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Plana-Ruiz S, Götz E, Neumann T, Schwesig P, Kolb U. Three-dimensional electron diffraction on clinkers: the belite α' H incommensurate modulated structure. Acta Crystallogr B Struct Sci Cryst Eng Mater 2024; 80:105-116. [PMID: 38488703 PMCID: PMC10994169 DOI: 10.1107/s205252062400146x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/13/2024] [Indexed: 04/06/2024]
Abstract
Traditional X-ray methods are extensively applied to commercial cement samples in order to determine their physical and chemical properties. Powder patterns are routinely used to quantify the composition of these phase mixtures, but structure determination becomes difficult because of reflection overlapping caused by the high number of different crystal structures. The fast-growing 3D electron diffraction technique and its related automated acquisition protocols arise as a potentially very interesting tool for the cement industry, since they enable the fast and systematic acquisition of diffraction data from individual particles. In this context, electron diffraction has been used in the investigation of the different crystalline phases present in various commercial clinkers for cement. Automated data collection procedures and subsequent data processing have enabled the structural characterization of the different crystal structures from which the α'H polymorph of Ca2SiO4 (belite) exhibited satellite reflections. Its average crystal structure has been known since 1971 and satellite reflections have been reported previously, yet the modulation was never fully described by means of the superspace formalism. Here, the incommensurately modulated structure is solved and refined using harmonic and crenel functions in the superspace group Pnma(α00)0ss, showing the potential of 3D electron diffraction for systematic crystallographic characterizations of cement. A full description of the different belite polymorphs is provided considering this modulated structure.
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Affiliation(s)
- Sergi Plana-Ruiz
- Servei de Recursos Científics i Tècnics, Universitat Rovira i Virgili, Avinguda Països Catalans 26, Tarragona, Catalonia 43007, Spain
- Institut für Angewandte Geowissenschaften, Technische Universität Darmstadt, Petersenstrasse 23, Darmstadt, Hessen 64287, Germany
| | - Emilia Götz
- Institut für Angewandte Geowissenschaften, Technische Universität Darmstadt, Petersenstrasse 23, Darmstadt, Hessen 64287, Germany
| | - Thomas Neumann
- Schwenk Zement GmbH & Co. Kg, Laudenbacher Weg 5, Karlstadt, Bavaria 97753, Germany
| | - Peter Schwesig
- Master Builders Solutions Deutschland GmbH, Dr.-Albert-Frank-Strasse 32, Trostberg, Bavaria 83308, Germany
| | - Ute Kolb
- Institut für Angewandte Geowissenschaften, Technische Universität Darmstadt, Petersenstrasse 23, Darmstadt, Hessen 64287, Germany
- Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg University of Mainz, Duesbergweg 10-14, Mainz, Rheinland-Pfalz 55128, Germany
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Thomas M, Cleverley A, Beanland R. Parameterized absorptive electron scattering factors. Acta Crystallogr A Found Adv 2024; 80:146-150. [PMID: 38270202 PMCID: PMC10913675 DOI: 10.1107/s2053273323010963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
In electron diffraction, thermal atomic motion produces incoherent scattering over a relatively wide angular range, which appears as a diffuse background that is usually subtracted from measurements of Bragg spot intensities in structure solution methods. The transfer of electron flux from Bragg spots to diffuse scatter is modelled using complex scattering factors f + if' in the Bloch wave methodology. In a two-beam Einstein model the imaginary `absorptive' scattering factor f' can be obtained by the evaluation of an integral containing f over all possible scattering angles. While more sophisticated models of diffuse scatter are widely used in the electron microscopy community, it is argued in this paper that this simple model is appropriate for current structure solution and refinement methods. The two-beam model is a straightforward numerical calculation, but even this simplistic approach can become time consuming for simulations of materials with large numbers of atoms in the unit cell and/or many incident beam orientations. Here, a parameterized form of f' is provided for 103 elements as neutral, spherical atoms that reduces calculation time considerably.
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Affiliation(s)
- M. Thomas
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - A. Cleverley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - R. Beanland
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
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Samperisi L, Zou X, Huang Z. How to get maximum structure information from anisotropic displacement parameters obtained by three-dimensional electron diffraction: an experimental study on metal-organic frameworks. IUCrJ 2022; 9:480-491. [PMID: 35844475 PMCID: PMC9252158 DOI: 10.1107/s2052252522005632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Three-dimensional electron diffraction (3D ED) has been used for ab initio structure determination of various types of nanocrystals, such as metal-organic frameworks (MOFs), zeolites, metal oxides and organic crystals. These crystals are often obtained as polycrystalline powders, which are too small for single-crystal X-ray diffraction (SCXRD). While it is now possible to obtain accurate atomic positions of nanocrystals by adopting kinematical refinement against 3D ED data, most new structures are refined with isotropic displacement parameters (U eq), which limits the detection of possible structure disorders and atomic motions. Anisotropic displacement parameters (ADPs, Uij ) obtained by anisotropic structure refinement, on the other hand, provide information about the average displacements of atoms from their mean positions in a crystal, which can provide insights with respect to displacive disorder and flexibility. Although ADPs have been obtained from some 3D ED studies of MOFs, they are seldom mentioned or discussed in detail. We report here a detailed study and interpretation of structure models refined anisotropically against 3D ED data. Three MOF samples with different structural complexity and symmetry, namely ZIF-EC1, MIL-140C and Ga(OH)(1,4-ndc) (1,4-ndcH2 is naphthalene-1,4-dicarboxylic acid), were chosen for the studies. We compare the ADPs refined against individual data sets and how they are affected by different data-merging strategies. Based on our results and analysis, we propose strategies for obtaining accurate structure models with interpretable ADPs based on kinematical refinement against 3D ED data. The ADPs of the obtained structure models provide clear and unambiguous information about linker motions in the MOFs.
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Affiliation(s)
- Laura Samperisi
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden 106 91, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden 106 91, Sweden
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden 106 91, Sweden
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Gao ZR, Balestra SRG, Li J, Camblor MA. HPM-16, a Stable Interrupted Zeolite with a Multidimensional Mixed Medium-Large Pore System Containing Supercages. Angew Chem Int Ed Engl 2021; 60:20249-20252. [PMID: 34309150 PMCID: PMC8456927 DOI: 10.1002/anie.202106734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/20/2021] [Indexed: 11/10/2022]
Abstract
HPM-16 is a highly porous germanosilicate zeolite with an interrupted framework that contains a three-dimensional system of 12+10×10(12)×12+10-membered ring (MR) pores. The 10(12) MR pore in the b direction is a 10 MR pore with long 12 MR stretches forming 30 Å long tubular supercages. Along one direction the 10 MR pores are fused, meaning that the separation between adjacent pores consists of a single tetrahedron that is, additionally, connected to only three additional tetrahedra (a Q3 ). These fused pores are thus decorated by T-OH groups along the whole diffusion path, creating a hydrophilic region embedded in an otherwise essentially hydrophobic environment. The structure is built from highly porous 12×12×12 MR uninterrupted layers that are connected to each other through Q3 producing a second system of 10×10×10 MR pores. This zeolite can be extensively degermanated yielding a material with high thermal stability, despite its interrupted nature.
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Affiliation(s)
- Zihao Rei Gao
- Instituto de Ciencia de Materiales de MadridConsejo Superior de Investigaciones Científicas (ICMM-CSIC)c/ Sor Juana Inés de la Cruz, 328049MadridSpain
| | - Salvador R. G. Balestra
- Instituto de Ciencia de Materiales de MadridConsejo Superior de Investigaciones Científicas (ICMM-CSIC)c/ Sor Juana Inés de la Cruz, 328049MadridSpain
| | - Jian Li
- Berzelii Center EXSELENT on Porous MaterialsDepartment of Materials and Environmental ChemistryStockholm University10691StockholmSweden
| | - Miguel A. Camblor
- Instituto de Ciencia de Materiales de MadridConsejo Superior de Investigaciones Científicas (ICMM-CSIC)c/ Sor Juana Inés de la Cruz, 328049MadridSpain
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Ge M, Wang Y, Carraro F, Liang W, Roostaeinia M, Siahrostami S, Proserpio DM, Doonan C, Falcaro P, Zheng H, Zou X, Huang Z. High-Throughput Electron Diffraction Reveals a Hidden Novel Metal-Organic Framework for Electrocatalysis. Angew Chem Int Ed Engl 2021; 60:11391-11397. [PMID: 33682282 PMCID: PMC8252586 DOI: 10.1002/anie.202016882] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 01/25/2023]
Abstract
Metal-organic frameworks (MOFs) are known for their versatile combination of inorganic building units and organic linkers, which offers immense opportunities in a wide range of applications. However, many MOFs are typically synthesized as multiphasic polycrystalline powders, which are challenging for studies by X-ray diffraction. Therefore, developing new structural characterization techniques is highly desired in order to accelerate discoveries of new materials. Here, we report a high-throughput approach for structural analysis of MOF nano- and sub-microcrystals by three-dimensional electron diffraction (3DED). A new zeolitic-imidazolate framework (ZIF), denoted ZIF-EC1, was first discovered in a trace amount during the study of a known ZIF-CO3 -1 material by 3DED. The structures of both ZIFs were solved and refined using 3DED data. ZIF-EC1 has a dense 3D framework structure, which is built by linking mono- and bi-nuclear Zn clusters and 2-methylimidazolates (mIm- ). With a composition of Zn3 (mIm)5 (OH), ZIF-EC1 exhibits high N and Zn densities. We show that the N-doped carbon material derived from ZIF-EC1 is a promising electrocatalyst for oxygen reduction reaction (ORR). The discovery of this new MOF and its conversion to an efficient electrocatalyst highlights the power of 3DED in developing new materials and their applications.
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Affiliation(s)
- Meng Ge
- Department of Materials and Environmental ChemistryStockholm University10691StockholmSweden
| | - Yanzhi Wang
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal UniversityXi'an710119China
| | - Francesco Carraro
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Weibin Liang
- Department of Chemistry and the Centre for Advanced NanomaterialsThe University of AdelaideAdelaide5005South AustraliaAustralia
| | - Morteza Roostaeinia
- Department of ChemistryUniversity of Calgary2500 University Drive NWCalgaryAlbertaT2N1N4Canada
| | - Samira Siahrostami
- Department of ChemistryUniversity of Calgary2500 University Drive NWCalgaryAlbertaT2N1N4Canada
| | - Davide M. Proserpio
- Dipartimento di ChimicaUniversità degli Studi di Milano20133MilanoItaly
- Samara Center for Theoretical Materials Science (SCTMS)Samara State Technical UniversitySamara443100Russia
| | - Christian Doonan
- Department of Chemistry and the Centre for Advanced NanomaterialsThe University of AdelaideAdelaide5005South AustraliaAustralia
| | - Paolo Falcaro
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Haoquan Zheng
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal UniversityXi'an710119China
| | - Xiaodong Zou
- Department of Materials and Environmental ChemistryStockholm University10691StockholmSweden
| | - Zhehao Huang
- Department of Materials and Environmental ChemistryStockholm University10691StockholmSweden
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Yun Y, Zou X, Hovmöller S, Wan W. Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders. IUCrJ 2015; 2:267-82. [PMID: 25866663 PMCID: PMC4392419 DOI: 10.1107/s2052252514028188] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 12/26/2014] [Indexed: 05/04/2023]
Abstract
Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni-Se-O-Cl crystals, zeolites, germanates, metal-organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.
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Affiliation(s)
- Yifeng Yun
- Berzelii Center EXSELENT on Porous Materials and Inorganic and Structural Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, SE-10691 Stockholm, Sweden
| | - Xiaodong Zou
- Berzelii Center EXSELENT on Porous Materials and Inorganic and Structural Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, SE-10691 Stockholm, Sweden
| | - Sven Hovmöller
- Berzelii Center EXSELENT on Porous Materials and Inorganic and Structural Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, SE-10691 Stockholm, Sweden
| | - Wei Wan
- Berzelii Center EXSELENT on Porous Materials and Inorganic and Structural Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, SE-10691 Stockholm, Sweden
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Wan W, Sun J, Su J, Hovmöller S, Zou X. Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing. J Appl Crystallogr 2013; 46:1863-1873. [PMID: 24282334 PMCID: PMC3831301 DOI: 10.1107/s0021889813027714] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/09/2013] [Indexed: 11/12/2022] Open
Abstract
Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05-0.20°) are combined with goniometer tilts at a coarse step (2.0-3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.
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Affiliation(s)
- Wei Wan
- Inorganic and Structural Chemistry and Berzelii Centre EXSELENT on Porous Materials, Department of Materials and Environmental Chemistry, Stockholm University, Arrhenius Laboratory, Stockholm SE-106 91, Sweden
| | - Junliang Sun
- Inorganic and Structural Chemistry and Berzelii Centre EXSELENT on Porous Materials, Department of Materials and Environmental Chemistry, Stockholm University, Arrhenius Laboratory, Stockholm SE-106 91, Sweden
| | - Jie Su
- Inorganic and Structural Chemistry and Berzelii Centre EXSELENT on Porous Materials, Department of Materials and Environmental Chemistry, Stockholm University, Arrhenius Laboratory, Stockholm SE-106 91, Sweden
| | - Sven Hovmöller
- Inorganic and Structural Chemistry and Berzelii Centre EXSELENT on Porous Materials, Department of Materials and Environmental Chemistry, Stockholm University, Arrhenius Laboratory, Stockholm SE-106 91, Sweden
| | - Xiaodong Zou
- Inorganic and Structural Chemistry and Berzelii Centre EXSELENT on Porous Materials, Department of Materials and Environmental Chemistry, Stockholm University, Arrhenius Laboratory, Stockholm SE-106 91, Sweden
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