Hongyi XuResearcher

Advanced TEM (PhD Course), teaching assistant from 2015 to 2018, and lecturer since 2019.
Electron Crystallography, lecture since 2022.
Bioanalytical Chemistry, guest lecturer since 2020.
Experimental Chemistry methods, guest lecturer since 2020.

 

Research Supervision

Current:

Postdoc: 1 (main supervisor), 3 (co-supervisor), Stockholm University, Sweden
PhD student: 2 (main supervisor), 4 (co-supervisor), Stockholm University, Sweden

Alumni:

Postdoc:

Dr. Clabbers, M.T.B., postdoc at UCLA, USA

PhD student:

Dr. Taimin Yang, postdoc at SU

Dr. Jingjing Zhao, postdoc at Rosalind Franklin Institute, UK

Dr. Meng Ge, postdoc at University of Basel, Switzerland

Dr. Laura Samperisi, postdoc at Jean Rouxel Institute of Materials in Nantes, France

Dr. Molly Lightowler, Trainee Patent Attorney at Potter Clarkson, Sweden

Master Student:

Henri Bwanika, Research Assistant at Karolinska Institute

I have also mentored a PhD student at the Karolinska Institute, Sweden (graduated in Jan 2022). In addition, I have been actively helping Master and PhD students in learning electron microscopy and electron crystallography at Stockholm University and other institutions. I have worked with more than 15 universities internationally to set up 3D ED/MicroED at their TEM facilities.
 

 

Knowing the 3D atomic structures of materials and biomolecules is crucial for understanding their functions. X-ray diffraction is currently the most important technique for determination of 3D atomic structures, but requires large crystals which are often difficult to obtain. Due to the strong interactions between electrons and matter, crystals that are considered as powder in X-ray crystallography can be treated as single crystals by 3D electron diffraction methods. This enables structure determination of materials and organic molecules from micron- to nanometer-sized 3D crystals that are too small for conventional X-ray diffraction.

Over the past decades, a number of 3D ED methods have been developed for structure determination. Thanks to the recent advancement in CMOS and hybrid detector technology, it is now feasible to collect diffraction data in movie mode while continuously rotating the crystal (continuous rotation election diffraction, cRED, also known as MicroED in structural biology). Benefiting from these technological advances, structure determination can now be accomplished within few hours. Recently, fully automated serial rotation electron diffraction data collection and processing have been realized by our group. By using 3D ED and MicroED methods, we have solved more than 180 novel crystal structures of small inorganic compounds (including zeolite, MOF, COF and minerals) and organic molecules (pharmaceuticals, small organic molecules, peptides and proteins) in the past 6 years. We aim to further develop new electron crystallography methods and more importantly spread them to labs around the world.

 

Competitive Funding

1.    Swedish Research Council, Starting Grant (2017-005333) SEK 3.4M – Development of electron crystallography methods for structural characterisation of submicron-sized protein crystals, 2018-2021
2.    Swedish Foundation for Strategic Research, SSF Works (ITM17-0301, co-applicant) SEK 8.0M (My part: SEK 2.5M) – A multidimensional toolkit for modern electron microscopy, 2019-2021
3.    Scilifelab Technology Development Grant (co-applicant) SEK 2.2M – MicroED @ Scilifelab, 2019-2021
4.    European Commission Innovative Training Network (co-applicant) 4M Euro (my part: 270k Euro) – NanED, 2021-2025
5.    Swedish Research Council, Research Project (2022-03596) SEK 4M – Study structures of intermediates in the urate oxidase reaction by MicroED, 2023 – 2026
6.    Australian Research Council, Linkage Infrastructure, Equipment and Facilities Grant (LE230100145) AUD 1.13M, Main Chief Investigator – Nanocrystal Electron Diffraction Facility, 2023

 

Publications

Google Scholar

2023

P. B. Klar, Y. Krysiak, H. Xu, G. Steciuk, J. Cho, X. Zou, L. Palatinus, Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data. Nat. Chem. (2023), doi:10.1038/s41557-023-01186-1.

Q. Yao, L. Liu, S. Malola, M. Ge, H. Xu, Z. Wu, T. Chen, Y. Cao, M. F. Matus, A. Pihlajamäki, Y. Han, H. Häkkinen, J. Xie, Supercrystal engineering of atomically precise gold nanoparticles promoted by surface dynamics. Nat. Chem. 15, 230–239 (2023).

S. Li, M. Lightowler, X. Ou, S. Huang, Y. Jiang, X. Li, X. Zou, H. Xu*, M. Lu, Direct structure determination of vemurafenib polymorphism from compact spherulites using 3D electron diffraction. Commun Chem. 6, 18 (2023).

 

2022

M. Ge, T. Yang, H. Xu, X. Zou, Z. Huang, Direct Location of Organic Molecules in Framework Materials by Three-Dimensional Electron Diffraction. J. Am. Chem. Soc. 144, 15165–15174 (2022).

T. Yang, H. Xu*, X. Zou, Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method. J Appl Crystallogr. 55, 1583–1591 (2022).

V. E. G. Bengtsson, L. Pacoste, J. M. de la Rosa-Trevin, G. Hofer, X. Zou, H. Xu*, Scipion-ED : a graphical user interface for batch processing and analysis of 3D ED/MicroED data. J Appl Crystallogr. 55, 638–646 (2022).

T. Yang, T. Willhammar, H. Xu*, X. Zou*, Z. Huang*, Single-crystal structure determination of nanosized metal–organic frameworks by three-dimensional electron diffraction. Nat Protoc (2022), doi:10.1038/s41596-022-00720-8.

M. Lightowler, S. Li, X. Ou, X. Zou, M. Lu, H. Xu*, Indomethacin Polymorph δ Revealed To Be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction: Correcting a 47‐Year‐Old Misunderstanding**. Angewandte Chemie Intl Edit (2022), doi:10.1002/anie.202114985. (Front Cover)

 

2021

J. Zhao, H. Xu*, H. Lebrette, M. Carroni, H. Taberman, M. Högbom*, X. Zou*, A simple pressure-assisted method for MicroED specimen preparation. Nat Commun. 12, 5036 (2021).

T. Yang, S. Waitschat, A. K. Inge, N. Stock, X. Zou, H. Xu*, A Comparison of Structure Determination of Small Organic Molecules by 3D Electron Diffraction at Cryogenic and Room Temperature. Symmetry. 13, 2131 (2021).

K. Xiao, T. Yang, J. Liang, A. Rawal, H. Liu, R. Fang, R. Amal, H. Xu*, D.-W. Wang*, Nanofluidic voidless electrode for electrochemical capacitance enhancement in gel electrolyte. Nat Commun. 12, 5515 (2021).

Z. Wu, Q. Yao, Z. Liu, H. Xu*, P. Guo, L. Liu, Y. Han, K. Zhang, Z. Lu, X. Li, J. Zhang, J. Xie*, Multiscale Assembly of [AgS 4 ] Tetrahedrons into Hierarchical Ag–S Networks for Robust Photonic Water. Adv. Mater. 33, 2006459 (2021).

M. T. B. Clabbers, H. Xu*, Macromolecular crystallography using microcrystal electron diffraction. Acta Crystallogr D Struct Biol. 77, 313–324 (2021).

M. T. B. Clabbers, S. Holmes, T. W. Muusse, P. R. Vajjhala, S. J. Thygesen, A. K. Malde, D. J. B. Hunter, T. I. Croll, L. Flueckiger, J. D. Nanson, Md. H. Rahaman, A. Aquila, M. S. Hunter, M. Liang, C. H. Yoon, J. Zhao, N. A. Zatsepin, B. Abbey, E. Sierecki, Y. Gambin, K. J. Stacey, C. Darmanin*, B. Kobe*, H. Xu*, T. Ve*, MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun. 12, 2578 (2021).

J. Cho, Y. Yun, H. Xu, J. Sun, A. W. Burton, K. G. Strohmaier, G. Terefenko, H. Vroman, M. Afeworki, G. Cao, H. Wang, X. Zou, T. Willhammar, EMM-25: The Structure of Two-Dimensional 11 × 10 Medium-Pore Borosilicate Zeolite Unraveled Using 3D Electron Diffraction. Chem. Mater. 33, 4146–4153 (2021).

E. T. Broadhurst, H. Xu*, S. Parsons*, F. Nudelman*, Revealing the early stages of carbamazepine crystallization by cryoTEM and 3D electron diffraction. IUCrJ. 8, 860–866 (2021).

 

2020

H. Xu, J. Ångström, T. Eklund, K. Amann-Winkel, Electron Beam-Induced Transformation in High-Density Amorphous Ices. J. Phys. Chem. B. 124, 9283–9288 (2020).

M. Roslova, S. Smeets, B. Wang, T. Thersleff, H. Xu, X. Zou, InsteaDMatic : towards cross-platform automated continuous rotation electron diffraction. J Appl Crystallogr. 53, 1217–1224 (2020).

S. Leubner, V. E. G. Bengtsson, K. Synnatschke, J. Gosch, A. Koch, H. Reinsch, H. Xu, C. Backes, X. Zou, N. Stock, Synthesis and Exfoliation of a New Layered Mesoporous Zr-MOF Comprising Hexa- and Dodecanuclear Clusters as Well as a Small Organic Linker Molecule. J. Am. Chem. Soc. 142, 15995–16000 (2020).

S. Leubner, V. E. G. Bengtsson, A. K. Inge, M. Wahiduzzaman, F. Steinke, A. Jaworski, H. Xu, S. Halis, P. Rönfeldt, H. Reinsch, G. Maurin, X. Zou, N. Stock, Hexahydroxytriphenylene for the synthesis of group 13 MOFs – a new inorganic building unit in a β-cristobalite type structure. Dalton Trans. 49, 3088–3092 (2020).

E. S. Grape, H. Xu, O. Cheung, M. Calmels, J. Zhao, C. Dejoie, D. M. Proserpio, X. Zou, A. K. Inge, Breathing Metal–Organic Framework Based on Flexible Inorganic Building Units. Crystal Growth & Design. 20, 320–329 (2020).

M. T. B. Clabbers, H. Xu*, Microcrystal electron diffraction in macromolecular and pharmaceutical structure determination. Drug Discovery Today: Technologies, S1740674920300354 (2020).

M. T. B. Clabbers, S. Z. Fisher, M. Coinçon, X. Zou, H. Xu*, Visualizing drug binding interactions using microcrystal electron diffraction. Commun Biol. 3, 417 (2020).

M. O. Cichocka, Z. Liang, D. Feng, S. Back, S. Siahrostami, X. Wang, L. Samperisi, Y. Sun, H. Xu, N. Hedin, H. Zheng, X. Zou, H.-C. Zhou, Z. Huang, A Porphyrinic Zirconium Metal–Organic Framework for Oxygen Reduction Reaction: Tailoring the Spacing between Active-Sites through Chain-Based Inorganic Building Units. J. Am. Chem. Soc. 142, 15386–15395 (2020).

E. T. Broadhurst, H. Xu*, M. T. B. Clabbers, M. Lightowler, F. Nudelman, X. Zou*, S. Parsons*, Polymorph evolution during crystal growth studied by 3D electron diffraction. IUCrJ. 7, 5–9 (2020).

 

2019

Grape, E.S.; Xu, H.; Cheung, O.; Calmels, M.; Zhao, J.; Dejoie, C.; Proserpio, D.M.; Zou, X.; Inge, A.K. Crystal Growth & Design 2019, 20, 320-329.

Xu, H.; Zou, X. Science 2019, 364, 632-633

Lenzen, D.; Zhao, J.; Ernst, S-J.; Wahiduzzaman, M.; Inge A.K.; Frohlich, D.; Xu, H.; Bart, H-J.; Janiak, C.; Henninger, S.; Maurin, G.; Zou, X.; Stock, N. Nature Communications 2019, 1, 1-9.

Xu, H.*; Lebrette, H.; Clabbers M.T.B.; Zhao, J.; Griese, J.J.; Zou, X.; Hogbom, M. Science advances 2019, 5, eaax4621.

Kapaca, E.; Burton, A.; Terefenko, E.; Vroman, H.; Weston, S.C.; Kochersperger, M.; Afeworki, M.; Paur, C.; Koziol, L.; Ravikovitch, P.; Xu, H.; Zou, X.; Willhammar, T. Inorganic Chemistry 2019, 58, 12854-12858.

 

2018

Xu, H.; Lebrette, H. (Equal Contribution); Yang, T.; Srinivas, V.; Hovmoller, S.; Hogbom, M.; Zou, X.D. Structure 2018, 26, 667-675.

Yuan, S.; Qin, J.S.; Xu, H.Q.; Su, J.; Rossi, D.; Chen, Y.P.; Zhang, L.L.; Lollar, C.; Wang, Q.; Jiang, H.L.; Son, D.H.; Xu, H.; Huang, Z.H.; Zou, X.D.; Zhou, H.C. ACS Central Science 2018, 4, 105-111.

Wang, L.; Xu, H.; Yan, N.N.; Correll, S.; Xu S.T.; Guo, P.; Tian, P.; Liu Z.M. CrystEngComm 2018, 20, 699-702.

Yan, N.N.; Xu, H.; Zhang, W.N.; Sun, T.T.; Guo, P.; Tian, P.; Liu, Z.M.  Microporous Mesoporous Mater. 2018, 264, 55-59.

Wang, Y.C.; Yan, T.M.; Xu, H.; Zou, X.D.; Wan, W.   J. Appl. Crystallogr. 2018, 51, 1094-1101.

Carmona, F. J.; Maldonado, C.R.; Ikemura, S.; Romao, C.C.; Huang, Z.H.; Xu, H.; Zou, X.D.; Kitagawa, S.; Furukawa, S.; Barea, E. ACS Appl. Mater. Interfaces 2018, 10, 31158-31167.

Wang, B.; Rhauderwiek, T.; Inge, A.K.; Xu, H.; Yang, T.M.; Huang, Z.H.; Stock, N.; Zou, X.D. Chemistry – A European Journal 2018, 24, 17429-17433.

 

2017

Wang, Y.; Takki, S.; Cheung, O.; Xu, H.; Wan, W; Ohrstrom, L.; Inge, A.K. Chemical Communications 2017, 53, 7018-7021.

 

2016

Inge, A.K.; Köppen, M.; Su, J.; Feyand, M.; Xu, H.; Zou, X.; O’Keeffe, M.; Stock, N. Journal of the American Chemical Society 2016, 138, 1970-1976.

Shin, J.; Xu, H. (equal contribution); Seo, S.; Guo, P.; Min, J.G.; Wright, P.; Zou, X.; Hong S.B. Angewandte Chemie International Edition 2016, In-Press (doi: 10.1002/anie.201510726).

 

2015

Xia, C.; Ju, L.; Zhao, Y.; Xu, H.; Zhu, B.; Gao, F.; Lin, M.; Dai, Z.; Zou, X.; Shu, X. Chinese Journal of Catalysis 2015, 36, 845-854.

 

2014

Zhang, Z.; Lu, Z.; Xu, H.; Chen, P.; Lu, W.; Zou J. Nano Research 2014, 7,1640-1649.

Yang, T.; Liu, J.; Zhou, R.; Chen, Z.; Xu, H.; Qiao, S.; Monteiro, M. Journal of Materials Chemistry A 2014, 2, 18139-18146.

Yun, Y.; Wan, W.; Rabbani, F.; Su, J.; Xu, H.; Hovmöller, S.; Johnsson, M.; Zou, X. Journal of Applied Crystallography 2014, 47, 2048-2054.

 

2013

Cheng, L. N.; Chen, Z. G.; Yang, L.; Han, G.; Xu, H. Y.; Snyder, G. J.; Lu, G. Q.; Zou, J. Journal of Physical Chemistry C 2013, 117, 12458-12464.

Guo, Y. N.; Xu, H. Y.; Auchterlonie, G. J.; Burgess, T.; Joyce, H. J.; Gao, Q.; Tan, H. H.; Jagadish, C.; Shu, H. B.; Chen, X. S.; Lu, W.; Kim, Y.; Zou, J. Nano Letters 2013, 13, 643-650.

Liao, Z. M.; Chen, Z. G.; Lu, Z. Y.; Xu, H. Y.; Guo, Y. N.; Sun, W.; Zhang, Z.; Yang, L.; Chen, P. P.; Lu, W.; Zou, J. Applied Physics Letters 2013, 102, 063106.

Niu, Y. T.; Yu, M. H.; Hartono, S. B.; Yang, J.; Xu, H. Y.; Zhang, H. W.; Zhang, J.; Zou, J.; Dexter, A.; Gu, W. Y.; Yu, C. Z. Advanced Materials 2013, 25, 6233-6237.

Qian, K.; Zhou, L.; Liu, J.; Yang, J.; Xu, H. Y.; Yu, M. H.; Nouwens, A.; Zou, J.; Monteiro, M. J.; Yu, C. Z. Scientific Reports 2013, 3, 1415.

Sun, W.; Guo, Y. N.; Xu, H. Y.; Gao, Q.; Tan, H. H.; Jagadish, C.; Zou, J. Applied Physics Letters 2013, 103, 4, 223104.

Sun, W.; Guo, Y. N.; Xu, H. Y.; Liao, Z. M.; Gao, Q.; Tan, H. H.; Jagadish, C.; Zou, J. Journal of Physical Chemistry C 2013, 117, 19234-19238.

Wang, S. L.; Chen, G. L.; Huang, H.; Ma, S. J.; Xu, H. Y.; He, Y. H.; Zou, J. Nanotechnology 2013, 24, 505705.

Xu, H. Y.; Guo, Y. N.; Liao, Z. M.; Sun, W.; Gao, Q.; Tan, H. H.; Jagadish, C.; Zou, J. Applied Physics Letters 2013, 102, 203108.

Yang, L.; Chen, Z. G.; Han, G.; Cheng, L. N.; Xu, H. Y.; Zou, J. Crystal Growth & Design 2013, 13, 4796-4802.

Zhang, Z.; Lu, Z. Y.; Chen, P. P.; Xu, H. Y.; Guo, Y. N.; Liao, Z. M.; Shi, S. X.; Lu, W.; Zou, J. Applied Physics Letters 2013, 103, 073109.

Zhou, L.; Xu, H. Y.; Zhang, H. W.; Yang, J.; Hartono, S. B.; Qian, K.; Zou, J.; Yu, C. Z. Chemical Communication 2013, 49, 8695-8697.

Zong, X.; Thaweesak, S.; Xu, H. Y.; Xing, Z.; Zou, J.; Lu, G. Q.; Wang, L. Z. Physical Chemistry Chemical Physics 2013, 15, 12314-12321.

 

2012

Cheng, L. N.; Chen, Z. G.; Ma, S.; Zhang, Z. D.; Wang, Y.; Xu, H. Y.; Yang, L.; Han, G.; Jack, K.; Lu, G. Q.; Zou, J. Journal of the American Chemical Society 2012, 134, 18920-18923.

Kang, J. H.; Gao, Q.; Parkinson, P.; Joyce, H. J.; Tan, H. H.; Kim, Y.; Guo, Y.; Xu, H.; Zou, J.; Jagadish, C. Nanotechnology 2012, 23, 415702.

Xia, H.; Lu, Z. Y.; Li, T. X.; Parkinson, P.; Liao, Z. M.; Liu, F. H.; Lu, W.; Hu, W. D.; Chen, P. P.; Xu, H. Y.; Zou, J.; Jagadish, C. Acs Nano 2012, 6, 6005-6013.

Xu, H. Y.; Guo, Y. N.; Sun, W.; Liao, Z. M.; Burgess, T.; Lu, H. F.; Gao, Q.; Tan, H. H.; Jagadish, C.; Zou, J. Nanoscale Research Letters 2012, 7, 589.

Xu, H. Y.; Wang, Y.; Guo, Y. N.; Liao, Z. M.; Gao, Q.; Jiang, N.; Tan, H. H.; Jagadish, C.; Zou, J. Crystal Growth & Design 2012, 12, 2018-2022.

Xu, H. Y.; Wang, Y.; Guo, Y. N.; Liao, Z. M.; Gao, Q.; Tan, H. H.; Jagadish, C.; Zou, J. Nano Letters 2012, 12, 5744-5749.

 

2011

Kang, J. H.; Gao, Q.; Joyce, H. J.; Tan, H. H.; Jagadish, C.; Kim, Y.; Guo, Y. A.; Xu, H. Y.; Zou, J.; Fickenscher, M. A.; Smith, L. M.; Jackson, H. E.; Yarrison-Rice, J. M. Crystal Growth & Design 2011, 11, 3109-3114.

Wang, Y.; Liao, Z. M.; Xu, H. Y.; Xiu, F. X.; Kou, X. F.; Wang, K. L.; Drennan, J.; Zou, J. Nanoscale Research Letters 2011, 6, 24.

Yuan, P.; Sun, J. L.; Xu, H. Y.; Zhou, L.; Liu, J. Z.; Zhang, D. L.; Wang, Y. H.; Jack, K. S.; Drennan, J.; Zhao, D. Y.; Lu, G. Q.; Zou, X. D.; Zou, J.; Yu, C. Z. Chemistry of Materials 2011, 23, 229-238.

Zhou, W.; Ge, L.; Chen, Z. G.; Liang, F. L.; Xu, H. Y.; Motuzas, J.; Julbe, A.; Zhu, Z. H. Chemistry of Materials 2011, 23, 4193-4198.

 

2010

Chen, Z. G.; Cheng, L. N.; Xu, H. Y.; Liu, J. Z.; Zou, J.; Sekiguchi, T.; Lu, G. Q.; Cheng, H. M. Advanced Materials 2010, 22, 2376-2380.

Fu, L. T.; Chen, Z. G.; Wang, D. W.; Cheng, L. N.; Xu, H. Y.; Liu, J. Z.; Cong, H. T.; Lu, G. Q.; Zou, J. Journal of Physical Chemistry C 2010, 114, 9627-9633.

Kang, J. H.; Gao, Q.; Joyce, H. J.; Tan, H. H.; Jagadish, C.; Kim, Y.; Choi, D. Y.; Guo, Y.; Xu, H.; Zou, J.; Fickenscher, M. A.; Smith, L. M.; Jackson, H. E.; Yarrison-Rice, J. M. Nanotechnology 2010, 21, 035604.

Liu, J. Z.; Chen, J. H.; Yang, X. B.; Ren, S.; Wu, C. L.; Xu, H. Y.; Zou, J. Scripta Materialia 2010, 63, 1061-1064.

Wang, Y.; Xiu, F. X.; Xu, H. Y.; Li, D.; Kou, X. F.; Wang, K. L.; Jacob, A. P.; Zou, J. Journal of Crystal Growth 2010, 312, 3034-3039.

 

2009

Xu, H. Y.; Guo, Y. N.; Wang, Y.; Zou, J.; Kang, J. H.; Gao, Q.; Tan, H. H.; Jagadish, C. Journal of Applied Physics 2009, 106, 083514.