie.201811318] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Indexed: 12/02/2022]
Abstract
Chemists of all fields currently publish about 50 000 crystal structures per year, the vast majority of which are X-ray structures. We determined two molecular structures by employing electron rather than X-ray diffraction. For this purpose, an EIGER hybrid pixel detector was fitted to a transmission electron microscope, yielding an electron diffractometer. The structure of a new methylene blue derivative was determined at 0.9 Å resolution from a crystal smaller than 1×2 μm2 . Several thousand active pharmaceutical ingredients (APIs) are only available as submicrocrystalline powders. To illustrate the potential of electron crystallography for the pharmaceutical industry, we also determined the structure of an API from its pill. We demonstrate that electron crystallography complements X-ray crystallography and is the technique of choice for all unsolved cases in which submicrometer-sized crystals were the limiting factor.
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Affiliation(s)
- Tim Gruene
- Department of Energy and EnvironmentPaul Scherrer InstitutForschungsstrasse 1115232Villigen PSISwitzerland
| | - Julian T. C. Wennmacher
- Department of Energy and EnvironmentPaul Scherrer InstitutForschungsstrasse 1115232Villigen PSISwitzerland
| | - Christan Zaubitzer
- Scientific Center for Optical and Electron MicroscopyETH ZürichAuguste-Piccard-Hof 18093ZürichSwitzerland
| | - Julian J. Holstein
- Department of Chemical and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Jonas Heidler
- Department of Biology and ChemistryPaul Scherrer InstitutForschungsstrasse 1115232Villigen PSISwitzerland
| | - Ariane Fecteau‐Lefebvre
- Center for Cellular Imaging and NanoAnalyticsUniversity of BaselMattenstrasse 264058BaselSwitzerland
| | | | - Elisabeth Müller
- Electron Microscopy FacilityPaul Scherrer InstitutForschungsstrasse 1115232Villigen PSISwitzerland
| | - Kenneth N. Goldie
- Center for Cellular Imaging and NanoAnalyticsUniversity of BaselMattenstrasse 264058BaselSwitzerland
| | - Irene Regeni
- Department of Chemical and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Teng Li
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | | | | | - Stephan Handschin
- Scientific Center for Optical and Electron MicroscopyETH ZürichAuguste-Piccard-Hof 18093ZürichSwitzerland
| | - Eric van Genderen
- Department of Biology and ChemistryPaul Scherrer InstitutForschungsstrasse 1115232Villigen PSISwitzerland
| | - Jeroen A. van Bokhoven
- Department of Energy and EnvironmentPaul Scherrer InstitutForschungsstrasse 1115232Villigen PSISwitzerland
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | - Guido H. Clever
- Department of Chemical and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Radosav Pantelic
- Department of Biology and ChemistryPaul Scherrer InstitutForschungsstrasse 1115232Villigen PSISwitzerland
- DECTRIS Ltd.Taefernweg 15405Baden-DaettwilSwitzerland
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24
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Gruene T, Wennmacher JTC, Zaubitzer C, Holstein JJ, Heidler J, Fecteau-Lefebvre A, De Carlo S, Müller E, Goldie KN, Regeni I, Li T, Santiso-Quinones G, Steinfeld G, Handschin S, van Genderen E, van Bokhoven JA, Clever GH, Pantelic R. Schnelle Strukturaufklärung mikrokristalliner molekularer Verbindungen durch Elektronenbeugung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811318] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tim Gruene
- Department of Energy and Environment; Paul Scherrer Institut; Forschungsstrasse 111 5232 Villigen PSI Schweiz
| | - Julian T. C. Wennmacher
- Department of Energy and Environment; Paul Scherrer Institut; Forschungsstrasse 111 5232 Villigen PSI Schweiz
| | - Christan Zaubitzer
- Scientific Center for Optical and Electron Microscopy; ETH Zürich; Auguste-Piccard-Hof 1 8093 Zürich Schweiz
| | - Julian J. Holstein
- Department of Chemical and Chemical Biology; TU Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Jonas Heidler
- Department of Biology and Chemistry; Paul Scherrer Institut; Forschungsstrasse 111 5232 Villigen PSI Schweiz
| | - Ariane Fecteau-Lefebvre
- Center for Cellular Imaging and NanoAnalytics; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
| | | | - Elisabeth Müller
- Electron Microscopy Facility; Paul Scherrer Institut; Forschungsstrasse 111 5232 Villigen PSI Schweiz
| | - Kenneth N. Goldie
- Center for Cellular Imaging and NanoAnalytics; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
| | - Irene Regeni
- Department of Chemical and Chemical Biology; TU Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Teng Li
- Department of Chemistry and Applied Biosciences; ETH Zürich; Vladimir-Prelog-Weg 1-5/10 8093 Zürich Schweiz
| | | | | | - Stephan Handschin
- Scientific Center for Optical and Electron Microscopy; ETH Zürich; Auguste-Piccard-Hof 1 8093 Zürich Schweiz
| | - Eric van Genderen
- Department of Biology and Chemistry; Paul Scherrer Institut; Forschungsstrasse 111 5232 Villigen PSI Schweiz
| | - Jeroen A. van Bokhoven
- Department of Energy and Environment; Paul Scherrer Institut; Forschungsstrasse 111 5232 Villigen PSI Schweiz
- Department of Chemistry and Applied Biosciences; ETH Zürich; Vladimir-Prelog-Weg 1-5/10 8093 Zürich Schweiz
| | - Guido H. Clever
- Department of Chemical and Chemical Biology; TU Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Radosav Pantelic
- Department of Biology and Chemistry; Paul Scherrer Institut; Forschungsstrasse 111 5232 Villigen PSI Schweiz
- DECTRIS Ltd.; Taefernweg 1 5405 Baden-Daettwil Schweiz
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25
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Wang Y, Yang T, Xu H, Zou X, Wan W. On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718007604] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The continuous rotation electron diffraction (cRED) method has the capability of providing fast three-dimensional electron diffraction data collection on existing and future transmission electron microscopes; unknown structures could be potentially solved and refined using cRED data collected from nano- and submicrometre-sized crystals. However, structure refinements of cRED data using SHELXL often lead to relatively high R1 values when compared with those refined against single-crystal X-ray diffraction data. It is therefore necessary to analyse the quality of the structural models refined against cRED data. In this work, multiple cRED data sets collected from different crystals of an oxofluoride (FeSeO3F) and a zeolite (ZSM-5) with known structures are used to assess the data consistency and quality and, more importantly, the accuracy of the structural models refined against these data sets. An evaluation of the precision and consistency of the cRED data by examination of the statistics obtained from the data processing software DIALS is presented. It is shown that, despite the high R1 values caused by dynamical scattering and other factors, the refined atomic positions obtained from the cRED data collected for different crystals are consistent with those of the reference models refined against single-crystal X-ray diffraction data. The results serve as a reference for the quality of the cRED data and the achievable accuracy of the structural parameters.
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26
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Gorelik TE, van de Streek J, Meier H, Andernach L, Opatz T. Crystal structure analysis of a star-shaped triazine compound: a combination of single-crystal three-dimensional electron diffraction and powder X-ray diffraction. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2018; 74:287-294. [PMID: 29927391 DOI: 10.1107/s2052520618006686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
The solid-state structure of star-shaped 2,4,6-tris{(E)-2-[4-(dimethylamino)-phenyl]ethenyl}-1,3,5-triazine is determined from a powder sample by exploiting the respective strengths of single-crystal three-dimensional electron diffraction and powder X-ray diffraction data. The unit-cell parameters were determined from single crystal electron diffraction data. Using this information, the powder X-ray diffraction data were indexed, and the crystal structure was determined from the powder diffraction profile. The compound crystallizes in a noncentrosymmetric space group, P212121. The molecular conformation in the crystal structure was used to calculate the molecular dipole moment of 3.22 Debye, which enables the material to show nonlinear optical effects.
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Affiliation(s)
- Tatiana E Gorelik
- Institute of Physical Chemistry, Johannes Gutenberg-University Mainz, Jakob Welder Weg 11, Mainz, 55099, Germany
| | - Jacco van de Streek
- Institute for Inorganic and Analytical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, Frankfurt am Main, 60438, Germany
| | - Herbert Meier
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
| | - Lars Andernach
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
| | - Till Opatz
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
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