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Paulson L, Narayanasamy SR, Shelby ML, Frank M, Trebbin M. Advanced manufacturing provides tailor-made solutions for crystallography with x-ray free-electron lasers. Struct Dyn 2024; 11:011101. [PMID: 38389979 PMCID: PMC10883715 DOI: 10.1063/4.0000229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Serial crystallography at large facilities, such as x-ray free-electron lasers and synchrotrons, evolved as a powerful method for the high-resolution structural investigation of proteins that are critical for human health, thus advancing drug discovery and novel therapies. However, a critical barrier to successful serial crystallography experiments lies in the efficient handling of the protein microcrystals and solutions at microscales. Microfluidics are the obvious approach for any high-throughput, nano-to-microliter sample handling, that also requires design flexibility and rapid prototyping to deal with the variable shapes, sizes, and density of crystals. Here, we discuss recent advances in polymer 3D printing for microfluidics-based serial crystallography research and present a demonstration of emerging, large-scale, nano-3D printing approaches leading into the future of 3D sample environment and delivery device fabrication from liquid jet gas-dynamic virtual nozzles devices to fixed-target sample environment technology.
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Affiliation(s)
- Lars Paulson
- Department of Chemistry & Research and Education in Energy, Environment and Water (RENEW), The State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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2
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Liu Z, Gu KK, Shelby ML, Gilbile D, Lyubimov AY, Russi S, Cohen AE, Narayanasamy SR, Botha S, Kupitz C, Sierra RG, Poitevin F, Gilardi A, Lisova S, Coleman MA, Frank M, Kuhl TL. A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography. Acta Crystallogr D Struct Biol 2023; 79:944-952. [PMID: 37747292 PMCID: PMC10565732 DOI: 10.1107/s2059798323007027] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip, 21, 4831-4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.
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Affiliation(s)
- Zhongrui Liu
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
| | - Kevin K. Gu
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Deepshika Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Fredric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Antonio Gilardi
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Radiation Oncology, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Matthias Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Tonya L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA
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3
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Gu KK, Liu Z, Narayanasamy SR, Shelby ML, Chan N, Coleman MA, Frank M, Kuhl TL. All polymer microfluidic chips-A fixed target sample delivery workhorse for serial crystallography. Biomicrofluidics 2023; 17:051302. [PMID: 37840537 PMCID: PMC10576627 DOI: 10.1063/5.0167164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around "workhorse" for serial crystallography measurements. This Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.
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Affiliation(s)
- Kevin K. Gu
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | - Zhongrui Liu
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Nicholas Chan
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | | | | | - Tonya L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
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4
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Jernigan RJ, Logeswaran D, Doppler D, Nagaratnam N, Sonker M, Yang JH, Ketawala G, Martin-Garcia JM, Shelby ML, Grant TD, Mariani V, Tolstikova A, Sheikh MZ, Yung MC, Coleman MA, Zaare S, Kaschner EK, Rabbani MT, Nazari R, Zacks MA, Hayes B, Sierra RG, Hunter MS, Lisova S, Batyuk A, Kupitz C, Boutet S, Hansen DT, Kirian RA, Schmidt M, Fromme R, Frank M, Ros A, Chen JJL, Botha S, Fromme P. Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser. Structure 2023; 31:138-151.e5. [PMID: 36630960 PMCID: PMC9830665 DOI: 10.1016/j.str.2022.12.009] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/08/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023]
Abstract
NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.
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Affiliation(s)
- Rebecca J Jernigan
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Dhenugen Logeswaran
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Diandra Doppler
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Nirupa Nagaratnam
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mukul Sonker
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jay-How Yang
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Gihan Ketawala
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jose M Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main Street, Buffalo, NY 14203, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Michelle Z Sheikh
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mimi Cho Yung
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Sahba Zaare
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Fulton School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Emily K Kaschner
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Mohammad Towshif Rabbani
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Reza Nazari
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Michele A Zacks
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Debra T Hansen
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Raimund Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Alexandra Ros
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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5
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, Ros A. Co-flow injection for serial crystallography at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:1-13. [PMID: 35153640 PMCID: PMC8805165 DOI: 10.1107/s1600576721011079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dai Hyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joe Chen
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Faisal H. M. Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jayhow Yang
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohamed Youssef
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Saša Bajt
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Megan L. Shelby
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Matt A. Coleman
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christopher Kuptiz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sahba Zaare
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Zachary Dobson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Erin Discianno
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Shangji Zhang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - James D. Zook
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | | | - Adam R. Round
- European XFEL, Schenefeld, Germany,School of Chemical and Physical Sciences, Keele University, Staffordshire, UK
| | - Patrik Vagovic
- European XFEL, Schenefeld, Germany,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | | | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Natasha E. Stander
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Tien L. Olson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Katherine Morin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jyotirmory Mondal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - José Domingo Meza-Aguilar
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,European XFEL, Schenefeld, Germany
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sara Vaiana
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, CSIC, Madrid, Spain
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Barry D. Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Adrian P. Mancuso
- European XFEL, Schenefeld, Germany,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Thomas Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Richard A. Kirian
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Correspondence e-mail:
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6
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Gilbile D, Shelby ML, Lyubimov AY, Wierman JL, Monteiro DCF, Cohen AE, Russi S, Coleman MA, Frank M, Kuhl TL. Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography. Lab Chip 2021; 21:4831-4845. [PMID: 34821226 PMCID: PMC8915944 DOI: 10.1039/d1lc00810b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The practice of serial X-ray crystallography (SX) depends on efficient, continuous delivery of hydrated protein crystals while minimizing background scattering. Of the two major types of sample delivery devices, fixed-target devices offer several advantages over widely adopted jet injectors, including: lower sample consumption, clog-free delivery, and the ability to control on-chip crystal density to improve hit rates. Here we present our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial measurements at both synchrotrons and X-ray free electron lasers (XFELs). Our design includes highly X-ray-transparent enclosing thin film layers tuned to minimize scatter background, adaptable sample flow layers tuned to match crystal size, and a large sample area compatible with both raster scanning and rotation based serial data collection. The optically transparent chips can be used both for in situ protein crystallization (to eliminate crystal handling) or crystal slurry loading, with prepared samples stable for weeks in a humidified environment and for several hours in ambient conditions. Serial oscillation crystallography, using a multi-crystal rotational data collection approach, at a microfocus synchrotron beamline (SSRL, beamline 12-1) was used to benchmark the performance of the chips. High-resolution structures (1.3-2.7 Å) were collected from five different proteins - hen egg white lysozyme, thaumatin, bovine liver catalase, concanavalin-A (type VI), and SARS-CoV-2 nonstructural protein NSP5. Overall, our modular fabrication approach enables precise control over the cross-section of materials in the X-ray beam path and facilitates chip adaption to different sample and beamline requirements for user-friendly, straightforward diffraction measurements at room temperature.
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Affiliation(s)
- Deepshika Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
| | - Megan L Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Artem Y Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Diana C F Monteiro
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew A Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Radiation Oncology, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Matthias Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Tonya L Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
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7
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Shelby ML, Wildman A, Hayes D, Mara MW, Lestrange PJ, Cammarata M, Balducci L, Artamonov M, Lemke HT, Zhu D, Seideman T, Hoffman BM, Li X, Chen LX. Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations. Proc Natl Acad Sci U S A 2021; 118:e2018966118. [PMID: 33782122 PMCID: PMC8040624 DOI: 10.1073/pnas.2018966118] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ultrafast structural dynamics with different spatial and temporal scales were investigated during photodissociation of carbon monoxide (CO) from iron(II)-heme in bovine myoglobin during the first 3 ps following laser excitation. We used simultaneous X-ray transient absorption (XTA) spectroscopy and X-ray transient solution scattering (XSS) at an X-ray free electron laser source with a time resolution of 80 fs. Kinetic traces at different characteristic X-ray energies were collected to give a global picture of the multistep pathway in the photodissociation of CO from heme. In order to extract the reaction coordinates along different directions of the CO departure, XTA data were collected with parallel and perpendicular relative polarizations of the laser pump and X-ray probe pulse to isolate the contributions of electronic spin state transition, bond breaking, and heme macrocycle nuclear relaxation. The time evolution of the iron K-edge X-ray absorption near edge structure (XANES) features along the two major photochemical reaction coordinates, i.e., the iron(II)-CO bond elongation and the heme macrocycle doming relaxation were modeled by time-dependent density functional theory calculations. Combined results from the experiments and computations reveal insight into interplays between the nuclear and electronic structural dynamics along the CO photodissociation trajectory. Time-resolved small-angle X-ray scattering data during the same process are also simultaneously collected, which show that the local CO dissociation causes a protein quake propagating on different spatial and temporal scales. These studies are important for understanding gas transport and protein deligation processes and shed light on the interplay of active site conformational changes and large-scale protein reorganization.
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Affiliation(s)
- Megan L Shelby
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Dugan Hayes
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
| | - Michael W Mara
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | | | - Marco Cammarata
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Lodovico Balducci
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Maxim Artamonov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Tamar Seideman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195;
| | - Lin X Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
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8
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Gisriel C, Coe J, Letrun R, Yefanov OM, Luna-Chavez C, Stander NE, Lisova S, Mariani V, Kuhn M, Aplin S, Grant TD, Dörner K, Sato T, Echelmeier A, Cruz Villarreal J, Hunter MS, Wiedorn MO, Knoska J, Mazalova V, Roy-Chowdhury S, Yang JH, Jones A, Bean R, Bielecki J, Kim Y, Mills G, Weinhausen B, Meza JD, Al-Qudami N, Bajt S, Brehm G, Botha S, Boukhelef D, Brockhauser S, Bruce BD, Coleman MA, Danilevski C, Discianno E, Dobson Z, Fangohr H, Martin-Garcia JM, Gevorkov Y, Hauf S, Hosseinizadeh A, Januschek F, Ketawala GK, Kupitz C, Maia L, Manetti M, Messerschmidt M, Michelat T, Mondal J, Ourmazd A, Previtali G, Sarrou I, Schön S, Schwander P, Shelby ML, Silenzi A, Sztuk-Dambietz J, Szuba J, Turcato M, White TA, Wrona K, Xu C, Abdellatif MH, Zook JD, Spence JCH, Chapman HN, Barty A, Kirian RA, Frank M, Ros A, Schmidt M, Fromme R, Mancuso AP, Fromme P, Zatsepin NA. Membrane protein megahertz crystallography at the European XFEL. Nat Commun 2019; 10:5021. [PMID: 31685819 PMCID: PMC6828683 DOI: 10.1038/s41467-019-12955-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/07/2019] [Indexed: 12/02/2022] Open
Abstract
The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs. The European X-ray free-electron laser (EuXFEL) in Hamburg is the first XFEL with a megahertz repetition rate. Here the authors present the 2.9 Å structure of the large membrane protein complex Photosystem I from T. elongatus that was determined at the EuXFEL.
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Affiliation(s)
- Chris Gisriel
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Jesse Coe
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Cesar Luna-Chavez
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Natasha E Stander
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Stella Lisova
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Manuela Kuhn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Thomas D Grant
- Hauptman-Woodward Institute, 700 Ellicott St, Buffalo, NY, 14203-1102, USA.,Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 700 Ellicott St, Buffalo, NY, 14203-1102, USA
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Austin Echelmeier
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Jorvani Cruz Villarreal
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Shatabdi Roy-Chowdhury
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Jay-How Yang
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Alex Jones
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Jose D Meza
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Saša Bajt
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Gerrit Brehm
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Institute for X-Ray Physics, University of Göttingen, 37077, Göttingen, Germany.,Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | | | - Sandor Brockhauser
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Barry D Bruce
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996.,Program in Energy Science and Engineering, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996.,Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | - Erin Discianno
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Zachary Dobson
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Hans Fangohr
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,University of Southampton, University Rd, Southampton, SO17 1BJ, UK
| | - Jose M Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstraße 20, 21079, Hamburg, Germany
| | - Steffen Hauf
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Friederike Januschek
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Gihan K Ketawala
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA.,Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Luis Maia
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Marc Messerschmidt
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas Michelat
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jyotirmoy Mondal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA, 37996
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | | | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | | | - Janusz Szuba
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Monica Turcato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Krzysztof Wrona
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Chen Xu
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Mohamed H Abdellatif
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - James D Zook
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - John C H Spence
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Alexandra Ros
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Raimund Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
| | - Nadia A Zatsepin
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA. .,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA. .,ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia.
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9
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Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
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Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
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10
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Wiedorn MO, Oberthür D, Bean R, Schubert R, Werner N, Abbey B, Aepfelbacher M, Adriano L, Allahgholi A, Al-Qudami N, Andreasson J, Aplin S, Awel S, Ayyer K, Bajt S, Barák I, Bari S, Bielecki J, Botha S, Boukhelef D, Brehm W, Brockhauser S, Cheviakov I, Coleman MA, Cruz-Mazo F, Danilevski C, Darmanin C, Doak RB, Domaracky M, Dörner K, Du Y, Fangohr H, Fleckenstein H, Frank M, Fromme P, Gañán-Calvo AM, Gevorkov Y, Giewekemeyer K, Ginn HM, Graafsma H, Graceffa R, Greiffenberg D, Gumprecht L, Göttlicher P, Hajdu J, Hauf S, Heymann M, Holmes S, Horke DA, Hunter MS, Imlau S, Kaukher A, Kim Y, Klyuev A, Knoška J, Kobe B, Kuhn M, Kupitz C, Küpper J, Lahey-Rudolph JM, Laurus T, Le Cong K, Letrun R, Xavier PL, Maia L, Maia FRNC, Mariani V, Messerschmidt M, Metz M, Mezza D, Michelat T, Mills G, Monteiro DCF, Morgan A, Mühlig K, Munke A, Münnich A, Nette J, Nugent KA, Nuguid T, Orville AM, Pandey S, Pena G, Villanueva-Perez P, Poehlsen J, Previtali G, Redecke L, Riekehr WM, Rohde H, Round A, Safenreiter T, Sarrou I, Sato T, Schmidt M, Schmitt B, Schönherr R, Schulz J, Sellberg JA, Seibert MM, Seuring C, Shelby ML, Shoeman RL, Sikorski M, Silenzi A, Stan CA, Shi X, Stern S, Sztuk-Dambietz J, Szuba J, Tolstikova A, Trebbin M, Trunk U, Vagovic P, Ve T, Weinhausen B, White TA, Wrona K, Xu C, Yefanov O, Zatsepin N, Zhang J, Perbandt M, Mancuso AP, Betzel C, Chapman H, Barty A. Megahertz serial crystallography. Nat Commun 2018; 9:4025. [PMID: 30279492 PMCID: PMC6168542 DOI: 10.1038/s41467-018-06156-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 08/21/2018] [Indexed: 01/08/2023] Open
Abstract
The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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Grants
- Project oriented funds Helmholtz-Gemeinschaft (Helmholtz Gemeinschaft)
- DFG-EXC1074 Deutsche Forschungsgemeinschaft (German Research Foundation)
- R01 GM117342 NIGMS NIH HHS
- R01 GM095583 NIGMS NIH HHS
- 609920 European Research Council
- Wellcome Trust
- : The Helmholtz organisation through program oriented funds; excellence cluster "The Hamburg Center for Ultrafast Imaging – Structure, Dynamics and Control of Matter at the Atomic Scale" of the Deutsche Forschungsgemeinschaft (CUI, DFG-EXC1074); the European Research Council, “Frontiers in Attosecond X-ray Science: Imaging and Spectroscopy (AXSIS)”, ERC-2013-SyG 609920 (2014-2018); the Gottfried Wilhelm Leibniz Program of the DFG; the project “X-probe” funded by the European Union’s 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant agreement 637295; the BMBF German-Russian Cooperation “SyncFELMed” grant 05K14CHA; European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the Consolidator Grant COMOTION (ERC-614507-Küpper); the Helmholtz Gemeinschaft through the "Impuls und Vernetzungsfond"; Helmholtz Initiative and Networking Fund through the Young Investigators Program and by the Deutsche Forschungsgemeinschaft SFB755/B03; the Swedish Research Council; the Knut and Alice Wallenberg Foundation; the Röntgen-Angström Cluster; the BMBF via projects 05K13GU7 and 05E13GU1; the from Ministry of Education, Science, Research and Sport of the Slovak Republic; the Joachim Herz Stiftung; the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence “Inflammation at interfaces” (EXC 306); the Swedish Research Council; the Swedish Foundation for Strategic Research; the Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011]; the Australian Nuclear Science and Technology Organisation (ANSTO); the International Synchrotron Access Program (ISAP) managed by the Australian Synchrotron, part of ANSTO, and funded by the Australian Government; The projects Structural dynamics of biomolecular systems (CZ.02.1.01/0.0/0.0/15_003/0000447) (ELIBIO) and Advanced research using high intensity laser produced photons and particles (CZ.02.1.01/0.0/0.0/16_019/0000789) (ADONIS) from European Regional Development Fund, the Ministry of Education, Youth and Sports as part of targeted support from the National Programme of Sustainability II; the Röntgen Ångström Cluster; the Chalmers Area of Advance, Material science; the Project DPI2016-78887-C3-1-R, Ministerio de Economía y Competitividad; the Wellcome Trust (studentship 075491/04); Rutgers University, Newark; the Max Planck Society; the NSF-STC “BioXFEL” through award STC-1231306; the Slovak Research and Development Agency under contract APVV-14-0181; the Wellcome Trust; Helmholtz Strategic Investment funds; Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011], Australian Nuclear Science and Technology Organisation (ANSTO); The Swedish Research Council, the Knut and Alice Wallenberg Foundation, and the Röntgen-Angström Cluster, BMBF via projects 05K13GU7 and 05E13GU1, Ministry of Education, Science, Research and Sport of the Slovak Republic; BMBF grants 05K16GUA and 05K12GU3; the Joachim Herz Foundation through and Add-on Fellowship; NHMRC project grants 1107804 and 1108859, ARC Discovery Early Career Research Award (DE170100783); National Health and Medical Research Council (NHMRC grants 1107804, 1071659). BK is NHMRC Principal Research Fellow (1110971); National Science Foundation Grant # 1565180, "ABI Innovation: New Algorithms for Biological X-ray Free Electron Laser Data"; Diamond Light Source and from a Strategic Award from the Wellcome Trust and the Biotechnology and Biological Sciences Research Council (grant 102593); use of the XBI biological sample preparation laboratory, enabled by the XBI User Consortium. This work was performed, in part, under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. MLS, MAC and MF were supported by NIH grant 1R01GM117342-01
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Affiliation(s)
- Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robin Schubert
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Nadine Werner
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aschkan Allahgholi
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Kartik Ayyer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Sabine Botha
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sandor Brockhauser
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Igor Cheviakov
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | | | - Connie Darmanin
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Yang Du
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Hans Fangohr
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Engineering and the Environment, University of Southampton, SO17 1BJ, Southampton, UK
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Alfonso M Gañán-Calvo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstr. 20, 21079, Hamburg, Germany
| | | | - Helen Mary Ginn
- Division of Structural Biology, Headington, Oxford, OX3 7BN, UK
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Heinz Graafsma
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Mid Sweden University, Holmgatan 10, 85170, Sundsvall, Sweden
| | - Rita Graceffa
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Göttlicher
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
| | - Steffen Hauf
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Michael Heymann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Susannah Holmes
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Daniel A Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Siegfried Imlau
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexander Klyuev
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Manuela Kuhn
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christopher Kupitz
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Janine Mia Lahey-Rudolph
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Karoline Le Cong
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Luis Maia
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, 94720, CA, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Davide Mezza
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Thomas Michelat
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Diana C F Monteiro
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Astrid Münnich
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Julia Nette
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Keith A Nugent
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Theresa Nuguid
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Allen M Orville
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Gisel Pena
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Pablo Villanueva-Perez
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jennifer Poehlsen
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Lars Redecke
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Winnie Maria Riekehr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tatiana Safenreiter
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Tokushi Sato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Bernd Schmitt
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, 106 91, Sweden
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Robert L Shoeman
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Claudiu A Stan
- Physics Department, Rutgers University Newark, Newark, NJ, 07102, USA
| | - Xintian Shi
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Trebbin
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University at Buffalo, 359 Natural Sciences Complex, Buffalo, NY, 14260, USA
- Institute of Nanostructure and Solid State Physics, Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Ulrich Trunk
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrik Vagovic
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Krzysztof Wrona
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Chen Xu
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Jiaguo Zhang
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Markus Perbandt
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | | | - Christian Betzel
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
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11
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Hong J, Kelley MS, Shelby ML, Hayes DK, Hadt RG, Rimmerman D, Zhang X, Chen LX. The Nature of the Long-Lived Excited State in a Ni II Phthalocyanine Complex Investigated by X-Ray Transient Absorption Spectroscopy. ChemSusChem 2018; 11:2421-2428. [PMID: 29851241 DOI: 10.1002/cssc.201800777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/24/2018] [Indexed: 06/08/2023]
Abstract
The nature of the photoexcited state of octabutoxy nickel(II) phthalocyanine (NiPcOBu8 ) with a 500 ps lifetime was investigated by X-ray transient absorption (XTA) spectroscopy. Previous optical, vibrational, and computational studies have suggested that this photoexcited state has a ligand-to-metal charge transfer (LMCT) nature. By using XTA, which provides unambiguous information on the local electronic and nuclear configuration around the Ni center, the nature of the excited state of NiPcOBu8 was reassessed. Using X-ray probe pulses from a synchrotron source, the ground- and excited-state X-ray absorption spectra of NiPcOBu8 were measured. Based on the results, we identified that the excited state exhibits spectral features that are characteristic of a Ni1, 3 (3dz2 ,3dx2-y2 ) state rather than a LMCT state with a transiently reduced Ni center. This state resembles the (d,d) state of nickel(II) tetramesitylphorphyrin. The XTA features are rationalized based on the inherent cavity sizes of the macrocycles. These results may provide useful guidance for the design of photocatalysts in the future.
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Affiliation(s)
- Jiyun Hong
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Matthew S Kelley
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Megan L Shelby
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Dugan K Hayes
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Ryan G Hadt
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Dolev Rimmerman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Xiaoyi Zhang
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Lin X Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
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12
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Kohler L, Hayes D, Hong J, Carter TJ, Shelby ML, Fransted KA, Chen LX, Mulfort KL. Synthesis, structure, ultrafast kinetics, and light-induced dynamics of CuHETPHEN chromophores. Dalton Trans 2018; 45:9871-83. [PMID: 26924711 DOI: 10.1039/c6dt00324a] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Five heteroleptic Cu(i)bis(phenanthroline) chromophores with distinct variation in the steric bulk at the 2,9-phenanthroline position were synthesized using the HETPHEN method, and their ground and excited state properties are described. Analysis of the crystal structures reveals a significant distortion from tetrahedral geometry around the Cu(i) centre which is attributed to favourable aromatic interactions between the two phenanthroline ligands. Ultrafast and nanosecond transient optical spectroscopies reveal that the excited state lifetime can be tuned across two orders of magnitude up to 74 nanoseconds in acetonitrile by changing the 2,9-substituent from hydrogen to sec-butyl. X-ray transient absorption spectroscopy at the Cu K-edge confirmed Cu(i) oxidation to Cu(ii) and revealed a decrease of the Cu-N bond lengths in the excited state. The ground and excited state characterization presented here will guide the integration of CuHETPHEN chromophores into complex electron donor-acceptor architectures.
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Affiliation(s)
- Lars Kohler
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL 60439, USA.
| | - Dugan Hayes
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL 60439, USA.
| | - Jiyun Hong
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Tyler J Carter
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL 60439, USA.
| | - Megan L Shelby
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Kelly A Fransted
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL 60439, USA.
| | - Lin X Chen
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL 60439, USA. and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Karen L Mulfort
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL 60439, USA.
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13
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Chen LX, Shelby ML, Lestrange PJ, Jackson NE, Haldrup K, Mara MW, Stickrath AB, Zhu D, Lemke H, Chollet M, Hoffman BM, Li X. Imaging ultrafast excited state pathways in transition metal complexes by X-ray transient absorption and scattering using X-ray free electron laser source. Faraday Discuss 2016; 194:639-658. [PMID: 27711898 PMCID: PMC5177475 DOI: 10.1039/c6fd00083e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This report will describe our recent studies of transition metal complex structural dynamics on the fs and ps time scales using an X-ray free electron laser source, Linac Coherent Light Source (LCLS). Ultrafast XANES spectra at the Ni K-edge of nickel(ii) tetramesitylporphyrin (NiTMP) were measured for optically excited states at a timescale from 100 fs to 50 ps, providing insight into its sub-ps electronic and structural relaxation processes. Importantly, a transient reduced state Ni(i) (π, 3dx2-y2) electronic state is captured through the interpretation of a short-lived excited state absorption on the low-energy shoulder of the edge, which is aided by the computation of X-ray transitions for postulated excited electronic states. The observed and computed inner shell to valence orbital transition energies demonstrate and quantify the influence of the electronic configuration on specific metal orbital energies. A strong influence of the valence orbital occupation on the inner shell orbital energies indicates that one should not use the transition energy from 1s to other orbitals to draw conclusions about the d-orbital energies. For photocatalysis, a transient electronic configuration could influence d-orbital energies up to a few eV and any attempt to steer the reaction pathway should account for this to ensure that external energies can be used optimally in driving desirable processes. NiTMP structural evolution and the influence of the porphyrin macrocycle conformation on relaxation kinetics can be likewise inferred from this study.
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Affiliation(s)
- Lin X Chen
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, USA. and Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
| | - Megan L Shelby
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, USA. and Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
| | | | - Nicholas E Jackson
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, USA. and Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
| | - Kristoffer Haldrup
- Physics Department, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Michael W Mara
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
| | - Andrew B Stickrath
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, USA.
| | - Diling Zhu
- LCLS, SLAC National Laboratory, Menlo Park, CA 94025, USA
| | - Henrik Lemke
- LCLS, SLAC National Laboratory, Menlo Park, CA 94025, USA
| | | | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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14
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Haldrup K, Dohn AO, Shelby ML, Mara MW, Stickrath AB, Harpham MR, Huang J, Zhang X, Møller KB, Chakraborty A, Castellano FN, Tiede DM, Chen LX. Butterfly Deformation Modes in a Photoexcited Pyrazolate-Bridged Pt Complex Measured by Time-Resolved X-Ray Scattering in Solution. J Phys Chem A 2016; 120:7475-83. [DOI: 10.1021/acs.jpca.6b07728] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kristoffer Haldrup
- Physics
Department, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Asmus O. Dohn
- Physics
Department, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Megan L. Shelby
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael W. Mara
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | | | | | - Klaus B. Møller
- Physics
Department, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Arnab Chakraborty
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Felix N. Castellano
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | | | - Lin X. Chen
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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15
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Shelby ML, Lestrange PJ, Jackson NE, Haldrup K, Mara MW, Stickrath AB, Zhu D, Lemke H, Chollet M, Hoffman BM, Li X, Chen LX. Ultrafast Excited State Relaxation of a Metalloporphyrin Revealed by Femtosecond X-ray Absorption Spectroscopy. J Am Chem Soc 2016; 138:8752-64. [PMID: 27286410 PMCID: PMC5074555 DOI: 10.1021/jacs.6b02176] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photoexcited Nickel(II) tetramesitylporphyrin (NiTMP), like many open-shell metalloporphyrins, relaxes rapidly through multiple electronic states following an initial porphyrin-based excitation, some involving metal centered electronic configuration changes that could be harnessed catalytically before excited state relaxation. While a NiTMP excited state present at 100 ps was previously identified by X-ray transient absorption (XTA) spectroscopy at a synchrotron source as a relaxed (d,d) state, the lowest energy excited state (J. Am. Chem. Soc., 2007, 129, 9616 and Chem. Sci., 2010, 1, 642), structural dynamics before thermalization were not resolved due to the ∼100 ps duration of the available X-ray probe pulse. Using the femtosecond (fs) X-ray pulses of the Linac Coherent Light Source (LCLS), the Ni center electronic configuration from the initial excited state to the relaxed (d,d) state has been obtained via ultrafast Ni K-edge XANES (X-ray absorption near edge structure) on a time scale from hundreds of femtoseconds to 100 ps. This enabled the identification of a short-lived Ni(I) species aided by time-dependent density functional theory (TDDFT) methods. Computed electronic and nuclear structure for critical excited electronic states in the relaxation pathway characterize the dependence of the complex's geometry on the electron occupation of the 3d orbitals. Calculated XANES transitions for these excited states assign a short-lived transient signal to the spectroscopic signature of the Ni(I) species, resulting from intramolecular charge transfer on a time scale that has eluded previous synchrotron studies. These combined results enable us to examine the excited state structural dynamics of NiTMP prior to thermal relaxation and to capture intermediates of potential photocatalytic significance.
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Affiliation(s)
- Megan L. Shelby
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | | | - Nicholas E. Jackson
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Kristoffer Haldrup
- Physics Department, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Michael W. Mara
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Andrew B. Stickrath
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Diling Zhu
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Henrik Lemke
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Matthieu Chollet
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Lin X. Chen
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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16
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Mara MW, Bowman DN, Buyukcakir O, Shelby ML, Haldrup K, Huang J, Harpham MR, Stickrath AB, Zhang X, Stoddart JF, Coskun A, Jakubikova E, Chen LX. Electron Injection from Copper Diimine Sensitizers into TiO2: Structural Effects and Their Implications for Solar Energy Conversion Devices. J Am Chem Soc 2015; 137:9670-84. [PMID: 26154849 DOI: 10.1021/jacs.5b04612] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Copper(I) diimine complexes have emerged as low cost replacements for ruthenium complexes as light sensitizers and electron donors, but their shorter metal-to-ligand-charge-transfer (MLCT) states lifetimes and lability of transient Cu(II) species impede their intended functions. Two carboxylated Cu(I) bis-2,9-diphenylphenanthroline (dpp) complexes [Cu(I)(dpp-O(CH2CH2O)5)(dpp-(COOH)2)](+) and [Cu(I)(dpp-O(CH2CH2O)5)(dpp-(Φ-COOH)2)](+) (Φ = tolyl) with different linker lengths were synthesized in which the MLCT-state solvent quenching pathways are effectively blocked, the lifetime of the singlet MLCT state is prolonged, and the transient Cu(II) ligands are stabilized. Aiming at understanding the mechanisms of structural influence to the interfacial charge transfer in the dye-sensitized solar cell mimics, electronic and geometric structures as well as dynamics for the MLCT state of these complexes and their hybrid with TiO2 nanoparticles were investigated using optical transient spectroscopy, X-ray transient absorption spectroscopy, time-dependent density functional theory, and quantum dynamics simulations. The combined results show that these complexes exhibit strong absorption throughout the visible spectrum due to the severely flattened ground state, and a long-lived charge-separated Cu(II) has been achieved via ultrafast electron injection (<300 fs) from the (1)MLCT state into TiO2 nanoparticles. The results also indicate that the TiO2-phen distance in these systems does not have significant effect on the efficiency of the interfacial electron-transfer process. The mechanisms for electron transfer in these systems are discussed and used to develop new strategies in optimizing copper(I) diimine complexes in solar energy conversion devices.
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Affiliation(s)
- Michael W Mara
- †Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - David N Bowman
- §Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
| | - Onur Buyukcakir
- ⊥Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Megan L Shelby
- †Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Kristoffer Haldrup
- ∥Centre for Molecular Movies, Department of Physics, NEXMAP Section, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | | | | | | | - J Fraser Stoddart
- †Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Ali Coskun
- ⊥Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Elena Jakubikova
- §Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
| | - Lin X Chen
- †Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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17
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Lohmiller T, Shelby ML, Long X, Yachandra VK, Yano J. Removal of Ca(2+) from the Oxygen-Evolving Complex in Photosystem II Has Minimal Effect on the Mn4O5 Core Structure: A Polarized Mn X-ray Absorption Spectroscopy Study. J Phys Chem B 2015; 119:13742-54. [PMID: 25989608 DOI: 10.1021/acs.jpcb.5b03559] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ca(2+)-depleted and Ca(2+)-reconstituted spinach photosystem II was studied using polarized X-ray absorption spectroscopy of oriented PS II preparations to investigate the structural and functional role of the Ca(2+) ion in the Mn4O5Ca cluster of the oxygen-evolving complex (OEC). Samples were prepared by low pH/citrate treatment as one-dimensionally ordered membrane layers and poised in the Ca(2+)-depleted S1 (S1') and S2 (S2') states, the S2'YZ(•) state, at which point the catalytic cycle of water oxidation is inhibited, and the Ca(2+)-reconstituted S1 state. Polarized Mn K-edge XANES and EXAFS spectra exhibit pronounced dichroism. Polarized EXAFS data of all states of Ca(2+)-depleted PS II investigated show only minor changes in distances and orientations of the Mn-Mn vectors compared to the Ca(2+)-containing OEC, which may be attributed to some loss of rigidity of the core structure. Thus, removal of the Ca(2+) ion does not lead to fundamental distortion or rearrangement of the tetranuclear Mn cluster, which indicates that the Ca(2+) ion in the OEC is not critical for structural maintenance of the cluster, at least in the S1 and S2 states, but fulfills a crucial catalytic function in the mechanism of the water oxidation reaction. On the basis of this structural information, reasons for the inhibitory effect of Ca(2+) removal are discussed, attributing to the Ca(2+) ion a fundamental role in organizing the surrounding (substrate) water framework and in proton-coupled electron transfer to YZ(•) (D1-Tyr161).
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Affiliation(s)
- Thomas Lohmiller
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Megan L Shelby
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Xi Long
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
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18
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Huang J, Mara MW, Stickrath AB, Kokhan O, Harpham MR, Haldrup K, Shelby ML, Zhang X, Ruppert R, Sauvage JP, Chen LX. A strong steric hindrance effect on ground state, excited state, and charge separated state properties of a Cu(I)-diimine complex captured by X-ray transient absorption spectroscopy. Dalton Trans 2015; 43:17615-23. [PMID: 25243795 DOI: 10.1039/c4dt02046d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photophysical and structural properties of a Cu(I) diimine complex with very strong steric hindrance, [Cu(I)(dppS)2](+) (dppS = 2,9-diphenyl-1,10-phenanthroline disulfonic acid disodium salt), are investigated by optical and X-ray transient absorption (OTA and XTA) spectroscopy. The bulky phenylsulfonic acid groups at 2,9 positions of phenanthroline ligands force the ground state and the metal-to-ligand charge-transfer (MLCT) excited state to adopt a flattened pseudo-tetrahedral coordination geometry in which the solvent access to the copper center is completely blocked. We analyzed the MLCT state dynamics and structures as well as those of the charge separated state resulting from the interfacial electron injection from the MLCT state to TiO2 nanoparticles (NPs). The OTA results show the absence of the sub-picosecond component previously assigned as the time constant for flattening, while the two observed time constants are assigned to a relatively slow intersystem crossing (ISC) rate (∼13.8 ps) and a decay rate (100 ns) of the [Cu(I)(dppS)2](+) MLCT state in water. These results correlate well with the XTA studies that resolved a flattened tetrahedral Cu(i) coordination geometry in the ground state. Probing the (3)MLCT state structure with XTA establishes that the (3)MLCT state has the same oxidation state as the copper center in [Cu(II)(dppS)2](2+) and the Cu-N distance is reduced by 0.06 Å compared to that of the ground state, accompanied by a rotation of phenyl rings located at 2,9 positions of phenanthroline. The structural dynamics of the photoinduced charge transfer process in the [Cu(I)(dppS)2](+)/TiO2 hybrid is also investigated, which suggests a more restricted environment for the complex upon binding to TiO2 NPs. Moreover, the Cu-N bond length of the oxidized state of [Cu(I)(dppS)2](+) after electron injection to TiO2 NPs shortens by 0.05 Å compared to that in the ground state. The interpretation of these observed structural changes associated with excited and charge separated states will be discussed. These results not only set an example for applying XTA in capturing the intermediate structure of metal complex/semiconductor NP hybrids but also provide guidance for designing efficient Cu(I) diimine complexes with optimized structures for application in solar-to-electricity conversion.
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Affiliation(s)
- J Huang
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA.
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19
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Abstract
The first ligand-exchange rate measurements of lanthanide ions in an ionic liquid are reported here. The trend of water-exchange rates in the ionic liquid is the opposite of the trend in water.
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Affiliation(s)
- Zhijin Lin
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA.
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20
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Shelby ML, Mara MW, Chen LX. New insight into metalloporphyrin excited state structures and axial ligand binding from X-ray transient absorption spectroscopic studies. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.05.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Fransted KA, Jackson NE, Zong R, Mara MW, Huang J, Harpham MR, Shelby ML, Thummel RP, Chen LX. Ultrafast Structural Dynamics of Cu(I)-Bicinchoninic Acid and Their Implications for Solar Energy Applications. J Phys Chem A 2014; 118:10497-506. [DOI: 10.1021/jp504294j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Kelly A. Fransted
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-3113, United States
| | - Nicholas E. Jackson
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60439, United States
| | - Ruifa Zong
- Department
of Chemistry, University of Houston, 4800 Calhoun Road, Houston, Texas 77204-5003, United States
| | - Michael W. Mara
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-3113, United States
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60439, United States
| | - Jier Huang
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-3113, United States
| | - Michael R. Harpham
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-3113, United States
| | - Megan L. Shelby
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-3113, United States
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60439, United States
| | - Randolph P. Thummel
- Department
of Chemistry, University of Houston, 4800 Calhoun Road, Houston, Texas 77204-5003, United States
| | - Lin X. Chen
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-3113, United States
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60439, United States
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22
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Bacchi M, Berggren G, Niklas J, Veinberg E, Mara MW, Shelby ML, Poluektov OG, Chen LX, Tiede DM, Cavazza C, Field MJ, Fontecave M, Artero V. Cobaloxime-Based Artificial Hydrogenases. Inorg Chem 2014; 53:8071-82. [DOI: 10.1021/ic501014c] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Marine Bacchi
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Gustav Berggren
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Jens Niklas
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Elias Veinberg
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR
CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | - Michael W. Mara
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Megan L. Shelby
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Lin X. Chen
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - David M. Tiede
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Christine Cavazza
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Martin J. Field
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR
CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | - Marc Fontecave
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 (Collège
de France, CNRS, Université Pierre et Marie Curie), 11 place Marcellin Berthelot 75005 Paris, France
| | - Vincent Artero
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
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23
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Vagnini MT, Mara MW, Harpham MR, Huang J, Shelby ML, Chen LX, Wasielewski MR. Interrogating the photogenerated Ir(iv) state of a water oxidation catalyst using ultrafast optical and X-ray absorption spectroscopy. Chem Sci 2013. [DOI: 10.1039/c3sc51511g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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24
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Khnayzer RS, Mara MW, Huang J, Shelby ML, Chen LX, Castellano FN. Structure and Activity of Photochemically Deposited “CoPi” Oxygen Evolving Catalyst on Titania. ACS Catal 2012. [DOI: 10.1021/cs3005192] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rony S. Khnayzer
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Michael W. Mara
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
Argonne, Illinois 60439, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113,
United States
| | - Jier Huang
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
Argonne, Illinois 60439, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113,
United States
| | - Megan L. Shelby
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
Argonne, Illinois 60439, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113,
United States
| | - Lin X. Chen
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
Argonne, Illinois 60439, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113,
United States
| | - Felix N. Castellano
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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