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Aragon M, Bowman SEJ, Chen CH, de la Cruz MJ, Decato DA, Eng ET, Flatt KM, Gulati S, Li Y, Lomba CJ, Mercado B, Miller J, Palatinus L, Rice WJ, Waterman D, Zimanyi CM. Applying 3D ED/MicroED workflows toward the next frontiers. Acta Crystallogr C Struct Chem 2024; 80:179-189. [PMID: 38712546 PMCID: PMC11150879 DOI: 10.1107/s2053229624004078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024] Open
Abstract
We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.
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Affiliation(s)
- Mahira Aragon
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Sarah E. J. Bowman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, New York 14203, USA
| | - Chun-Hsing Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - M. Jason de la Cruz
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Daniel A. Decato
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Kristen M. Flatt
- Materials Research Laboratory, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
| | | | - Yuchen Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Charles J. Lomba
- Department of Physics, Quantitative Biology Institute, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-8103, USA
| | - Brandon Mercado
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jessalyn Miller
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Lukáš Palatinus
- Institute of Physics of the CAS/NanED, Na Slovance 1999/2, Prague 192000, Czech Republic
| | - William J. Rice
- Department of Cell Biology, NYU Grossman School of Medicine, 540 First Ave, New York, New York 10016, USA
| | - David Waterman
- Research Complex at Harwell, UKRI–STFC Rutherford Appleton Laboratory, Harwell, Didcot, Oxfordshire, OX11 0FA, England, United Kingdom
| | - Christina M. Zimanyi
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
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Peña Corredor A, Wendling L, Preziosi D, Schlur L, Leuvrey C, Thiaudière D, Elklaim E, Blanc N, Grenier S, Roulland F, Viart N, Lefevre C. Oxygen crystallographic positions in thin films by non-destructive resonant elastic X-ray scattering. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576722003673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Precisely locating oxygen atoms in nanosized systems is a real challenge. The traditional strategies used for bulk samples fail at probing samples with much less matter. Resonant elastic X-ray scattering (REXS) experiments in the X-ray absorption near-edge structure (XANES) domain have already proved their efficiency in probing transition metal cations in thin films, but it is not feasible to perform such experiments at the low-energy edges of lighter atoms – such as oxygen. In this study, the adequacy of using REXS in the extended X-ray absorption fine structure (EXAFS) domain, also known as extended diffraction absorption fine structure (EDAFS), to solve this issue is shown. The technique has been validated on a bulk FeV2O4 sample, through comparison with results obtained with conventional X-ray diffraction measurements. Subsequently, the positions of oxygen atoms in a thin film were unveiled by using the same strategy. The approach described in this study can henceforth be applied to solve the crystallographic structure of oxides, and will help in better understanding the properties and functionalities which are dictated by the positions of the oxygen atoms in functional nanosized materials.
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Kloda M, Plecháček T, Ondrušová S, Brázda P, Chalupský P, Rohlíček J, Demel J, Hynek J. Phosphinate MOFs Formed from Tetratopic Ligands as Proton-Conductive Materials. Inorg Chem 2022; 61:7506-7512. [PMID: 35512292 DOI: 10.1021/acs.inorgchem.2c00194] [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
Metal-organic frameworks (MOFs) are attracting attention as potential proton conductors. There are two main advantages of MOFs in this application: the possibility of rational design and tuning of the properties and clear conduction pathways given by their crystalline structure. We hereby present two new MOF structures, ICR-10 and ICR-11, based on tetratopic phosphinate ligands. The structures of both MOFs were determined by 3D electron diffraction. They both crystallize in the P3̅ space group and contain arrays of parallel linear pores lined with hydrophilic noncoordinated phosphinate groups. This, together with the adsorbed water molecules, facilitates proton transfer via the Grotthuss mechanism, leading to a proton conductivity of up to 4.26 × 10-4 S cm-1 for ICR-11. The presented study demonstrates the high potential of phosphinate MOFs for the fabrication of proton conductors.
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Affiliation(s)
- Matouš Kloda
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Tomáš Plecháček
- Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Soňa Ondrušová
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Petr Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Praha, Czech Republic
| | - Petr Chalupský
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Jan Rohlíček
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Praha, Czech Republic
| | - Jan Demel
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Jan Hynek
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
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Determination of Spinel Content in Cycled Li1.2Ni0.13Mn0.54Co0.13O2 Using Three-Dimensional Electron Diffraction and Precession Electron Diffraction. Symmetry (Basel) 2021. [DOI: 10.3390/sym13111989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Among lithium battery cathode materials, Li1.2Ni0.13Mn0.54Co0.13O2 (LR-NMC) has a high theoretical capacity, but suffers from voltage and capacity fade during cycling. This is partially ascribed to transition metal cation migration, which involves the local transformation of the honeycomb layered structure to spinel-like nano-domains. Determination of the honeycomb layered/spinel phase ratio from powder X-ray diffraction data is hindered by the nanoscale of the functional material and the domains, diverse types of twinning, stacking faults, and the possible presence of the rock salt phase. Determining the phase ratio from transmission electron microscopy imaging can only be done for thin regions near the surfaces of the crystals, and the intense beam that is needed for imaging induces the same transformation to spinel as cycling does. In this article, it is demonstrated that the low electron dose sufficient for electron diffraction allows the collection of data without inducing a phase transformation. Using calculated electron diffraction patterns, we demonstrate that it is possible to determine the volume ratio of the different phases in the particles using a pair-wise comparison of the intensities of the reflections. Using this method, the volume ratio of spinel structure to honeycomb layered structure is determined for a submicron sized crystal from experimental three-dimensional electron diffraction (3D ED) and precession electron diffraction (PED) data. Both twinning and the possible presence of the rock salt phase are taken into account. After 150 charge–discharge cycles, 4% of the volume in LR-NMC particles was transformed irreversibly from the honeycomb layered structure to the spinel structure. The proposed method would be applicable to other multi-phase materials as well.
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Gemmi M, Mugnaioli E, Gorelik TE, Kolb U, Palatinus L, Boullay P, Hovmöller S, Abrahams JP. 3D Electron Diffraction: The Nanocrystallography Revolution. ACS CENTRAL SCIENCE 2019; 5:1315-1329. [PMID: 31482114 PMCID: PMC6716134 DOI: 10.1021/acscentsci.9b00394] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Indexed: 05/20/2023]
Abstract
Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.
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Affiliation(s)
- Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Tatiana E. Gorelik
- University
of Ulm, Central Facility for Electron Microscopy, Electron Microscopy
Group of Materials Science (EMMS), Albert Einstein Allee 11, 89081 Ulm, Germany
| | - Ute Kolb
- Institut
für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
- Institut
für Angewandte Geowissenschaften, Technische Universität Darmstadt, Schnittspahnstraße 9, 64287 Darmstadt, Germany
| | - Lukas Palatinus
- Department
of Structure Analysis, Institute of Physics
of the CAS, Na Slovance 2, 182 21 Prague 8, Czechia
| | - Philippe Boullay
- CRISMAT,
Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Cedex Caen, France
| | - Sven Hovmöller
- Inorganic
and Structural Chemistry, Department of Materials and Environmental
Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Jan Pieter Abrahams
- Center
for Cellular Imaging and NanoAnalytics (C−CINA), Biozentrum, Basel University, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Department
of Biology and Chemistry, Paul Scherrer
Institut (PSI), CH-5232 Villigen PSI, Switzerland
- Leiden
Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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