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Decato D, Palatinus L, Stierle A, Stierle D. Absolute structure determination of Berkecoumarin by X-ray and electron diffraction. Acta Crystallogr C Struct Chem 2024; 80:S2053229624003061. [PMID: 38598330 DOI: 10.1107/s2053229624003061] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024] Open
Abstract
X-ray and electron diffraction methods independently identify the S-enantiomer of Berkecoumarin [systematic name: (S)-8-hydroxy-3-(2-hydroxypropyl)-6-methoxy-2H-chromen-2-one]. Isolated from Berkeley Pit Lake Penicillium sp., Berkecoumarin is a natural product with a light-atom composition (C13H14O5) that challenges in-house absolute structure determination by anomalous scattering. This study further demonstrates the utility of dynamical refinement of electron-diffraction data for absolute structure determination.
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Affiliation(s)
- Daniel Decato
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| | - Lukáš Palatinus
- Institute of Physics of the CAS, Na Slovance 1999/2, Prague 19200, Czech Republic
| | - Andrea Stierle
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| | - Donald Stierle
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
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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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Yue Q, Steciuk G, Mazur M, Zhang J, Petrov O, Shamzhy M, Liu M, Palatinus L, Čejka J, Opanasenko M. Catching a New Zeolite as a Transition Material during Deconstruction. J Am Chem Soc 2023; 145:9081-9091. [PMID: 37040083 PMCID: PMC10141410 DOI: 10.1021/jacs.3c00423] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Zeolites are key materials in both basic research and industrial applications. However, their synthesis is neither diverse nor applicable to labile frameworks because classical procedures require harsh hydrothermal conditions, whereas post-synthesis methods are limited to a few suitable parent materials. Remaining frameworks can fail due to amorphization, dissolution, and other decomposition processes. Nevertheless, stopping degradation at intermediate structures could yield new zeolites. Here, by optimizing the design and synthesis parameters of the parent zeolite IWV, we "caught" a new, highly crystalline, and siliceous zeolite during its degradation. IWV seed-assisted crystallization followed by gentle transformation into the water-alcohol system yielded the highly crystalline daughter zeolite IPC-20, whose structure was solved by precession-assisted three-dimensional electron diffraction. Without additional requirements, as in conventional (direct or post-synthesis) strategies, our approach may be applied to any chemically labile material with a staged structure.
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Affiliation(s)
- Qiudi Yue
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 43, Czech Republic
| | - Gwladys Steciuk
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Na Slovance 2, Prague 8 182 21, Czech Republic
| | - Michal Mazur
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 43, Czech Republic
| | - Jin Zhang
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 43, Czech Republic
| | - Oleg Petrov
- Department of Low-Temperature Physics, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, Prague 8 180 00, Czech Republic
| | - Mariya Shamzhy
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 43, Czech Republic
| | - Mingxiu Liu
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 43, Czech Republic
| | - Lukáš Palatinus
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Na Slovance 2, Prague 8 182 21, Czech Republic
| | - Jiří Čejka
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 43, Czech Republic
| | - Maksym Opanasenko
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 43, Czech Republic
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Navrátilová T, Tatar A, Havlík M, Hajduch J, Drozdová M, Gurung K, Palatinus L, Čejka J, Sedláček J, Anzenbacher P, Dolenský B. Preparation and Characterization of Metalloporphyrin Tröger’s and Spiro-Tröger’s Base Derivatives. J Org Chem 2022; 87:15178-15186. [DOI: 10.1021/acs.joc.2c01716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tereza Navrátilová
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
| | - Ameneh Tatar
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
| | - Martin Havlík
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
| | - Jan Hajduch
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
| | - Michaela Drozdová
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
| | - Kshitij Gurung
- Institute of Physics of the Czech Academy of Sciences, 182 21 Prague 8, Czech Republic
| | - Lukáš Palatinus
- Institute of Physics of the Czech Academy of Sciences, 182 21 Prague 8, Czech Republic
| | - Jan Čejka
- Department of Solid State Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
| | - Jakub Sedláček
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
| | - Pavel Anzenbacher
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Bohumil Dolenský
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, 166 28 Prague 6, Czech Republic
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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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Gurung K, Brázda P, Palatinus L. Crystal structure study of xenon compounds using 3D electron diffraction. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322091513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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7
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Barrier N, Debost M, Grand J, Boullay P, Clatworthy E, Päcklar A, Klar P, Brázda P, Nesterenko N, Dath J, Gilson J, Palatinus L, Mintova S. In situ characterizations of the selective CO 2 adsorption in free-template nanosized zeolites RHO and CHA. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322090672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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8
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Brazda P, Palatinus L, Jegorov A, Gavenda A, Vraspir P. Absolute structure of pharmaceutical salts of vilanterol using 3D ED – from Earth to the Space Station and back. Acta Cryst Sect A 2022. [DOI: 10.1107/s205327332209533x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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9
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Klementova M, Palatinus L, Bursik J, Zobac O. (3+3)D incommensurately modulated structure of the τ phase in the Al–Cu–Zn system. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322095419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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10
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Cabaj M, Palatinus L, Andrusenko I, Gemmi M. The influence of energy filtering on kinematical and dynamical structure refinement from 3D ED data. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322091525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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11
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Chintakindi H, Palatinus L. Dynamical refinement of 3D ED data: comparison of CCD and HPD data. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322091458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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12
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Gruza B, Brázda P, Palatinus L, Dominiak P. TAAM refinement in dynamical approach against electron diffraction data. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322091501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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13
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Palatinus L, Klar P. Frame-based kinematical refinement: a way to quantify dynamical effects in 3D electron diffraction. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322095353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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14
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Schmidt E, Krysiak Y, Klar P, Palatinus L, Goodwin A. Using 3D-ΔPDFs from electron diffraction data to determine local structure. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322095389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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15
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Krysiak Y, Maslyk M, Silva BNN, Plana-Ruiz S, Moura HM, Munsignatti EO, Vaiss VS, Kolb U, Tremel W, Palatinus L, Leitão AA, Marler B, Pastore HO. The long-time elusive structure of magadiite, solved by 3D electron diffraction and model building. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s010876732109351x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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Sasaki S, Caldes MT, Guillot-Deudon C, Braems I, Steciuk G, Palatinus L, Gautron E, Frapper G, Janod E, Corraze B, Jobic S, Cario L. Design of metastable oxychalcogenide phases by topochemical (de)intercalation of sulfur in La 2O 2S 2. Nat Commun 2021; 12:3605. [PMID: 34127660 PMCID: PMC8203606 DOI: 10.1038/s41467-021-23677-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/22/2021] [Indexed: 11/17/2022] Open
Abstract
Designing and synthesising new metastable compounds is a major challenge of today’s material science. While exploration of metastable oxides has seen decades-long advancement thanks to the topochemical deintercalation of oxygen as recently spotlighted with the discovery of nickelate superconductor, such unique synthetic pathway has not yet been found for chalcogenide compounds. Here we combine an original soft chemistry approach, structure prediction calculations and advanced electron microscopy techniques to demonstrate the topochemical deintercalation/reintercalation of sulfur in a layered oxychalcogenide leading to the design of novel metastable phases. We demonstrate that La2O2S2 may react with monovalent metals to produce sulfur-deintercalated metastable phases La2O2S1.5 and oA-La2O2S whose lamellar structures were predicted thanks to an evolutionary structure-prediction algorithm. This study paves the way to unexplored topochemistry of mobile chalcogen anions. Great progress has been made in topochemistry of mobile oxygen anions, but metastable compounds have not yet been achieved by deintercalation of sulfur anions. Here, the authors prepare metastable oxychalcogenide phases by taking advantage of redox-reactive sulfur dimers embedded in a layered oxysulfide.
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Affiliation(s)
- Shunsuke Sasaki
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France
| | - Maria Teresa Caldes
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France
| | | | - Isabelle Braems
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France
| | - Gwladys Steciuk
- Institute of Physics ASCR, v.v.i., Na Slovance 1999/2, Praha 8, 18221, Czechia
| | - Lukáš Palatinus
- Institute of Physics ASCR, v.v.i., Na Slovance 1999/2, Praha 8, 18221, Czechia
| | - Eric Gautron
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France
| | - Gilles Frapper
- Institut de Chimie des Milieux et Matériaux de Poitiers, 4 rue Michel Brunet, Poitiers cedex 09, 86073, France
| | - Etienne Janod
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France
| | - Benoît Corraze
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France
| | - Stéphane Jobic
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France.
| | - Laurent Cario
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, F-44000, France.
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Steciuk G, Schäf O, Tortet L, Pizzala H, Palatinus L, Hornfeck W, Paillaud J. A New Lithium‐Rich Zeolitic 10‐MR Zincolithosilicate MZS‐1 Hydrothermally Synthesized under High Pressure and Characterized by 3D Electron Diffraction. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202000939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Gwladys Steciuk
- Institute of Physics of the AS CR v.v.i., Na Slovance 2 182 21 Prague Czech Republic
| | - Oliver Schäf
- Laboratoire MADIREL, UMR7246 Aix-Marseille Université CNRS Campus Scientifique de St. Jérôme, 20 13397 Marseille Cedex France
| | - Laurence Tortet
- Laboratoire MADIREL, UMR7246 Aix-Marseille Université CNRS Campus Scientifique de St. Jérôme, 20 13397 Marseille Cedex France
| | - Hélène Pizzala
- Institut de Chimie Radicalaire, UMR7273 Aix-Marseille Université, CNRS Campus Universitaire de Saint-Jérôme 52 Avenue Escadrille Normandie Niemen 13013 Marseille France
| | - Lukáš Palatinus
- Institute of Physics of the AS CR v.v.i., Na Slovance 2 182 21 Prague Czech Republic
| | - Wolfgang Hornfeck
- Institute of Physics of the AS CR v.v.i., Na Slovance 2 182 21 Prague Czech Republic
| | - Jean‐Louis Paillaud
- Institut de Science des Matériaux de Mulhouse (IS2M) UMR 7361 CNRS Université de Haute-Alsace 68100 Mulhouse France
- Université de Strasbourg Strasbourg France
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Brázda P, Palatinus L, Babor M. Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal. Science 2019; 364:667-669. [PMID: 31097664 DOI: 10.1126/science.aaw2560] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/03/2019] [Indexed: 01/19/2023]
Abstract
Determination of the absolute configuration of organic molecules is essential in drug development and the subsequent approval process. We show that this determination is possible through electron diffraction using nanocrystalline material. Ab initio structure determination by electron diffraction has so far been limited to compounds that maintain their crystallinity after a dose of one electron per square angstrom or more. We present a complete structure analysis of a pharmaceutical cocrystal of sofosbuvir and l-proline, which is about one order of magnitude less stable. Data collection on multiple positions of a crystal and an advanced-intensity extraction procedure enabled us to solve the structure ab initio. We further show that dynamical diffraction effects are strong enough to permit unambiguous determination of the absolute structure of material composed of light scatterers.
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Affiliation(s)
- Petr Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 18200 Prague 8, Czech Republic.
| | - Lukáš Palatinus
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 18200 Prague 8, Czech Republic
| | - Martin Babor
- University of Chemistry and Technology, Technická 3, 16628 Prague 6, Czech Republic.,Zentiva, U Kabelovny 130, 10237 Prague 10, Czech Republic
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Smeets S, Zones SI, Xie D, Palatinus L, Pascual J, Hwang S, Schmidt JE, McCusker LB. SSZ-27: A Small-Pore Zeolite with Large Heart-Shaped Cavities Determined by Using Multi-crystal Electron Diffraction. Angew Chem Int Ed Engl 2019; 58:13080-13086. [PMID: 31347746 PMCID: PMC6773097 DOI: 10.1002/anie.201905049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 11/10/2022]
Abstract
The high-silica zeolite SSZ-27 was synthesized using one of the isomers of the organic structure-directing agent that is known to produce the large-pore zeolite SSZ-26 (CON). The structure of the as-synthesized form was solved using multi-crystal electron diffraction data. Data were collected on eighteen crystals, and to obtain a high-quality and complete data set for structure refinement, hierarchical cluster analysis was employed to select the data sets most suitable for merging. The framework structure of SSZ-27 can be described as a combination of two types of cavities, one of which is shaped like a heart. The cavities are connected through shared 8-ring windows to create straight channels that are linked together in pairs to form a one-dimensional channel system. Once the framework structure was known, molecular modelling was used to find the best fitting isomer, and this, in turn, was isolated to improve the synthesis conditions for SSZ-27.
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Affiliation(s)
- Stef Smeets
- Department of Materials and Environmental ChemistryStockholm University10691StockholmSweden
- Kavli Institute of NanoscienceDelft University of Technology2629HZDelftThe Netherlands
| | | | - Dan Xie
- Chevron Energy Technology CompanyRichmondCA94802USA
| | - Lukáš Palatinus
- Institute of Physics of the Czech Academy of SciencesNa Slovance 2PragueCzech Republic
| | | | - Son‐Jong Hwang
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCA91125USA
| | | | - Lynne B. McCusker
- Department of MaterialsETH ZurichVladimir-Prelog-Weg 58093ZurichSwitzerland
- Department of Chemical EngineeringUniversity of California, Santa BarbaraCA93106USA
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Smeets S, Zones SI, Xie D, Palatinus L, Pascual J, Hwang S, Schmidt JE, McCusker LB. SSZ‐27: A Small‐Pore Zeolite with Large Heart‐Shaped Cavities Determined by Using Multi‐crystal Electron Diffraction. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Stef Smeets
- Department of Materials and Environmental Chemistry Stockholm University 10691 Stockholm Sweden
- Kavli Institute of Nanoscience Delft University of Technology 2629 HZ Delft The Netherlands
| | | | - Dan Xie
- Chevron Energy Technology Company Richmond CA 94802 USA
| | - Lukáš Palatinus
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2 Prague Czech Republic
| | - Jesus Pascual
- Chevron Energy Technology Company Richmond CA 94802 USA
| | - Son‐Jong Hwang
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA 91125 USA
| | | | - Lynne B. McCusker
- Department of Materials ETH Zurich Vladimir-Prelog-Weg 5 8093 Zurich Switzerland
- Department of Chemical Engineering University of California, Santa Barbara CA 93106 USA
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Palatinus L, Brázda P, Jelínek M, Hrdá J, Steciuk G, Klementová M. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Crystallogr B Struct Sci Cryst Eng Mater 2019; 75:512-522. [DOI: 10.1107/s2052520619007534] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/23/2019] [Indexed: 11/10/2022]
Abstract
Electron diffraction tomography (EDT) data are in many ways similar to X-ray diffraction data. However, they also present certain specifics. One of the most noteworthy is the specific rocking curve observed for EDT data collected using the precession electron diffraction method. This double-peaked curve (dubbed `the camel') may be described with an approximation based on a circular integral of a pseudo-Voigt function and used for intensity extraction by profile fitting. Another specific aspect of electron diffraction data is the high likelihood of errors in the estimation of the crystal orientation, which may arise from the inaccuracies of the goniometer reading, crystal deformations or crystal movement during the data collection. A method for the refinement of crystal orientation for each frame individually is proposed based on the least-squares optimization of simulated diffraction patterns. This method provides typical angular accuracy of the frame orientations of less than 0.05°. These features were implemented in the computer program PETS 2.0. The implementation of the complete data processing workflow in the program PETS and the incorporation of the features specific for electron diffraction data is also described.
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Affiliation(s)
- Joke Hadermann
- Department of Physics, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Lukáš Palatinus
- Institute of Physics of the AS CR, v.v.i, Cukrovarnicka 10, 162 00 Prague 6, Czech Republic
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Steciuk G, David A, Petříček V, Palatinus L, Mercey B, Prellier W, Pautrat A, Boullay P. Precession electron diffraction tomography on twinned crystals: application to CaTiO 3 thin films. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719005569] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Strain engineering via epitaxial thin-film synthesis is an efficient way to modify the crystal structure of a material in order to induce new features or improve existing properties. One of the challenges in this approach is to quantify structural changes occurring in these films. While X-ray diffraction is the most widely used technique for obtaining accurate structural information from bulk materials, severe limitations appear in the case of epitaxial thin films. This past decade, precession electron diffraction tomography has emerged as a relevant technique for the structural characterization of nano-sized materials. While its usefulness has already been demonstrated for solving the unknown structure of materials deposited in the form of thin films, the frequent existence of orientation variants within the film introduces a severe bias in the structure refinement, even when using the dynamical diffraction theory to calculate diffracted intensities. This is illustrated here using CaTiO3 films deposited on SrTiO3 substrates as a case study. By taking into account twinning in the structural analysis, it is shown that the structure of the CaTiO3 films can be refined with an accuracy comparable to that obtained by dynamical refinement from non-twinned data. The introduction of the possibility to handle twin data sets is undoubtedly a valuable add-on and, notably, paves the way for a successful use of precession electron diffraction tomography for accurate structural analyses of thin films.
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Wiedemann D, Lüdtke T, Palatinus L, Willinger E, Willinger MG, Mühlbauer MJ, Lerch M. At the Gates: The Tantalum-Rich Phase Hf 3Ta 2O 11 and its Commensurately Modulated Structure. Inorg Chem 2018; 57:14435-14442. [PMID: 30379071 DOI: 10.1021/acs.inorgchem.8b02642] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Generic mixtures in the system (Zr,Hf)O2-(Nb,Ta)2O5 are employed as tunable gate materials for field-effect transistors. Whereas production processes and target compositions are well-defined, resulting crystal structures are vastly unexplored. In this study, we summarize the sparse reported findings and present the new phase Hf3Ta2O11 as synthesized via a sol-gel route. Its commensurately modulated structure represents the hitherto unknown, metal(V)-richest member of the family (Zr,Hf) x(Nb,Ta)2O2 x+5. Based on electron, neutron, and X-ray diffraction, the crystal structure is described within modern superspace [Hf1.2Ta0.8O4.4, Z = 2, a = 4.7834(13), b = 5.1782(17), c = 5.064(3) Å, q = 1/5 c*, orthorhombic, superspace group Xmcm(00γ) s00] and supercell formalisms [Hf3Ta2O11, Z = 4, a = 4.7834(13), b = 5.1782(17), c = 25.320(13) Å, orthorhombic, space group Pbnm]. Transmission electron microscopy shows the microscopic structure from film-like aggregates down to atomic resolution. Cation ordering within the different available coordination environments is possible, but no significant hint at it is found within the limits of standard diffraction techniques. Hf3Ta2O11 is an unpredicted compound in the above-mentioned oxide systems, in which stability ranges have been disputably fuzzy and established only by syntheses via solid-state routes so far.
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Affiliation(s)
- Dennis Wiedemann
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | - Tobias Lüdtke
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | - Lukáš Palatinus
- Institute of Physics , Czech Academy of Sciences , 18221 Prague 8 , Czech Republic
| | - Elena Willinger
- Abteilung Anorganische Chemie , Fritz-Haber-Institut , 14195 Berlin , Germany
| | - Marc G Willinger
- Abteilung Anorganische Chemie , Fritz-Haber-Institut , 14195 Berlin , Germany
| | - Martin J Mühlbauer
- Heinz Maier-Leibnitz Zentrum (MLZ) , Technische Universität München , 85747 Garching , Germany
| | - Martin Lerch
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
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Palatinus L. Crystallography in the 21st century: the age of electron? Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318095268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Steciuk G, Chateigner D, Palatinus L. Unravelling the structure of vaterite using precession electron diffraction tomography. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318090277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Palatinus L, Brázda P. Riding the camel: the double-peaked rocking curve and its use in the processing of precession electron diffraction data. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318090460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Bowden D, Krysiak Y, Palatinus L, Tsivoulas D, Plana-Ruiz S, Sarakinou E, Kolb U, Stewart D, Preuss M. A high-strength silicide phase in a stainless steel alloy designed for wear-resistant applications. Nat Commun 2018; 9:1374. [PMID: 29636474 PMCID: PMC5893616 DOI: 10.1038/s41467-018-03875-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/20/2018] [Indexed: 11/09/2022] Open
Abstract
Hardfacing alloys provide strong, wear-resistant and corrosion-resistant coatings for extreme environments such as those within nuclear reactors. Here, we report an ultra-high-strength Fe-Cr-Ni silicide phase, named π-ferrosilicide, within a hardfacing Fe-based alloy. Electron diffraction tomography has allowed the determination of the atomic structure of this phase. Nanohardness testing indicates that the π-ferrosilicide phase is up to 2.5 times harder than the surrounding austenite and ferrite phases. The compressive strength of the π-ferrosilicide phase is exceptionally high and does not yield despite loading in excess of 1.6 GPa. Such a high-strength silicide phase could not only provide a new type of strong, wear-resistant and corrosion-resistant Fe-based coating, replacing more costly and hazardous Co-based alloys for nuclear applications, but also lead to the development of a new class of high-performance silicide-strengthened stainless steels, no longer reliant on carbon for strengthening.
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Affiliation(s)
- D Bowden
- School of Materials, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Y Krysiak
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University Mainz, Jakob-Welder-Weg 11, 55099, Mainz, Germany
| | - L Palatinus
- Academy of Sciences of the Czech Republic, Institute of Physics, Na Slovance 2, 18040, Praha 8, Czech Republic
| | - D Tsivoulas
- School of Materials, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Wood plc, 601 Faraday Street, Birchwood Park, Warrington, WA3 6GN, UK
| | - S Plana-Ruiz
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University Mainz, Jakob-Welder-Weg 11, 55099, Mainz, Germany.,LENS, MIND/IN2UB, Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona, Martí i Franquès, 1-11, 08028, Barcelona, Catalonia, Spain
| | - E Sarakinou
- School of Materials, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Interface Analysis Centre, University of Bristol, Bristol, BS8 1TL, UK
| | - U Kolb
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University Mainz, Jakob-Welder-Weg 11, 55099, Mainz, Germany
| | - D Stewart
- Rolls-Royce plc, Derby, DE24 8BJ, UK
| | - M Preuss
- School of Materials, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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Mayorga-Martinez CC, Sofer Z, Luxa J, Huber Š, Sedmidubský D, Brázda P, Palatinus L, Mikulics M, Lazar P, Medlín R, Pumera M. TaS 3 Nanofibers: Layered Trichalcogenide for High-Performance Electronic and Sensing Devices. ACS Nano 2018; 12:464-473. [PMID: 29227684 DOI: 10.1021/acsnano.7b06853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Layered materials, like transition metal dichalcogenides, exhibit broad spectra with outstanding properties with huge application potential, whereas another group of related materials, layered transition metal trichalcogenides, remains unexplored. Here, we show the broad application potential of this interesting structural type of layered tantalum trisulfide prepared in a form of nanofibers. This material shows tailorable attractive electronic properties dependent on the tensile strain applied to it. Structure of this so-called orthorhombic phase of TaS3 grown in a form of long nanofibers has been solved and refined. Taking advantage of these capabilities, we demonstrate a highly specific impedimetric NO gas sensor based on TaS3 nanofibers as well as construction of photodetectors with excellent responsivity and field-effect transistors. Various flexible substrates were used for the construction of a NO gas sensor. Such a device exhibits a low limit of detection of 0.48 ppb, well under the allowed value set by environmental agencies for NOx (50 ppb). Moreover, this NO gas sensor also showed excellent selectivity in the presence of common interferences formed during fuel combustion. TaS3 nanofibers produced in large scale exhibited excellent broad application potential for various types of devices covering nanoelectronic, optoelectronic, and gas-sensing applications.
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Affiliation(s)
- Carmen C Mayorga-Martinez
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences Nanyang Technological University , Nanyang Link 21, Singapore 637371
| | - Zdeněk Sofer
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague 6, Czech Republic
| | - Jan Luxa
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague 6, Czech Republic
| | - Štěpán Huber
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague 6, Czech Republic
| | - David Sedmidubský
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague 6, Czech Republic
| | - Petr Brázda
- Institute of Physics of the CAS , v.v.i., Na Slovance 2, 182 00 Prague 8, Czech Republic
| | - Lukáš Palatinus
- Institute of Physics of the CAS , v.v.i., Na Slovance 2, 182 00 Prague 8, Czech Republic
| | - Martin Mikulics
- Peter Grünberg Institute (PGI-9), Forschungszentrum Jülich, and Jülich-Aachen Research Alliance, JARA, Fundamentals of Future Information Technology, D-52425 Jülich, Germany
| | - Petr Lazar
- Department of Physical Chemistry and Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc , tř. 17. Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Rostislav Medlín
- New Technologies - Research Centre, University of West Bohemia , Univerzitní 8, 306 14 Plzeň, Czech Republic
| | - Martin Pumera
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences Nanyang Technological University , Nanyang Link 21, Singapore 637371
- Department of Inorganic Chemistry, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague 6, Czech Republic
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Antunes Correa C, Poupon M, Pérez O, Král R, Zemenová P, Lecourt J, Kopeček J, Brázda P, Klementová M, Palatinus L. Phase transitions and crystal structures of η′′-Cu (3+x)Si and η′′′-Cu (3+x)Si. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317084522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Palatinus L, Brázda P, Boullay P, Perez O, Klementová M, Petit S, Eigner V, Zaarour M, Mintova S. Hydrogen positions in single nanocrystals revealed by electron diffraction. Science 2017; 355:166-169. [PMID: 28082587 DOI: 10.1126/science.aak9652] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/22/2016] [Indexed: 01/18/2023]
Abstract
The localization of hydrogen atoms is an essential part of crystal structure analysis, but it is difficult because of their small scattering power. We report the direct localization of hydrogen atoms in nanocrystalline materials, achieved using the recently developed approach of dynamical refinement of precession electron diffraction tomography data. We used this method to locate hydrogen atoms in both an organic (paracetamol) and an inorganic (framework cobalt aluminophosphate) material. The results demonstrate that the technique can reliably reveal fine structural details, including the positions of hydrogen atoms in single crystals with micro- to nanosized dimensions.
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Affiliation(s)
- L Palatinus
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, Prague, Czech Republic.
| | - P Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, Prague, Czech Republic
| | - P Boullay
- CRISMAT (Laboratoire de Cristallographie et Sciences des Matériaux), Normandie Université, ENSICAEN (Ecole Nationale Supérieure d'Ingénieurs de Caen), UNICAEN (Université de Caen), CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Caen, France.
| | - O Perez
- CRISMAT (Laboratoire de Cristallographie et Sciences des Matériaux), Normandie Université, ENSICAEN (Ecole Nationale Supérieure d'Ingénieurs de Caen), UNICAEN (Université de Caen), CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Caen, France
| | - M Klementová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, Prague, Czech Republic
| | - S Petit
- CRISMAT (Laboratoire de Cristallographie et Sciences des Matériaux), Normandie Université, ENSICAEN (Ecole Nationale Supérieure d'Ingénieurs de Caen), UNICAEN (Université de Caen), CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Caen, France
| | - V Eigner
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, Prague, Czech Republic
| | - M Zaarour
- LCS (Laboratoire Catalyse et Spectrochimie), Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6506, 6 Bd Maréchal Juin, F-14050 Caen, France
| | - S Mintova
- LCS (Laboratoire Catalyse et Spectrochimie), Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6506, 6 Bd Maréchal Juin, F-14050 Caen, France
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Corrêa CA, Perez O, Kopeček J, Brázda P, Klementová M, Palatinus L. Crystal structures of η''-Cu 3+xSi and η'''-Cu 3+xSi. Acta Crystallogr B Struct Sci Cryst Eng Mater 2017; 73:767-774. [PMID: 28762986 DOI: 10.1107/s2052520617006163] [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] [Received: 01/09/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
The binary phase diagram of Cu-Si is unexpectedly complex in the vicinity of Cu3+xSi. The low-temperature region contains three closely related incommensurately modulated phases denoted, in order of increasing temperature of stability, η''', η'' and η'. The structure analysis of η' has been reported previously [Palatinus et al. (2011). Inorg. Chem. 50, 3743]. Here the structure model for the phases η'' and η''' is reported. The structures could be solved in superspace, but no superspace structure model could be constructed due to the complexity of the modulation functions. Therefore, the structures were described in a supercell approximation, which involved a 4 × 4 × 3 supercell for the η'' phase and a 14 × 14 × 3 supercell for the η''' phase. Both structures are very similar and differ only by a subtle symmetry lowering from η'' to η'''. A comparison of the structure models of η'' and η''' with the reported structure of η' suggests that the reported structure model of η' contains an incorrect assignment of atomic types.
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Affiliation(s)
| | - Olivier Perez
- CRISMAT, Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6508, 6 Bd Marechal Juin, F-14050 Caen Cedex 4, France
| | - Jaromír Kopeček
- Institute of Physics of the AS CR, Na Slovance 2, Prague, Czechia
| | - Petr Brázda
- Institute of Physics of the AS CR, Na Slovance 2, Prague, Czechia
| | | | - Lukáš Palatinus
- Institute of Physics of the AS CR, Na Slovance 2, Prague, Czechia
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Zaarour M, Perez O, Boullay P, Martens J, Mihailova B, Karaghiosoff K, Palatinus L, Mintova S. Synthesis of new cobalt aluminophosphate framework by opening a cobalt methylphosphonate layered material. CrystEngComm 2017. [DOI: 10.1039/c7ce01129f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly stable, cobalt rich, template free Co–AlPO material was prepared by opening the structure of CoMeP under hydrothermal treatment in the presence of aluminium.
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Affiliation(s)
- Moussa Zaarour
- Laboratoire Catalyse et Spectrochimie
- Normandie Université
- CNRS
- ENSICAEN
- 14000 Caen
| | | | | | - Jörn Martens
- Department of Chemistry
- Ludwig-Maximilians-Universität München (LMU)
- Munich
- Germany
| | - Boriana Mihailova
- Mineralogisch-Petrographisches Institut
- University of Hamburg
- D-20146 Hamburg
- Germany
| | | | | | - Svetlana Mintova
- Laboratoire Catalyse et Spectrochimie
- Normandie Université
- CNRS
- ENSICAEN
- 14000 Caen
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Corrêa CA, Brázda P, Kopeček J, Klementová M, Palatinus L. Incommensurately modulated crystal structures of Cu 3Si. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316098521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Wallen CM, Palatinus L, Bacsa J, Scarborough CC. Hydrogen Peroxide Coordination to Cobalt(II) Facilitated by Second-Sphere Hydrogen Bonding. Angew Chem Int Ed Engl 2016; 55:11902-6. [PMID: 27560462 DOI: 10.1002/anie.201606561] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 07/06/2016] [Indexed: 11/11/2022]
Abstract
M(H2 O2 ) adducts have been postulated as intermediates in biological and industrial processes; however, only one observable M(H2 O2 ) adduct has been reported, where M is redox-inactive zinc. Herein, direct solution-phase detection of an M(H2 O2 ) adduct with a redox-active metal, cobalt(II), is described. This Co(II) (H2 O2 ) compound is made observable by incorporating second-sphere hydrogen-bonding interactions between bound H2 O2 and the supporting ligand, a trianionic trisulfonamido ligand. Thermodynamics of H2 O2 binding and decay kinetics of the Co(II) (H2 O2 ) species are described, as well as the reaction of this Co(II) (H2 O2 ) species with Group 2 cations.
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Affiliation(s)
- Christian M Wallen
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
| | - Lukáš Palatinus
- Department of Structure Analysis, Institute of Physics of the AS CR, Prague, Czechia
| | - John Bacsa
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
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Abstract
The combination of PXRD and ED is applied to determine modulated structures which resist solution by more conventional methods.
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Affiliation(s)
- Zhengyang Zhou
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- People's Republic of China
- College of Chemistry and Chemical Engineering
| | - Lukáš Palatinus
- Institute of Physics of the CAS
- v.v.i
- 182 21 Prague
- Czech Republic
| | - Junliang Sun
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- People's Republic of China
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Palatinus L, Corrêa CA, Steciuk G, Jacob D, Roussel P, Boullay P, Klementová M, Gemmi M, Kopeček J, Domeneghetti MC, Cámara F, Petříček V. Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data. Acta Crystallogr B Struct Sci Cryst Eng Mater 2015; 71:740-51. [DOI: 10.1107/s2052520615017023] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022]
Abstract
The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235–244] has been applied to a set of experimental data sets from five different samples – Ni2Si, PrVO3, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.
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Palatinus L, Correa CA, Boullay P, Steciuk G, Gemmi M, Jacob D, Klementová M, Roussel P. Accurate structure refinement from electron diffraction tomography data. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315099192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Corrêa CA, Klementová M, Palatinus L. Dynamically refined PEDT of Ni 2Si compared to XRD. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315093973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brázda P, Palatinus L, Klementová M, Buršík J, Knížek K. Mapping of reciprocal space of La0.30CoO2 in 3D: Analysis of superstructure diffractions and intergrowths with Co3O4. J SOLID STATE CHEM 2015. [DOI: 10.1016/j.jssc.2015.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Palatinus L. Taking a closer look for a broader view: combining powder diffraction with electron crystallography for a better understanding of modulated structures. Acta Crystallogr B Struct Sci Cryst Eng Mater 2015; 71:125-126. [PMID: 25827365 DOI: 10.1107/s2052520615005910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 06/04/2023]
Abstract
Electron crystallography has made enormous progress over the last decade. It can provide the necessary information that complements powder diffraction data and allows for successful structure analysis of (not only) modulated structures.
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Affiliation(s)
- Lukáš Palatinus
- Department of Structure Analysis, Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague, Czech Republic
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Palatinus L, Petříček V, Corrêa CA. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Crystallogr A Found Adv 2015; 71:235-44. [DOI: 10.1107/s2053273315001266] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/21/2015] [Indexed: 05/28/2023]
Abstract
Accurate structure refinement from electron-diffraction data is not possible without taking the dynamical-diffraction effects into account. A complete three-dimensional model of the structure can be obtained only from a sufficiently complete three-dimensional data set. In this work a method is presented for crystal structure refinement from the data obtained by electron diffraction tomography, possibly combined with precession electron diffraction. The principle of the method is identical to that used in X-ray crystallography: data are collected in a series of small tilt steps around a rotation axis, then intensities are integrated and the structure is optimized by least-squares refinement against the integrated intensities. In the dynamical theory of diffraction, the reflection intensities exhibit a complicated relationship to the orientation and thickness of the crystal as well as to structure factors of other reflections. This complication requires the introduction of several special parameters in the procedure. The method was implemented in the freely available crystallographic computing systemJana2006.
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Corrêa C, Klementová M, Palatinus L. Structural analysis of Ni 3Si 2by EDT and dynamical refinement. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314096272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Transition metal silicides are known for properties such as low resistivity, high melting point, low cost and low toxicity, which are of great interest for applications in current silicon nanotechnology such as nano-complementary metal-oxide semiconductor (CMOS) devices, photovoltaics and ohmic contacts. In all these technologies the materials are used on nanoscale. To gain better insight into their properties, it is necessary to be able to determine the structure of the nanoparticles of these materials. Electron diffraction tomography combined with the precession electron diffraction (PED) are ideal techniques for structural analysis of nanocrystals. In this work Ni3Si2 nanowires with diameter of 25 nm were analyzed by EDT both with and without PED. The structure was refined using the kinematical and dynamical diffraction theory. The results show that the best results can be obtained of EDT and PED.
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Palatinus L, Corrêa C, Mouillard G, Boullay P, Jacob D. Accurate structure refinement from 3D electron diffraction data. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314096259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Structure determination from electron diffraction data has seen an enormous progress over the past few years. At present, complex structures with hundreds of atoms in the unit cell can be solved from electron diffraction using the concept of electron diffraction tomography (EDT), possibly combined with precession electron diffraction (PED) [1]. Unfortunately, the initial model is typically optimized using the kinematical approximation to calculate model diffracted intensities. This approximation is quite inaccurate for electron diffraction and leads to high figures of merit and inaccurate results with unrealistically low standard uncertainties. The obvious remedy to the problem is the use of dynamical diffraction theory to calculate the model intensities in structure refinement. This technique has been known and used before, but it has not become very popular, because good fits could be obtained only for sufficiently perfect and sufficiently thin crystals. It has been shown recently on several zone-axis patterns [2] that the quality of the refinement can be improved by using precession electron diffraction. In the present contribution we demonstrate that the same approach can be successfully used to refine crystal structures against non-oriented patterns acquired by EDT combined with PED (PEDT in short). Because the PEDT technique provides three-dimensional diffraction information, it can be used for a complete structure refinement. Several test examples demonstrate that the dynamical structure refinement yields better figures of merit and more accurate results than the refinement using kinematical approximation.
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Abstract
Abstract
JANA2006 is a freely available program for structure determination of standard, modulated and magnetic samples based on X-ray or neutron single crystal/ powder diffraction or on electron diffraction. The system has been developed for 30 years from specialized tool for refinement of modulated structures to a universal program covering standard as well as advanced crystallography. The aim of this article is to describe the basic features of JANA2006 and explain its scope and philosophy. It will also serve as a basis for future publications detailing tools and methods of JANA.
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Affiliation(s)
- Václav Petříček
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Na Slovance 2, 180 40 Praha 8, Czech Republic
| | - Michal Dušek
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Na Slovance 2, 180 40 Praha 8, Czech Republic
| | - Lukáš Palatinus
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i., Na Slovance 2, 180 40 Praha 8, Czech Republic
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Ackerbauer SV, Borrmann H, Bürgi HB, Flack HD, Grin Y, Linden A, Palatinus L, Schweizer WB, Warshamanage R, Wörle M. TiGePt--a study of Friedel differences. Acta Crystallogr B Struct Sci Cryst Eng Mater 2013; 69:457-464. [PMID: 24056354 DOI: 10.1107/s2052519213021635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/02/2013] [Indexed: 06/02/2023]
Abstract
The X-ray single-crystal diffraction intensities of the intermetallic compound TiGePt were analysed. These showed beyond doubt that the crystal structure is non-centrosymmetric. The analysis revolves around the resonant-scattering contribution to differences in intensity between Friedel opposites hkl and \bar h\bar k\bar l. The following techniques were used: R(merge) factors on the average (A) and difference (D) of Friedel opposites; statistical estimates of the resonant-scattering contribution to Friedel opposites; plots of 2A(obs) against 2A(model) and of D(obs) against D(model); the antisymmetric D-Patterson function. Moreover it was possible to show that a non-standard atomic model was unnecessary to describe TiGePt. Two data sets are compared. That measured with Ag Kα radiation at 295 K to a resolution of 1.25 Å(-1) is less conclusive than the one measured with Mo Kα radiation at 100 K to the lower resolution of 0.93 Å(-1). This result is probably due to the fact that the resonant scattering of Pt is larger for Mo Kα than for AgKα radiation.
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Affiliation(s)
- Sarah Virginia Ackerbauer
- Chemische Metallkunde, Max-Planck-Institut für Chemische Physik fester Stoffe, Nöthnitzer Strasse 40, D-01187 Dresden, Germany
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Palatinus L, Jacob D, Cuvillier P, Klementová M, Sinkler W, Marks LD. Structure refinement from precession electron diffraction data. Acta Crystallogr A 2013; 69:171-88. [PMID: 23403968 DOI: 10.1107/s010876731204946x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [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: 07/27/2012] [Accepted: 12/02/2012] [Indexed: 11/10/2022] Open
Abstract
Electron diffraction is a unique tool for analysing the crystal structures of very small crystals. In particular, precession electron diffraction has been shown to be a useful method for ab initio structure solution. In this work it is demonstrated that precession electron diffraction data can also be successfully used for structure refinement, if the dynamical theory of diffraction is used for the calculation of diffracted intensities. The method is demonstrated on data from three materials - silicon, orthopyroxene (Mg,Fe)(2)Si(2)O(6) and gallium-indium tin oxide (Ga,In)(4)Sn(2)O(10). In particular, it is shown that atomic occupancies of mixed crystallographic sites can be refined to an accuracy approaching X-ray or neutron diffraction methods. In comparison with conventional electron diffraction data, the refinement against precession diffraction data yields significantly lower figures of merit, higher accuracy of refined parameters, much broader radii of convergence, especially for the thickness and orientation of the sample, and significantly reduced correlations between the structure parameters. The full dynamical refinement is compared with refinement using kinematical and two-beam approximations, and is shown to be superior to the latter two.
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Affiliation(s)
- Lukáš Palatinus
- Institute of Physics of the AS CR, v.v.i., Na Slovance 2, 182 21 Prague, Czech Republic.
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Abstract
The charge-flipping algorithm (CFA) is a member of the diverse family of dual-space iterative phasing algorithms. These algorithms use alternating modifications in direct and reciprocal space to find a solution to the phase problem. The current state-of-the-art CFA is reviewed and it is put in the context of related dual-space algorithms with relevance for crystallography. The CFA has found applications in many crystallographic problems. The principal applications in various fields are described with sections devoted to routine structure solution, the solution of complex structures from powder diffraction data, the solution of incommensurately modulated crystals and quasicrystals, macromolecular crystallography and single-particle imaging.
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Affiliation(s)
- Lukáš Palatinus
- Institute of Physics of the ASCR, v.v.i., Na Slovance 2, 18221 Prague, Czech Republic.
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Collet E, Watanabe H, Bréfuel N, Palatinus L, Roudaut L, Toupet L, Tanaka K, Tuchagues JP, Fertey P, Ravy S, Toudic B, Cailleau H. Aperiodic spin state ordering of bistable molecules and its photoinduced erasing. Phys Rev Lett 2012; 109:257206. [PMID: 23368495 DOI: 10.1103/physrevlett.109.257206] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 06/01/2023]
Abstract
We describe a novel type of ordering phenomenon associated with the incommensurate occupational modulation of bistable molecular magnetic state in a spin-crossover material. This unusual type of aperiodicity resulting from the ordering of multistable electronic states opens new possibilities for addressing such materials by light. Here we show that light can switch the crystal from four- to three-dimensional periodic structure. Mixing aperiodicity, multistability, and photoinduced phenomenà opens new perspectives for directing complex order and function in material science.
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Affiliation(s)
- E Collet
- Institut de Physique de Rennes, Université de Rennes I-CNRS, UMR 6251, F-35042 Rennes, France
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Palatinus L, Klementova M, Jacob D, Cuvillier P, Sinkler W, Marks L. Structure refinement against precession electron diffraction data. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312098844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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