1
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Dodia M, Rouxel JR, Cho D, Zhang Y, Keefer D, Bonn M, Nagata Y, Mukamel S. Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer. J Chem Theory Comput 2024; 20:4254-4264. [PMID: 38727197 DOI: 10.1021/acs.jctc.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
We propose an X-ray Raman pump-X-ray diffraction probe scheme to follow solvation dynamics upon charge migration in a solute molecule. The X-ray Raman pump selectively prepares a valence electronic wavepacket in the solute, while the probe provides information about the entire molecular ensemble. A combination of molecular dynamics and ab initio quantum chemistry simulations is applied to a Zn-Ni porphyrin dimer in water. Using time-resolved X-ray diffraction and pair distribution functions, we extracted solvation shell dynamics.
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Affiliation(s)
- Mayank Dodia
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Jérémy R Rouxel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Daeheum Cho
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yu Zhang
- Ames National Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Daniel Keefer
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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2
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Wallick R, Chakrabarti S, Burke JH, Gnewkow R, Chae JB, Rossi TC, Mantouvalou I, Kanngießer B, Fondell M, Eckert S, Dykstra C, Smith LE, Vura-Weis J, Mirica LM, van der Veen RM. Excited-State Identification of a Nickel-Bipyridine Photocatalyst by Time-Resolved X-ray Absorption Spectroscopy. J Phys Chem Lett 2024; 15:4976-4982. [PMID: 38691639 PMCID: PMC11089568 DOI: 10.1021/acs.jpclett.4c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/18/2024] [Accepted: 04/16/2024] [Indexed: 05/03/2024]
Abstract
Photoassisted catalysis using Ni complexes is an emerging field for cross-coupling reactions in organic synthesis. However, the mechanism by which light enables and enhances the reactivity of these complexes often remains elusive. Although optical techniques have been widely used to study the ground and excited states of photocatalysts, they lack the specificity to interrogate the electronic and structural changes at specific atoms. Herein, we report metal-specific studies using transient Ni L- and K-edge X-ray absorption spectroscopy of a prototypical Ni photocatalyst, (dtbbpy)Ni(o-tol)Cl (dtb = 4,4'-di-tert-butyl, bpy = bipyridine, o-tol = ortho-tolyl), in solution. We unambiguously confirm via direct experimental evidence that the long-lived (∼5 ns) excited state is a tetrahedral metal-centered triplet state. These results demonstrate the power of ultrafast X-ray spectroscopies to unambiguously elucidate the nature of excited states in important transition-metal-based photocatalytic systems.
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Affiliation(s)
- Rachel
F. Wallick
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Sagnik Chakrabarti
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - John H. Burke
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Richard Gnewkow
- Department
of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin 14109, Germany
- Institute
of Optics and Atomic Physics, Technische
Universität Berlin, Berlin 10623, Germany
| | - Ju Byeong Chae
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Thomas C. Rossi
- Department
of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin 14109, Germany
| | - Ioanna Mantouvalou
- Department
of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin 14109, Germany
- Institute
of Optics and Atomic Physics, Technische
Universität Berlin, Berlin 10623, Germany
| | - Birgit Kanngießer
- Department
of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin 14109, Germany
- Institute
of Optics and Atomic Physics, Technische
Universität Berlin, Berlin 10623, Germany
| | - Mattis Fondell
- Department
of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin 14109, Germany
| | - Sebastian Eckert
- Department
of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin 14109, Germany
| | - Conner Dykstra
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Laura E. Smith
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Josh Vura-Weis
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Liviu M. Mirica
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Renske M. van der Veen
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
- Department
of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin 14109, Germany
- Institute
of Optics and Atomic Physics, Technische
Universität Berlin, Berlin 10623, Germany
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3
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Chen LX, Yano J. Deciphering Photoinduced Catalytic Reaction Mechanisms in Natural and Artificial Photosynthetic Systems on Multiple Temporal and Spatial Scales Using X-ray Probes. Chem Rev 2024; 124:5421-5469. [PMID: 38663009 DOI: 10.1021/acs.chemrev.3c00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Utilization of renewable energies for catalytically generating value-added chemicals is highly desirable in this era of rising energy demands and climate change impacts. Artificial photosynthetic systems or photocatalysts utilize light to convert abundant CO2, H2O, and O2 to fuels, such as carbohydrates and hydrogen, thus converting light energy to storable chemical resources. The emergence of intense X-ray pulses from synchrotrons, ultrafast X-ray pulses from X-ray free electron lasers, and table-top laser-driven sources over the past decades opens new frontiers in deciphering photoinduced catalytic reaction mechanisms on the multiple temporal and spatial scales. Operando X-ray spectroscopic methods offer a new set of electronic transitions in probing the oxidation states, coordinating geometry, and spin states of the metal catalytic center and photosensitizers with unprecedented energy and time resolution. Operando X-ray scattering methods enable previously elusive reaction steps to be characterized on different length scales and time scales. The methodological progress and their application examples collected in this review will offer a glimpse into the accomplishments and current state in deciphering reaction mechanisms for both natural and synthetic systems. Looking forward, there are still many challenges and opportunities at the frontier of catalytic research that will require further advancement of the characterization techniques.
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Affiliation(s)
- Lin X Chen
- Chemical Science and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Junko Yano
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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De Angelis D, Longetti L, Bonano G, Pelli Cresi JS, Foglia L, Pancaldi M, Capotondi F, Pedersoli E, Bencivenga F, Krstulovic M, Menk RH, D'Addato S, Orlando S, de Simone M, Ingle RA, Bleiner D, Coreno M, Principi E, Chergui M, Masciovecchio C, Mincigrucci R. A sub-100 nm thickness flat jet for extreme ultraviolet to soft X-ray absorption spectroscopy. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:605-612. [PMID: 38592969 DOI: 10.1107/s1600577524001875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Experimental characterization of the structural, electronic and dynamic properties of dilute systems in aqueous solvents, such as nanoparticles, molecules and proteins, are nowadays an open challenge. X-ray absorption spectroscopy (XAS) is probably one of the most established approaches to this aim as it is element-specific. However, typical dilute systems of interest are often composed of light elements that require extreme-ultraviolet to soft X-ray photons. In this spectral regime, water and other solvents are rather opaque, thus demanding radical reduction of the solvent volume and removal of the liquid to minimize background absorption. Here, we present an experimental endstation designed to operate a liquid flat jet of sub-micrometre thickness in a vacuum environment compatible with extreme ultraviolet/soft XAS measurements in transmission geometry. The apparatus developed can be easily connected to synchrotron and free-electron-laser user-facility beamlines dedicated to XAS experiments. The conditions for stable generation and control of the liquid flat jet are analyzed and discussed. Preliminary soft XAS measurements on some test solutions are shown.
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Affiliation(s)
- Dario De Angelis
- CNR - Istituto Officina dei Materiali (IOM), Basovizza, Area Science Park, 34149 Trieste, Italy
| | - Luca Longetti
- Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Gabriele Bonano
- Dipartimento FIM, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/a, 41125 Modena, Italy
| | | | - Laura Foglia
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Matteo Pancaldi
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Flavio Capotondi
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Emanuele Pedersoli
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Filippo Bencivenga
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Marija Krstulovic
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Ralf Hendrik Menk
- Sezione di Trieste, Istituto Nazionale di Fisica Nucleare, Via Valerio 2, 34127 Trieste, Italy
| | - Sergio D'Addato
- Dipartimento FIM, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/a, 41125 Modena, Italy
| | - Stefano Orlando
- ISM-CNR, Trieste Branch, in Basovizza Area Science Park, 34149 Trieste, Italy
| | - Monica de Simone
- CNR - Istituto Officina dei Materiali (IOM), Basovizza, Area Science Park, 34149 Trieste, Italy
| | - Rebecca A Ingle
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Davide Bleiner
- Laboratory for Advanced Analytical Technologies, EMPA, Uberlandstrasse 129, CH-8600 Dübendorf, Switzerland
| | - Marcello Coreno
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Emiliano Principi
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Majed Chergui
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
| | - Riccardo Mincigrucci
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5, Basovizza, 34149 Trieste, Italy
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5
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Yang S, Liu X, Li S, Yuan W, Yang L, Wang T, Zheng H, Cao R, Zhang W. The mechanism of water oxidation using transition metal-based heterogeneous electrocatalysts. Chem Soc Rev 2024. [PMID: 38646825 DOI: 10.1039/d3cs01031g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The water oxidation reaction, a crucial process for solar energy conversion, has garnered significant research attention. Achieving efficient energy conversion requires the development of cost-effective and durable water oxidation catalysts. To design effective catalysts, it is essential to have a fundamental understanding of the reaction mechanisms. This review presents a comprehensive overview of recent advancements in the understanding of the mechanisms of water oxidation using transition metal-based heterogeneous electrocatalysts, including Mn, Fe, Co, Ni, and Cu-based catalysts. It highlights the catalytic mechanisms of different transition metals and emphasizes the importance of monitoring of key intermediates to explore the reaction pathway. In addition, advanced techniques for physical characterization of water oxidation intermediates are also introduced, for the purpose of providing information for establishing reliable methodologies in water oxidation research. The study of transition metal-based water oxidation electrocatalysts is instrumental in providing novel insights into understanding both natural and artificial energy conversion processes.
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Affiliation(s)
- Shujiao Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Xiaohan Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Sisi Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Wenjie Yuan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Luna Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Ting Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Haoquan Zheng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Rui Cao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
| | - Wei Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.
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6
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Bergmann U. Stimulated X-ray emission spectroscopy. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01080-y. [PMID: 38619702 DOI: 10.1007/s11120-024-01080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/24/2024] [Indexed: 04/16/2024]
Abstract
We describe an emerging hard X-ray spectroscopy technique, stimulated X-ray emission spectroscopy (S-XES). S-XES has the potential to characterize the electronic structure of 3d transition metal complexes with spectral information currently not reachable and might lead to the development of new ultrafast X-ray sources with properties beyond the state of the art. S-XES has become possible with the emergence of X-ray free-electron lasers (XFELs) that provide intense femtosecond X-ray pulses that can be employed to generate a population inversion of core-hole excited states resulting in stimulated X-ray emission. We describe the instrumentation, the various types of S-XES, the potential applications, the experimental challenges, and the feasibility of applying S-XES to characterize dilute systems, including the Mn4Ca cluster in the oxygen evolving complex of photosystem II.
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Affiliation(s)
- Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA.
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7
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De Santis E, Alleva S, Minicozzi V, Morante S, Stellato F. Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders. Chempluschem 2024:e202300712. [PMID: 38526934 DOI: 10.1002/cplu.202300712] [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: 12/01/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.
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Affiliation(s)
- Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Stefania Alleva
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Velia Minicozzi
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Silvia Morante
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Francesco Stellato
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
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8
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Liu MF, Zhang C, Wang J, Han X, Hu W, Deng Y. Recent research progresses of Sn/Bi/In-based electrocatalysts for electroreduction CO 2 to formate. Chemistry 2024; 30:e202303711. [PMID: 38143240 DOI: 10.1002/chem.202303711] [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: 11/08/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
Carbon dioxide electroreduction reaction (CO2RR) can take full advantage of sustainable power to reduce the continuously increasing carbon emissions. Recycling CO2 to produce formic acid or formate is a technologically and economically viable route to accomplish CO2 cyclic utilization. Developing efficient and cost-effective electrocatalysts with high selectivity towards formate is prioritized for the industrialized applications of CO2RR electrolysis. From the previous explored CO2RR catalysts, Sn, Bi and In based materials have drawn increasing attentions due to the high selectivity towards formate. However, there are still confronted with several challenges for the practical applications of these materials. Therefore, a rational design of the catalysts for formate is urgently needed for the target of industrialized applications. Herein, we comprehensively summarized the recent development in the advanced electrocatalysts for the CO2RR to formate. Firstly, the reaction mechanism of CO2RR is introduced. Then the preparation and design strategies of the highly active electrocatalysts are presented. Especially the innovative design mechanism in engineering materials for promoting catalytic performance, and the efforts on mechanistic exploration using in situ (ex situ) characterization techniques are reviewed. Subsequently, some perspectives and expectations are proposed about current challenges and future potentials in CO2RR research.
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Affiliation(s)
- Ms Fei Liu
- Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Chen Zhang
- Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiajun Wang
- Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Xiaopeng Han
- Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Wenbin Hu
- Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Yida Deng
- Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Materials Science and Engineering, Hainan University, Haikou, 570228, P. R. China
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9
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Biró L, Csehi A. Attosecond Probing of Nuclear Vibrations in the D 2+ and HeH + Molecular Ions. J Phys Chem A 2024; 128:858-867. [PMID: 38277484 DOI: 10.1021/acs.jpca.3c07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
We study the ultrafast photodissociation of small diatomic molecules using attosecond laser pulses of moderate intensity in the (extreme) ultraviolet regime. The simultaneous application of subfemtosecond laser pulses with different photon energies─resonant in the region of the molecular motion─allows one to monitor the vibrational dynamics of simple diatomics, like the D2+ and HeH+ molecular ions. In our real-time wave packet simulations, the nuclear dynamics is initiated either by sudden ionization (D2+) or by explicit pump pulses (HeH+) via distortion of the potential energy of the molecule. The application of time-delayed attosecond pulses leads to the breakup of the molecules, and the information on the underlying bound-state dynamics is imprinted in the kinetic energy release (KER) spectra of the outgoing fragments. We show that the KER-delay spectrograms generated in our ultrafast pump-probe schemes are able to reconstruct the most important features of the molecular motion within a given electronic state, such as the time period or amplitude of oscillations, interference patterns, or the revival and splitting of the nuclear wave packet. The impact of probe pulse duration, which is key to the applicability of the presented mapping scheme, is investigated in detail.
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Affiliation(s)
- László Biró
- Department of Theoretical Physics, Faculty of Science and Technology, University of Debrecen, H-4002 Debrecen, P.O. Box 400, Hungary
| | - András Csehi
- Department of Theoretical Physics, Faculty of Science and Technology, University of Debrecen, H-4002 Debrecen, P.O. Box 400, Hungary
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10
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Choi S, Park S, Kim J, Kim H, Cho S, Kim S, Park J, Kim C. X-ray free-electron laser induced acoustic microscopy (XFELAM). PHOTOACOUSTICS 2024; 35:100587. [PMID: 38312809 PMCID: PMC10835452 DOI: 10.1016/j.pacs.2024.100587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/06/2024]
Abstract
The X-ray free-electron laser (XFEL) has remarkably advanced X-ray imaging technology and enabled important scientific achievements. The XFEL's extremely high power, short pulse width, low emittance, and high coherence make possible such diverse imaging techniques as absorption/emission spectroscopy, diffraction imaging, and scattering imaging. Here, we demonstrate a novel XFEL-based imaging modality that uses the X-ray induced acoustic (XA) effect, which we call X-ray free-electron laser induced acoustic microscopy (XFELAM). Initially, we verified the XA effect by detecting XA signals from various materials, then we validated the experimental results with simulation outcomes. Next, in resolution experiments, we successfully imaged a patterned tungsten target with drilled various-sized circles at a spatial resolution of 7.8 ± 5.1 µm, which is the first micron-scale resolution achieved by XA imaging. Our results suggest that the novel XFELAM can expand the usability of XFEL in various areas of fundamental scientific research.
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Affiliation(s)
- Seongwook Choi
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Sinyoung Park
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Jiwoong Kim
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Hyunhee Kim
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Seonghee Cho
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Sunam Kim
- Pohang Accelerator Laboratory, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Jaeku Park
- Pohang Accelerator Laboratory, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Chulhong Kim
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
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11
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Botella R, Cao W, Celis J, Fernández-Catalá J, Greco R, Lu L, Pankratova V, Temerov F. Activating two-dimensional semiconductors for photocatalysis: a cross-dimensional strategy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:141501. [PMID: 38086082 DOI: 10.1088/1361-648x/ad14c8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
The emerging two-dimensional (2D) semiconductors substantially extend materials bases for versatile applications such as semiconductor photocatalysis demanding semiconductive matrices and large surface areas. The dimensionality, while endowing 2D semiconductors the unique properties to host photocatalytic functionality of pollutant removal and hydrogen evolution, hurdles the activation paths to form heterogenous photocatalysts where the photochemical processes are normally superior over these on the mono-compositional counterparts. In this perspective, we present a cross-dimensional strategy to employ thenD (n= 0-2) clusters or nanomaterials as activation partners to boost the photocatalytic activities of the 2D semiconductors. The formation principles of heterogenous photocatalysts are illustrated specifically for the 2D matrices, followed by selection criteria of them among the vast 2D database. The computer investigations are illustrated in the density functional theory route and machine learning benefitted from the vast samples in the 2D library. Synthetic realizations and characterizations of the 2D heterogenous systems are introduced with an emphasis on chemical methods and advanced techniques to understand materials and mechanistic studies. The perspective outlooks cross-dimensional activation strategies of the 2D materials for other applications such as CO2removal, and materials matrices in other dimensions which may inspire incoming research within these fields.
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Affiliation(s)
- R Botella
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
| | - W Cao
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
| | - J Celis
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
| | - J Fernández-Catalá
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
| | - R Greco
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
| | - L Lu
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
| | - V Pankratova
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
| | - F Temerov
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, Oulu, FIN-90014, Finland
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12
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Garratt D, Matthews M, Marangos J. Toward ultrafast soft x-ray spectroscopy of organic photovoltaic devices. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:010901. [PMID: 38250136 PMCID: PMC10799687 DOI: 10.1063/4.0000214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/17/2023] [Indexed: 01/23/2024]
Abstract
Novel ultrafast x-ray sources based on high harmonic generation and at x-ray free electron lasers are opening up new opportunities to resolve complex ultrafast processes in condensed phase systems with exceptional temporal resolution and atomic site specificity. In this perspective, we present techniques for resolving charge localization, transfer, and separation processes in organic semiconductors and organic photovoltaic devices with time-resolved soft x-ray spectroscopy. We review recent results in ultrafast soft x-ray spectroscopy of these systems and discuss routes to overcome the technical challenges in performing time-resolved x-ray experiments on photosensitive materials with poor thermal conductivity and low pump intensity thresholds for nonlinear effects.
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13
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Trebbin M. Thinner than a knife's edge: 3D-printed liquid sheet jet technology for solution phase XFEL experiments. IUCRJ 2023; 10:638-641. [PMID: 37910141 PMCID: PMC10619446 DOI: 10.1107/s2052252523009429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
In this commentary, we explore the pioneering implementation of 3D-printed thin liquid sheet devices for advanced X-ray scattering and spectroscopy experiments at high-repetition rate XFELs.
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Affiliation(s)
- Martin Trebbin
- University at Buffalo, Department of Chemistry & Research and Education in eNergy, Environment and Water (RENEW), 760 Natural Sciences Complex, Buffalo, NY 14260, USA
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14
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Lima FA, Otte F, Vakili M, Ardana-Lamas F, Biednov M, Dall’Antonia F, Frankenberger P, Gawelda W, Gelisio L, Han H, Huang X, Jiang Y, Kloos M, Kluyver T, Knoll M, Kubicek K, Bermudez Macias IJ, Schulz J, Turkot O, Uemura Y, Valerio J, Wang H, Yousef H, Zalden P, Khakhulin D, Bressler C, Milne C. Experimental capabilities for liquid jet samples at sub-MHz rates at the FXE Instrument at European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:1168-1182. [PMID: 37860937 PMCID: PMC10624029 DOI: 10.1107/s1600577523008159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
The Femtosecond X-ray Experiments (FXE) instrument at the European X-ray Free-Electron Laser (EuXFEL) provides an optimized platform for investigations of ultrafast physical, chemical and biological processes. It operates in the energy range 4.7-20 keV accommodating flexible and versatile environments for a wide range of samples using diverse ultrafast X-ray spectroscopic, scattering and diffraction techniques. FXE is particularly suitable for experiments taking advantage of the sub-MHz repetition rates provided by the EuXFEL. In this paper a dedicated setup for studies on ultrafast biological and chemical dynamics in solution phase at sub-MHz rates at FXE is presented. Particular emphasis on the different liquid jet sample delivery options and their performance is given. Our portfolio of high-speed jets compatible with sub-MHz experiments includes cylindrical jets, gas dynamic virtual nozzles and flat jets. The capability to perform multi-color X-ray emission spectroscopy (XES) experiments is illustrated by a set of measurements using the dispersive X-ray spectrometer in von Hamos geometry. Static XES data collected using a multi-crystal scanning Johann-type spectrometer are also presented. A few examples of experimental results on ultrafast time-resolved X-ray emission spectroscopy and wide-angle X-ray scattering at sub-MHz pulse repetition rates are given.
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Affiliation(s)
- F. A. Lima
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - F. Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Fakultät für Physik, Technical University Dortmund, Dortmund, Germany
| | - M. Vakili
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - M. Biednov
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - W. Gawelda
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - L. Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - X. Huang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - T. Kluyver
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Knoll
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - K. Kubicek
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | | | - J. Schulz
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - O. Turkot
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Wang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - P. Zalden
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - D. Khakhulin
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - C. Bressler
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | - C. Milne
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
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15
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Konold PE, You T, Bielecki J, Valerio J, Kloos M, Westphal D, Bellisario A, Varma Yenupuri T, Wollter A, Koliyadu JCP, Koua FH, Letrun R, Round A, Sato T, Mészáros P, Monrroy L, Mutisya J, Bódizs S, Larkiala T, Nimmrich A, Alvarez R, Adams P, Bean R, Ekeberg T, Kirian RA, Martin AV, Westenhoff S, Maia FRNC. 3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers. IUCRJ 2023; 10:662-670. [PMID: 37721770 PMCID: PMC10619454 DOI: 10.1107/s2052252523007972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
X-ray free-electron lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit involves the delivery of samples to the X-ray interaction point in such a way that produces data of the highest possible quality and with maximal efficiency. This is hampered by intrinsic constraints posed by the light source and operation within a beamline environment. For liquid samples, the solution typically involves some form of high-speed liquid jet, capable of keeping up with the rate of X-ray pulses. However, conventional jets are not ideal because of radiation-induced explosions of the jet, as well as their cylindrical geometry combined with the X-ray pointing instability of many beamlines which causes the interaction volume to differ for every pulse. This complicates data analysis and contributes to measurement errors. An alternative geometry is a liquid sheet jet which, with its constant thickness over large areas, eliminates the problems related to X-ray pointing. Since liquid sheets can be made very thin, the radiation-induced explosion is reduced, boosting their stability. These are especially attractive for experiments which benefit from small interaction volumes such as fluctuation X-ray scattering and several types of spectroscopy. Although their use has increased for soft X-ray applications in recent years, there has not yet been wide-scale adoption at XFELs. Here, gas-accelerated liquid sheet jet sample injection is demonstrated at the European XFEL SPB/SFX nano focus beamline. Its performance relative to a conventional liquid jet is evaluated and superior performance across several key factors has been found. This includes a thickness profile ranging from hundreds of nanometres to 60 nm, a fourfold increase in background stability and favorable radiation-induced explosion dynamics at high repetition rates up to 1.13 MHz. Its minute thickness also suggests that ultrafast single-particle solution scattering is a possibility.
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Affiliation(s)
- Patrick E. Konold
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Tong You
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Alfredo Bellisario
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Tej Varma Yenupuri
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - August Wollter
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | | | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Petra Mészáros
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Szabolcs Bódizs
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Taru Larkiala
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Bagley Hall, Seattle, WA 98195, USA
| | - Roberto Alvarez
- Department of Physics, Arizona State University, 550 E. Tyler Drive, Tempe, AZ 85287, USA
| | - Patrick Adams
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Richard A. Kirian
- Department of Physics, Arizona State University, 550 E. Tyler Drive, Tempe, AZ 85287, USA
| | - Andrew V. Martin
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Sebastian Westenhoff
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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16
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Di Felice R, Mayes ML, Richard RM, Williams-Young DB, Chan GKL, de Jong WA, Govind N, Head-Gordon M, Hermes MR, Kowalski K, Li X, Lischka H, Mueller KT, Mutlu E, Niklasson AMN, Pederson MR, Peng B, Shepard R, Valeev EF, van Schilfgaarde M, Vlaisavljevich B, Windus TL, Xantheas SS, Zhang X, Zimmerman PM. A Perspective on Sustainable Computational Chemistry Software Development and Integration. J Chem Theory Comput 2023; 19:7056-7076. [PMID: 37769271 PMCID: PMC10601486 DOI: 10.1021/acs.jctc.3c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 09/30/2023]
Abstract
The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.
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Affiliation(s)
- Rosa Di Felice
- Departments
of Physics and Astronomy and Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- CNR-NANO
Modena, Modena 41125, Italy
| | - Maricris L. Mayes
- Department
of Chemistry and Biochemistry, University
of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States
| | | | | | - Garnet Kin-Lic Chan
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Wibe A. de Jong
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Niranjan Govind
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Martin Head-Gordon
- Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew R. Hermes
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Karol Kowalski
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Xiaosong Li
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Hans Lischka
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Karl T. Mueller
- Physical
and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Erdal Mutlu
- Advanced
Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Anders M. N. Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Mark R. Pederson
- Department
of Physics, The University of Texas at El
Paso, El Paso, Texas 79968, United States
| | - Bo Peng
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Ron Shepard
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, United States
| | - Edward F. Valeev
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Bess Vlaisavljevich
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - Theresa L. Windus
- Department
of Chemistry, Iowa State University and
Ames Laboratory, Ames, Iowa 50011, United States
| | - Sotiris S. Xantheas
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced
Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xing Zhang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Paul M. Zimmerman
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Wang J, Hsu CS, Wu TS, Chan TS, Suen NT, Lee JF, Chen HM. In situ X-ray spectroscopies beyond conventional X-ray absorption spectroscopy on deciphering dynamic configuration of electrocatalysts. Nat Commun 2023; 14:6576. [PMID: 37852958 PMCID: PMC10584842 DOI: 10.1038/s41467-023-42370-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Realizing viable electrocatalytic processes for energy conversion/storage strongly relies on an atomic-level understanding of dynamic configurations on catalyst-electrolyte interface. X-ray absorption spectroscopy (XAS) has become an indispensable tool to in situ investigate dynamic natures of electrocatalysts but still suffers from limited energy resolution, leading to significant electronic transitions poorly resolved. Herein, we highlight advanced X-ray spectroscopies beyond conventional XAS, with emphasis on their unprecedented capabilities of deciphering key configurations of electrocatalysts. The profound complementarities of X-ray spectroscopies from various aspects are established in a probing energy-dependent "in situ spectroscopy map" for comprehensively understanding the solid-liquid interface. This perspective establishes an indispensable in situ research model for future studies and offers exciting research prospects for scientists and spectroscopists.
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Affiliation(s)
- Jiali Wang
- Department of Chemistry and Center for Emerging Materials and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-Shuo Hsu
- Department of Chemistry and Center for Emerging Materials and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan
| | - Tai-Sing Wu
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.
| | - Nian-Tzu Suen
- College of Chemistry & Chemical Engineering, Yangzhou University, 225002, Yangzhou, China
| | - Jyh-Fu Lee
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Hao Ming Chen
- Department of Chemistry and Center for Emerging Materials and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan.
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.
- Graduate Institute of Nanomedicine and Medical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.
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18
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Lipp V, Grünert J, Liu J, Ziaja B. Picosecond to microsecond dynamics of X-ray irradiated materials at MHz pulse repetition rate. Sci Rep 2023; 13:16344. [PMID: 37770502 PMCID: PMC10539529 DOI: 10.1038/s41598-023-42943-z] [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: 05/10/2023] [Accepted: 09/16/2023] [Indexed: 09/30/2023] Open
Abstract
Modern X-ray free-electron lasers (XFELs) produce intense femtosecond X-ray pulses able to cause significant damage to irradiated targets. Energetic photoelectrons created upon X-ray absorption, and Auger electrons emitted after relaxation of core-hole states trigger secondary electron cascades, which contribute to the increasing transient free electron density on femtosecond timescales. Further evolution may involve energy and particle diffusion, creation of point defects, and lattice heating. This long-timescale (up to a microsecond) X-ray-induced dynamics is discussed on the example of silicon in two-dimensional geometry. For modeling, we apply an extended Two-Temperature model with electron density dynamics, nTTM, which describes relaxation of an irradiated sample between two successive X-ray pulses, emitted from XFEL at MHz pulse repetition rate. It takes into account ambipolar carrier diffusion, electronic and atomic heat conduction, as well as electron-ion coupling. To solve the nTTM system of equations in two dimensions, we developed a dedicated finite-difference integration algorithm based on Alternating Direction Implicit method with an additional predictor-corrector scheme. We show first results obtained with the model and discuss its possible applications for XFEL optics, detectors, and for diagnostics tools. In particular, the model can estimate the timescale of material relaxation relevant for beam diagnostic applications during MHz operation of contemporary and future XFELs.
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Affiliation(s)
- Vladimir Lipp
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland.
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
| | - Jan Grünert
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jia Liu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
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19
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Makita H, Zhang M, Yano J, Kern J. Room temperature crystallography and X-ray spectroscopy of metalloenzymes. Methods Enzymol 2023; 688:307-348. [PMID: 37748830 PMCID: PMC10799221 DOI: 10.1016/bs.mie.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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20
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Follmer AH, Borovik AS. The role of basicity in selective C-H bond activation by transition metal-oxidos. Dalton Trans 2023; 52:11005-11016. [PMID: 37497779 PMCID: PMC10619463 DOI: 10.1039/d3dt01781h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The development of (bio)catalysts capable of selectively activating strong C-H bonds is a continuing challenge in modern chemistry. In both metalloenzymes and synthetic systems capable of activating C-H bonds, transition metal-oxido intermediates serve as the active species for reactivity whose thermodynamic properties influence the bond strengths they are capable of activating. In this Frontier article, we present current ideas of how the basicity of transition metal-oxidos impacts their reactivity with C-H bonds and present new opportunities within this field. We highlight recent insights into the role basicity plays in the activation process and its influence on mechanism, as well as the important role that secondary coordination sphere effects, such as hydrogen bonds, in tuning the basicity of the metal-oxido species is discussed.
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Affiliation(s)
- Alec H Follmer
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697-3900, USA.
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697-3900, USA.
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21
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Chen R, Chen J, Gong Z, Zhang X, Zhu X, Yang Y, Kaminer I, Chen H, Zhang B, Lin X. Free-electron Brewster-transition radiation. SCIENCE ADVANCES 2023; 9:eadh8098. [PMID: 37566659 PMCID: PMC10421060 DOI: 10.1126/sciadv.adh8098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/12/2023] [Indexed: 08/13/2023]
Abstract
We reveal a mechanism to enhance particle-matter interactions by exploiting the pseudo-Brewster effect of gain materials, presenting an enhancement of at least four orders of magnitude for light emission. This mechanism is enabled by the emergence of an unprecedented phase diagram that maps all phenomena of free-electron transition radiation into three distinct phases in a gain-thickness parameter space, namely, the conventional, intermediate, and Brewster phases, when an electron penetrates a dielectric slab with a modest gain and a finite thickness. Essentially, our revealed mechanism corresponds to the free-electron transition radiation in the Brewster phase, which also features ultrahigh directionality, always at the Brewster angle, regardless of the electron velocity. Counterintuitively, we find that the intensity of this free-electron Brewster-transition radiation is insensitive to the Fabry-Pérot resonance condition and, thus, the variation of slab thickness, and moreover, a weaker gain could lead to a stronger enhancement for light emission.
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Affiliation(s)
- Ruoxi Chen
- Interdisciplinary Center for Quantum Information, State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Information Science & Electronic Engineering, Zhejiang University, Hangzhou 310027, China
- International Joint Innovation Center, The Electromagnetics Academy at Zhejiang University, Zhejiang University, Haining 314400, China
| | - Jialin Chen
- Interdisciplinary Center for Quantum Information, State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Information Science & Electronic Engineering, Zhejiang University, Hangzhou 310027, China
- International Joint Innovation Center, The Electromagnetics Academy at Zhejiang University, Zhejiang University, Haining 314400, China
- Department of Electrical and Computer Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Zheng Gong
- Interdisciplinary Center for Quantum Information, State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Information Science & Electronic Engineering, Zhejiang University, Hangzhou 310027, China
- International Joint Innovation Center, The Electromagnetics Academy at Zhejiang University, Zhejiang University, Haining 314400, China
| | - Xinyan Zhang
- Interdisciplinary Center for Quantum Information, State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Information Science & Electronic Engineering, Zhejiang University, Hangzhou 310027, China
- International Joint Innovation Center, The Electromagnetics Academy at Zhejiang University, Zhejiang University, Haining 314400, China
| | - Xingjian Zhu
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Yi Yang
- Department of Physics, University of Hong Kong, Hong Kong 999077, China
| | - Ido Kaminer
- Department of Electrical and Computer Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hongsheng Chen
- Interdisciplinary Center for Quantum Information, State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Information Science & Electronic Engineering, Zhejiang University, Hangzhou 310027, China
- International Joint Innovation Center, The Electromagnetics Academy at Zhejiang University, Zhejiang University, Haining 314400, China
- Key Laboratory of Advanced Micro/Nano Electronic Devices & Smart Systems of Zhejiang, Jinhua Institute of Zhejiang University, Zhejiang University, Jinhua 321099, China
- Shaoxing Institute of Zhejiang University, Zhejiang University, Shaoxing 312000, China
| | - Baile Zhang
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- Centre for Disruptive Photonic Technologies, Nanyang Technological University, Singapore 637371, Singapore
| | - Xiao Lin
- Interdisciplinary Center for Quantum Information, State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Information Science & Electronic Engineering, Zhejiang University, Hangzhou 310027, China
- International Joint Innovation Center, The Electromagnetics Academy at Zhejiang University, Zhejiang University, Haining 314400, China
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22
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Tang J, Zhang Z, Morgan J, Hemsing E, Huang Z. Active Q-Switched X-Ray Regenerative Amplifier Free-Electron Laser. PHYSICAL REVIEW LETTERS 2023; 131:055001. [PMID: 37595223 DOI: 10.1103/physrevlett.131.055001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/29/2023] [Indexed: 08/20/2023]
Abstract
Despite tremendous progress in x-ray free-electron laser (FEL) science over the last decade, future applications still demand fully coherent, stable x rays that have not been demonstrated in existing x-ray FEL facilities. In this Letter, we describe an active Q-switched x-ray regenerative amplifier FEL scheme to produce fully coherent, high-brightness, hard x rays at a high-repetition rate. By using simple electron-beam phase space manipulation, we show this scheme is flexible in controlling the x-ray cavity quality factor Q and hence the output radiation. We report both theoretical and numerical studies on this scheme with a wide range of accelerator, x-ray cavity, and undulator parameters.
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Affiliation(s)
- Jingyi Tang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Zhen Zhang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jenny Morgan
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Erik Hemsing
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Zhirong Huang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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23
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Bogacz I, Makita H, Simon PS, Zhang M, Doyle MD, Chatterjee R, Fransson T, Weninger C, Fuller F, Gee L, Sato T, Seaberg M, Alonso-Mori R, Bergmann U, Yachandra VK, Kern J, Yano J. Room temperature X-ray absorption spectroscopy of metalloenzymes with drop-on-demand sample delivery at XFELs. PURE APPL CHEM 2023; 95:891-897. [PMID: 38013689 PMCID: PMC10505480 DOI: 10.1515/pac-2023-0213] [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] [Indexed: 11/29/2023]
Abstract
X-ray crystallography and X-ray spectroscopy using X-ray free electron lasers plays an important role in understanding the interplay of structural changes in the protein and the chemical changes at the metal active site of metalloenzymes through their catalytic cycles. As a part of such an effort, we report here our recent development of methods for X-ray absorption spectroscopy (XAS) at XFELs to study dilute biological samples, available in limited volumes. Our prime target is Photosystem II (PS II), a multi subunit membrane protein complex, that catalyzes the light-driven water oxidation reaction at the Mn4CaO5 cluster. This is an ideal system to investigate how to control multi-electron/proton chemistry, using the flexibility of metal redox states, in coordination with the protein and the water network. We describe the method that we have developed to collect XAS data using PS II samples with a Mn concentration of <1 mM, using a drop-on-demand sample delivery method.
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Affiliation(s)
- Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Margaret D. Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Thomas Fransson
- Department of Theoretical chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Franklin Fuller
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | - Leland Gee
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | - Takahiro Sato
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | - Matthew Seaberg
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | | | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, 53706, Madison, WI, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
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24
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Ash R, Abhari Z, Candela R, Welke N, Murawski J, Gardezi SM, Venkatasubramanian N, Munawar M, Siewert F, Sokolov A, LaDuca Z, Kawasaki J, Bergmann U. X-FAST: A versatile, high-throughput, and user-friendly XUV femtosecond absorption spectroscopy tabletop instrument. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:073004. [PMID: 37462459 DOI: 10.1063/5.0146137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/25/2023] [Indexed: 07/21/2023]
Abstract
We present the X-FAST (XUV Femtosecond Absorption Spectroscopy Tabletop) instrument at the University of Wisconsin-Madison. The instrument produces femtosecond extreme ultraviolet photon pulses via high-harmonic generation in the range of 40-72 eV, as well as optical pump pulses for transient-absorption experiments. The system implements a gas-cooled sample cell that enables studying the dynamics of thermally sensitive thin-film samples. This paper provides potential users with specifications of the optical, vacuum, data acquisition, and sample cooling systems of the X-FAST instrument, along with performance metrics and data of an ultrafast laser-induced phase transition in a Ni2MnGa Heusler thin film.
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Affiliation(s)
- Ryan Ash
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
| | - Zain Abhari
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
| | - Roberta Candela
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
| | - Noah Welke
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
| | - Jake Murawski
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
| | - S Minhal Gardezi
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
| | | | - Muneeza Munawar
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
| | - Frank Siewert
- Helmholtz Zentrum Berlin für Materialien und Energie, Department of Optics and Beamlines, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Andrey Sokolov
- Helmholtz Zentrum Berlin für Materialien und Energie, Department of Optics and Beamlines, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Zachary LaDuca
- Department of Materials Science and Engineering, University of Wisconsin Madison, 1509 University Ave., Madison, Wisconsin 53706, USA
| | - Jason Kawasaki
- Department of Materials Science and Engineering, University of Wisconsin Madison, 1509 University Ave., Madison, Wisconsin 53706, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
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25
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Sension RJ, McClain TP, Lamb RM, Alonso-Mori R, Lima FA, Ardana-Lamas F, Biednov M, Chollet M, Chung T, Deb A, Dewan PA, Gee LB, Huang Ze En J, Jiang Y, Khakhulin D, Li J, Michocki LB, Miller NA, Otte F, Uemura Y, van Driel TB, Penner-Hahn JE. Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin. J Am Chem Soc 2023. [PMID: 37327324 DOI: 10.1021/jacs.3c04099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Femtosecond time-resolved X-ray absorption (XANES) at the Co K-edge, X-ray emission (XES) in the Co Kβ and valence-to-core regions, and broadband UV-vis transient absorption are combined to probe the femtosecond to picosecond sequential atomic and electronic dynamics following photoexcitation of two vitamin B12 compounds, hydroxocobalamin and aquocobalamin. Polarized XANES difference spectra allow identification of sequential structural evolution involving first the equatorial and then the axial ligands, with the latter showing rapid coherent bond elongation to the outer turning point of the excited state potential followed by recoil to a relaxed excited state structure. Time-resolved XES, especially in the valence-to-core region, along with polarized optical transient absorption suggests that the recoil results in the formation of a metal-centered excited state with a lifetime of 2-5 ps. This combination of methods provides a uniquely powerful tool to probe the electronic and structural dynamics of photoactive transition-metal complexes and will be applicable to a wide variety of systems.
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Affiliation(s)
- Roseanne J Sension
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States
| | - Taylor P McClain
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Ryan M Lamb
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Frederico Alves Lima
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Fernando Ardana-Lamas
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Mykola Biednov
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Taewon Chung
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Paul A Dewan
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Joel Huang Ze En
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Yifeng Jiang
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Dmitry Khakhulin
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Jianhao Li
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Lindsay B Michocki
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Nicholas A Miller
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Florian Otte
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yohei Uemura
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tim B van Driel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
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26
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Weakly RB, Liekhus-Schmaltz CE, Poulter BI, Biasin E, Alonso-Mori R, Aquila A, Boutet S, Fuller FD, Ho PJ, Kroll T, Loe CM, Lutman A, Zhu D, Bergmann U, Schoenlein RW, Govind N, Khalil M. Revealing core-valence interactions in solution with femtosecond X-ray pump X-ray probe spectroscopy. Nat Commun 2023; 14:3384. [PMID: 37291130 DOI: 10.1038/s41467-023-39165-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Femtosecond pump-probe spectroscopy using ultrafast optical and infrared pulses has become an essential tool to discover and understand complex electronic and structural dynamics in solvated molecular, biological, and material systems. Here we report the experimental realization of an ultrafast two-color X-ray pump X-ray probe transient absorption experiment performed in solution. A 10 fs X-ray pump pulse creates a localized excitation by removing a 1s electron from an Fe atom in solvated ferro- and ferricyanide complexes. Following the ensuing Auger-Meitner cascade, the second X-ray pulse probes the Fe 1s → 3p transitions in resultant novel core-excited electronic states. Careful comparison of the experimental spectra with theory, extracts +2 eV shifts in transition energies per valence hole, providing insight into correlated interactions of valence 3d with 3p and deeper-lying electrons. Such information is essential for accurate modeling and predictive synthesis of transition metal complexes relevant for applications ranging from catalysis to information storage technology. This study demonstrates the experimental realization of the scientific opportunities possible with the continued development of multicolor multi-pulse X-ray spectroscopy to study electronic correlations in complex condensed phase systems.
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Affiliation(s)
- Robert B Weakly
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | | | - Benjamin I Poulter
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Phay J Ho
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Thomas Kroll
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Caroline M Loe
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Alberto Lutman
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Robert W Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Munira Khalil
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA.
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27
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Makita H, Simon PS, Kern J, Yano J, Yachandra VK. Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography. Curr Opin Struct Biol 2023; 80:102604. [PMID: 37148654 PMCID: PMC10793627 DOI: 10.1016/j.sbi.2023.102604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023]
Abstract
With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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28
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Reinhard M, Gallo A, Guo M, Garcia-Esparza AT, Biasin E, Qureshi M, Britz A, Ledbetter K, Kunnus K, Weninger C, van Driel T, Robinson J, Glownia JM, Gaffney KJ, Kroll T, Weng TC, Alonso-Mori R, Sokaras D. Ferricyanide photo-aquation pathway revealed by combined femtosecond Kβ main line and valence-to-core x-ray emission spectroscopy. Nat Commun 2023; 14:2443. [PMID: 37147295 PMCID: PMC10163258 DOI: 10.1038/s41467-023-37922-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/30/2023] [Indexed: 05/07/2023] Open
Abstract
Reliably identifying short-lived chemical reaction intermediates is crucial to elucidate reaction mechanisms but becomes particularly challenging when multiple transient species occur simultaneously. Here, we report a femtosecond x-ray emission spectroscopy and scattering study of the aqueous ferricyanide photochemistry, utilizing the combined Fe Kβ main and valence-to-core emission lines. Following UV-excitation, we observe a ligand-to-metal charge transfer excited state that decays within 0.5 ps. On this timescale, we also detect a hitherto unobserved short-lived species that we assign to a ferric penta-coordinate intermediate of the photo-aquation reaction. We provide evidence that bond photolysis occurs from reactive metal-centered excited states that are populated through relaxation of the charge transfer excited state. Beyond illuminating the elusive ferricyanide photochemistry, these results show how current limitations of Kβ main line analysis in assigning ultrafast reaction intermediates can be circumvented by simultaneously using the valence-to-core spectral range.
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Affiliation(s)
- Marco Reinhard
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
| | | | - Meiyuan Guo
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Elisa Biasin
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Kathryn Ledbetter
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Clemens Weninger
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- MAX IV Laboratory, Lund University, Lund, Sweden
| | - Tim van Driel
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | | | | | - Thomas Kroll
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Tsu-Chien Weng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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29
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Zhao Y, Adiyeri Saseendran DP, Huang C, Triana CA, Marks WR, Chen H, Zhao H, Patzke GR. Oxygen Evolution/Reduction Reaction Catalysts: From In Situ Monitoring and Reaction Mechanisms to Rational Design. Chem Rev 2023; 123:6257-6358. [PMID: 36944098 DOI: 10.1021/acs.chemrev.2c00515] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) are core steps of various energy conversion and storage systems. However, their sluggish reaction kinetics, i.e., the demanding multielectron transfer processes, still render OER/ORR catalysts less efficient for practical applications. Moreover, the complexity of the catalyst-electrolyte interface makes a comprehensive understanding of the intrinsic OER/ORR mechanisms challenging. Fortunately, recent advances of in situ/operando characterization techniques have facilitated the kinetic monitoring of catalysts under reaction conditions. Here we provide selected highlights of recent in situ/operando mechanistic studies of OER/ORR catalysts with the main emphasis placed on heterogeneous systems (primarily discussing first-row transition metals which operate under basic conditions), followed by a brief outlook on molecular catalysts. Key sections in this review are focused on determination of the true active species, identification of the active sites, and monitoring of the reactive intermediates. For in-depth insights into the above factors, a short overview of the metrics for accurate characterizations of OER/ORR catalysts is provided. A combination of the obtained time-resolved reaction information and reliable activity data will then guide the rational design of new catalysts. Strategies such as optimizing the restructuring process as well as overcoming the adsorption-energy scaling relations will be discussed. Finally, pending current challenges and prospects toward the understanding and development of efficient heterogeneous catalysts and selected homogeneous catalysts are presented.
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Affiliation(s)
- Yonggui Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | | | - Chong Huang
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Carlos A Triana
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Walker R Marks
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hang Chen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Han Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Greta R Patzke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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30
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Time-resolved transmission electron microscopy for nanoscale chemical dynamics. Nat Rev Chem 2023; 7:256-272. [PMID: 37117417 DOI: 10.1038/s41570-023-00469-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2023] [Indexed: 02/24/2023]
Abstract
The ability of transmission electron microscopy (TEM) to image a structure ranging from millimetres to Ångströms has made it an indispensable component of the toolkit of modern chemists. TEM has enabled unprecedented understanding of the atomic structures of materials and how structure relates to properties and functions. Recent developments in TEM have advanced the technique beyond static material characterization to probing structural evolution on the nanoscale in real time. Accompanying advances in data collection have pushed the temporal resolution into the microsecond regime with the use of direct-electron detectors and down to the femtosecond regime with pump-probe microscopy. Consequently, studies have deftly applied TEM for understanding nanoscale dynamics, often in operando. In this Review, time-resolved in situ TEM techniques and their applications for probing chemical and physical processes are discussed, along with emerging directions in the TEM field.
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31
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Evlyukhin E, Cifligu P, Pravica M, Bhowmik PK, Kim E, Popov D, Park C. Experimental demonstration of necessary conditions for X-ray induced synthesis of cesium superoxide. Phys Chem Chem Phys 2023; 25:1799-1807. [PMID: 36597992 DOI: 10.1039/d2cp04767e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Absorption of sufficiently energetic X-ray photons by a molecular system results in a cascade of ultrafast electronic relaxation processes which leads to a distortion and dissociation of its molecular structure. Here, we demonstrate that only decomposition of powdered cesium oxalate monohydrate induced by monochromatic X-ray irradiation under high pressure leads to the formation of cesium superoxide. Whereas, for an unhydrated form of cesium oxalate subjected to the same extreme conditions, only degradation of the electron density distribution is observed. Moreover, the corresponding model of X-ray induced electronic relaxation cascades with an emphasis on water molecules' critical role is proposed. Our experimental results suggest that the presence of water molecules in initially solid-state systems (i.e. additional electronic relaxation channels) together with applied high pressure (reduced interatomic/intermolecular distance) could potentially be a universal criteria for chemical and structural synthesis of novel compounds via X-ray induced photochemistry.
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Affiliation(s)
- Egor Evlyukhin
- Department of Physics and Astronomy, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
| | - Petrika Cifligu
- Department of Physics and Astronomy, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
| | - Michael Pravica
- Department of Physics and Astronomy, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
| | - Pradip K Bhowmik
- Department of Chemistry and Biochemistry, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Eunja Kim
- Department of Physics, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Dmitry Popov
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Changyong Park
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
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32
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Emamian S, Ireland KA, Purohit V, McWhorter KL, Maximova O, Allen W, Jensen S, Casa DM, Pushkar Y, Davis KM. X-ray Emission Spectroscopy of Single Protein Crystals Yields Insights into Heme Enzyme Intermediates. J Phys Chem Lett 2023; 14:41-48. [PMID: 36566390 PMCID: PMC9990082 DOI: 10.1021/acs.jpclett.2c03018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Enzyme reactivity is often enhanced by changes in oxidation state, spin state, and metal-ligand covalency of associated metallocofactors. The development of spectroscopic methods for studying these processes coincidentally with structural rearrangements is essential for elucidating metalloenzyme mechanisms. Herein, we demonstrate the feasibility of collecting X-ray emission spectra of metalloenzyme crystals at a third-generation synchrotron source. In particular, we report the development of a von Hamos spectrometer for the collection of Fe Kβ emission optimized for analysis of dilute biological samples. We further showcase its application in crystals of the immunosuppressive heme-dependent enzyme indoleamine 2,3-dioxygenase. Spectra from protein crystals in different states were compared with relevant reference compounds. Complementary density functional calculations assessing covalency support our spectroscopic analysis and identify active site conformations that correlate to high- and low-spin states. These experiments validate the suitability of an X-ray emission approach for determining spin states of previously uncharacterized metalloenzyme reaction intermediates.
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Affiliation(s)
- Sahand Emamian
- Department of Physics, Emory University, Atlanta, GA 30322, USA
| | | | - Vatsal Purohit
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | - Olga Maximova
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Winter Allen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Scott Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Diego M. Casa
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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33
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Simon PS, Makita H, Bogacz I, Fuller F, Bhowmick A, Hussein R, Ibrahim M, Zhang M, Chatterjee R, Cheah MH, Chernev P, Doyle MD, Brewster AS, Alonso-Mori R, Sauter NK, Bergmann U, Dobbek H, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs. FEBS Lett 2023; 597:30-37. [PMID: 36310373 PMCID: PMC9839502 DOI: 10.1002/1873-3468.14527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/17/2023]
Abstract
Ever since the discovery that Mn was required for oxygen evolution in plants by Pirson in 1937 and the period-four oscillation in flash-induced oxygen evolution by Joliot and Kok in the 1970s, understanding of this process has advanced enormously using state-of-the-art methods. The most recent in this series of innovative techniques was the introduction of X-ray free-electron lasers (XFELs) a decade ago, which led to another quantum leap in the understanding in this field, by enabling operando X-ray structural and X-ray spectroscopy studies at room temperature. This review summarizes the current understanding of the structure of Photosystem II (PS II) and its catalytic centre, the Mn4 CaO5 complex, in the intermediate Si (i = 0-4)-states of the Kok cycle, obtained using XFELs.
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Affiliation(s)
- Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Franklin Fuller
- Pulse Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roberto Alonso-Mori
- LINAC Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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34
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Penfold TJ, Rankine CD. A deep neural network for valence-to-core X-ray emission spectroscopy. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2123406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- T. J. Penfold
- Chemistry–School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - C. D. Rankine
- Chemistry–School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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35
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Soley M, Videla PE, Nibbering ETJ, Batista VS. Ultrafast Charge Relocation Dynamics in Enol-Keto Tautomerization Monitored with a Local Soft-X-ray Probe. J Phys Chem Lett 2022; 13:8254-8263. [PMID: 36018775 PMCID: PMC9465716 DOI: 10.1021/acs.jpclett.2c02037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Proton-coupled electron transfer (PCET) is the underlying mechanism governing important reactions ranging from water splitting in photosynthesis to oxygen reduction in hydrogen fuel cells. The interplay of proton and electronic charge distribution motions can vary from sequential to concerted schemes, with elementary steps occurring on ultrafast time scales. We demonstrate with a simulation study that femtosecond soft-X-ray spectroscopy provides key insights into the PCET mechanism of a photoinduced intramolecular enol* → keto* tautomerization reaction. A full quantum treatment of the electronic and nuclear dynamics of 2-(2'-hydroxyphenyl)benzothiazole upon electronic excitation reveals how spectral signatures of local excitations from core to frontier orbitals display the distinctly different stages of charge relocation for the H atom, donating, and accepting sites. Our findings indicate that ultraviolet/X-ray pump-probe spectroscopy provides a unique way to probe ultrafast electronic structure rearrangements in photoinduced chemical reactions essential to understanding the mechanism of PCET.
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Affiliation(s)
- Micheline
B. Soley
- Department
of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
- Yale
Quantum Institute, Yale University, P.O. Box 208334, New Haven, Connecticut 06520-8263, United States
| | - Pablo E. Videla
- Department
of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
- Energy
Sciences Institute, Yale University, P.O. Box 27394, West Haven, Connecticut 06516-7394, United States
| | - Erik T. J. Nibbering
- Max
Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max Born Strasse 2A, 12489 Berlin, Germany
| | - Victor S. Batista
- Department
of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
- Yale
Quantum Institute, Yale University, P.O. Box 208334, New Haven, Connecticut 06520-8263, United States
- Energy
Sciences Institute, Yale University, P.O. Box 27394, West Haven, Connecticut 06516-7394, United States
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36
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Cutsail GE, Banerjee R, Rice DB, McCubbin Stepanic O, Lipscomb JD, DeBeer S. Determination of the iron(IV) local spin states of the Q intermediate of soluble methane monooxygenase by Kβ X-ray emission spectroscopy. J Biol Inorg Chem 2022; 27:573-582. [PMID: 35988092 PMCID: PMC9470658 DOI: 10.1007/s00775-022-01953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/07/2022] [Indexed: 11/29/2022]
Abstract
Soluble methane monooxygenase (sMMO) facilitates the conversion of methane to methanol at a non-heme FeIV2 intermediate MMOHQ, which is formed in the active site of the sMMO hydroxylase component (MMOH) during the catalytic cycle. Other biological systems also employ high-valent FeIV sites in catalysis; however, MMOHQ is unique as Nature’s only identified FeIV2 intermediate. Previous 57Fe Mössbauer spectroscopic studies have shown that MMOHQ employs antiferromagnetic coupling of the two FeIV sites to yield a diamagnetic cluster. Unfortunately, this lack of net spin prevents the determination of the local spin state (Sloc) of each of the irons by most spectroscopic techniques. Here, we use Fe Kβ X-ray emission spectroscopy (XES) to characterize the local spin states of the key intermediates of the sMMO catalytic cycle, including MMOHQ trapped by rapid-freeze-quench techniques. A pure XES spectrum of MMOHQ is obtained by subtraction of the contributions from other reaction cycle intermediates with the aid of Mössbauer quantification. Comparisons of the MMOHQ spectrum with those of known Sloc = 1 and Sloc = 2 FeIV sites in chemical and biological models reveal that MMOHQ possesses Sloc = 2 iron sites. This experimental determination of the local spin state will help guide future computational and mechanistic studies of sMMO catalysis.
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Affiliation(s)
- George E Cutsail
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany.
| | - Rahul Banerjee
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Derek B Rice
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Olivia McCubbin Stepanic
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
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37
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Medvedev N, Akhmetov F, Rymzhanov RA, Voronkov R, Volkov AE. Modeling Time‐Resolved Kinetics in Solids Induced by Extreme Electronic Excitation. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nikita Medvedev
- Institute of Physics Czech Academy of Sciences Na Slovance 1999/2 Prague 8 182 21 Czech Republic
- Institute of Plasma Physics Czech Academy of Sciences Za Slovankou 3 Prague 8 182 00 Czech Republic
| | - Fedor Akhmetov
- Industrial Focus Group XUV Optics MESA+ Institute for Nanotechnology University of Twente Drienerlolaan 5 NB Enschede 7522 The Netherlands
| | - Ruslan A. Rymzhanov
- Joint Institute for Nuclear Research Joliot‐Curie 6 Dubna Moscow Region 141980 Russia
- The Institute of Nuclear Physics Ibragimov St. 1 Almaty 050032 Kazakhstan
| | - Roman Voronkov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences Leninskij pr., 53 Moscow 119991 Russia
| | - Alexander E. Volkov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences Leninskij pr., 53 Moscow 119991 Russia
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38
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Cutsail III GE, DeBeer S. Challenges and Opportunities for Applications of Advanced X-ray Spectroscopy in Catalysis Research. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- George E. Cutsail III
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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39
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Yano J, Gaffney KJ, Gregoire J, Hung L, Ourmazd A, Schrier J, Sethian JA, Toma FM. The case for data science in experimental chemistry: examples and recommendations. Nat Rev Chem 2022; 6:357-370. [PMID: 37117931 DOI: 10.1038/s41570-022-00382-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2022] [Indexed: 12/31/2022]
Abstract
The physical sciences community is increasingly taking advantage of the possibilities offered by modern data science to solve problems in experimental chemistry and potentially to change the way we design, conduct and understand results from experiments. Successfully exploiting these opportunities involves considerable challenges. In this Expert Recommendation, we focus on experimental co-design and its importance to experimental chemistry. We provide examples of how data science is changing the way we conduct experiments, and we outline opportunities for further integration of data science and experimental chemistry to advance these fields. Our recommendations include establishing stronger links between chemists and data scientists; developing chemistry-specific data science methods; integrating algorithms, software and hardware to 'co-design' chemistry experiments from inception; and combining diverse and disparate data sources into a data network for chemistry research.
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40
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Zhang Y, Kroll T, Weninger C, Michine Y, Fuller FD, Zhu D, Alonso-Mori R, Sokaras D, Lutman AA, Halavanau A, Pellegrini C, Benediktovitch A, Yabashi M, Inoue I, Inubushi Y, Osaka T, Yamada J, Babu G, Salpekar D, Sayed FN, Ajayan PM, Kern J, Yano J, Yachandra VK, Yoneda H, Rohringer N, Bergmann U. Generation of intense phase-stable femtosecond hard X-ray pulse pairs. Proc Natl Acad Sci U S A 2022; 119:e2119616119. [PMID: 35290124 PMCID: PMC8944280 DOI: 10.1073/pnas.2119616119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/02/2022] [Indexed: 11/18/2022] Open
Abstract
Coherent nonlinear spectroscopies and imaging in the X-ray domain provide direct insight into the coupled motions of electrons and nuclei with resolution on the electronic length scale and timescale. The experimental realization of such techniques will strongly benefit from access to intense, coherent pairs of femtosecond X-ray pulses. We have observed phase-stable X-ray pulse pairs containing more than 3 × 107 photons at 5.9 keV (2.1 Å) with ∼1 fs duration and 2 to 5 fs separation. The highly directional pulse pairs are manifested by interference fringes in the superfluorescent and seeded stimulated manganese Kα emission induced by an X-ray free-electron laser. The fringes constitute the time-frequency X-ray analog of Young’s double-slit interference, allowing for frequency domain X-ray measurements with attosecond time resolution.
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Affiliation(s)
- Yu Zhang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Clemens Weninger
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- MAX IV Laboratory, Lund University, Lund 224 84, Sweden
| | - Yurina Michine
- Institute for Laser Science, The University of Electro-Communications, Chofu,Tokyo 182-8585, Japan
| | - Franklin D. Fuller
- 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
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Alberto A. Lutman
- Linac & FEL Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Aliaksei Halavanau
- Accelerator Research Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Claudio Pellegrini
- Accelerator Research Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andrei Benediktovitch
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Makina Yabashi
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Ichiro Inoue
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuichi Inubushi
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Taito Osaka
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Jumpei Yamada
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Ganguli Babu
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Devashish Salpekar
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Farheen N. Sayed
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Pulickel M. Ajayan
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Hitoki Yoneda
- Institute for Laser Science, The University of Electro-Communications, Chofu,Tokyo 182-8585, Japan
| | - Nina Rohringer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Department of Physics, Universität Hamburg, Hamburg 20355, Germany
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Physics, University of Wisconsin–Madison, Madison, WI 53706
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41
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Lipp V, Milov I, Medvedev N. Quantifying electron cascade size in various irradiated materials for free-electron laser applications. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:323-330. [PMID: 35254294 PMCID: PMC8900838 DOI: 10.1107/s1600577522000339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Studying electron- and X-ray-induced electron cascades in solids is essential for various research areas at free-electron laser facilities, such as X-ray imaging, crystallography, pulse diagnostics or X-ray-induced damage. To better understand the fundamental factors that define the duration and spatial size of such cascades, this work investigates the electron propagation in ten solids relevant for the applications of X-ray lasers: Au, B4C, diamond, Ni, polystyrene, Ru, Si, SiC, Si3N4 and W. Using classical Monte Carlo simulation in the atomic approximation, we study the dependence of the cascade size on the incident electron or photon energy and on the target parameters. The results show that an electron-induced cascade is systematically larger than a photon-induced cascade. Moreover, in contrast with the common assumption, the maximal cascade size does not necessarily coincide with the electron range. It was found that the cascade size can be controlled by careful selection of the photon energy for a particular material. Photon energy, just above an ionization potential, can essentially split the absorbed energy between two electrons (photo- and Auger), reducing their initial energy and thus shrinking the cascade size. This analysis suggests a way of tailoring the electron cascades for applications requiring either small cascades with a high density of excited electrons or large-spread cascades with lower electron densities.
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Affiliation(s)
- Vladimir Lipp
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Igor Milov
- Industrial Focus Group XUV Optics, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Nikita Medvedev
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 3, 18200 Prague 8, Czech Republic
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42
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Toward accurate and efficient dynamic computational strategy for heterogeneous catalysis: Temperature-dependent thermodynamics and kinetics for the chemisorbed on-surface CO. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.03.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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Liekhus-Schmaltz C, Fox ZW, Andersen A, Kjaer KS, Alonso-Mori R, Biasin E, Carlstad J, Chollet M, Gaynor JD, Glownia JM, Hong K, Kroll T, Lee JH, Poulter BI, Reinhard M, Sokaras D, Zhang Y, Doumy G, March AM, Southworth SH, Mukamel S, Cordones AA, Schoenlein RW, Govind N, Khalil M. Femtosecond X-ray Spectroscopy Directly Quantifies Transient Excited-State Mixed Valency. J Phys Chem Lett 2022; 13:378-386. [PMID: 34985900 DOI: 10.1021/acs.jpclett.1c03613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantifying charge delocalization associated with short-lived photoexcited states of molecular complexes in solution remains experimentally challenging, requiring local element specific femtosecond experimental probes of time-evolving electron transfer. In this study, we quantify the evolving valence hole charge distribution in the photoexcited charge transfer state of a prototypical mixed valence bimetallic iron-ruthenium complex, [(CN)5FeIICNRuIII(NH3)5]-, in water by combining femtosecond X-ray spectroscopy measurements with time-dependent density functional theory calculations of the excited-state dynamics. We estimate the valence hole charge that accumulated at the Fe atom to be 0.6 ± 0.2, resulting from excited-state metal-to-metal charge transfer, on an ∼60 fs time scale. Our combined experimental and computational approach provides a spectroscopic ruler for quantifying excited-state valency in solvated complexes.
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Affiliation(s)
| | - Zachary W Fox
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Amity Andersen
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kasper S Kjaer
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Julia Carlstad
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - James D Gaynor
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Kiryong Hong
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jae Hyuk Lee
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Benjamin I Poulter
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Marco Reinhard
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Yu Zhang
- Department of Chemistry and Department of Physics & Astronomy, University of California, Irvine, California 94025, United States
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Anne Marie March
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Stephen H Southworth
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics & Astronomy, University of California, Irvine, California 94025, United States
| | - Amy A Cordones
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Robert W Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Niranjan Govind
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Munira Khalil
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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44
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Vogt M, Smolentsev G. Time‐Resolved X‐Ray Spectroscopy to Study Luminophores with Relevance for OLEDs. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Matthias Vogt
- Fakultät für Naturwissenschaften II, Institut für Chemie Martin-Luther-Universität Halle-Wittenberg Kurt-Mothes-Str. 2 06120 Halle (Saale) Germany
| | - Grigory Smolentsev
- Energy and Environment Research Division Paul Scherrer Institute Forschungsstrasse 111 5232 Villigen-PSI Switzerland
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45
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Jay RM, Kunnus K, Wernet P, Gaffney KJ. Capturing Atom-Specific Electronic Structural Dynamics of Transition-Metal Complexes with Ultrafast Soft X-Ray Spectroscopy. Annu Rev Phys Chem 2022; 73:187-208. [DOI: 10.1146/annurev-physchem-082820-020236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The atomic specificity of X-ray spectroscopies provides a distinct perspective on molecular electronic structure. For 3 d metal coordination and organometallic complexes, the combination of metal- and ligand-specific X-ray spectroscopies directly interrogates metal–ligand covalency—the hybridization of metal and ligand electronic states. Resonant inelastic X-ray scattering (RIXS), the X-ray analog of resonance Raman scattering, provides access to all classes of valence excited states in transition-metal complexes, making it a particularly powerful means of characterizing the valence electronic structure of 3 d metal complexes. Recent advances in X-ray free-electron laser sources have enabled RIXS to be extended to the ultrafast time domain. We review RIXS studies of two archetypical photochemical processes: charge-transfer excitation in ferricyanide and ligand photodissociation in iron pentacarbonyl. These studies demonstrate femtosecond-resolution RIXS can directly characterize the time-evolving electronic structure, including the evolution of the metal–ligand covalency. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Raphael M. Jay
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden;,
| | - Kristjan Kunnus
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Philippe Wernet
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden;,
| | - Kelly J. Gaffney
- PULSE Institute, SLAC National Accelerator Laboratory and Stanford University, Menlo Park, California, USA
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46
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Banerjee R, Srinivas V, Lebrette H. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Subcell Biochem 2022; 99:109-153. [PMID: 36151375 DOI: 10.1007/978-3-031-00793-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France.
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47
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Kaila VRI. Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I. Acc Chem Res 2021; 54:4462-4473. [PMID: 34894649 PMCID: PMC8697550 DOI: 10.1021/acs.accounts.1c00524] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
Biological energy conversion is catalyzed by membrane-bound proteins
that transduce chemical or light energy into energy forms that power
endergonic processes in the cell. At a molecular level, these catalytic
processes involve elementary electron-, proton-, charge-, and energy-transfer
reactions that take place in the intricate molecular machineries of
cell respiration and photosynthesis. Recent developments in structural
biology, particularly cryo-electron microscopy (cryoEM), have resolved
the molecular architecture of several energy transducing proteins,
but detailed mechanistic principles of their charge transfer reactions
still remain poorly understood and a major challenge for modern biochemical
research. To this end, multiscale molecular simulations provide a
powerful approach to probe mechanistic principles on a broad range
of time scales (femtoseconds to milliseconds) and spatial resolutions
(101–106 atoms), although technical challenges
also require balancing between the computational accuracy, cost, and
approximations introduced within the model. Here we discuss how the
combination of atomistic (aMD) and hybrid quantum/classical molecular
dynamics (QM/MM MD) simulations with free energy (FE) sampling methods
can be used to probe mechanistic principles of enzymes responsible
for biological energy conversion. We present mechanistic explorations
of long-range proton-coupled electron transfer (PCET) dynamics in
the highly intricate respiratory chain enzyme Complex I, which functions
as a redox-driven proton pump in bacterial and mitochondrial respiratory
chains by catalyzing a 300 Å fully reversible PCET process. This
process is initiated by a hydride (H–) transfer
between NADH and FMN, followed by long-range (>100 Å) electron
transfer along a wire of 8 FeS centers leading to a quinone biding
site. The reduction of the quinone to quinol initiates dissociation
of the latter to a second membrane-bound binding site, and triggers
proton pumping across the membrane domain of complex I, in subunits
up to 200 Å away from the active site. Our simulations across
different size and time scales suggest that transient charge transfer
reactions lead to changes in the internal hydration state of key regions,
local electric fields, and the conformation of conserved ion pairs,
which in turn modulate the dynamics of functional steps along the
reaction cycle. Similar functional principles, which operate on much
shorter length scales, are also found in some unrelated proteins,
suggesting that enzymes may employ conserved principles in the catalysis
of biological energy transduction processes.
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Affiliation(s)
- Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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48
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Chen Z, Wang X, Mills JP, Du C, Kim J, Wen J, Wu YA. Two-dimensional materials for electrochemical CO 2 reduction: materials, in situ/ operando characterizations, and perspective. NANOSCALE 2021; 13:19712-19739. [PMID: 34817491 DOI: 10.1039/d1nr06196h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Electrochemical CO2 reduction (CO2 ECR) is an efficient approach to achieving eco-friendly energy generation and environmental sustainability. This approach is capable of lowering the CO2 greenhouse gas concentration in the atmosphere while producing various valuable fuels and products. For catalytic CO2 ECR, two-dimensional (2D) materials stand as promising catalyst candidates due to their superior electrical conductivity, abundant dangling bonds, and tremendous amounts of surface active sites. On the other hand, the investigations on fundamental reaction mechanisms in CO2 ECR are highly demanded but usually require advanced in situ and operando multimodal characterizations. This review summarizes recent advances in the development, engineering, and structure-activity relationships of 2D materials for CO2 ECR. Furthermore, we overview state-of-the-art in situ and operando characterization techniques, which are used to investigate the catalytic reaction mechanisms with the spatial resolution from the micron-scale to the atomic scale, and with the temporal resolution from femtoseconds to seconds. Finally, we conclude this review by outlining challenges and opportunities for future development in this field.
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Affiliation(s)
- Zuolong Chen
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Materials Interface Foundry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Xiyang Wang
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Materials Interface Foundry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Joel P Mills
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Materials Interface Foundry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Cheng Du
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Materials Interface Foundry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Jintae Kim
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Materials Interface Foundry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - John Wen
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Materials Interface Foundry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Yimin A Wu
- Department of Mechanical and Mechatronics Engineering, Waterloo Institute for Nanotechnology, Materials Interface Foundry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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49
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Fransson T, Alonso-Mori R, Chatterjee R, Cheah MH, Ibrahim M, Hussein R, Zhang M, Fuller F, Gul S, Kim IS, Simon PS, Bogacz I, Makita H, de Lichtenberg C, Song S, Batyuk A, Sokaras D, Massad R, Doyle M, Britz A, Weninger C, Zouni A, Messinger J, Yachandra VK, Yano J, Kern J, Bergmann U. Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:064302. [PMID: 34849380 PMCID: PMC8610604 DOI: 10.1063/4.0000130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/24/2021] [Indexed: 05/21/2023]
Abstract
In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.
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Affiliation(s)
- Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Mohamed Ibrahim
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Miao Zhang
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Franklin Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ramzi Massad
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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50
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Larsson HR, Tannor DJ. Control of concerted back-to-back double ionization dynamics in helium. J Chem Phys 2021; 155:144105. [PMID: 34654299 DOI: 10.1063/5.0063056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Double ionization (DI) is a fundamental process that despite its apparent simplicity provides rich opportunities for probing and controlling the electronic motion. Even for the simplest multielectron atom, helium, new DI mechanisms are still being found. To first order in the field strength, a strong external field doubly ionizes the electrons in helium such that they are ejected into the same direction (front-to-back motion). The ejection into opposite directions (back-to-back motion) cannot be described to first order, making it a challenging target for control. Here, we address this challenge and optimize the field with the objective of back-to-back double ionization using a (1 + 1)-dimensional model. The optimization is performed using four different control procedures: (1) short-time control, (2) derivative-free optimization of basis expansions of the field, (3) the Krotov method, and (4) control of the classical equations of motion. All four procedures lead to fields with dominant back-to-back motion. All the fields obtained exploit essentially the same two-step mechanism leading to back-to-back motion: first, the electrons are displaced by the field into the same direction. Second, after the field turns off, the nuclear attraction and the electron-electron repulsion combine to generate the final motion into opposite directions for each electron. By performing quasi-classical calculations, we confirm that this mechanism is essentially classical.
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Affiliation(s)
- Henrik R Larsson
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - David J Tannor
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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