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Park J, Nam KH. Experimental approaches for time-resolved serial femtosecond crystallography at PAL-XFEL. Methods Enzymol 2024; 709:131-160. [PMID: 39608942 DOI: 10.1016/bs.mie.2024.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2024]
Abstract
Understanding the structures and dynamics of biomolecules and chemical compounds is crucial for deciphering their molecular functions and mechanisms. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) is a useful technique for determining structures at room temperature, while minimizing radiation damage. Time-resolved serial femtosecond crystallography (TR-SFX), which uses an optical laser or a mixing device, allows molecular dynamic visualization during a reaction at specific time points. Because the XFEL beamline has unique properties for beams and instruments, understanding the beamline system is essential to conduct TR-SFX experiments and develop related technologies. In this study, we introduce an experimental system for performing TR-SFX using a Nano Crystallography and Coherent Imaging (NCI) experimental hutch at the Pohang Accelerator Laboratory XFEL (PAL-XFEL). Specifically, we present the XFEL properties of the PAL-XFEL and the main instruments in the NCI experimental hutch. In addition, the characteristics and uses of the sample delivery methods for TR-SFX and the general sample preparation process are discussed. Furthermore, the general time schedule and experimental procedures for TR-SFX during the beam time are outlined, along with data analysis programs. This chapter contributes to understanding the performance of TR-SFX experiments conducted at the PAL-XFEL NCI experimental hutch.
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Affiliation(s)
- Jaehyun Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.
| | - Ki Hyun Nam
- College of General Education, Kookmin University, Seoul, Republic of Korea.
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Choi TK, Park J, Kim G, Jang H, Park SY, Sohn JH, Cho BI, Kim H, Kim KS, Nam I, Chun SH. Resonant X-ray emission spectroscopy using self-seeded hard X-ray pulses at PAL-XFEL. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:1038-1047. [PMID: 37738032 PMCID: PMC10624040 DOI: 10.1107/s1600577523007312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
Self-seeded hard X-ray pulses at PAL-XFEL were used to commission a resonant X-ray emission spectroscopy experiment with a von Hamos spectrometer. The self-seeded beam, generated through forward Bragg diffraction of the [202] peak in a 100 µm-thick diamond crystal, exhibited an average bandwidth of 0.54 eV at 11.223 keV. A coordinated scanning scheme of electron bunch energy, diamond crystal angle and silicon monochromator allowed us to map the Ir Lβ2 X-ray emission lines of IrO2 powder across the Ir L3-absorption edge, from 11.212 to 11.242 keV with an energy step of 0.3 eV. This work provides a reference for hard X-ray emission spectroscopy experiments utilizing self-seeded pulses with a narrow bandwidth, eventually applicable for pump-probe studies in solid-state and diluted systems.
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Affiliation(s)
- Tae-Kyu Choi
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jaeku Park
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyujin Kim
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hoyoung Jang
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sang-Youn Park
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jang Hyeob Sohn
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Byoung Ick Cho
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hyunjung Kim
- Department of Physics, Sogang University, Seoul 04107, Republic of Korea
| | - Kyung Sook Kim
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Inhyuk Nam
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sae Hwan Chun
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
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Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
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Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
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Singh JP, Paidi AK, Chae KH, Lee S, Ahn D. Synchrotron radiation based X-ray techniques for analysis of cathodes in Li rechargeable batteries. RSC Adv 2022; 12:20360-20378. [PMID: 35919598 PMCID: PMC9277717 DOI: 10.1039/d2ra01250b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/15/2022] [Indexed: 01/21/2023] Open
Abstract
Li-ion rechargeable batteries are promising systems for large-scale energy storage solutions. Understanding the electrochemical process in the cathodes of these batteries using suitable techniques is one of the crucial steps for developing them as next-generation energy storage devices. Due to the broad energy range, synchrotron X-ray techniques provide a better option for characterizing the cathodes compared to the conventional laboratory-scale characterization instruments. This work gives an overview of various synchrotron radiation techniques for analyzing cathodes of Li-rechargeable batteries by depicting instrumental details of X-ray diffraction, X-ray absorption spectroscopy, X-ray imaging, and X-ray near-edge fine structure-imaging. Analysis and simulation procedures to get appropriate information of structural order, local electronic/atomic structure, chemical phase mapping and pores in cathodes are discussed by taking examples of various cathode materials. Applications of these synchrotron techniques are also explored to investigate oxidation state, metal-oxygen hybridization, quantitative local atomic structure, Ni oxidation phase and pore distribution in Ni-rich layered oxide cathodes.
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Affiliation(s)
- Jitendra Pal Singh
- Pohang Accelerator Laboratory, Pohang University of Science and Technology Pohang-37673 Republic of Korea
- Department of Physics, Manav Rachna University Faridabad-121004 Haryana India
| | - Anil Kumar Paidi
- Pohang Accelerator Laboratory, Pohang University of Science and Technology Pohang-37673 Republic of Korea
| | - Keun Hwa Chae
- Advanced Analysis Center, Korea Institute of Science and Technology Seoul-02792 Republic of Korea
| | - Sangsul Lee
- Pohang Accelerator Laboratory, Pohang University of Science and Technology Pohang-37673 Republic of Korea
- Xavisoptics Pohang-37673 Republic of Korea
| | - Docheon Ahn
- Pohang Accelerator Laboratory, Pohang University of Science and Technology Pohang-37673 Republic of Korea
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