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Antolini C, Sosa Alfaro V, Reinhard M, Chatterjee G, Ribson R, Sokaras D, Gee L, Sato T, Kramer PL, Raj SL, Hayes B, Schleissner P, Garcia-Esparza AT, Lim J, Babicz JT, Follmer AH, Nelson S, Chollet M, Alonso-Mori R, van Driel TB. The Liquid Jet Endstation for Hard X-ray Scattering and Spectroscopy at the Linac Coherent Light Source. Molecules 2024; 29:2323. [PMID: 38792184 PMCID: PMC11124266 DOI: 10.3390/molecules29102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The ability to study chemical dynamics on ultrafast timescales has greatly advanced with the introduction of X-ray free electron lasers (XFELs) providing short pulses of intense X-rays tailored to probe atomic structure and electronic configuration. Fully exploiting the full potential of XFELs requires specialized experimental endstations along with the development of techniques and methods to successfully carry out experiments. The liquid jet endstation (LJE) at the Linac Coherent Light Source (LCLS) has been developed to study photochemistry and biochemistry in solution systems using a combination of X-ray solution scattering (XSS), X-ray absorption spectroscopy (XAS), and X-ray emission spectroscopy (XES). The pump-probe setup utilizes an optical laser to excite the sample, which is subsequently probed by a hard X-ray pulse to resolve structural and electronic dynamics at their intrinsic femtosecond timescales. The LJE ensures reliable sample delivery to the X-ray interaction point via various liquid jets, enabling rapid replenishment of thin samples with millimolar concentrations and low sample volumes at the 120 Hz repetition rate of the LCLS beam. This paper provides a detailed description of the LJE design and of the techniques it enables, with an emphasis on the diagnostics required for real-time monitoring of the liquid jet and on the spatiotemporal overlap methods used to optimize the signal. Additionally, various scientific examples are discussed, highlighting the versatility of the LJE.
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Affiliation(s)
- Cali Antolini
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Victor Sosa Alfaro
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Marco Reinhard
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Gourab Chatterjee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Ryan Ribson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Dimosthenis Sokaras
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Leland Gee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Takahiro Sato
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Patrick L. Kramer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Sumana Laxmi Raj
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Brandon Hayes
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Pamela Schleissner
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Angel T. Garcia-Esparza
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Jinkyu Lim
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
- Department of Energy and Environmental Engineering, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Jeffrey T. Babicz
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Alec H. Follmer
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA;
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Matthieu Chollet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
| | - Tim B. van Driel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; (C.A.); (V.S.A.); (M.R.); (G.C.); (R.R.); (D.S.); (L.G.); (T.S.); (P.L.K.); (S.L.R.); (B.H.); (P.S.); (A.T.G.-E.); (J.L.); (J.T.B.J.); (S.N.); (M.C.)
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Bacellar C, Kinschel D, Cannelli O, Sorokin B, Katayama T, Mancini GF, Rouxel JR, Obara Y, Nishitani J, Ito H, Ito T, Kurahashi N, Higashimura C, Kudo S, Cirelli C, Knopp G, Nass K, Johnson PJM, Wach A, Szlachetko J, Lima FA, Milne CJ, Yabashi M, Suzuki T, Misawa K, Chergui M. Femtosecond X-ray spectroscopy of haem proteins. Faraday Discuss 2021; 228:312-328. [PMID: 33565544 DOI: 10.1039/d0fd00131g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discuss our recently reported femtosecond (fs) X-ray emission spectroscopy results on the ligand dissociation and recombination in nitrosylmyoglobin (MbNO) in the context of previous studies on ferrous haem proteins. We also present a preliminary account of femtosecond X-ray absorption studies on MbNO, pointing to the presence of more than one species formed upon photolysis.
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Affiliation(s)
- Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Dominik Kinschel
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Oliviero Cannelli
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Boris Sorokin
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198, Japan
| | - Giulia F Mancini
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jeremy R Rouxel
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Yuki Obara
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Junichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hironori Ito
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Terumasa Ito
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Naoya Kurahashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, 7-1, Chiyoda, 102-8554 Tokyo, Japan
| | - Chika Higashimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Shotaro Kudo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Claudio Cirelli
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Karol Nass
- SwissFEL, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | | | - Anna Wach
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | | | | | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kazuhiko Misawa
- Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Bacellar C, Kinschel D, Mancini GF, Ingle RA, Rouxel J, Cannelli O, Cirelli C, Knopp G, Szlachetko J, Lima FA, Menzi S, Pamfilidis G, Kubicek K, Khakhulin D, Gawelda W, Rodriguez-Fernandez A, Biednov M, Bressler C, Arrell CA, Johnson PJM, Milne CJ, Chergui M. Spin cascade and doming in ferric hemes: Femtosecond X-ray absorption and X-ray emission studies. Proc Natl Acad Sci U S A 2020; 117:21914-21920. [PMID: 32848065 PMCID: PMC7486745 DOI: 10.1073/pnas.2009490117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The structure-function relationship is at the heart of biology, and major protein deformations are correlated to specific functions. For ferrous heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobins. Cytochrome c (Cyt c) has evolved to become an important electron-transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe Kα and Kβ X-ray emission spectroscopy (XES) with Fe K-edge X-ray absorption near-edge structure (XANES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the iron ion, causing the ferric heme to undergo doming, which we identify. We also argue that this pattern is common to a wide diversity of ferric heme proteins, raising the question of the biological relevance of doming in such proteins.
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Affiliation(s)
- Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Dominik Kinschel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giulia F Mancini
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Rebecca A Ingle
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jérémy Rouxel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Oliviero Cannelli
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Claudio Cirelli
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Kraków, Poland
| | | | - Samuel Menzi
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Georgios Pamfilidis
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | | | | | - Wojciech Gawelda
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznan, Poland
| | | | - Mykola Biednov
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
| | | | - Christopher A Arrell
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Christopher J Milne
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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Abstract
The well-known spherical complex optical potential (SCOP) and complex scattering potential-ionization contribution (CSP-ic) methods with appropriate modifications are applied to the CH3X (X = F, Cl, Br, and I) molecules to compute positron scattering cross sections, which rather is the first theoretical attempt to report the same. Besides, various inelastic cross sections are also predicted for the first time in this Article. We have utilized the multiscattering spherical complex optical potential (MSCOP) approach to derive these cross sections. In general, a reasonable accordance has been found between the present total cross sections and the experimental measurements. Apart from the inconsistency between the present theoretical and previous experimental cross sections in the low energy region, the present theory is found to produce consistent and reliable results at all other energies.
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Affiliation(s)
- Nidhi Sinha
- Atomic and Molecular Physics Lab, Department of Applied Physics , Indian Institute of Technology (Indian School of Mines) , Dhanbad - 826004 , Jharkhand , India
| | - Paresh Modak
- Atomic and Molecular Physics Lab, Department of Applied Physics , Indian Institute of Technology (Indian School of Mines) , Dhanbad - 826004 , Jharkhand , India
| | - Suvam Singh
- Atomic and Molecular Physics Lab, Department of Applied Physics , Indian Institute of Technology (Indian School of Mines) , Dhanbad - 826004 , Jharkhand , India
| | - Bobby Antony
- Atomic and Molecular Physics Lab, Department of Applied Physics , Indian Institute of Technology (Indian School of Mines) , Dhanbad - 826004 , Jharkhand , India
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Chergui M, Collet E. Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods. Chem Rev 2017; 117:11025-11065. [DOI: 10.1021/acs.chemrev.6b00831] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Majed Chergui
- Laboratoire
de Spectroscopie Ultrarapide (LSU), ISIC, and Lausanne Centre for
Ultrafast Science (LACUS), Faculté des Sciences de Base, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Eric Collet
- Univ Rennes 1, CNRS, Institut de Physique de Rennes, UMR 6251, UBL, Rennes F-35042, France
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Wang H, Yu C, Wei X, Gao Z, Xu GL, Sun DR, Li Z, Zhou Y, Li QJ, Zhang BB, Xu JQ, Wang L, Zhang Y, Tan YL, Tao Y. Development of picosecond time-resolved X-ray absorption spectroscopy by high-repetition-rate laser pump/X-ray probe at Beijing Synchrotron Radiation Facility. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:667-673. [PMID: 28452759 DOI: 10.1107/s1600577517003277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/28/2017] [Indexed: 05/23/2023]
Abstract
A new setup and commissioning of transient X-ray absorption spectroscopy are described, based on the high-repetition-rate laser pump/X-ray probe method, at the 1W2B wiggler beamline at the Beijing Synchrotron Radiation Facility. A high-repetition-rate and high-power laser is incorporated into the setup with in-house-built avalanche photodiodes as detectors. A simple acquisition scheme was applied to obtain laser-on and laser-off signals simultaneously. The capability of picosecond transient X-ray absorption spectroscopy measurement was demonstrated for a photo-induced spin-crossover iron complex in 6 mM solution with 155 kHz repetition rate.
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Affiliation(s)
- Hao Wang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Can Yu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Xu Wei
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Zhenhua Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Guang Lei Xu
- Accelerator Division, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Da Rui Sun
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Zhenjie Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Yangfan Zhou
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Qiu Ju Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Bing Bing Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Jin Qiang Xu
- Accelerator Division, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Lin Wang
- Accelerator Division, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Yan Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Ying Lei Tan
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
| | - Ye Tao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100049, People's Republic of China
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Kim KH, Kim J, Oang KY, Lee JH, Grolimund D, Milne CJ, Penfold TJ, Johnson SL, Galler A, Kim TW, Kim JG, Suh D, Moon J, Kim J, Hong K, Guérin L, Kim TK, Wulff M, Bressler C, Ihee H. Identifying the major intermediate species by combining time-resolved X-ray solution scattering and X-ray absorption spectroscopy. Phys Chem Chem Phys 2015; 17:23298-302. [PMID: 26300122 DOI: 10.1039/c5cp03686k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Identifying the intermediate species along a reaction pathway is a first step towards a complete understanding of the reaction mechanism, but often this task is not trivial. There has been a strong on-going debate: which of the three intermediates, the CHI2 radical, the CHI2-I isomer, and the CHI2(+) ion, is the dominant intermediate species formed in the photolysis of iodoform (CHI3)? Herein, by combining time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TR-XAS), we present strong evidence that the CHI2 radical is dominantly formed from the photolysis of CHI3 in methanol at 267 nm within the available time resolution of the techniques (∼20 ps for TRXL and ∼100 ps for TR-XAS). The TRXL measurement, conducted using the time-slicing scheme, detected no CHI2-I isomer within our signal-to-noise ratio, indicating that, if formed, the CHI2-I isomer must be a minor intermediate. The TR-XAS transient spectra measured at the iodine L1 and L3 edges support the same conclusion. The present work demonstrates that the application of these two complementary time-resolved X-ray methods to the same system can provide a detailed understanding of the reaction mechanism.
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Affiliation(s)
- Kyung Hwan Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea.
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NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy. Proc Natl Acad Sci U S A 2015; 112:12922-7. [PMID: 26438842 DOI: 10.1073/pnas.1424446112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diatomic ligands in hemoproteins and the way they bind to the active center are central to the protein's function. Using picosecond Fe K-edge X-ray absorption spectroscopy, we probe the NO-heme recombination kinetics with direct sensitivity to the Fe-NO binding after 532-nm photoexcitation of nitrosylmyoglobin (MbNO) in physiological solutions. The transients at 70 and 300 ps are identical, but they deviate from the difference between the static spectra of deoxymyoglobin and MbNO, showing the formation of an intermediate species. We propose the latter to be a six-coordinated domed species that is populated on a timescale of ∼ 200 ps by recombination with NO ligands. This work shows the feasibility of ultrafast pump-probe X-ray spectroscopic studies of proteins in physiological media, delivering insight into the electronic and geometric structure of the active center.
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Levantino M, Lemke HT, Schirò G, Glownia M, Cupane A, Cammarata M. Observing heme doming in myoglobin with femtosecond X-ray absorption spectroscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041713. [PMID: 26798812 PMCID: PMC4711634 DOI: 10.1063/1.4921907] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/20/2015] [Indexed: 05/19/2023]
Abstract
We report time-resolved X-ray absorption measurements after photolysis of carbonmonoxy myoglobin performed at the LCLS X-ray free electron laser with nearly 100 fs (FWHM) time resolution. Data at the Fe K-edge reveal that the photoinduced structural changes at the heme occur in two steps, with a faster (∼70 fs) relaxation preceding a slower (∼400 fs) one. We tentatively attribute the first relaxation to a structural rearrangement induced by photolysis involving essentially only the heme chromophore and the second relaxation to a residual Fe motion out of the heme plane that is coupled to the displacement of myoglobin F-helix.
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Affiliation(s)
- M Levantino
- Department of Physics and Chemistry, University of Palermo , Viale delle Scienze, 90128 Palermo, Italy
| | - H T Lemke
- LCLS, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - G Schirò
- CNRS - Institut de Biologie Structurale , Grenoble 38044, France
| | - M Glownia
- LCLS, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - A Cupane
- Department of Physics and Chemistry, University of Palermo , Viale delle Scienze, 90128 Palermo, Italy
| | - M Cammarata
- Department of Physics , UMR UR1-CNRS 6251, University of Rennes 1 , Rennes, France
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10
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11
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Lima FA, Penfold TJ, van der Veen RM, Reinhard M, Abela R, Tavernelli I, Rothlisberger U, Benfatto M, Milne CJ, Chergui M. Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy. Phys Chem Chem Phys 2014; 16:1617-31. [PMID: 24317683 DOI: 10.1039/c3cp53683a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.
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Affiliation(s)
- Frederico A Lima
- École Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, CH, Switzerland.
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13
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In-situ Characterization of Molecular Processes in Liquids by Ultrafast X-ray Absorption Spectroscopy. IN-SITU MATERIALS CHARACTERIZATION 2014. [DOI: 10.1007/978-3-642-45152-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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14
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Chen LX, Zhang X, Shelby ML. Recent advances on ultrafast X-ray spectroscopy in the chemical sciences. Chem Sci 2014. [DOI: 10.1039/c4sc01333f] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular snapshots obtained by ultrafast X-ray spectroscopy reveal new insight into fundamental reaction mechanisms at single electron and atomic levels.
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Affiliation(s)
- L. X. Chen
- Chemical Sciences and Engineering Division
- Argonne National Laboratory
- Lemont, USA
- Department of Chemistry
- Northwestern University
| | - X. Zhang
- X-ray Science Division
- Advance Photon Source
- Argonne National Laboratory
- Lemont, USA
| | - M. L. Shelby
- Department of Chemistry
- Northwestern University
- Evanston, USA
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15
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Mara MW, Shelby M, Stickrath A, Harpham M, Huang J, Zhang X, Hoffman BM, Chen LX. Electronic and Nuclear Structural Snapshots in Ligand Dissociation and Recombination Processes of Iron Porphyrin in Solution: A Combined Optical/X-ray Approach. J Phys Chem B 2013; 117:14089-98. [DOI: 10.1021/jp407094u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael W. Mara
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | - Megan Shelby
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | | | | | | | | | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | - Lin X. Chen
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
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16
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Borfecchia E, Garino C, Salassa L, Lamberti C. Synchrotron ultrafast techniques for photoactive transition metal complexes. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120132. [PMID: 23776294 DOI: 10.1098/rsta.2012.0132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In the last decade, the use of time-resolved X-ray techniques has revealed the structure of light-generated transient species for a wide range of samples, from small organic molecules to proteins. Time resolutions of the order of 100 ps are typically reached, allowing one to monitor thermally equilibrated excited states and capture their structure as a function of time. This review aims at providing a general overview of the application of time-resolved X-ray solution scattering (TR-XSS) and time-resolved X-ray absorption spectroscopy (TR-XAS), the two techniques prevalently employed in the investigation of light-triggered structural changes of transition metal complexes. In particular, we herein describe the fundamental physical principles for static XSS and XAS and illustrate the theory of time-resolved XSS and XAS together with data acquisition and analysis strategies. Selected pioneering examples of photoactive transition metal complexes studied by TR-XSS and TR-XAS are discussed in depth.
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Affiliation(s)
- Elisa Borfecchia
- Department of Chemistry, NIS Centre of Excellence, University of Turin, via P. Giuria 7, 10125 Turin, Italy
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18
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Stickrath AB, Mara MW, Lockard JV, Harpham MR, Huang J, Zhang X, Attenkofer K, Chen LX. Detailed Transient Heme Structures of Mb-CO in Solution after CO Dissociation: An X-ray Transient Absorption Spectroscopic Study. J Phys Chem B 2012; 117:4705-12. [DOI: 10.1021/jp3086705] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew B. Stickrath
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Michael W. Mara
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, 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
| | - Jenny V. Lockard
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Michael R. Harpham
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Jier Huang
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Xiaoyi Zhang
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Klaus Attenkofer
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Lin X. Chen
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, 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
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19
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Xu W, Marcelli A, Hampai D, Malfatti L, Innocenzi P, Schade U, Wu Z. New opportunity to investigate physico-chemical phenomena: time-resolved X-ray and IR concurrent analysis. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2011. [DOI: 10.1007/s12210-011-0145-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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20
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Lima FA, Milne CJ, Amarasinghe DCV, Rittmann-Frank MH, van der Veen RM, Reinhard M, Pham VT, Karlsson S, Johnson SL, Grolimund D, Borca C, Huthwelker T, Janousch M, van Mourik F, Abela R, Chergui M. A high-repetition rate scheme for synchrotron-based picosecond laser pump/x-ray probe experiments on chemical and biological systems in solution. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:063111. [PMID: 21721678 DOI: 10.1063/1.3600616] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We present the extension of time-resolved optical pump/x-ray absorption spectroscopy (XAS) probe experiments towards data collection at MHz repetition rates. The use of a high-power picosecond laser operating at an integer fraction of the repetition rate of the storage ring allows exploitation of up to two orders of magnitude more x-ray photons than in previous schemes based on the use of kHz lasers. Consequently, we demonstrate an order of magnitude increase in the signal-to-noise of time-resolved XAS of molecular systems in solution. This makes it possible to investigate highly dilute samples at concentrations approaching physiological conditions for biological systems. The simplicity and compactness of the scheme allows for straightforward implementation at any synchrotron beamline and for a wide range of x-ray probe techniques, such as time-resolved diffraction or x-ray emission studies.
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Affiliation(s)
- Frederico A Lima
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, 1015 Lausanne, Switzerland
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21
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Bressler C, Chergui M. Molecular Structural Dynamics Probed by Ultrafast X-Ray Absorption Spectroscopy. Annu Rev Phys Chem 2010; 61:263-82. [DOI: 10.1146/annurev.physchem.012809.103353] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, Station 6, CH-1015 Lausanne, Switzerland;
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22
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Westenhoff S, Nazarenko E, Malmerberg E, Davidsson J, Katona G, Neutze R. Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches. Acta Crystallogr A 2010; 66:207-19. [PMID: 20164644 PMCID: PMC2824530 DOI: 10.1107/s0108767309054361] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 12/16/2009] [Indexed: 11/26/2022] Open
Abstract
Time-resolved structural studies of proteins have undergone several significant developments during the last decade. Recent developments using time-resolved X-ray methods, such as time-resolved Laue diffraction, low-temperature intermediate trapping, time-resolved wide-angle X-ray scattering and time-resolved X-ray absorption spectroscopy, are reviewed. Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein’s resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein’s conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein’s reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.
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Affiliation(s)
- Sebastian Westenhoff
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
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23
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Chergui M. Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems. Acta Crystallogr A 2010; 66:229-39. [DOI: 10.1107/s010876730904968x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Accepted: 11/19/2009] [Indexed: 11/10/2022] Open
Abstract
The need to visualize molecular structure in the course of a chemical reaction, a phase transformation or a biological function has been a dream of scientists for decades. The development of time-resolved X-ray and electron-based methods is making this true. X-ray absorption spectroscopy is ideal for the study of structural dynamics in liquids, because it can be implemented in amorphous media. Furthermore, it is chemically selective. Using X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) in laser pump/X-ray probe experiments allows the retrieval of the local geometric structure of the system under study, but also the underlying photoinduced electronic structure changes that drive the structural dynamics. Recent developments in picosecond and femtosecond X-ray absorption spectroscopy applied to molecular systems in solution are reviewed: examples on ultrafast photoinduced processes such as intramolecular electron transfer, low-to-high spin change, and bond formation are presented.
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24
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Chergui M, Zewail AH. Electron and X-Ray Methods of Ultrafast Structural Dynamics: Advances and Applications. Chemphyschem 2009; 10:28-43. [DOI: 10.1002/cphc.200800667] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Cole JM. Photocrystallography. Acta Crystallogr A 2007; 64:259-71. [DOI: 10.1107/s0108767307065324] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 12/03/2007] [Indexed: 11/10/2022] Open
Abstract
This review describes the development and application of a new crystallographic technique that is starting to enable the three-dimensional structural determination of molecules in their photo-activated states. So called `photocrystallography' has wide applicability, particularly in the currently exciting area of photonics, and a discussion of this applied potential is put into context in this article. Studies are classified into four groups: photo-structural changes that are (i) irreversible; (ii) long-lived but reversible under certain conditions; (iii) transient with photo-active lifetimes of the order of microseconds; (iv) very short lived, existing at the nanosecond or even picosecond level. As photo-structural changes relative to the `ground state' can be subtle, this article necessarily concentrates on small-molecule single-crystal X-ray diffraction given that high atomic resolution is possible. That said, where it is pertinent, references are also made to related major advances in photo-induced macromolecular crystallography. The review concludes with an outlook on this new research area, including the future possibility of studying even more ephemeral, femtosecond-lived, photo-active species.
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26
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Affiliation(s)
- Christian Bressler
- Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB-BSP, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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27
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Saes M, Gawelda W, Kaiser M, Tarnovsky A, Bressler C, Chergui M, Johnson SL, Grolimund D, Abela R. Ultrafast time‐resolved X‐ray absorption spectroscopy of chemical systems. ACTA ACUST UNITED AC 2003. [DOI: 10.1080/08940880308603029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Saes M, Bressler C, Abela R, Grolimund D, Johnson SL, Heimann PA, Chergui M. Observing photochemical transients by ultrafast x-ray absorption spectroscopy. PHYSICAL REVIEW LETTERS 2003; 90:047403. [PMID: 12570459 DOI: 10.1103/physrevlett.90.047403] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Indexed: 05/24/2023]
Abstract
Accurate determination of the transient electronic structures, which drive photochemical reactions, is crucial in chemistry and biology. We report the detection of transient chemical changes on the picosecond time scale by x-ray-absorption near-edge structure of photoexcited aqueous [Ru(bpy)(3)](2+). Upon ultrashort laser pulse excitation a charge transfer excited state having a 300 ns lifetime is formed. We detect the change of oxidation state of the central Ru atom at its L3 and L2 edges, at a temporal resolution of 100 ps with the zero of time unambiguously determined.
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Affiliation(s)
- Melanie Saes
- Institut de Physique de la Matière Condensée, Université de Lausanne, BSP, CH-1015 Lausanne, Switzerland
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29
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Oulianov DA, Tomov IV, Dvornikov AS, Rentzepis PM. Structures of bromoalkanes' photodissociation in solution by means of ultrafast extended x-ray absorption fine-structure spectroscopy. Proc Natl Acad Sci U S A 2002; 99:12556-61. [PMID: 12239341 PMCID: PMC130498 DOI: 10.1073/pnas.192447199] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2002] [Indexed: 11/18/2022] Open
Abstract
The structures of initial and final products of bromoalkanes' photodisociation reaction in cyclohexane solution have been measured with a bond length accuracy of 0.02 A by means of ultrafast time-resolved extended x-ray absorption fine structure spectroscopy. The photoredaction mechanism is also discussed.
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Affiliation(s)
- D A Oulianov
- Department of Chemistry, University of California, Irvine, CA 92697, USA
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30
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Chen LX, Jennings G, Liu T, Gosztola DJ, Hessler JP, Scaltrito DV, Meyer GJ. Rapid excited-state structural reorganization captured by pulsed X-rays. J Am Chem Soc 2002; 124:10861-7. [PMID: 12207541 DOI: 10.1021/ja017214g] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Visible light excitation of [Cu(I)(dmp)(2)](BArF), where dmp is 2,9-dimethyl-1,10-phenanthroline and BArF is tetrakis(3,5-bis(trifluoromethylphenyl))borate, in toluene produces a photoluminescent, metal-to-ligand charge-transfer (MLCT) excited state with a lifetime of 98 +/- 5 ns. Probing this state within 14 ns after photoexcitation with pulsed X-rays establishes that a Cu(II) center, borne in a Cu(I) geometry, binds an additional ligand to form a five-coordinate complex with increased bond lengths and a coordination geometry of distorted trigonal bipyramid. The average Cu-N bond length increases in the excited state by 0.07 A. The transiently formed five-coordinate MLCT state is photoluminescent under the condition studied, indicating that the absorptive and emissive states have distinct geometries. The data represent the first X-ray characterization of a molecular excited state in fluid solution on a nanosecond time scale.
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Affiliation(s)
- Lin X Chen
- Chemistry Division and Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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31
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Schoenlein R, Chong H, Glover T, Heimann P, Leemans W, Padmore H, Shank C, Zholents AA, Zolotorev MS, Corlett JS. Femtosecond X-rays from relativistic electrons: new tools for probing structural dynamics. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1296-2147(01)01277-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Chen LX, Jäger WJ, Jennings G, Gosztola DJ, Munkholm A, Hessler JP. Capturing a photoexcited molecular structure through time-domain x-ray absorption fine structure. Science 2001; 292:262-4. [PMID: 11303096 DOI: 10.1126/science.1057063] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The determination of the structure of transient molecules, such as photoexcited states, in disordered media (such as in solution) usually requires methods with high temporal resolution. The transient molecular structure of a reaction intermediate produced by photoexcitation of NiTPP-L2 (NiTPP, nickeltetraphenylporphyrin; L, piperidine) in solution was determined by x-ray absorption fine structure (XAFS) data obtained on a 14-nanosecond time scale from a third-generation synchrotron source. The XAFS measurements confirm that photoexcitation leads to the rapid removal of both axial ligands to produce a transient square-planar intermediate, NiTPP, with a lifetime of 28 nanoseconds. The transient structure of the photodissociated intermediate is nearly identical to that of the ground state NiTPP, suggesting that the intermediate adopts the same structure as the ground state in a noncoordinating solvent before it recombines with two ligands to form the more stable octahedrally coordinated NiTPP-L2.
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Affiliation(s)
- L X Chen
- Chemistry Division and, Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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Schnurer M, Streli C, Wobrauschek P, Hentschel M, Kienberger R, Spielmann C, Krausz F. Femtosecond X-Ray fluorescence. PHYSICAL REVIEW LETTERS 2000; 85:3392-3395. [PMID: 11030904 DOI: 10.1103/physrevlett.85.3392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2000] [Indexed: 05/23/2023]
Abstract
Using few-cycle-driven coherent laser harmonics, K-shell vacancies have been created in light elements, such as boron (E(B) = 188 eV) and carbon (E(B) = 284 eV), on a time scale of a few femtoseconds for the first time. The capability of detecting x-ray fluorescence excited by few-femtosecond radiation with an accuracy of the order of 1 eV paves the way for probing the evolution of the microscopic environment of selected atoms in chemical and biochemical reactions on previously inaccessible time scales (<100 fs) by tracing the temporal evolution of the "chemical shift" of peaks associated with inner-shell electronic transitions in time-resolved x-ray fluorescence and photoelectron spectra.
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Affiliation(s)
- M Schnurer
- Institut fur Photonik, Technische Universitat Wien, Gusshausstrasse 27-29, A-1040 Wien, Austria
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Brown FLH, Wilson KR, Cao J. Ultrafast extended x-ray absorption fine structure (EXAFS)—theoretical considerations. J Chem Phys 1999. [DOI: 10.1063/1.479928] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ozutsumi K, Ohtaki H. Structure Analysis of Reaction Intermediates in Metal Substitution Reactions in Solution by the Stopped-Flow EXAFS Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1999. [DOI: 10.1246/bcsj.72.1947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Chen LX, Lee PL, Gosztola D, Svec WA, Montano PA, Wasielewski MR. Time-Resolved X-ray Absorption Determination of Structural Changes following Photoinduced Electron Transfer within Bis-porphyrin Heme Protein Models. J Phys Chem B 1999. [DOI: 10.1021/jp990056j] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lin X. Chen
- Chemistry Division, Experimental Facilities Division and Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4831, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Peter L. Lee
- Chemistry Division, Experimental Facilities Division and Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4831, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - David Gosztola
- Chemistry Division, Experimental Facilities Division and Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4831, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Walter A. Svec
- Chemistry Division, Experimental Facilities Division and Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4831, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Pedro A. Montano
- Chemistry Division, Experimental Facilities Division and Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4831, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Michael R. Wasielewski
- Chemistry Division, Experimental Facilities Division and Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4831, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
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Bae IT, Scherson DA. In Situ X-ray Absorption of a Carbon Monoxide−Iron Porphyrin Adduct Adsorbed on High-Area Carbon in an Aqueous Electrolyte. J Phys Chem B 1998. [DOI: 10.1021/jp973124f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- In Tae Bae
- Ernest B. Yeager Center for Electrochemical Sciences and the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078
| | - Daniel A. Scherson
- Ernest B. Yeager Center for Electrochemical Sciences and the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078
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Wang H, Peng G, Miller LM, Scheuring EM, George SJ, Chance MR, Cramer SP. Iron L-Edge X-ray Absorption Spectroscopy of Myoglobin Complexes and Photolysis Products. J Am Chem Soc 1997. [DOI: 10.1021/ja961446b] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongxin Wang
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Gang Peng
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Lisa M. Miller
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Eva M. Scheuring
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - S. J. George
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Mark R. Chance
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Stephen P. Cramer
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
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Edwards AB, Garner CD, Roberts KJ. In Situ QXAFS Study of the Pyrolytic Decomposition of Nickel Formate Dihydrate. J Phys Chem B 1997. [DOI: 10.1021/jp961488m] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Bryan Edwards
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - C. David Garner
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Kevin J. Roberts
- Centre for Molecular and Interface Engineering, Department of Mechanical and Chemical Engineering, Heriot-Watt University, Edinburgh, EH14 4AS, U.K., and CCLRC Daresbury Laboratory, Warrington WA4 4AD, U.K
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Scheuring EM, Clavin W, Wirt MD, Miller LM, Fischetti RF, Lu Y, Mahoney N, Xie A, Wu JJ, Chance MR. Time-Resolved X-ray Absorption Spectroscopy of Photoreduced Base-off Cob(II)alamin Compared to the Co(II) Species in Clostridium thermoaceticum. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp943066n] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eva M. Scheuring
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Whitney Clavin
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Michael D. Wirt
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Lisa M. Miller
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Robert F. Fischetti
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Yun Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Nicole Mahoney
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Aihua Xie
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Jing-jing Wu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Mark R. Chance
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, and Regional Center for Time-Resolved Synchrotron Spectroscopy, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
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Della Longa S D, Ascone I, Fontaine A, Congiu Castellano A, Bianconi A. Intermediate states in ligand photodissociation of carboxymyoglobin studies by dispersive X-ray absorption. EUROPEAN BIOPHYSICS JOURNAL : EBJ 1994; 23:361-8. [PMID: 7835320 DOI: 10.1007/bf00188660] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The ligand photodissociation of sperm whale carboxymyoglobin (MbCO) at low temperature (15K-100K) under extended illumination has been studied by X-ray Absorption Near Edge Structure (XANES) spectroscopy using the dispersive technique. XANES simulations through the multiple scattering (MS) approach allow one to interpret the spectroscopic data in structural terms, and to investigate the Fe site structure configurations of the states that follow the CO photodissociation as a function of temperature. The Fe site in the photoproduct is unbound, with an overall structure similar to the deoxy-form (Mb) of the protein. The Fe site structure changes from T < 30K(Mb*) to T > 50K (Mb**), revealing the existence of a slower unbound state Mb**. A model is proposed which includes the faster state (Mb*) as a planar porphyrin ring with a displacement of Fe from the heme plane of less than 0.3 A, and the slower state (Mb**) with a domed heme.
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Affiliation(s)
- D Della Longa S
- Dipartimento di Medicina Sperimentale, Università dell'Aquila, Italy
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Saigo S, Hashimoto H, Shibayama N, Nomura M, Nagamura T. X-ray absorption spectroscopic studies of a transient intermediate in the reaction of cyanide metmyoglobin with dithionite by using rapid freezing. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1202:99-106. [PMID: 8373831 DOI: 10.1016/0167-4838(93)90069-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The reaction of cyanide metmyoglobin (Mb+CN-) with dithionite produces a transient intermediate, supposed to be cyanide-ligated ferrous myoglobin. The Fe K-edge X-ray absorption spectrum of the intermediate has been measured by using rapid freezing and compared with those of Mb+CN- and deoxymyoglobin (deoxyMb). The shapes of the XANES (X-ray Absorption Near Edge Structure) spectra of Mb+CN- and the intermediate are very similar, including the intensity ratios of the peak C1 to D. This indicates that CN- remains bound with a linear Fe-C-N configuration in the intermediate. The absorption edge of the intermediate is shifted to 1.2 eV lower energy than that of Mb+CN-, reflecting a valence change in the heme iron. The EXAFS (Extended X-ray Absorption Fine Structure) spectrum of the intermediate closely resembles that of Mb+CN- but significantly differs from that of deoxyMb. Analysis shows that the average iron-nearest neighbor atom distance is 1.99 +/- 0.01 A for both Mb+CN- and the intermediate and 2.05 +/- 0.01 A for deoxyMb. These results imply that the local structure around the heme iron of Mb+CN- does not change upon reduction until the cyanide ligand is released.
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Affiliation(s)
- S Saigo
- Department of Physics, Jichi Medical School, Tochigi, Japan
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Stern EA, Kalman Z, Lewis A, Lieberman K. Simple method for focusing x rays using tapered capillaries. APPLIED OPTICS 1988; 27:5135-5139. [PMID: 20539708 DOI: 10.1364/ao.27.005135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A new method of focusing x rays is described using appropriately tapered capillaries. The x rays are incident on the inner surface of the capillary below the critical glancing angle and reflect due to total external reflection. By appropriately narrowing the capillary, the x rays can thus be focused in a broad band of energies. The theory of the effect and optimum taper is described. A measurement verifying the focusing capability of the method is presented. The method appears practical for focusing bending magnet synchrotron radiation around 8 keV down to a diameter of 10 mum from an initial dimension of 1-mm(2) incident cross section with an attenuation of the total energy of ~2, i.e., an increase in the intensity per unit area of 6.5 x 10(3). Greater focusing is possible with softer x rays and from undulator sources. The wide-ranging applicability of the technique is discussed.
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