1
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Carrillo-Cabrera W, Dreimann O, Grasser MA, Santra P, Kretschmer S, Krasheninnikov AV, Ruck M. Electron Diffraction Tomography on Two-Phase Nanolamellae of Topochemically Synthesized Cu(Sb 2S 3)Cl. Inorg Chem 2024. [PMID: 38850238 DOI: 10.1021/acs.inorgchem.4c01674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
The dark red semiconductor Cu(Sb2S3)Cl was obtained by leaching the layered precursor Cu(Sb2S3)[AlCl4] in a 0.1 M aqueous HCl solution. The selective extraction of AlCl3 yielded a mica-like lamellar product of poor crystallinity. Misalignment of lamellae down to the nanoscale prevented structure determination by conventional single-crystal X-ray diffraction, but a combination of transmission electron microscopy, selected area electron diffraction, and selected area electron precession diffraction tomography on a nanoscale spot with largely ordered crystalline lamellae revealed the crystal structures of two intergrown modifications. Orthorhombic o-Cu(Sb2S3)Cl and monoclinic m-Cu(Sb2S3)Cl have similar layers to the precursor and differ only in the stacking of the layers. These consist of uncharged Sb2S3 strands, whose sulfide ions, together with chloride ions, coordinate the copper(I) cations. Only one chloride ion remained from the [AlCl4]- group. DFT calculations confirm the structure solution for the orthorhombic form and suggest that the monoclinic structure is metastable against transformation to o-Cu(Sb2S3)Cl.
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Affiliation(s)
| | - Oliver Dreimann
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
| | - Matthias A Grasser
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
| | - Prosun Santra
- Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
| | | | | | - Michael Ruck
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
- Max Planck Institut für Chemische Physik fester Stoffe, 01187 Dresden, Germany
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2
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Sala A, Faye Diouf MD, Marchetti D, Pasquale L, Gemmi M. Mechanochemical Synthesis and Three-Dimensional Electron Diffraction Structure Solution of a Novel Cu-Based Protocatechuate Metal-Organic Framework. CRYSTAL GROWTH & DESIGN 2024; 24:3246-3255. [PMID: 38659659 PMCID: PMC11036354 DOI: 10.1021/acs.cgd.3c01494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 04/26/2024]
Abstract
Mechanochemical synthesis is a powerful approach to obtain new materials, limiting costs, and times. However, defected and submicrometrical-sized crystal products make critical their characterization through classical single-crystal X-ray diffraction. A valid alternative is represented by three-dimensional (3D) electron diffraction, in which a transmission electron microscope is used, like a diffractometer. This work matches a green water-based mechanochemical synthesis and 3D electron diffraction to obtain and characterize a Cu-based protocatechuate metal-organic framework (PC-MOF). Its structure has been fully refined through dynamical diffraction theory, and free water molecules could be detected in the channels of the framework. Thermal characterization, focused on the dehydration profile determination, leads to the formation of a novel high-temperature 2D coordination polymer, fully solved with 3D electron diffraction data. At last, the strong activity of the PC-MOF against cationic dyes like methylene blue has been reported.
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Affiliation(s)
- Andrea Sala
- Electron
Crystallography, Istituto Italiano di Tecnologia, viale Rinaldo Piaggio 34, Pontedera 56025, Italy
| | - Moussa D. Faye Diouf
- Electron
Crystallography, Istituto Italiano di Tecnologia, viale Rinaldo Piaggio 34, Pontedera 56025, Italy
- Dipartimento
di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Danilo Marchetti
- Electron
Crystallography, Istituto Italiano di Tecnologia, viale Rinaldo Piaggio 34, Pontedera 56025, Italy
- Dipartimento
di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Lea Pasquale
- Materials
Characterization Facility, Istituto Italiano
di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Mauro Gemmi
- Electron
Crystallography, Istituto Italiano di Tecnologia, viale Rinaldo Piaggio 34, Pontedera 56025, Italy
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3
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Bertocchi F, Marchetti D, Doria S, di Donato M, Sissa C, Gemmi M, Dalcanale E, Pinalli R, Lapini A. Tuning the Optical Properties Through Hydrogen Bond-assisted H-aggregate Formation: The ODIN Case. Chemistry 2024; 30:e202302619. [PMID: 37788976 DOI: 10.1002/chem.202302619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/05/2023]
Abstract
The current work focuses on the investigation of two functionalized naphthyridine derivatives, namely ODIN-EtPh and ODIN-But, to gain insights into the hydrogen bond-assisted H-aggregate formation and its impact on the optical properties of ODIN molecules. By employing a combination of X-ray and electron crystallography, absorption and emission spectroscopy, time resolved fluorescence and ultrafast pump-probe spectroscopy (visible and infrared) we unravel the correlation between the structure and light-matter response, with a particular emphasis on the influence of the polarity of the surrounding environment. Our experimental results and simulations confirm that in polar and good hydrogen-bond acceptor solvents (DMSO), the formation of dimers for ODIN derivatives is strongly inhibited. The presence of a phenyl group linked to the ureidic unit favors the folding of ODIN derivatives (forming an intramolecular hydrogen bond) leading to the stabilization of a charge-transfer excited state which almost completely quenches its fluorescence emission. In solvents with a poor aptitude for forming hydrogen bonds, the formation of dimers is favored and gives rise to H aggregates, with a consequent considerable reduction in the fluorescence emission. The urea-bound phenyl group furtherly stabilizes the dimers in chloroform.
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Affiliation(s)
- Francesco Bertocchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze17/A, 43124, Parma, Italy
| | - Danilo Marchetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze17/A, 43124, Parma, Italy
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, 56025, Pontedera, Italy
| | - Sandra Doria
- ICCOM-CNR, via Madonna del Piano 10, I-50019, Sesto Fiorentino, FI, Italy
- LENS (European Laboratory for Non-Linear Spectroscopy), Via N. Carrara 1, 5001, Sesto Fiorentino, FI, Italy
| | - Mariangela di Donato
- ICCOM-CNR, via Madonna del Piano 10, I-50019, Sesto Fiorentino, FI, Italy
- LENS (European Laboratory for Non-Linear Spectroscopy), Via N. Carrara 1, 5001, Sesto Fiorentino, FI, Italy
| | - Cristina Sissa
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze17/A, 43124, Parma, Italy
| | - Mauro Gemmi
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, 56025, Pontedera, Italy
| | - Enrico Dalcanale
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze17/A, 43124, Parma, Italy
| | - Roberta Pinalli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze17/A, 43124, Parma, Italy
| | - Andrea Lapini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze17/A, 43124, Parma, Italy
- LENS (European Laboratory for Non-Linear Spectroscopy), Via N. Carrara 1, 5001, Sesto Fiorentino, FI, Italy
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4
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Hogan-Lamarre P, Luo Y, Bücker R, Miller RJD, Zou X. STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials. IUCRJ 2024; 11:62-72. [PMID: 38038991 PMCID: PMC10833385 DOI: 10.1107/s2052252523009661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.
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Affiliation(s)
- Pascal Hogan-Lamarre
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
| | - Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
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5
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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 CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 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] [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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6
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Aleksich M, Paley DW, Schriber EA, Linthicum W, Oklejas V, Mittan-Moreau DW, Kelly RP, Kotei PA, Ghodsi A, Sierra RG, Aquila A, Poitevin F, Blaschke JP, Vakili M, Milne CJ, Dall'Antonia F, Khakhulin D, Ardana-Lamas F, Lima F, Valerio J, Han H, Gallo T, Yousef H, Turkot O, Bermudez Macias IJ, Kluyver T, Schmidt P, Gelisio L, Round AR, Jiang Y, Vinci D, Uemura Y, Kloos M, Hunter M, Mancuso AP, Huey BD, Parent LR, Sauter NK, Brewster AS, Hohman JN. XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates. J Am Chem Soc 2023; 145:17042-17055. [PMID: 37524069 DOI: 10.1021/jacs.3c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.
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Affiliation(s)
- Mariya Aleksich
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Elyse A Schriber
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Will Linthicum
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Vanessa Oklejas
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David W Mittan-Moreau
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ryan P Kelly
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Patience A Kotei
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Anita Ghodsi
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Johannes P Blaschke
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | | | | | | | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tamires Gallo
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- MAX IV Laboratory, Lund University, Box 118, SE-22100 Lund, Sweden
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | | | - Luca Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam R Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yifeng Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Doriana Vinci
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yohei Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Mark Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe University, Melbourne 3086, Australia
- Diamond Light Source, Harwell Science & Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Bryan D Huey
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Materials Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lucas R Parent
- Innovation Partnership Building, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - J Nathan Hohman
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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7
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Landers D, Clancy I, Weber D, Dunin-Borkowski RE, Stewart A. TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation. J Appl Crystallogr 2023; 56:1267-1276. [PMID: 37555218 PMCID: PMC10405588 DOI: 10.1107/s1600576723005174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/09/2023] [Indexed: 08/10/2023] Open
Abstract
An interactive simulation of a transmission electron microscope (TEM) called TEMGYM Basic is developed here, which enables users to understand how to operate and control an electron beam without the need to access an instrument. TEMGYM Basic allows users to familiarize themselves with alignment procedures offline, reducing the time and money required to become a proficient TEM operator. In addition to teaching the basics of electron beam alignments, the software enables users to create bespoke microscope configurations and develop an understanding of how to operate the configurations without sitting at a microscope. TEMGYM Basic also creates static ray diagram figures for a given lens configuration. The available components include apertures, lenses, quadrupoles, deflectors and biprisms. The software design uses first-order ray transfer matrices to calculate ray paths through each electron microscope component, and the program is developed entirely in Python to facilitate compatibility with machine-learning packages for future exploration of automated control.
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Affiliation(s)
- David Landers
- Department of Physics, University of Limerick, Limerick, Munster V94 T9PX, Ireland
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Ian Clancy
- Department of Physics, University of Limerick, Limerick, Munster V94 T9PX, Ireland
| | - Dieter Weber
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, North Rhine-Westphalia 52428, Germany
| | - Rafal E. Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, North Rhine-Westphalia 52428, Germany
| | - Andrew Stewart
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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8
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Prabhakaran A, Dhanabalan B, Andrusenko I, Pianetti A, Lauciello S, Prato M, Marras S, Solokha P, Gemmi M, Brovelli S, Manna L, Arciniegas MP. Stable Sn-Based Hybrid Perovskite-Related Structures with Tunable Color Coordinates via Organic Cations in Low-Temperature Synthesis. ACS ENERGY LETTERS 2023; 8:2630-2640. [PMID: 37324542 PMCID: PMC10262684 DOI: 10.1021/acsenergylett.3c00791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023]
Abstract
Organic-inorganic Pb-free layered perovskites are efficient broadband emitters and thus are promising materials for lighting applications. However, their synthetic protocols require a controlled atmosphere, high temperature, and long preparation time. This hinders the potential tunability of their emission through organic cations, as is instead common practice in Pb-based structures. Here, we present a set of Sn-Br layered perovskite-related structures that display different chromaticity coordinates and photoluminescence quantum yield (PLQY) up to 80%, depending on the choice of the organic monocation. We first develop a synthetic protocol that is performed under air and at 4 °C, requiring only a few steps. X-ray and 3D electron diffraction analyses show that the structures exhibit diverse octahedra connectivity (disconnected and face-sharing) and thus optical properties, while preserving the organic-inorganic layer intercalation. These results provide key insight into a previously underexplored strategy to tune the color coordinates of Pb-free layered perovskites through organic cations with complex molecular configurations.
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Affiliation(s)
- Aarya Prabhakaran
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università
degli Studi di Genova, Via Dodecaneso, 31, 16146 Genova, Italy
| | - Balaji Dhanabalan
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Iryna Andrusenko
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025 Pontedera, Italy
| | - Andrea Pianetti
- Dipartimento
di Scienza dei Materiali, Università
degli Studi di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Simone Lauciello
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Mirko Prato
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sergio Marras
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Pavlo Solokha
- Dipartimento
di Chimica e Chimica Industriale, Università
degli Studi di Genova, Via Dodecaneso, 31, 16146 Genova, Italy
| | - Mauro Gemmi
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025 Pontedera, Italy
| | - Sergio Brovelli
- Dipartimento
di Scienza dei Materiali, Università
degli Studi di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Liberato Manna
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Milena P. Arciniegas
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
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9
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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: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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10
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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: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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11
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Marchetti D, Portone F, Mezzadri F, Dalcanale E, Gemmi M, Pedrini A, Massera C. Selective and Reversible Solvent Uptake in Tetra-4-(4-pyridyl)phenylmethane-based Supramolecular Organic Frameworks. Chemistry 2022; 28:e202202977. [PMID: 36161363 PMCID: PMC10092063 DOI: 10.1002/chem.202202977] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 12/29/2022]
Abstract
The dynamic behavior of supramolecular organic frameworks (SOFs) based on the rigid tetra-4-(4-pyridyl)phenylmethane (TPPM) organic tecton has been elucidated through 3D electron diffraction, X-ray powder diffraction and differential scanning calorimetry (DSC) analysis. The SOF undergoes a reversible single-crystal-to-single-crystal transformation when exposed to vapours of selected organic solvents, moving from a closed structure with isolated small voids to an expanded structure with solvated channels along the b axis. The observed selectivity is dictated by the fitting of the guest in the expanded SOF, following the degree of packing coefficient. The effect of solvent uptake on TPPM solid-state fluorescence was investigated, evidencing a significant variation in the emission profile only in the presence of chloroform.
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Affiliation(s)
- Danilo Marchetti
- Department of Chemistry, Life Sciences and Environmental Sustainability INSTM UdR Parma, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy.,Center for Materials Interfaces Electron Crystallography, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Italy
| | - Francesca Portone
- Department of Chemistry, Life Sciences and Environmental Sustainability INSTM UdR Parma, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Francesco Mezzadri
- Department of Chemistry, Life Sciences and Environmental Sustainability INSTM UdR Parma, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Enrico Dalcanale
- Department of Chemistry, Life Sciences and Environmental Sustainability INSTM UdR Parma, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Mauro Gemmi
- Center for Materials Interfaces Electron Crystallography, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Italy
| | - Alessandro Pedrini
- Department of Chemistry, Life Sciences and Environmental Sustainability INSTM UdR Parma, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Chiara Massera
- Department of Chemistry, Life Sciences and Environmental Sustainability INSTM UdR Parma, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
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12
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Toso S, Imran M, Mugnaioli E, Moliterni A, Caliandro R, Schrenker NJ, Pianetti A, Zito J, Zaccaria F, Wu Y, Gemmi M, Giannini C, Brovelli S, Infante I, Bals S, Manna L. Halide perovskites as disposable epitaxial templates for the phase-selective synthesis of lead sulfochloride nanocrystals. Nat Commun 2022; 13:3976. [PMID: 35803933 PMCID: PMC9270429 DOI: 10.1038/s41467-022-31699-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/29/2022] [Indexed: 11/11/2022] Open
Abstract
Colloidal chemistry grants access to a wealth of materials through simple and mild reactions. However, even few elements can combine in a variety of stoichiometries and structures, potentially resulting in impurities or even wrong products. Similar issues have been long addressed in organic chemistry by using reaction-directing groups, that are added to a substrate to promote a specific product and are later removed. Inspired by such approach, we demonstrate the use of CsPbCl3 perovskite nanocrystals to drive the phase-selective synthesis of two yet unexplored lead sulfochlorides: Pb3S2Cl2 and Pb4S3Cl2. When homogeneously nucleated in solution, lead sulfochlorides form Pb3S2Cl2 nanocrystals. Conversely, the presence of CsPbCl3 triggers the formation of Pb4S3Cl2/CsPbCl3 epitaxial heterostructures. The phase selectivity is guaranteed by the continuity of the cationic subnetwork across the interface, a condition not met in a hypothetical Pb3S2Cl2/CsPbCl3 heterostructure. The perovskite domain is then etched, delivering phase-pure Pb4S3Cl2 nanocrystals that could not be synthesized directly. Phase-selective approaches, such using reaction-directing groups, are often seen in traditional organic chemistry and catalysis. Here authors use perovskite nanocrystals as disposable templates to drive the phase-selective synthesis of two colloidal nanomaterials, the lead sulfohalides Pb3S2Cl2 and Pb4S3Cl2.
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Affiliation(s)
- Stefano Toso
- Department of Nanochemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,International Doctoral Program in Science, Università Cattolica del Sacro Cuore, 25121, Brescia, Italy
| | - Muhammad Imran
- Department of Nanochemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.
| | - Enrico Mugnaioli
- Electron Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Italy
| | - Anna Moliterni
- Istituto di Cristallografia - Consiglio Nazionale delle Ricerche (IC-CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
| | - Rocco Caliandro
- Istituto di Cristallografia - Consiglio Nazionale delle Ricerche (IC-CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
| | - Nadine J Schrenker
- Electron Microscopy for Materials Science (EMAT) and NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Andrea Pianetti
- Dipartimento di Scienza dei Materiali, Università degli Studi di Milano-Bicocca, Via Roberto Cozzi 55, 20125, Milano, Italy
| | - Juliette Zito
- Department of Nanochemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Genova, Via Dodecaneso 31, 16146, Genova, Italy
| | - Francesco Zaccaria
- Department of Nanochemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Ye Wu
- Department of Nanochemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Mauro Gemmi
- Electron Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Italy.
| | - Cinzia Giannini
- Istituto di Cristallografia - Consiglio Nazionale delle Ricerche (IC-CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
| | - Sergio Brovelli
- Dipartimento di Scienza dei Materiali, Università degli Studi di Milano-Bicocca, Via Roberto Cozzi 55, 20125, Milano, Italy.
| | - Ivan Infante
- Department of Nanochemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.
| | - Sara Bals
- Electron Microscopy for Materials Science (EMAT) and NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.
| | - Liberato Manna
- Department of Nanochemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.
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13
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Zhang D, Zou XN, Wang XG, Su J, Luan TX, Fan W, Li PZ, Zhao Y. Highly Effective Photocatalytic Radical Reactions Triggered by a Photoactive Metal-Organic Framework. ACS APPLIED MATERIALS & INTERFACES 2022; 14:23518-23526. [PMID: 35537034 DOI: 10.1021/acsami.2c04331] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
On account of their inherent reactive properties, radical reactions play an important role in organic syntheses. The booming photochemistry provides a feasible approach to trigger the generation of radical intermediates in organic reaction processes. Thus, developing effective photocatalysts becomes the key step in radical reactions. In this work, the triphenylamine moiety with photoactivity is successfully embedded in a highly porous and stable metal-organic framework (MOF), and the obtained MOF, namely, Zr-TCA, naturally displays a photoactive property derived from the triphenylamine-based ligand. In photocatalytic studies, the triphenylamine-based Zr-TCA not only exhibits a high catalytic activity on the aerobic oxidation of sulfides via the generation of the superoxide radical anion (O2•-) under light irradiation but also shows good efficiency in the trifluoromethylation of arenes and heteroarenes by the formation of the trifluoromethyl radical (CF3•) as an intermediate. Moreover, the high performance of Zr-TCA can be well maintained over a wide range of substrates in these radical reactions, and the recycled Zr-TCA still retains its excellent photocatalytic activity. The high recyclability and catalytic efficiency to various substrates make the constructed triphenylamine-based Zr-TCA a promising photocatalyst in diverse radical reactions.
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Affiliation(s)
- Deshan Zhang
- School of Chemistry and Chemical Engineering, Shandong University, No. 27 Shanda South Road, Ji'nan 250100 Shandong Province, P. R. China
| | - Xin-Nan Zou
- School of Chemistry and Chemical Engineering, Shandong University, No. 27 Shanda South Road, Ji'nan 250100 Shandong Province, P. R. China
| | - Xiao-Ge Wang
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Jie Su
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Tian-Xiang Luan
- School of Chemistry and Chemical Engineering, Shandong University, No. 27 Shanda South Road, Ji'nan 250100 Shandong Province, P. R. China
| | - Weiliu Fan
- School of Chemistry and Chemical Engineering, Shandong University, No. 27 Shanda South Road, Ji'nan 250100 Shandong Province, P. R. China
| | - Pei-Zhou Li
- School of Chemistry and Chemical Engineering, Shandong University, No. 27 Shanda South Road, Ji'nan 250100 Shandong Province, P. R. China
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
- Science Center for Material Creation and Energy Conversion, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237 Shandong Province, P. R. China
| | - Yanli Zhao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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14
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Two New Organic Co-Crystals Based on Acetamidophenol Molecules. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Herein we present two new organic co-crystals obtained through a simple solution growth process based on an acetamidophenol molecule, either paracetamol or metacetamol, and on 7,7,8,8-tetracyanoquinodimethane (TCNQ). These co-crystals are part of a family of potential organic charge transfer complexes, where the acetamidophenol molecule behaves as an electron donor and TCNQ behaves as an electron acceptor. Due to the sub-micron size of the crystalline domains, 3D electron diffraction was employed for the structure characterization of both systems. Paracetamol-TCNQ structure was solved by standard direct methods, while the analysis of metacetamol-TCNQ was complicated by the low resolution of the available diffraction data and by the low symmetry of the system. The structure determination of metacetamol-TCNQ was eventually achieved after merging two data sets and combining direct methods with simulated annealing. Our study reveals that both paracetamol-TCNQ and metacetamol-TCNQ systems crystallize in a 1:1 stoichiometry, assembling in a mixed-stack configuration and adopting a non-centrosymmetric P1 symmetry. It appears that paracetamol and metacetamol do not form a strong structural scaffold based on hydrogen bonding, as previously observed for orthocetamol-TCNQ and orthocetamol-TCNB (1,2,4,5-tetracyanobenzene) co-crystals.
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15
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Chen P, Liu Y, Zhang C, Huang F, Liu L, Sun J. Crystalline Sponge Method by Three-Dimensional Electron Diffraction. Front Mol Biosci 2022; 8:821927. [PMID: 35198600 PMCID: PMC8859408 DOI: 10.3389/fmolb.2021.821927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
Abstract
The crystalline sponge method has shown to be a novel strategy for the structure determination of noncrystalline, oily, or trace amount of a compound. A target compound was absorbed and oriented orderly in the pregrown porous crystal for x-ray diffraction analysis. However, the diffusion in the micron-sized crystals is rather difficult. Lots of trial-and-error experiments are needed to optimize the guest-soaking process and to improve data quality. Nanocrystals are better in diffusion, yet it could not conduct a single crystal x-ray diffraction (SCXRD) analysis. Three-dimensional electron diffraction (3D-ED) is a powerful diffraction tool for the structure determination of small crystals. In this work, we successfully carried out the crystalline sponge method by 3D-ED technique using {(ZnI2)3-[2,4,6-tris(4-pyridyl)-1,3,5-triazine]2·x(guest)}n (1-Guest) porous complex nanocrystals. On account of the better diffuse ability of nanocrystals, the time needed for solvent exchange and guest soaking protocols are shortened 50-fold faster versus the original protocol. The crystal structure of the crystalline sponge incorporated with three different guests was fully resolved using a merged dataset. The structure model was identical to previously reported ones using x-ray, showing that the accuracy of the 3D-ED was comparable with SCXRD. The refinement results can also give the precise occupancy of the guest molecule soaked in the porous crystal. This work not only provides a new data collection strategy for crystalline sponge method but also demonstrates the potential of 3D-ED techniques to study host-guest interaction by solving the fine structure of porous material.
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Affiliation(s)
- Pohua Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yang Liu
- ReadCrystal Technology Co., Jiangsu, China
| | | | - Fei Huang
- ReadCrystal Technology Co., Jiangsu, China
| | | | - Junliang Sun
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- *Correspondence: Junliang Sun,
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16
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A Comparison of Structure Determination of Small Organic Molecules by 3D Electron Diffraction at Cryogenic and Room Temperature. Symmetry (Basel) 2021. [DOI: 10.3390/sym13112131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a rapid, accurate, and robust method for structure determination of submicron-sized crystals. 3D ED has mainly been applied in material science until 2013, when MicroED was developed for studying macromolecular crystals. MicroED was considered as a cryo-electron microscopy method, as MicroED data collection is usually carried out in cryogenic conditions. As a result, some researchers may consider that 3D ED/MicroED data collection on crystals of small organic molecules can only be performed in cryogenic conditions. In this work, we determined the structure for sucrose and azobenzene tetracarboxylic acid (H4ABTC). The structure of H4ABTC is the first crystal structure ever reported for this molecule. We compared data quality and structure accuracy among datasets collected under cryogenic conditions and room temperature. With the improvement in data quality by data merging, it is possible to reveal hydrogen atom positions in small organic molecule structures under both temperature conditions. The experimental results showed that, if the sample is stable in the vacuum environment of a transmission electron microscope (TEM), the data quality of datasets collected under room temperature is at least as good as data collected under cryogenic conditions according to various indicators (resolution, I/σ(I), CC1/2 (%), R1, Rint, ADRA).
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17
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Andrusenko I, Hamilton V, Lanza AE, Hall CL, Mugnaioli E, Potticary J, Buanz A, Gaisford S, Piras AM, Zambito Y, Hall SR, Gemmi M. Structure determination, thermal stability and dissolution rate of δ-indomethacin. Int J Pharm 2021; 608:121067. [PMID: 34481012 DOI: 10.1016/j.ijpharm.2021.121067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/17/2022]
Abstract
The structure solution of the δ-polymorph of indomethacin was obtained using three-dimensional electron diffraction. This form shows a significantly enhanced dissolution rate compared with the more common and better studied α- and γ-polymorphs, indicating better biopharmaceutical properties for medicinal applications. The structure was solved in non-centrosymmetric space group P21 and comprises two molecules in the asymmetric unit. Packing and molecule conformation closely resemble indomethacin methyl ester and indomethacin methanol solvate. Knowledge of the structure allowed the rational interpretation of spectroscopic IR and Raman data for δ-polymorph and a tentative interpretation for still unsolved indomethacin polymorphs. Finally, we observed a solid-solid transition from δ-polymorph to α-polymorph that can be driven by similarities in molecular conformation.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Victoria Hamilton
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Arianna E Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Charlie L Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Asma Buanz
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Simon Gaisford
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Anna M Piras
- Department of Pharmacy, University of Pisa, Via Bonanno 33, Pisa 56126, Italy
| | - Ylenia Zambito
- Department of Pharmacy, University of Pisa, Via Bonanno 33, Pisa 56126, Italy.
| | - Simon R Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy.
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18
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Steciuk G, Kiefer B, Hornfeck W, Kasatkin AV, Plášil J. Molybdenum Disorder in Hydrated Sedovite, Ideally U(MoO 4) 2· nH 2O, a Microporous Nanocrystalline Mineral Characterized by Three-Dimensional Electron Diffraction, Density Functional Theory Computations, and Complexity Analysis. Inorg Chem 2021; 60:15169-15179. [PMID: 34559506 DOI: 10.1021/acs.inorgchem.1c01506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sedovite, U4+(Mo6+O4)2·nH2O, is reported as being one of the earliest supergene minerals formed of the secondary zone. The difficulty of isolating enough pure material limits studies to techniques that can access the nanoscale combined with theoretical analyses. The crystal structure of sedovite has been solved and refined using the dynamical approach from three-dimensional electron diffraction data collected on natural nanocrystals found among iriginite. At 100 K, sedovite is monoclinic a ≈ 6.96 Å, b ≈ 9.07 Å, c ≈ 12.27 Å, and V ≈ 775 Å3 with space group C2/c. The microporous structure presents a characteristic framework built from uranium polyhedra and disordered Mo pyramids creating pore hosting water molecules. To confirm the formula U4+(Mo6+O4)2·nH2O, the possible presence of a hydroxyl group that would promote Mo5+ was tested with density functional theory (DFT) computations at the ambient temperature. DFT predicts that sedovite is a ferromagnetic insulator with a fundamental bandgap of Eg ∼ 1.7 eV with its chemical and physical properties dominated by U4+ rather than Mo6+. The structural complexity, IG,tot, of sedovite was evaluated in order to get indirect information about the missing formation conditions.
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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
| | - Boris Kiefer
- Department of Physics, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Wolfgang Hornfeck
- Department of Structure Analysis, Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, Prague 8 182 21, Czech Republic
| | - Anatoly V Kasatkin
- Fersman Mineralogical Museum of Russian Academy of Sciences, Leninsky Prospekt 18-2, 119071 Moscow, Russia
| | - 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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19
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Gruene T, Mugnaioli E. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Chem Rev 2021; 121:11823-11834. [PMID: 34533919 PMCID: PMC8517952 DOI: 10.1021/acs.chemrev.1c00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 01/26/2023]
Abstract
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.
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Affiliation(s)
- Tim Gruene
- University
of Vienna, Faculty of Chemistry,
Department of Inorganic Chemistry, AT-1090 Vienna, Austria
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, IT-56127 Pisa, Italy
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20
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Hall CL, Andrusenko I, Potticary J, Gao S, Liu X, Schmidt W, Marom N, Mugnaioli E, Gemmi M, Hall SR. 3D Electron Diffraction Structure Determination of Terrylene, a Promising Candidate for Intermolecular Singlet Fission. Chemphyschem 2021; 22:1631-1637. [PMID: 34117821 PMCID: PMC8457070 DOI: 10.1002/cphc.202100320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/05/2021] [Indexed: 12/13/2022]
Abstract
Herein we demonstrate the prowess of the 3D electron diffraction approach by unveiling the structure of terrylene, the third member in the series of peri‐condensed naphthalene analogues, which has eluded structure determination for 65 years. The structure was determined by direct methods using electron diffraction data and corroborated by dispersion‐inclusive density functional theory optimizations. Terrylene crystalizes in the monoclinic space group P21/a, arranging in a sandwich‐herringbone packing motif, similar to analogous compounds. Having solved the crystal structure, we use many‐body perturbation theory to evaluate the excited‐state properties of terrylene in the solid‐state. We find that terrylene is a promising candidate for intermolecular singlet fission, comparable to tetracene and rubrene.
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Affiliation(s)
- Charlie L Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Iryna Andrusenko
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Siyu Gao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xingyu Liu
- 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
| | - Enrico Mugnaioli
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Mauro Gemmi
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Simon R Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
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21
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22
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Duong NT, Aoyama Y, Kawamoto K, Yamazaki T, Nishiyama Y. Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments. Molecules 2021; 26:molecules26154652. [PMID: 34361806 PMCID: PMC8347922 DOI: 10.3390/molecules26154652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine.
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Affiliation(s)
- Nghia Tuan Duong
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | | | | | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
- JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
- Correspondence:
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23
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Bücker R, Hogan-Lamarre P, Miller RJD. Serial Electron Diffraction Data Processing With diffractem and CrystFEL. Front Mol Biosci 2021; 8:624264. [PMID: 34095217 PMCID: PMC8171297 DOI: 10.3389/fmolb.2021.624264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 04/28/2021] [Indexed: 12/03/2022] Open
Abstract
Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.
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Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - R J Dwayne Miller
- Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
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24
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Sekharan S, Liu X, Yang Z, Liu X, Deng L, Ruan S, Abramov Y, Sun G, Li S, Zhou T, Shi B, Zeng Q, Zeng Q, Chang C, Jin Y, Shi X. Selecting a stable solid form of remdesivir using microcrystal electron diffraction and crystal structure prediction. RSC Adv 2021; 11:17408-17412. [PMID: 35479679 PMCID: PMC9033196 DOI: 10.1039/d1ra03100g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/20/2022] Open
Abstract
Therapeutic options in response to the coronavirus disease 2019 (COVID-19) outbreak are urgently needed. In this communication, we demonstrate how to support selection of a stable solid form of an antiviral drug remdesivir in quick time using the microcrystal electron diffraction (MicroED) technique and a cloud-based and artificial intelligence implemented crystal structure prediction platform. We present the MicroED structures of remdesivir forms II and IV and conclude that form II is more stable than form IV at ambient temperature in agreement with experimental observations. The combined experimental and theoretical study can serve as a template for formulation scientists in the pharmaceutical industry.
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Affiliation(s)
| | - Xuetao Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Zhuocen Yang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xiang Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Li Deng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Shigang Ruan
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yuriy Abramov
- XtalPi Inc. 245 Main St, Floor 11 Cambridge MA 02142 USA
| | - GuangXu Sun
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Sizhu Li
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Tian Zhou
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Baime Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qun Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qiao Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Chao Chang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yingdi Jin
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xuekun Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
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25
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Three-Dimensional Electron Diffraction for Structural Analysis of Beam-Sensitive Metal-Organic Frameworks. CRYSTALS 2021. [DOI: 10.3390/cryst11030263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Electrons interact strongly with matter, which makes it possible to obtain high-resolution electron diffraction data from nano- and submicron-sized crystals. Using electron beam as a radiation source in a transmission electron microscope (TEM), ab initio structure determination can be conducted from crystals that are 6–7 orders of magnitude smaller than using X-rays. The rapid development of three-dimensional electron diffraction (3DED) techniques has attracted increasing interests in the field of metal-organic frameworks (MOFs), where it is often difficult to obtain large and high-quality crystals for single-crystal X-ray diffraction. Nowadays, a 3DED dataset can be acquired in 15–250 s by applying continuous crystal rotation, and the required electron dose rate can be very low (<0.1 e s−1 Å−2). In this review, we describe the evolution of 3DED data collection techniques and how the recent development of continuous rotation electron diffraction techniques improves data quality. We further describe the structure elucidation of MOFs using 3DED techniques, showing examples of using both low- and high-resolution 3DED data. With an improved data quality, 3DED can achieve a high accuracy, and reveal more structural details of MOFs. Because the physical and chemical properties of MOFs are closely associated with their crystal structures, we believe 3DED will only increase its importance in developing MOF materials.
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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] [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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27
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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] [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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28
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Andrusenko I, Potticary J, Hall SR, Gemmi M. A new olanzapine cocrystal obtained from volatile deep eutectic solvents and determined by 3D electron diffraction. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:1036-1044. [PMID: 33289715 DOI: 10.1107/s2052520620012779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 06/12/2023]
Abstract
A previously unknown cocrystal of olanzapine and phenol was identified from a volatile deep eutectic solvent as the intermediate species in the crystallization of olanzapine. This new nanocrystalline phase was investigated by electron diffraction, powder X-ray diffraction and differential scanning calorimetry. The structure was determined by simulated annealing using 3D electron diffraction data and confirmed using DFT-D optimizations. Olanzapine and phenol cocrystallize in the triclinic space group P1, supporting the hypothesis of a dimeric growth unit, where a centrosymmetric dimer is stabilized by multiple weak C-H...π interactions and forms double N-H...N hydrogen bonding with adjacent dimers.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Simon R Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
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29
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Mugnaioli E, Bonaccorsi E, Lanza AE, Elkaim E, Diez-Gómez V, Sobrados I, Gemmi M, Gregorkiewitz M. The structure of kaliophilite KAlSiO 4, a long-lasting crystallographic problem. IUCRJ 2020; 7:1070-1083. [PMID: 33209318 PMCID: PMC7642771 DOI: 10.1107/s2052252520012270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/04/2020] [Indexed: 05/04/2023]
Abstract
Kaliophilite is a feldspathoid mineral found in two Italian magmatic provinces and represents one of the 12 known phases with composition close to KAlSiO4. Despite its apparently simple formula, the structure of this mineral revealed extremely complex and resisted structure solution for more than a century. Samples from the Vesuvius-Monte Somma and Alban Hills volcanic areas were analyzed through a multi-technique approach, and finally the crystal structure of kaliophilite was solved using 3D electron diffraction and refined against X-ray diffraction data of a twinned crystal. Results were also ascertained by the Rietveld method using synchrotron powder intensities. It was found that kaliophilite crystallizes in space group P3 with unit-cell parameters a = 27.0597 (16), c = 8.5587 (6) Å, V = 5427.3 (7) Å3 and Z = 54. The kaliophilite framework is a variant of the tridymite topology, with alternating SiO4 and AlO4 tetrahedra forming sheets of six-membered rings (63 nets), which are connected along [001] by sharing the apical oxygen atoms. Considering the up (U) and down (D) orientations of the linking vertex, kaliophilite is the first framework that contains three different ring topologies: nine (1-3-5) (UDUDUD) rings, six (1-2-3) (UUUDDD) rings and twelve (1-2-4) (UUDUDD) rings. This results in a relatively open (19.9 tetrahedra nm-3) channel system with multiple connections between the double six-ring cavities. Such a framework requires a surprisingly large unit cell, 27 times larger than the cell of kalsilite, the simplest phase with the same composition. The occurrence of some Na for K substitution (3-10%) may be related to the characteristic structural features of kaliophilite. Micro-twinning, pseudo-symmetries and anisotropic hkl-dependent peak broadening were also detected, and they may account for the elusive character of the kaliophilite crystal structure.
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Affiliation(s)
- Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza S. Silvestro 12, Pisa, 56127, Italy
| | - Elena Bonaccorsi
- Dipartimento di Scienze della Terra, Università di Pisa, Via Santa Maria 53, Pisa, 56126, Italy
- Correspondence e-mail: , ,
| | - Arianna E. Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza S. Silvestro 12, Pisa, 56127, Italy
| | - Erik Elkaim
- Synchrotron Soleil, L’Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, 91192, France
| | - Virginia Diez-Gómez
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (ICMM-CSIC), Sor Juana Inés de la Cruz 3, Madrid, 28049, Spain
| | - Isabel Sobrados
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (ICMM-CSIC), Sor Juana Inés de la Cruz 3, Madrid, 28049, Spain
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza S. Silvestro 12, Pisa, 56127, Italy
- Correspondence e-mail: , ,
| | - Miguel Gregorkiewitz
- Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Università di Siena, Via Laterina 8, Siena, 53100, Italy
- Correspondence e-mail: , ,
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30
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Mugnaioli E, Lanza AE, Bortolozzi G, Righi L, Merlini M, Cappello V, Marini L, Athanassiou A, Gemmi M. Electron Diffraction on Flash-Frozen Cowlesite Reveals the Structure of the First Two-Dimensional Natural Zeolite. ACS CENTRAL SCIENCE 2020; 6:1578-1586. [PMID: 32999933 PMCID: PMC7517411 DOI: 10.1021/acscentsci.9b01100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Indexed: 05/24/2023]
Abstract
Cowlesite, ideally Ca6Al12Si18O60·36H2O, is to date the only natural zeolite whose structure could not be determined by X-ray methods. In this paper, we present the ab initio structure determination of this mineral obtained by three-dimensional (3D) electron diffraction data collected from single-crystal domains of a few hundreds of nanometers. The structure of cowlesite consists of an alternation of rigid zeolitic layers and low-density interlayers supported by water and cations. This makes cowlesite the only two-dimensional (2D) zeolite known in nature. When cowlesite gets in contact with a transmission electron microscope vacuum, a phase transition to a conventional 3D zeolite framework occurs in few seconds. The original cowlesite structure could be preserved only by adopting a cryo-plunging sample preparation protocol usually employed for macromolecular samples. Such a protocol allows the investigation by 3D electron diffraction of very hydrated and very beam-sensitive inorganic materials, which were previously considered intractable by transmission electron microscopy crystallographic methods.
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Affiliation(s)
- Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Arianna E. Lanza
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Giorgio Bortolozzi
- Associazione
Micromineralogica Italiana (AMI), via Gioconda 3, 26100 Cremona, Italy
| | - Lara Righi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43124, Italy
- IMEM-CNR, Parco Area
delle Scienze 37/A, 43123 Parma, Italy
| | - Marco Merlini
- Dipartimento
di Scienze della Terra, Università
degli Studi di Milano, Via Botticelli 23, 20133 Milano, Italy
| | - Valentina Cappello
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Lara Marini
- Smart Materials, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | | | - Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
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31
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Toso S, Akkerman QA, Martín-García B, Prato M, Zito J, Infante I, Dang Z, Moliterni A, Giannini C, Bladt E, Lobato I, Ramade J, Bals S, Buha J, Spirito D, Mugnaioli E, Gemmi M, Manna L. Nanocrystals of Lead Chalcohalides: A Series of Kinetically Trapped Metastable Nanostructures. J Am Chem Soc 2020; 142:10198-10211. [PMID: 32374173 PMCID: PMC7737912 DOI: 10.1021/jacs.0c03577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 11/28/2022]
Abstract
We report the colloidal synthesis of a series of surfactant-stabilized lead chalcohalide nanocrystals. Our work is mainly focused on Pb4S3Br2, a chalcohalide phase unknown to date that does not belong to the ambient-pressure PbS-PbBr2 phase diagram. The Pb4S3Br2 nanocrystals herein feature a remarkably narrow size distribution (with a size dispersion as low as 5%), a good size tunability (from 7 to ∼30 nm), an indirect bandgap, photoconductivity (responsivity = 4 ± 1 mA/W), and stability for months in air. A crystal structure is proposed for this new material by combining the information from 3D electron diffraction and electron tomography of a single nanocrystal, X-ray powder diffraction, and density functional theory calculations. Such a structure is closely related to that of the recently discovered high-pressure chalcohalide Pb4S3I2 phase, and indeed we were able to extend our synthesis scheme to Pb4S3I2 colloidal nanocrystals, whose structure matches the one that has been published for the bulk. Finally, we could also prepare nanocrystals of Pb3S2Cl2, which proved to be a structural analogue of the recently reported bulk Pb3Se2Br2 phase. It is remarkable that one high-pressure structure (for Pb4S3I2) and two metastable structures that had not yet been reported (for Pb4S3Br2 and Pb3S2Cl2) can be prepared on the nanoscale by wet-chemical approaches. This highlights the important role of colloidal chemistry in the discovery of new materials and motivates further exploration into metal chalcohalide nanocrystals.
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Affiliation(s)
- Stefano Toso
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Dipartimento
di Matematica e Fisica and Interdisciplinary Laboratories for Advanced
Materials Physics, Università Cattolica
del Sacro Cuore, Via
Musei 41, I-25121 Brescia, Italy
| | - Quinten A. Akkerman
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Beatriz Martín-García
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Mirko Prato
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Juliette Zito
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Ivan Infante
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Department
of Theoretical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Zhiya Dang
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Anna Moliterni
- Istituto
di Cristallografia−Consiglio Nazionale delle Ricerche (IC−CNR), Via Amendola 122/O, I-70126 Bari, Italy
| | - Cinzia Giannini
- Istituto
di Cristallografia−Consiglio Nazionale delle Ricerche (IC−CNR), Via Amendola 122/O, I-70126 Bari, Italy
| | - Eva Bladt
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- NANOlab
Center of Excellence, University of Antwerp, 2020 Antwerp, Belgium
| | - Ivan Lobato
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- NANOlab
Center of Excellence, University of Antwerp, 2020 Antwerp, Belgium
| | - Julien Ramade
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- NANOlab
Center of Excellence, University of Antwerp, 2020 Antwerp, Belgium
| | - Sara Bals
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- NANOlab
Center of Excellence, University of Antwerp, 2020 Antwerp, Belgium
| | - Joka Buha
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Davide Spirito
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro, 12, 56127 Pisa, Italy
| | - Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro, 12, 56127 Pisa, Italy
| | - Liberato Manna
- Department
of Nanochemistry and Materials Characterization Facility, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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Gallagher-Jones M, Bustillo KC, Ophus C, Richards LS, Ciston J, Lee S, Minor AM, Rodriguez JA. Atomic structures determined from digitally defined nanocrystalline regions. IUCRJ 2020; 7:490-499. [PMID: 32431832 PMCID: PMC7201287 DOI: 10.1107/s2052252520004030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/22/2020] [Indexed: 06/11/2023]
Abstract
Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.
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Affiliation(s)
- Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Karen C. Bustillo
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Logan S. Richards
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jim Ciston
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Andrew M. Minor
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
- Department of Materials Science and Engineering, University of California, Berkeley, California, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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Woollam GR, Das PP, Mugnaioli E, Andrusenko I, Galanis AS, van de Streek J, Nicolopoulos S, Gemmi M, Wagner T. Structural analysis of metastable pharmaceutical loratadine form II, by 3D electron diffraction and DFT+D energy minimisation. CrystEngComm 2020. [DOI: 10.1039/d0ce01216e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coupling 3D electron diffraction and density functional theory provided the metastable pharmaceutical crystal structure within nanometre range, under ambient conditions.
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Affiliation(s)
| | | | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | - Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | | | | | | | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research
- Basel 4002
- Switzerland
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Jensen TT, Hall CL, Potticary J, Andrusenko I, Gemmi M, Hall SR. An experimental and computational study into the crystallisation propensity of 2nd generation sulflower. Chem Commun (Camb) 2019; 55:14586-14589. [PMID: 31750483 DOI: 10.1039/c9cc08346d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystallisation propensity of the newly synthesised molecule persulfurated coronene has been investigated through a number of experimental methods. Electrostatic potential calculations and multi-molecular optimisations show that face-face interactions are far more favorable than edge-face interactions, severely restricting the ability of the molecule to crystallise.
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Affiliation(s)
- Torsten T Jensen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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Blake AJ, de Boissieu M, Nangia A. Electron crystallography. IUCRJ 2019; 6:786-787. [PMID: 31576211 PMCID: PMC6760451 DOI: 10.1107/s2052252519011497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A Special Issue on the topic of Electron Crystallography, now available in the August 2019 issue of Acta Crystallographica, Section B, contains contributions which we hope will interest readers of IUCrJ.
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Affiliation(s)
- Alexander J. Blake
- School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | | | - Ashwini Nangia
- Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008, India
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Hadermann J, Palatinus L. Introduction to the special issue on electron crystallography. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:462. [PMID: 32830703 DOI: 10.1107/s2052520619010783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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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