Bin Wang Development of rotation electron Development of rotation electron diffraction as a fully automated and accurate method for structure determination and accurate automated as a fully diffraction electron of rotation Development diffraction as a fully automated and accurate method for structure determination Bin Wang Bin Wang was born in Shanghai, China. He received his B.Sc in chemistry from Fudan University in China in 2013, and M.Sc in material chemistry from Cornell University in the US in 2015. His research mainly focused on method development for TEM. ISBN 978-91-7797-646-2 Department of Materials and Environmental Chemistry Doctoral Thesis in Inorganic Chemistry at Stockholm University, Sweden 2019 Development of rotation electron diffraction as a fully automated and accurate method for structure determination Bin Wang Academic dissertation for the Degree of Doctor of Philosophy in Inorganic Chemistry at Stockholm University to be publicly defended on Monday 10 June 2019 at 13.00 in Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B. Abstract Over the past decade, electron diffraction methods have aroused more and more interest for micro-crystal structure determination. Compared to traditional X-ray diffraction, electron diffraction breaks the size limitation of the crystals studied, but at the same time it also suffers from much stronger dynamical effects. While X-ray crystallography has been almost thoroughly developed, electron crystallography is still under active development. To be able to perform electron diffraction experiments, adequate skills for using a TEM are usually required, which makes ED experiments less accessible to average users than X-ray diffraction. Moreover, the relatively poor data statistics from ED data prevented electron crystallography from being widely accepted in the crystallography community. The thesis focused on both application and method development of continuous rotation electron diffraction (cRED) technique. The cRED method was first applied to a beam sensitive metal-organic framework sample, Co-CAU-36, and the structure was determined and refined within one working day. More importantly, the guest molecules in the pores were also located using only electron diffraction data. To facilitate general users to perform cRED data collection for useful data, software was developed to automate the overall data collection procedure. Through combination of hierarchical cluster analysis tools, the automatically collected data showed comparable quality to those from recent publications, and thus were useful for structure determination and even phase identification. To deal with dynamical refinement for ED data, a frame orientation refinement algorithm was designed to calculate accurate frame orientations for rotation data. Accuracy for the method was validated and compared to an existing software, and the behavior of TEM goniometer was studied by applying the method to an experimental data set. Keywords: electron crystallography, structure determination, structure refinement, metal-organic framework, guest molecules, software development, automation, hierarchical cluster analyses, high-throughput data processing, data merging, frame orientations, least-squares optimization, data processing, TEM goniometer. Stockholm 2019 http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-168157 ISBN 978-91-7797-646-2 ISBN 978-91-7797-647-9 Department of Materials and Environmental Chemistry (MMK) Stockholm University, 106 91 Stockholm DEVELOPMENT OF ROTATION ELECTRON DIFFRACTION AS A FULLY AUTOMATED AND ACCURATE METHOD FOR STRUCTURE DETERMINATION Bin Wang Development of rotation electron diffraction as a fully automated and accurate method for structure determination Bin Wang ©Bin Wang, Stockholm University 2019 ISBN print 978-91-7797-646-2 ISBN PDF 978-91-7797-647-9 Printed in Sweden by Universitetsservice US-AB, Stockholm 2019 To those who are interested in my study Doctoral Thesis 2019 Department of Materials and Environmental Chemistry Arrhenius Laboratory, Stockholm University SE-106 91 Stockholm, Sweden Faculty opponent: Docent Andy Stewart Department of Physics and the Bernal Institute, University of Limerick, Ireland Evaluation committee: Docent Gulaim Seisenbaeva Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Sweden Docent Cesar Pay Gómez Department of Chemistry, Uppsala University, Sweden Docent Jonas Weissenrieder Department of Materials and Nanophysics, Royal Institute of Technology (KTH), Sweden Substitute: Docent Lars Eriksson Department of Materials and Environmental Chemistry, Stockholm University, Sweden Abstract Over the past decade, electron diffraction methods have aroused more and more interest for micro-crystal structure determination. Compared to tradi- tional X-ray diffraction, electron diffraction breaks the size limitation of the crystals studied, but at the same time it also suffers from much stronger dy- namical effects. While X-ray crystallography has been almost thoroughly developed, electron crystallography is still under active development. To be able to perform electron diffraction experiments, adequate skills for using a TEM are usually required, which makes ED experiments less accessible to average users than X-ray diffraction. Moreover, the relatively poor data sta- tistics from ED data prevented electron crystallography from being widely accepted in the crystallography community. The thesis focused on both application and method development of continu- ous rotation electron diffraction (cRED) technique. The cRED method was first applied to a beam sensitive metal-organic framework sample, Co-CAU- 36, and the structure was determined and refined within one working day. More importantly, the guest molecules in the pores were also located using only electron diffraction data. To facilitate general users to perform cRED data collection for useful data, software was developed to automate the over- all data collection procedure. Through combination of hierarchical cluster analysis tools, the automatically collected data showed comparable quality to those from recent publications, and thus were useful for structure determina- tion and even phase identification. To deal with dynamical refinement for ED data, a frame orientation refinement algorithm was designed to calculate accurate frame orientations for rotation data. Accuracy for the method was validated and compared to an existing software, and the behavior of TEM goniometer was studied by applying the method to an experimental data set. Keywords: electron crystallography; structure determination; structure re- finement; metal-organic framework; guest molecules; software development; automation; hierarchical cluster analyses; high-throughput data processing; data merging; frame orientations; least-squares optimization; data pro- cessing; TEM goniometer. List of papers Paper I: A porous cobalt tetraphosphonate metal-organic framework: accurate struc- ture and guest molecule location determined by continuous-rotation electron diffraction Bin Wang#, Timo Rhauderwiek#, A. Ken Inge, Hongyi Xu, Taimin Yang, Zhehao Huang, Norbert Stock, Xiaodong Zou. Chem. Eur. J., 2018, 24, 17429-17433. (# Equal contribution) Scientific contributions: I determined the structure using the cRED data and compared numerically the refinement results from different data sets. I wrote the manuscript. Paper II: Automated serial rotation electron diffraction combined with cluster analy- sis: an efficient multi-crystal workflow for structure determination Bin Wang, Xiaodong Zou, Stef Smeets. IUCrJ., 2019. Under review. Scientific contributions: I designed and scripted the automated experiment workflow in Python, and conducted the experiments for the test samples. I processed the automatically collected data using the hierarchical cluster analysis scripts and performed structure determination and refinement. I wrote the manuscript. Paper III: High-throughput continuous rotation electron diffraction data acquisition via software automation Magdalena Ola Cichocka, Jonas Ångström, Bin Wang, Xiaodong Zou, Stef Smeets. J. Appl. Cryst., 2018, 51, 1652-1661. Scientific contributions: I did early work of scripting the cRED method in Python as well as image format conversions. I assisted in manuscript writing. Paper IV: A method for accurate orientation determination for rotation electron diffrac- tion patterns Bin Wang, Wei Wan, David Waterman, Sven Hovmöller, Xiaodong Zou. In manuscript. Scientific contributions: I designed and implemented the algorithm in MATLAB, and conducted all the accuracy validation and test on the experi- mental data sets. I wrote the manuscript. Paper V: A method for determination of angular accuracy of the goniometer on a transmission electron microscope Bin Wang, Xiaodong Zou, Sven Hovmöller. In manuscript. Scientific contributions: I applied the method described in Paper IV on an experimental data set, and studied the goniometer and beam tilt accuracy in our microscope. I wrote the manuscript. Software I: Instamatic Stef Smeets, Bin Wang, Magdalena Ola Cichocka, Jonas Ångström, Wei Wan. Zenodo. 2018. DOI: 10.5281/zenodo.2026774. Scientific contributions: I implemented the cRED workflow in the software project, designed and implemented the SerialRED workflow, and some other minor contributions. I also mapped the interface for the Thermo Fisher Themis Z microscope and did some initial test. Contents Abbreviations .................................................................................................