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Olech B, Brázda P, Palatinus L, Dominiak PM. Dynamical refinement with multipolar electron scattering factors. IUCrJ 2024; 11:309-324. [PMID: 38512772 PMCID: PMC11067749 DOI: 10.1107/s2052252524001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.
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Affiliation(s)
- Barbara Olech
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Petr Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czechia
| | - Lukas Palatinus
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czechia
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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2
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Beanland R. 3D electron diffraction goes multipolar. IUCrJ 2024; 11:277-278. [PMID: 38700231 PMCID: PMC11067748 DOI: 10.1107/s2052252524003774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Over 30 years ago, it was shown that bonding between atoms has a noticeable effect on convergent beam electron diffraction patterns. The paper by Olech et al. [(2024). IUCrJ, 11, 309-324] demonstrates that its influence is also clearly present in 3D electron diffraction data, opening up new possibilities for quantum crystallography.
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Affiliation(s)
- R. Beanland
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
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3
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Lv ZP, Srivastava D, Conley K, Ruoko TP, Xu H, Lightowler M, Hong X, Cui X, Huang Z, Yang T, Wang HY, Karttunen AJ, Bergström L. Visualizing Noncovalent Interactions and Property Prediction of Submicron-Sized Charge-Transfer Crystals from ab-initio Determined Structures. Small Methods 2024:e2301229. [PMID: 38528393 DOI: 10.1002/smtd.202301229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/03/2024] [Indexed: 03/27/2024]
Abstract
The charge-transfer (CT) interactions between organic compounds are reflected in the (opto)electronic properties. Determining and visualizing crystal structures of CT complexes are essential for the design of functional materials with desirable properties. Complexes of pyranine (PYR), methyl viologen (MV), and their derivatives are the most studied water-based CT complexes. Nevertheless, very few crystal structures of CT complexes have been reported so far. In this study, the structures of two PYRs-MVs CT crystals and a map of the noncovalent interactions using 3D electron diffraction (3DED) are reported. Physical properties, e.g., band structure, conductivity, and electronic spectra of the CT complexes and their crystals are investigated and compared with a range of methods, including solid and liquid state spectroscopies and highly accurate quantum chemical calculations based on density functional theory (DFT). The combination of 3DED, spectroscopy, and DFT calculation can provide important insight into the structure-property relationship of crystalline CT materials, especially for submicrometer-sized crystals.
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Affiliation(s)
- Zhong-Peng Lv
- Department of Applied Physics, Aalto University, Espoo, FI 02150, Finland
| | - Divya Srivastava
- Department of Chemistry and Materials Science, Aalto University, Espoo, FI 02150, Finland
| | - Kevin Conley
- Department of Chemistry and Materials Science, Aalto University, Espoo, FI 02150, Finland
| | - Tero-Petri Ruoko
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, FI-33720, Finland
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Molly Lightowler
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Xiaodan Hong
- Department of Applied Physics, Aalto University, Espoo, FI 02150, Finland
| | - Xiaoqi Cui
- Department of Electronics and Nanoengineering, Aalto University, Espoo, FI 02150, Finland
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Taimin Yang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Hai-Ying Wang
- School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, P. R. China
| | - Antti J Karttunen
- Department of Chemistry and Materials Science, Aalto University, Espoo, FI 02150, Finland
| | - Lennart Bergström
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
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4
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Gurung K, Šimek P, Jegorov A, Palatinus L. Structure and absolute configuration of natural fungal product beauveriolide I, isolated from Cordyceps javanica, determined by 3D electron diffraction. Acta Crystallogr C Struct Chem 2024; 80:56-61. [PMID: 38411548 PMCID: PMC10913083 DOI: 10.1107/s2053229624001359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/11/2024] [Indexed: 02/28/2024] Open
Abstract
Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methylpropyl)-1-oxa-4,7,10-triazacyclotridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclodepsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclodepsipeptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Å and β = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enantiomorphs of beauveriolide I.
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Affiliation(s)
- Kshitij Gurung
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Petr Šimek
- Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice 2, 370 05, Czech Republic
| | - Alexandr Jegorov
- Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice 2, 370 05, Czech Republic
| | - Lukáš Palatinus
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
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5
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Elizebath D, Lim JH, Nishiyama Y, Vedhanarayanan B, Saeki A, Ogawa Y, Praveen VK. Nonclassical Crystal Growth of Supramolecular Polymers in Aqueous Medium. Small 2024; 20:e2306175. [PMID: 37771173 DOI: 10.1002/smll.202306175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Indexed: 09/30/2023]
Abstract
A mechanistic understanding of the principles governing the hierarchical organization of supramolecular polymers offers a paradigm for tailoring synthetic molecular architectures at the nano to micrometric scales. Herein, the unconventional crystal growth mechanism of a supramolecular polymer of superbenzene(coronene)-diphenylalanine conjugate (Cr-FFOEt ) is demonstrated. 3D electron diffraction (3D ED), a technique underexplored in supramolecular chemistry, is effectively utilized to gain a molecular-level understanding of the gradual growth of the initially formed poorly crystalline hairy, fibril-like supramolecular polymers into the ribbon-like crystallites. The further evolution of these nanosized flat ribbons into microcrystals by oriented attachment and lateral fusion is probed by time-resolved microscopy and electron diffraction. The gradual morphological and structural changes reveal the nonclassical crystal growth pathway, where the balance of strong and weak intermolecular interactions led to a structure beyond the nanoscale. The role of distinct π-stacking and H-bonding interactions that drive the nonclassical crystallization process of Cr-FFOEt supramolecular polymers is analyzed in comparison to analogous molecules, Py-FFOEt and Cr-FF forming helical and twisted fibers, respectively. Furthermore, the Cr-FFOEt crystals formed through nonclassical crystallization are found to improve the functional properties.
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Affiliation(s)
- Drishya Elizebath
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jia Hui Lim
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, 38000, France
| | | | - Balaraman Vedhanarayanan
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
| | - Akinori Saeki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yu Ogawa
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, 38000, France
| | - Vakayil K Praveen
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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6
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Poppe R, Roth N, Neder RB, Palatinus L, Iversen BB, Hadermann J. Refining short-range order parameters from the three-dimensional diffuse scattering in single-crystal electron diffraction data. IUCrJ 2024; 11:82-91. [PMID: 38096038 PMCID: PMC10833392 DOI: 10.1107/s2052252523010254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024]
Abstract
Our study compares short-range order parameters refined from the diffuse scattering in single-crystal X-ray and single-crystal electron diffraction data. Nb0.84CoSb was chosen as a reference material. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms were refined from the diffuse scattering using a Monte Carlo refinement in DISCUS. The difference between the Sb and Co displacements refined from the diffuse scattering and the Sb and Co displacements refined from the Bragg reflections in single-crystal X-ray diffraction data is 0.012 (7) Å for the refinement on diffuse scattering in single-crystal X-ray diffraction data and 0.03 (2) Å for the refinement on the diffuse scattering in single-crystal electron diffraction data. As electron diffraction requires much smaller crystals than X-ray diffraction, this opens up the possibility of refining short-range order parameters in many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available.
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Affiliation(s)
- Romy Poppe
- University of Antwerp, Department of Physics, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Nikolaj Roth
- University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Reinhard B. Neder
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Kirstallographie und Strukturphysik, Staudtstraße 3, 91058 Erlangen, Germany
| | - Lukas Palatinus
- Czech Academy of Sciences, Department of Structure Analysis, Na Slovance 2, 182 21 Prague, Czechia
| | - Bo Brummerstedt Iversen
- Aarhus University, Department of Chemistry and iNANO, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Joke Hadermann
- University of Antwerp, Department of Physics, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
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7
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Marchetti D, Pedrini A, Massera C, Faye Diouf MD, Jandl C, Steinfeld G, Gemmi M. 3D electron diffraction analysis of a novel, mechanochemically synthesized supramolecular organic framework based on tetrakis-4-(4-pyridyl)phenylmethane. Acta Crystallogr B Struct Sci Cryst Eng Mater 2023; 79:432-436. [PMID: 37811771 PMCID: PMC10833357 DOI: 10.1107/s2052520623007680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Tetrakis-4-(4-pyridyl)phenylmethane (TPPM) is a tetrahedral rigid molecule that crystallizes forming a dynamically responsive supramolecular organic framework (SOF). When exposed to different stimuli, this supramolecular network can reversibly switch from an empty to a filled solvated solid phase. This article describes a novel expanded form of a TPPM-based SOF that has been mechanochemically synthesized and whose crystal structure has been determined by 3D electron diffraction analysis using a novel electron diffractometer.
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Affiliation(s)
- Danilo Marchetti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
- Center for Materials Interfaces, Electron Crystallography, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, 56025, Italy
| | - Alessandro Pedrini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
| | - Chiara Massera
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
| | - Moussa Diame Faye Diouf
- Center for Materials Interfaces, Electron Crystallography, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, 56025, Italy
| | - Christian Jandl
- ELDICO Scientific AG, PARK INNOVAARE: deliveryLAB, Villigen, 5234, Switzerland
| | - Gunther Steinfeld
- ELDICO Scientific AG, PARK INNOVAARE: deliveryLAB, Villigen, 5234, Switzerland
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron Crystallography, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, 56025, Italy
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8
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Parkhurst JM, Crawshaw AD, Siebert CA, Dumoux M, Owen CD, Nunes P, Waterman D, Glen T, Stuart DI, Naismith JH, Evans G. Investigation of the milling characteristics of different focused-ion-beam sources assessed by three-dimensional electron diffraction from crystal lamellae. IUCrJ 2023; 10:270-287. [PMID: 36952226 PMCID: PMC10161776 DOI: 10.1107/s2052252523001902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/01/2023] [Indexed: 05/06/2023]
Abstract
Three-dimensional electron diffraction (3DED) from nanocrystals of biological macromolecules requires the use of very small crystals. These are typically less than 300 nm-thick in the direction of the electron beam due to the strong interaction between electrons and matter. In recent years, focused-ion-beam (FIB) milling has been used in the preparation of thin samples for 3DED. These instruments typically use a gallium liquid metal ion source. Inductively coupled plasma (ICP) sources in principle offer faster milling rates. Little work has been done to quantify the damage these sources cause to delicate biological samples at cryogenic temperatures. Here, an analysis of the effect that milling with plasma FIB (pFIB) instrumentation has on lysozyme crystals is presented. This work evaluates both argon and xenon plasmas and compares them with crystals milled with a gallium source. A milling protocol was employed that utilizes an overtilt to produce wedge-shaped lamellae with a shallow thickness gradient which yielded very thin crystalline samples. 3DED data were then acquired and standard data-processing statistics were employed to assess the quality of the diffraction data. An upper bound to the depth of the pFIB-milling damage layer of between 42.5 and 50 nm is reported, corresponding to half the thickness of the thinnest lamellae that resulted in usable diffraction data. A lower bound of between 32.5 and 40 nm is also reported, based on a literature survey of the minimum amount of diffracting material required for 3DED.
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Affiliation(s)
- James M Parkhurst
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - Adam D Crawshaw
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - C Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - Maud Dumoux
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - Pedro Nunes
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - David Waterman
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, Oxford OX11 0FA, United Kingdom
| | - Thomas Glen
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - David I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - James H Naismith
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - Gwyndaf Evans
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
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9
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Gorelik TE, Bekő SL, Teteruk J, Heyse W, Schmidt MU. Analysis of diffuse scattering in electron diffraction data for the crystal structure determination of Pigment Orange 13, C 32H 24Cl 2N 8O 2. Acta Crystallogr B Struct Sci Cryst Eng Mater 2023; 79:122-137. [PMID: 36920875 PMCID: PMC10088482 DOI: 10.1107/s2052520623000720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/26/2023] [Indexed: 03/05/2023]
Abstract
The crystallographic study of two polymorphs of the industrial pyrazolone Pigment Orange 13 (P.O.13) is reported. The crystal structure of the β phase was determined using single-crystal X-ray analysis of a tiny needle. The α phase was investigated using three-dimensional electron diffraction. The electron diffraction data contain sharp Bragg reflections and strong diffuse streaks, associated with severe stacking disorder. The structure was solved by careful analysis of the diffuse scattering, and similarities of the unit-cell parameters with the β phase. The structure solution is described in detail and this provides a didactic example of solving molecular crystal structures in the presence of diffuse scattering. Several structural models were constructed and optimized by lattice-energy minimization with dispersion-corrected DFT. A four-layer model was found, which matches the electron diffraction data, including the diffuse scattering, and agrees with X-ray powder data. Additionally, five further phases of P.O.13 are described.
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Affiliation(s)
- Tatiana E Gorelik
- Ulm University, Central Facility of Electron Microscopy, Materials Science Electron Microscopy, Albert Einstein Allee 11, 89069 Ulm, Germany
| | - Sàndor L Bekő
- Goethe University, Institute of Inorganic and Analytical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jaroslav Teteruk
- Goethe University, Institute of Inorganic and Analytical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Winfried Heyse
- Sanofi, R&D / PDP / TIDES Analytical Sciences, Building H770, 65926 Frankfurt am Main, Germany
| | - Martin U Schmidt
- Goethe University, Institute of Inorganic and Analytical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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10
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Simoncic P, Romeijn E, Hovestreydt E, Steinfeld G, Santiso-Quiñones G, Merkelbach J. Electron crystallography and dedicated electron-diffraction instrumentation. Acta Crystallogr E Crystallogr Commun 2023; 79:410-422. [PMID: 37151820 PMCID: PMC10162091 DOI: 10.1107/s2056989023003109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.
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Affiliation(s)
- Petra Simoncic
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
- Correspondence e-mail:
| | - Eva Romeijn
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Eric Hovestreydt
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Gunther Steinfeld
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | | | - Johannes Merkelbach
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
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11
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Storm A, Köster J, Ghorbani-Asl M, Kretschmer S, Gorelik TE, Kinyanjui MK, Krasheninnikov AV, Kaiser U. Electron-Beam- and Thermal-Annealing-Induced Structural Transformations in Few-Layer MnPS 3. ACS Nano 2023; 17:4250-4260. [PMID: 36802543 DOI: 10.1021/acsnano.2c05895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Quasi-two-dimensional (2D) manganese phosphorus trisulfide, MnPS3, which exhibits antiferromagnetic ordering, is a particularly interesting material in the context of magnetism in a system with reduced dimensionality and its potential technological applications. Here, we present an experimental and theoretical study on modifying the properties of freestanding MnPS3 by local structural transformations via electron irradiation in a transmission electron microscope and by thermal annealing under vacuum. In both cases we find that MnS1-xPx phases (0 ≤ x < 1) form in a crystal structure different from that of the host material, namely that of the α- or γ-MnS type. These phase transformations can both be locally controlled by the size of the electron beam as well as by the total applied electron dose and simultaneously imaged at the atomic scale. For the MnS structures generated in this process, our ab initio calculations indicate that their electronic and magnetic properties strongly depend on both in-plane crystallite orientation and thickness. Moreover, the electronic properties of the MnS phases can be further tuned by alloying with phosphorus. Therefore, our results show that electron beam irradiation and thermal annealing can be utilized to grow phases with distinct properties starting from freestanding quasi-2D MnPS3.
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Affiliation(s)
- Alexander Storm
- Electron Microscopy Group of Materials Science, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Janis Köster
- Electron Microscopy Group of Materials Science, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Mahdi Ghorbani-Asl
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Centre Dresden-Rossendorf, 01328 Dresden, Germany
| | - Silvan Kretschmer
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Centre Dresden-Rossendorf, 01328 Dresden, Germany
| | - Tatiana E Gorelik
- Electron Microscopy Group of Materials Science, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Michael Kiarie Kinyanjui
- Electron Microscopy Group of Materials Science, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Arkady V Krasheninnikov
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Centre Dresden-Rossendorf, 01328 Dresden, Germany
- Department of Applied Physics, Aalto University, PO Box 14100, 00076 Aalto, Finland
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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12
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Cleverley A, Beanland R. Modelling fine-sliced three dimensional electron diffraction data with dynamical Bloch-wave simulations. IUCrJ 2023; 10:118-130. [PMID: 36598507 PMCID: PMC9812222 DOI: 10.1107/s2052252522011290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Recent interest in structure solution and refinement using electron diffraction (ED) has been fuelled by its inherent advantages when applied to crystals of sub-micrometre size, as well as its better sensitivity to light elements. Currently, data are often processed with software written for X-ray diffraction, using the kinematic theory of diffraction to generate model intensities - despite the inherent differences in diffraction processes in ED. Here, dynamical Bloch-wave simulations are used to model continuous-rotation electron diffraction data, collected with a fine angular resolution (crystal orientations of ∼0.1°). This fine-sliced data allows a re-examination of the corrections applied to ED data. A new method is proposed for optimizing crystal orientation, and the angular range of the incident beam and the varying slew rate are taken into account. Observed integrated intensities are extracted and accurate comparisons are performed with simulations using rocking curves for a (110) lamella of silicon 185 nm thick. R1 is reduced from 26% with the kinematic model to 6.8% using dynamical simulations.
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Affiliation(s)
- Anton Cleverley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Richard Beanland
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
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13
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Andrusenko I, Hall CL, Mugnaioli E, Potticary J, Hall SR, Schmidt W, Gao S, Zhao K, Marom N, Gemmi M. True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications. IUCrJ 2023; 10:131-142. [PMID: 36598508 PMCID: PMC9812223 DOI: 10.1107/s205225252201154x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet-triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.
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Affiliation(s)
- Iryna Andrusenko
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
| | - Charlie L. Hall
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Enrico Mugnaioli
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
- Department of Earth Sciences, University of Pisa, Pisa 56126, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Simon R. Hall
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Siyu Gao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Kaiji Zhao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Mauro Gemmi
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
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14
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Yang T, Xu H, Zou X. Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method. J Appl Crystallogr 2022; 55:1583-1591. [PMID: 36570655 PMCID: PMC9721325 DOI: 10.1107/s1600576722009633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R 1 values improved by 10-30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.
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Affiliation(s)
- Taimin Yang
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden
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15
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Gorelik TE. Towards a new level of quantitative treatment of 3D electron diffraction data - in-pattern optical distortions. IUCrJ 2022; 9:715-717. [PMID: 36381149 PMCID: PMC9634610 DOI: 10.1107/s2052252522010326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Electron diffraction patterns unavoidably contain in-plane distortions introduced by electromagnetic lens systems. Geometric correction of different distortion types allows the accuracy of lattice parameter determination to be improved in 3D electron diffraction data.
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Affiliation(s)
- Tatiana E. Gorelik
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University Campus, Saarbrucken, 66123, Germany
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16
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Brázda P, Klementová M, Krysiak Y, Palatinus L. Accurate lattice parameters from 3D electron diffraction data. I. Optical distortions. IUCrJ 2022; 9:735-755. [PMID: 36381142 PMCID: PMC9634609 DOI: 10.1107/s2052252522007904] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/05/2022] [Indexed: 05/24/2023]
Abstract
Determination of lattice parameters from 3D electron diffraction (3D ED) data measured in a transmission electron microscope is hampered by a number of effects that seriously limit the achievable accuracy. The distortion of the diffraction patterns by the optical elements of the microscope is often the most severe problem. A thorough analysis of a number of experimental datasets shows that, in addition to the well known distortions, namely barrel-pincushion, spiral and elliptical, an additional distortion, dubbed parabolic, may be observed in the data. In precession electron diffraction data, the parabolic distortion leads to excitation-error-dependent shift and splitting of reflections. All distortions except for the elliptical distortion can be determined together with lattice parameters from a single 3D ED data set. However, the parameters of the elliptical distortion cannot be determined uniquely due to correlations with the lattice parameters. They can be determined and corrected either by making use of the known Laue class of the crystal or by combining data from two or more crystals. The 3D ED data can yield lattice parameter ratios with an accuracy of about 0.1% and angles with an accuracy better than 0.03°.
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Affiliation(s)
- Petr Brázda
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Mariana Klementová
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Yaşar Krysiak
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
- Institute of Inorganic Chemistry, Leibniz University of Hannover, Callinstraße 9, Hannover, 30167, Germany
| | - Lukáš Palatinus
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
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17
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Poppe R, Vandemeulebroucke D, Neder RB, Hadermann J. Quantitative analysis of diffuse electron scattering in the lithium-ion battery cathode material Li 1.2Ni 0.13Mn 0.54Co 0.13O 2. IUCrJ 2022; 9:695-704. [PMID: 36071802 PMCID: PMC9438490 DOI: 10.1107/s2052252522007746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
In contrast to perfectly periodic crystals, materials with short-range order produce diffraction patterns that contain both Bragg reflections and diffuse scattering. To understand the influence of short-range order on material properties, current research focuses increasingly on the analysis of diffuse scattering. This article verifies the possibility to refine the short-range order parameters in submicrometre-sized crystals from diffuse scattering in single-crystal electron diffraction data. The approach was demonstrated on Li1.2Ni0.13Mn0.54Co0.13O2, which is a state-of-the-art cathode material for lithium-ion batteries. The intensity distribution of the 1D diffuse scattering in the electron diffraction patterns of Li1.2Ni0.13Mn0.54Co0.13O2 depends on the number of stacking faults and twins in the crystal. A model of the disorder in Li1.2Ni0.13Mn0.54Co0.13O2 was developed and both the stacking fault probability and the percentage of the different twins in the crystal were refined using an evolutionary algorithm in DISCUS. The approach was applied on reciprocal space sections reconstructed from 3D electron diffraction data since they exhibit less dynamical effects compared with in-zone electron diffraction patterns. A good agreement was achieved between the calculated and the experimental intensity distribution of the diffuse scattering. The short-range order parameters in submicrometre-sized crystals can thus successfully be refined from the diffuse scattering in single-crystal electron diffraction data using an evolutionary algorithm in DISCUS.
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Affiliation(s)
- Romy Poppe
- University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium
| | | | - Reinhard B. Neder
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 3, D-91058 Erlangen, Germany
| | - Joke Hadermann
- University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium
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18
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Broadhurst ET, Xu H, Parsons S, Nudelman F. Revealing the early stages of carbamazepine crystallization by cryoTEM and 3D electron diffraction. IUCrJ 2021; 8:860-866. [PMID: 34804540 PMCID: PMC8562671 DOI: 10.1107/s2052252521010101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Time-resolved carbamazepine crystallization from wet ethanol has been monitored using a combination of cryoTEM and 3D electron diffraction. Carbamazepine is shown to crystallize exclusively as a dihydrate after 180 s. When the timescale was reduced to 30 s, three further polymorphs could be identified. At 20 s, the development of early stage carbamazepine dihydrate was observed through phase separation. This work reveals two possible crystallization pathways present in this active pharmaceutical ingredient.
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Affiliation(s)
- Edward T. Broadhurst
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, United Kingdom
| | - Hongyi Xu
- Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Simon Parsons
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, United Kingdom
| | - Fabio Nudelman
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, United Kingdom
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19
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Gorelik TE, Nergis B, Schöner T, Köster J, Kaiser U. 3D electron diffraction of mono- and few-layer MoS 2. Micron 2021; 146:103071. [PMID: 33892437 DOI: 10.1016/j.micron.2021.103071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 11/20/2022]
Abstract
Mono- and few-layer MoS2 were studied by three-dimensional electron diffraction (3D ED) showing distinctly different symmetry for crystals consisting of odd and even number of layers. Experimentally obtained intensity distributions along the relrods match qualitatively kinematically simulated data. Our findings allow to differentiate unambiguously between 1-, 2-, 3- 4- and 5-layers MoS2 crystals.
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Affiliation(s)
- Tatiana E Gorelik
- Electron Microscopy of Materials Science (EMMS), Central Facility for Electron Microscopy, Ulm University, Albert Einstein Allee 11, 89081, Ulm, Germany.
| | - Berkin Nergis
- Electron Microscopy of Materials Science (EMMS), Central Facility for Electron Microscopy, Ulm University, Albert Einstein Allee 11, 89081, Ulm, Germany
| | - Tobias Schöner
- Electron Microscopy of Materials Science (EMMS), Central Facility for Electron Microscopy, Ulm University, Albert Einstein Allee 11, 89081, Ulm, Germany
| | - Janis Köster
- Electron Microscopy of Materials Science (EMMS), Central Facility for Electron Microscopy, Ulm University, Albert Einstein Allee 11, 89081, Ulm, Germany
| | - Ute Kaiser
- Electron Microscopy of Materials Science (EMMS), Central Facility for Electron Microscopy, Ulm University, Albert Einstein Allee 11, 89081, Ulm, Germany
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20
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Abstract
Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
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Affiliation(s)
- Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
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21
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Steciuk G, Majzlan J, Plášil J. Hydrogen disorder in kaatialaite Fe[AsO 2(OH) 2]5H 2O from Jáchymov, Czech Republic: determination from low-temperature 3D electron diffraction. IUCrJ 2021; 8:116-123. [PMID: 33520247 PMCID: PMC7793002 DOI: 10.1107/s2052252520015626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Kaatialaite mineral Fe[AsO2(OH)2]5H2O from Jáchymov, Czech Republic forms white aggregates of needle-shaped crystals with micrometric size. Its structure at ambient temperature has already been reported but hydrogen atoms could not be identified from single-crystal X-ray diffraction. An analysis using 3D electron diffraction at low temperature brings to light the hydrogen positions and the existence of hydrogen disorder. At 100 K, kaatialaite is described in a monoclinic unit cell of a = 15.46, b = 19.996, c = 4.808 Å, β = 91.64° and V = 1485.64 Å3 with space group P21/n. The hydrogen sites were revealed after refinements both considering the dynamical effects and ignoring them. The possibility to access most of the hydrogen positions, including partially occupied ones among heavy atoms, from the kinematical refinement is due to the recent developments in the analysis of 3D electron data. The hydrogen bonding observed in kaatialaite provides examples of H2O configurations that have not been observed before in the structures of oxysalts with the presence of unusual inverse transformer H2O groups.
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Affiliation(s)
- Gwladys Steciuk
- Department of Structure Analysis, Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 182 21, Czech Republic
| | - Juraj Majzlan
- Institute of Geosciences, Friedrich-Schiller University, Burgweg 11, Jena, 07749, Germany
| | - Jakub Plášil
- Department of Structure Analysis, Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 182 21, Czech Republic
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22
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Sun T, Hughes CE, Guo L, Wei L, Harris KDM, Zhang YB, Ma Y. Direct-Space Structure Determination of Covalent Organic Frameworks from 3D Electron Diffraction Data. Angew Chem Int Ed Engl 2020; 59:22638-22644. [PMID: 32885575 DOI: 10.1002/anie.202009922] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Indexed: 02/06/2023]
Abstract
Structure determination of covalent organic frameworks (COFs) with atomic precision is a bottleneck that hinders the development of COF chemistry. Although three-dimensional electron diffraction (3D-ED) data has been used to solve structures of sub-micrometer-sized COFs, successful structure solution is not guaranteed as the data resolution is usually low. We demonstrate that the direct-space strategy for structure solution, implemented using a genetic algorithm (GA), is a successful approach for structure determination of COF-300 from 3D-ED data. Structural models with different geometric constraints were considered in the GA calculations, with successful structure solution achieved from room-temperature 3D-ED data with a resolution as low as ca. 3.78 Å. The generality of this strategy was further verified for different phases of COF-300. This study demonstrates a viable strategy for structure solution of COF materials from 3D-ED data of limited resolution, which may facilitate the discovery of new COF materials in the future.
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Affiliation(s)
- Tu Sun
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Colan E Hughes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Linshuo Guo
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Lei Wei
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Kenneth D M Harris
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China.,School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Yue-Biao Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Yanhang Ma
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
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23
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Roslova M, Smeets S, Wang B, Thersleff T, Xu H, Zou X. InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction. J Appl Crystallogr 2020; 53:1217-1224. [PMID: 33117109 PMCID: PMC7534539 DOI: 10.1107/s1600576720009590] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/14/2020] [Indexed: 11/26/2022] Open
Abstract
A DigitalMicrograph script named InsteaDMatic has been developed for automated continuous rotation electron diffraction (cRED) data acquisition. InsteaDMatic coordinates functions of the transmission electron microscope goniometer and camera in order to tune up diffraction-frame recording simultaneously with crystal rotation. Exploiting fast and automated data collection, the influence of the electron dose rate on the quality of cRED data was studied, and structural models obtained for two different parallel-beam illumination modes (aperture selection and nanoprobe) were compared. A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.
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Affiliation(s)
- Maria Roslova
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Stef Smeets
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Bin Wang
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Thomas Thersleff
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
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24
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Krysiak Y, Marler B, Barton B, Plana-Ruiz S, Gies H, Neder RB, Kolb U. New zeolite-like RUB-5 and its related hydrous layer silicate RUB-6 structurally characterized by electron microscopy. IUCrJ 2020; 7:522-534. [PMID: 32431835 PMCID: PMC7201290 DOI: 10.1107/s2052252520003991] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
This study made use of a recently developed combination of advanced methods to reveal the atomic structure of a disordered nanocrystalline zeolite using exit wave reconstruction, automated diffraction tomography, disorder modelling and diffraction pattern simulation. By applying these methods, it was possible to determine the so far unknown structures of the hydrous layer silicate RUB-6 and the related zeolite-like material RUB-5. The structures of RUB-5 and RUB-6 contain the same dense layer-like building units (LLBUs). In the case of RUB-5, these building units are interconnected via additional SiO4/2 tetrahedra, giving rise to a framework structure with a 2D pore system consisting of intersecting 8-ring channels. In contrast, RUB-6 contains these LLBUs as separate silicate layers terminated by silanol/sil-oxy groups. Both RUB-6 and RUB-5 show stacking disorder with intergrowths of different polymorphs. The unique structure of RUB-6, together with the possibility for an interlayer expansion reaction to form RUB-5, make it a promising candidate for interlayer expansion with various metal sources to include catalytically active reaction centres.
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Affiliation(s)
- Yaşar Krysiak
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, Mainz D-55128, Germany
- Department of Materials and Geoscience, Technische Universität Darmstadt, Petersenstrasse 23, Darmstadt D-64287, Germany
- Department of Structure Analysis of the Institute of Physics, Czech Academy of Sciences, Cukrovarnická 10/112, Prague 162 00, Czech Republic
| | - Bernd Marler
- Departure of Geology, Mineralogy and Geophysics, Ruhr University Bochum, Universitätsstrasse 150, Bochum D-44801, Germany
| | - Bastian Barton
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, Mainz D-55128, Germany
| | - Sergi Plana-Ruiz
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, Mainz D-55128, Germany
- LENS, MIND/IN2UB, Engineer department: Electronics section, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | - Hermann Gies
- Departure of Geology, Mineralogy and Geophysics, Ruhr University Bochum, Universitätsstrasse 150, Bochum D-44801, Germany
| | - Reinhard B. Neder
- Chair for Crystallography and Structural Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 3, Erlangen D-91058, Germany
| | - Ute Kolb
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, Mainz D-55128, Germany
- Department of Materials and Geoscience, Technische Universität Darmstadt, Petersenstrasse 23, Darmstadt D-64287, Germany
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25
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Liu X, Luo Y, Mao W, Jiang J, Xu H, Han L, Sun J, Wu P. 3D Electron Diffraction Unravels the New Zeolite ECNU-23 from the "Pure" Powder Sample of ECNU-21. Angew Chem Int Ed Engl 2020; 59:1166-1170. [PMID: 31674090 DOI: 10.1002/anie.201912488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 11/09/2022]
Abstract
A novel crystalline high-silica zeolite with 12×8-membered ring (R) channel system is prepared with the aid of the 3D electron diffraction (3D ED) technique. A crystal with the same topology as one of the predicted daughter structures of CIT-13 germanosilicate, named ECNU-23 (East China Normal University 23) was coincidentally detected by the 3D ED investigation during the structure characterization of the "pure" powder sample of existing one-dimension (1D) 10-R ECNU-21. By controlling the alkaline-assisted hydrolysis under moderate conditions, we purified the phase of ECNU-23 by selectively breaking and removing the chemically weak Ge(Si)-O-Ge and metastable Si-O-Si bonds. Its structure was determined based on the 3D ED data, and confirmed by high-resolution TEM images and powder X-ray diffraction (PXRD) data. The aluminosilicate Al-ECNU-23 shows unique catalytic properties in the isomerization/ disproportionation of m-xylene as solid-acid catalyst.
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Affiliation(s)
- Xue Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, North Zhongshan Road 3663, Shanghai, 200062, P. R. China.,College of Science, Agricultural University of Hebei, Lingyusi Road 289, Baoding, 071001, P. R. China
| | - Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Wenting Mao
- State Key Laboratory of Metal Matrix Composites, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, P. R. China
| | - Jingang Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, North Zhongshan Road 3663, Shanghai, 200062, P. R. China
| | - Hao Xu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, North Zhongshan Road 3663, Shanghai, 200062, P. R. China
| | - Lu Han
- School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, P. R. China
| | - Junliang Sun
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden.,College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, P. R. China
| | - Peng Wu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, North Zhongshan Road 3663, Shanghai, 200062, P. R. China
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26
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Azough F, Gholinia A, Alvarez-Ruiz DT, Duran E, Kepaptsoglou DM, Eggeman AS, Ramasse QM, Freer R. Self-Nanostructuring in SrTiO 3: A Novel Strategy for Enhancement of Thermoelectric Response in Oxides. ACS Appl Mater Interfaces 2019; 11:32833-32843. [PMID: 31419381 DOI: 10.1021/acsami.9b06483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanostructuring is recognized as an efficient route for enhancing thermoelectric response. Here, we report a new synthesis strategy for nanostructuring oxide ceramics and demonstrate its effectiveness on an important n-type thermoelectric SrTiO3. Ceramics of Sr0.9La0.1TiO3 with additions of B2O3 were synthesized by the mixed oxide route. Samples were sintered in air followed by annealing in a reducing atmosphere. Crystallographic data from X-ray and electron diffraction showed Pm3̅m cubic symmetry for all the samples. High-resolution transmission electron microscopy (HRTEM) showed the formation of a core-shell type structure within the grains for the annealed ceramics. The cores contain nanosize features comprising pairs of nanosize voids and particles; the feature sizes depend on annealing time. Atomic-resolution, high-angle annular-dark-field imaging and electron energy loss spectroscopy in the scanning transmission electron microscopy (STEM-HAADF-EELS) showed the particles to be rich in Ti and the areas around the voids to contain high concentrations of Ti3+. Additionally, dislocations were observed, with significantly higher densities in the shell areas. The observed dislocations are combined (100) and (110) edge dislocations. The major impact of the core-shell type microstructures, with nanosize inclusions, is the reduction of the thermal conductivity. Sr0.9La0.1TiO3 ceramics containing grain boundary shells of size ≈ 1 μm and inclusions in the core of 60-80 nm exhibit a peak power factor of 1600 μW/m·K2 at 540 K; at 1000 K, they exhibit a low thermal conductivity (2.75 W/m·K) and a power factor of 1050 μW/m·K2 leading to a high of ZT of 0.39 ± 0.03. This is the highest ZT reported so far for Sr0.9La0.1TiO3 based-compositions. This nanostructuring strategy should be readily applicable to other functional oxides.
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Affiliation(s)
- Feridoon Azough
- School of Materials , University of Manchester , Manchester , M13 9PL , U.K
| | - Ali Gholinia
- School of Materials , University of Manchester , Manchester , M13 9PL , U.K
| | | | - Ercin Duran
- School of Materials , University of Manchester , Manchester , M13 9PL , U.K
| | - Demie M Kepaptsoglou
- SuperSTEM Laboratory , STFC Daresbury Campus , Daresbury WA4 4AD , U.K
- Jeol Nanocentre and Department of Physics , University of York , Heslington, York YO10 5DD , U.K
| | | | - Quentin M Ramasse
- SuperSTEM Laboratory , STFC Daresbury Campus , Daresbury WA4 4AD , U.K
- School of Chemical and Process Engineering and School of Physics , University of Leeds , Leeds LS2 9JT , U.K
| | - Robert Freer
- School of Materials , University of Manchester , Manchester , M13 9PL , U.K
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27
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Andrusenko I, Hamilton V, Mugnaioli E, Lanza A, Hall C, Potticary J, Hall SR, Gemmi M. The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction. Angew Chem Int Ed Engl 2019; 58:10919-10922. [PMID: 31210373 DOI: 10.1002/anie.201904564] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Orthocetamol is a regioisomer of the well-known pain medication paracetamol and a promising analgesic and an anti-arthritic medicament itself. However, orthocetamol cannot be grown as single crystals suitable for X-ray diffraction, so its crystal structure has remained a mystery for more than a century. Here, we report the ab-initio structure determination of orthocetamol obtained by 3D electron diffraction, combining a low-dose acquisition method and a dedicated single-electron detector for recording the diffracted intensities. The structure is monoclinic, with a pseudo-tetragonal cell that favors multiple twinning on a scale of a few tens of nanometers. The successful application of 3D electron diffraction to orthocetamol introduces a new gold standard of total structure solution in all cases where X-ray diffraction and electron-microscope imaging methods fail.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Victoria Hamilton
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,Bristol Centre for Functional Nanomaterials, Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol, BS8 1FD, UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Arianna Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Charlie Hall
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,Centre for Doctoral Training in Condensed Matter Physics, HH Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Jason Potticary
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Simon R Hall
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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