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Publications (10 of 16) Show all publications
Wang, B., Zou, X. & Smeets, S. (2019). Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination. IUCrJ, 6, 854-867
Open this publication in new window or tab >>Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination
2019 (English)In: IUCrJ, E-ISSN 2052-2525, Vol. 6, p. 854-867Article in journal (Refereed) Published
Abstract [en]

Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal-organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool.

Keywords
serial crystallography, automated data collection, hierarchical cluster analysis, structure determination, electron diffraction, microED
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-175094 (URN)10.1107/S2052252519007681 (DOI)000484171300011 ()31576219 (PubMedID)
Available from: 2019-10-22 Created: 2019-10-22 Last updated: 2022-09-28Bibliographically approved
Smeets, S., Ångström, J. & Olsson, C.-O. A. (2019). Quantitative Phase Analysis for Carbide Characterization in Steel Using Automated Electron Diffraction. Steel Research International, 90(1), Article ID 1800300.
Open this publication in new window or tab >>Quantitative Phase Analysis for Carbide Characterization in Steel Using Automated Electron Diffraction
2019 (English)In: Steel Research International, ISSN 1611-3683, E-ISSN 1869-344X, Vol. 90, no 1, article id 1800300Article in journal (Refereed) Published
Abstract [en]

Carbides are critical to many different properties in a steel. In this paper, the quantification of a carbide powder extracted from a stainless steel analyzed with profile refinement of X-ray powder diffraction patterns, is compared to a novel technique for automated electron diffraction pattern collection with a transmission electron microscope. The automated analysis has the advantage of collecting patterns from individual particles, hence avoiding issues such as overlapping reflections in powder diffractograms. Electron diffraction patterns with satisfactory quality are selected through a deep convoluted neural network and matched to a library of pre-calculated diffraction patterns, corresponding to a set of selected carbide crystal structures. The quantitative results from the automated particle analysis are in good agreement with the phases identified by powder profile refinement.

Keywords
carbide, powder profile refinement, stainless steel, transmission electron microscopy, x-ray diffraction
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-165787 (URN)10.1002/srin.201800300 (DOI)000454790200015 ()
Available from: 2019-02-20 Created: 2019-02-20 Last updated: 2022-02-26Bibliographically approved
Smeets, S., Zones, S. I., Xie, D., Palatinus, L., Pascual, J., Hwang, S.-J., . . . McCusker, L. B. (2019). SSZ-27: A Small-Pore Zeolite with Large Heart-Shaped Cavities Determined by using Multi-crystal Electron Diffraction. Angewandte Chemie International Edition, 58(37), 13080-13086
Open this publication in new window or tab >>SSZ-27: A Small-Pore Zeolite with Large Heart-Shaped Cavities Determined by using Multi-crystal Electron Diffraction
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2019 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 58, no 37, p. 13080-13086Article, review/survey (Refereed) Published
Abstract [en]

The high-silica zeolite SSZ-27 was synthesized using one of the isomers of the organic structure-directing agent that is known to produce the large-pore zeolite SSZ-26 (CON). The structure of the as-synthesized form was solved using multi-crystal electron diffraction data. Data were collected on eighteen crystals, and to obtain a high-quality and complete data set for structure refinement, hierarchical cluster analysis was employed to select the data sets most suitable for merging. The framework structure of SSZ-27 can be described as a combination of two types of cavities, one of which is shaped like a heart. The cavities are connected through shared 8-ring windows to create straight channels that are linked together in pairs to form a one-dimensional channel system. Once the framework structure was known, molecular modelling was used to find the best fitting isomer, and this, in turn, was isolated to improve the synthesis conditions for SSZ-27.

Keywords
zeolites, electron diffraction, SSZ-27, structure determination, structure-directing agents (SDAs)
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-173127 (URN)10.1002/anie.201905049 (DOI)000482403000001 ()31347746 (PubMedID)
Available from: 2019-10-02 Created: 2019-10-02 Last updated: 2022-03-23Bibliographically approved
Luo, Y., Smeets, S., Wang, Z., Sun, J. & Yang, W. (2019). Synthesis and Structure Determination of SCM-15: A 3D Large Pore Zeolite with Interconnected Straight 12x12x10-Ring Channels. Chemistry - A European Journal, 25(9), 2184-2188
Open this publication in new window or tab >>Synthesis and Structure Determination of SCM-15: A 3D Large Pore Zeolite with Interconnected Straight 12x12x10-Ring Channels
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2019 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, no 9, p. 2184-2188Article in journal (Refereed) Published
Abstract [en]

A new germanosilicate zeolite named SCM-15 (Sinopec Composite Material No. 15), the first zeolite containing a 3-dimensional (3D) channel system with interconnected 12-, 12-, and 10-ring channels (pore sizes: 6.1 x 7.2, 6.1 x 7.4, and 5.2 x 5.9 angstrom), has been synthesized using neutral 4-pyrrolidinopyridine as organic structure-directing agents (OSDAs). Its structure has been determined by combining single-crystal electron diffraction (SCED) and synchrotron powder X-ray diffraction (SPXD) data. The unique open framework structure of SCM-15 is related to that of FOS-5 (BEC), ITQ-7 (ISV), PKU-16 (POS), ITQ-26 (IWS), ITQ-21, Beta polymorph B, and SU-78B, since all these framework structures can be constructed from similar chains which are connected through shared 4-ring or double 4-ring (d4r) units. Based on this relation, six topologically reasonable 3D large or extra-large pore hypothetical zeolites are predicted.

Keywords
channel system, organic structure-directing agent, structure determination, synthetic methods, zeolites
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-167532 (URN)10.1002/chem.201805187 (DOI)000461084900008 ()30521132 (PubMedID)
Available from: 2019-04-17 Created: 2019-04-17 Last updated: 2022-02-26Bibliographically approved
Rzepka, P., Wardecki, D., Smeets, S., Müller, M., Gies, H., Zou, X. & Hedin, N. (2018). CO2-Induced Displacement of Na+ and K+ in Zeolite INaKI-A. The Journal of Physical Chemistry C, 122(30), 17211-17220
Open this publication in new window or tab >>CO2-Induced Displacement of Na+ and K+ in Zeolite INaKI-A
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2018 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 30, p. 17211-17220Article in journal (Refereed) Published
Abstract [en]

Adsorption technologies offer opportunities to remove CO2 from gas mixtures, and zeolite A has good properties that include a high capacity for the adsorption of CO2 . It has been argued that its abilities to separate CO2 from N-2 in flue gas and CO2 from CH4 in raw biogas can be further enhanced by replacing Na+ with K+ in the controlling pore window apertures. In this study, several compositions of I Na12-xKxI-A were prepared and studied with respect to the adsorption of CO2 N-2, and CH4, and the detailed structural changes were induced by the adsorption of CO2. The adsorption of CO2 gradually decreased on an increasing content of K+, whereas the adsorption of N-2 and CH4 was completely nulled already at relatively small contents of K. Of the studied samples, INa9K3I-A exhibited the highest CO2 over N-2/CH4 selectivities, with a(CO2/N-2 ) > 21 000 and a(CO2/CH4) > 8000. For samples with and without adsorbed CO2 analyses of powder X-ray diffraction (PXRD) data revealed that K+ preferred to substitute Na+ at the eight-ring sites. The Na(+ )ions at the six-ring sites were gradually replaced by K+ on an increasing content, and these sites split into two positions on both sides of the six-ring mirror plane. It was observed that both the eight-ring and six-ring sites tailored the maximum adsorption capacity for CO2 and possibly also the diffusion of CO2 into the alpha-cavities of INa12-xKxI-A. The adsorption of CH4 and N-2 on the other hand appeared to be controlled by the K+ ions blocking the eight-ring windows. The in situ PXRD study revealed that the positions of the extra-framework cations were displaced into the a-cavities of INa12(_)x,KxI-A on the adsorption of CO2 . For samples with a low content of K+, the repositioning of the cations was consistent with a mutual attraction with the adsorbed CO(2 )molecules.

National Category
Chemical Sciences Nano Technology Materials Engineering
Research subject
Materials Chemistry
Identifiers
urn:nbn:se:su:diva-158906 (URN)10.1021/acs.jpcc.8b03899 (DOI)000440956200023 ()
Available from: 2018-08-20 Created: 2018-08-20 Last updated: 2022-02-26Bibliographically approved
Cichocka, M. O., Ångström, J., Wang, B., Zou, X. & Smeets, S. (2018). High-throughput continuous rotation electron diffraction data acquisition via software automation. Journal of applied crystallography, 51(6), 1652-1661
Open this publication in new window or tab >>High-throughput continuous rotation electron diffraction data acquisition via software automation
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2018 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 51, no 6, p. 1652-1661Article in journal (Refereed) Published
Abstract [en]

Single-crystal electron diffraction (SCED) is emerging as an effective technique to determine and refine the structures of unknown nano-sized crystals. In this work, the implementation of the continuous rotation electron diffraction (cRED) method for high-throughput data collection is described. This is achieved through dedicated software that controls the transmission electron microscope and the camera. Crystal tracking can be performed by defocusing every nth diffraction pattern while the crystal rotates, which addresses the problem of the crystal moving out of view of the selected area aperture during rotation. This has greatly increased the number of successful experiments with larger rotation ranges and turned cRED data collection into a high-throughput method. The experimental parameters are logged, and input files for data processing software are written automatically. This reduces the risk of human error, and makes data collection more reproducible and accessible for novice and irregular users. In addition, it is demonstrated how data from the recently developed serial electron diffraction technique can be used to supplement the cRED data collection by automatic screening for suitable crystals using a deep convolutional neural network that can identify promising crystals through the corresponding diffraction data. The screening routine and cRED data collection are demonstrated using a sample of the zeolite mordenite, and the quality of the cRED data is assessed on the basis of the refined crystal structure.

Keywords
single-crystal electron diffraction, high throughput, crystal screening, structure analysis
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-162656 (URN)10.1107/S1600576718015145 (DOI)000451833600016 ()
Available from: 2018-12-05 Created: 2018-12-05 Last updated: 2022-03-23Bibliographically approved
Smeets, S., Wang, B., Cichocka, M., Ångström, J. & Wan, W. (2018). Instamatic.
Open this publication in new window or tab >>Instamatic
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2018 (English)Other (Other academic)
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-168156 (URN)10.5281/zenodo.2026774 (DOI)
Note

Instamatic is a Python program that is being developed with the aim to automate the collection of electron diffraction data. At the core is a Python library for transmission electron microscope experimental control with bindings for the JEOL microscope and interfaces to the gatan/timepix cameras. Routines have been implemented for collecting serial electron diffraction (serialED), continuous rotation electron diffraction (cRED), and stepwise rotation electron diffraction (RED) data.

Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2022-03-17Bibliographically approved
Smeets, S. & McCusker, L. B. (2018). Location of Organic Structure-Directing Agents in Zeolites Using Diffraction Techniques. In: Luis Gómez-Hortigüela (Ed.), Insights into the Chemistry of Organic Structure-Directing Agents in the Synthesis of Zeolitic Materials: (pp. 43-73). New York: Springer, 175
Open this publication in new window or tab >>Location of Organic Structure-Directing Agents in Zeolites Using Diffraction Techniques
2018 (English)In: Insights into the Chemistry of Organic Structure-Directing Agents in the Synthesis of Zeolitic Materials / [ed] Luis Gómez-Hortigüela, New York: Springer , 2018, Vol. 175, p. 43-73Chapter in book (Refereed)
Abstract [en]

In this chapter, we delve into the X-ray diffraction techniques that can be used to address the question as to where the organic structure-directing agents (OSDAs) are located in the pores of a zeolite framework structure and give an overview of some of the practical issues involved. By examining the results of such investigations, we attempt to establish whether the OSDAs are really disordered, as is often claimed, or if it is the methods we use that give this impression. In fact, the non-framework species in the channels of a zeolite appear to be arranged quite logically in a chemically sensible manner. In most cases, the OSDA within the pores can be described well as a superposition of just a few discrete, symmetryrelated positions, provided the discrepancies between the OSDA and framework symmetries can be resolved. On the basis of some selected examples, we show that their arrangements can be extracted from experimental data using a systematic strategy and sometimes supplementary information.

Place, publisher, year, edition, pages
New York: Springer, 2018
Series
Structure and Bonding, ISSN 0081-5993 ; volume 175
Keywords
Simulated annealing, Structure-directing agents, X-ray (powder) diffraction, Zeolites
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-166880 (URN)10.1007/430_2017_7 (DOI)000457975500003 ()978-3-319-74289-2 (ISBN)978-3-319-74288-5 (ISBN)
Available from: 2019-03-06 Created: 2019-03-06 Last updated: 2022-02-26Bibliographically approved
Cichocka, M. O., Lorgouilloux, Y., Smeets, S., Su, J., Wan, W., Caullet, P., . . . Zou, X. (2018). Multidimensional Disorder in Zeolite IM-18 Revealed by Combining Transmission Electron Microscopy and X-ray Powder Diffraction Analyses. Crystal Growth & Design, 18(4), 2441-2451
Open this publication in new window or tab >>Multidimensional Disorder in Zeolite IM-18 Revealed by Combining Transmission Electron Microscopy and X-ray Powder Diffraction Analyses
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2018 (English)In: Crystal Growth & Design, ISSN 1528-7483, E-ISSN 1528-7505, Vol. 18, no 4, p. 2441-2451Article in journal (Refereed) Published
Abstract [en]

A new medium-pore germanosilicate, denoted IM-18, with a three-dimensional 8 x 8 x 10-ring channel system, has been prepared hydrothermally using 4-dimethylaminopyridine as an organic structure-directing agent (OSDA). Due to the presence of stacking disorder, the structure elucidation of IM-18 was challenging, and a combination of different techniques, including electron diffraction, high-resolution transmission electron microscopy (HRTEM), and Rietveld refinement using synchrotron powder diffraction data, was necessary to elucidate the details of the structure and to understand the nature of the disorder. Rotation electron diffraction data were used to determine the average structure of IM-18, HRTEM images to characterize the stacking disorder, and Rietveld refinement to locate the Ge in the framework and the OSDA occluded in the channels.

National Category
Chemical Sciences Materials Engineering
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-155967 (URN)10.1021/acs.cgd.8b00078 (DOI)000429508200057 ()
Available from: 2018-05-16 Created: 2018-05-16 Last updated: 2022-02-26Bibliographically approved
Smeets, S., Zou, X. & Wan, W. (2018). Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials. Journal of applied crystallography, 51, 1262-1273
Open this publication in new window or tab >>Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials
2018 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 51, p. 1262-1273Article in journal (Refereed) Published
Abstract [en]

Serial electron crystallography has been developed as a fully automated method to collect diffraction data on polycrystalline materials using a transmission electron microscope. This enables useful data to be collected on materials that are sensitive to the electron beam and thus difficult to measure using the conventional methods that require long exposure of the same crystal. The data collection strategy combines goniometer translation with electron beam shift, which allows the entire sample stage to be probed. At each position of the goniometer, the locations of the crystals are identified using image recognition techniques. Diffraction data are then collected on each crystal using a quasi-parallel focused beam with a predefined size (usually 300-500nm). It is shown that with a fast and sensitive Timepix hybrid pixel area detector it is possible to collect diffraction data of up to 3500 crystals per hour. These data can be indexed using a brute-force forward-projection algorithm. Results from several test samples show that 100-200 frames are enough for structure determination using direct methods or dual-space methods. The large number of crystals examined enables quantitative phase analysis and automatic screening of materials for known and unknown phases.

Keywords
serial crystallography, electron diffraction, structure determination, phase analysis
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-161053 (URN)10.1107/S1600576718009500 (DOI)000445614800001 ()30279637 (PubMedID)
Available from: 2018-10-15 Created: 2018-10-15 Last updated: 2022-03-23Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-5413-9038

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