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Markmann V, Pan J, Hansen BL, Haubro ML, Nimmrich A, Lenzen P, Levantino M, Katayama T, Adachi SI, Gorski-Bilke S, Temps F, Dohn AO, Møller KB, Nielsen MM, Haldrup K. Real-time structural dynamics of the ultrafast solvation process around photo-excited aqueous halides. Chem Sci 2024; 15:11391-11401. [PMID: 39055005 PMCID: PMC11268492 DOI: 10.1039/d4sc01912a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024] Open
Abstract
This work investigates and describes the structural dynamics taking place following charge-transfer-to-solvent photo-abstraction of electrons from I- and Br- ions in aqueous solution following single- and 2-photon excitation at 202 nm and 400 nm, respectively. A Time-Resolved X-ray Solution Scattering (TR-XSS) approach with direct sensitivity to the structure of the surrounding solvent as the water molecules adopt a new equilibrium configuration following the electron-abstraction process is utilized to investigate the structural dynamics of solvent shell expansion and restructuring in real-time. The structural sensitivity of the scattering data enables a quantitative evaluation of competing models for the interaction between the nascent neutral species and surrounding water molecules. Taking the I0-O distance as the reaction coordinate, we find that the structural reorganization is delayed by 0.1 ps with respect to the photoexcitation and completes on a time scale of 0.5-1 ps. On longer time scales we determine from the evolution of the TR-XSS difference signal that I0: e- recombination takes place on two distinct time scales of ∼20 ps and 100 s of picoseconds. These dynamics are well captured by a simple model of diffusive evolution of the initial photo-abstracted electron population where the charge-transfer-to-solvent process gives rise to a broad distribution of electron ejection distances, a significant fraction of which are in the close vicinity of the nascent halogen atoms and recombine on short time scales.
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Affiliation(s)
- Verena Markmann
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
| | - Jaysree Pan
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
| | - Bianca L Hansen
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
| | - Morten L Haubro
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
| | - Amke Nimmrich
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
- Department of Chemistry and Molecular Biology, University of Gothenburg Gothenburg Sweden
| | - Philipp Lenzen
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
| | - Matteo Levantino
- European Synchrotron Radiation Facility CS40220 Grenoble 38043 Cedex 9 France
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute Kouto 1-1-1, Sayo Hyogo 679-5198 Japan
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho, Tsukuba Ibaraki 305-0801 Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science 1-1 Oho, Tsukuba Ibaraki 305-0801 Japan
| | | | - Friedrich Temps
- Christian-Albrechts-University Kiel Olshausenstr. 40 24098 Kiel Germany
| | - Asmus O Dohn
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
- Science Institute, University of Iceland 107 Reykjavík Iceland
| | - Klaus B Møller
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
| | - Martin M Nielsen
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
| | - Kristoffer Haldrup
- Technical University of Denmark Anker Engelunds Vej 1 2800 Lyngby Denmark
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2
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Polonius S, Lehrner D, González L, Mai S. Resolving Photoinduced Femtosecond Three-Dimensional Solute-Solvent Dynamics through Surface Hopping Simulations. J Chem Theory Comput 2024; 20:4738-4750. [PMID: 38768386 PMCID: PMC11171268 DOI: 10.1021/acs.jctc.4c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Photoinduced dynamics in solution is governed by mutual solute-solvent interactions, which give rise to phenomena like solvatochromism, the Stokes shift, dual fluorescence, or charge transfer. Understanding these phenomena requires simulating the solute's photoinduced dynamics and simultaneously resolving the three-dimensional solvent distribution dynamics. If using trajectory surface hopping (TSH) to this aim, thousands of trajectories are required to adequately sample the time-dependent three-dimensional solvent distribution functions, and thus resolve the solvent dynamics with sub-Ångstrom and femtosecond accuracy and sufficiently low noise levels. Unfortunately, simulating thousands of trajectories with TSH in the framework of hybrid quantum mechanical/molecular mechanical (QM/MM) can be prohibitively expensive when employing ab initio electronic structure methods. To tackle this challenge, we recently introduced a computationally efficient approach that combines efficient linear vibronic coupling models with molecular mechanics (LVC/MM) via electrostatic embedding [Polonius et al., JCTC 2023, 19, 7171-7186]. This method provides solvent-embedded, nonadiabatically coupled potential energy surfaces while scaling similarly to MM force fields. Here, we employ TSH with LVC/MM to unravel the photoinduced dynamics of two small thiocarbonyl compounds solvated in water. We describe how to estimate the number of trajectories required to produce nearly noise-free three-dimensional solvent distribution functions and present an analysis based on approximately 10,000 trajectories propagated for 3 ps. In the electronic ground state, both molecules exhibit in-plane hydrogen bonds to the sulfur atom. Shortly after excitation, these bonds are broken and reform perpendicular to the molecular plane on timescales that differ by an order of magnitude due to steric effects. We also show that the solvent relaxation dynamics is coupled to the electronic dynamics, including intersystem crossing. These findings are relevant to advance the understanding of the coupled solute-solvent dynamics of solvated photoexcited molecules, e.g., biologically relevant thio-nucleobases.
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Affiliation(s)
- Severin Polonius
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090 Vienna, Austria
| | - David Lehrner
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
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3
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Selenius E, Sigurdarson AE, Schmerwitz YLA, Levi G. Orbital-Optimized Versus Time-Dependent Density Functional Calculations of Intramolecular Charge Transfer Excited States. J Chem Theory Comput 2024; 20:3809-3822. [PMID: 38695313 DOI: 10.1021/acs.jctc.3c01319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
The performance of time-independent, orbital-optimized calculations of excited states is assessed with respect to charge transfer excitations in organic molecules in comparison to the linear-response time-dependent density functional theory (TD-DFT) approach. A direct optimization method to converge on saddle points of the electronic energy surface is used to carry out calculations with the local density approximation (LDA) and the generalized gradient approximation (GGA) functionals PBE and BLYP for a set of 27 excitations in 15 molecules. The time-independent approach is fully variational and provides a relaxed excited state electron density from which the extent of charge transfer is quantified. The TD-DFT calculations are generally found to provide larger charge transfer distances compared to the orbital-optimized calculations, even when including orbital relaxation effects with the Z-vector method. While the error on the excitation energy relative to theoretical best estimates is found to increase with the extent of charge transfer up to ca. -2 eV for TD-DFT, no correlation is observed for the orbital-optimized approach. The orbital-optimized calculations with the LDA and the GGA functionals provide a mean absolute error of ∼0.7 eV, outperforming TD-DFT with both local and global hybrid functionals for excitations with a long-range charge transfer character. Orbital-optimized calculations with the global hybrid functional B3LYP and the range-separated hybrid functional CAM-B3LYP on a selection of states with short- and long-range charge transfer indicate that inclusion of exact exchange has a small effect on the charge transfer distance, while it significantly improves the excitation energy, with the best-performing functional CAM-B3LYP providing an absolute error typically around 0.15 eV.
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Affiliation(s)
- Elli Selenius
- Science Institute of the University of Iceland, Reykjavík 107, Iceland
| | | | | | - Gianluca Levi
- Science Institute of the University of Iceland, Reykjavík 107, Iceland
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4
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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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5
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Lee Y, Oang KY, Kim D, Ihee H. A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:031301. [PMID: 38706888 PMCID: PMC11065455 DOI: 10.1063/4.0000249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.
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Affiliation(s)
| | - Key Young Oang
- Radiation Center for Ultrafast Science, Korea Atomic Energy Research Institute (KAERI), Daejeon 34057, South Korea
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6
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Thompson NB, Mulfort KL, Tiede DM. Toward a quantitative description of solvation structure: a framework for differential solution scattering measurements. IUCRJ 2024; 11:423-433. [PMID: 38700232 PMCID: PMC11067739 DOI: 10.1107/s2052252524003282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024]
Abstract
Appreciating that the role of the solute-solvent and other outer-sphere interactions is essential for understanding chemistry and chemical dynamics in solution, experimental approaches are needed to address the structural consequences of these interactions, complementing condensed-matter simulations and coarse-grained theories. High-energy X-ray scattering (HEXS) combined with pair distribution function analysis presents the opportunity to probe these structures directly and to develop quantitative, atomistic models of molecular systems in situ in the solution phase. However, at concentrations relevant to solution-phase chemistry, the total scattering signal is dominated by the bulk solvent, prompting researchers to adopt a differential approach to eliminate this unwanted background. Though similar approaches are well established in quantitative structural studies of macromolecules in solution by small- and wide-angle X-ray scattering (SAXS/WAXS), analogous studies in the HEXS regime-where sub-ångström spatial resolution is achieved-remain underdeveloped, in part due to the lack of a rigorous theoretical description of the experiment. To address this, herein we develop a framework for differential solution scattering experiments conducted at high energies, which includes concepts of the solvent-excluded volume introduced to describe SAXS/WAXS data, as well as concepts from the time-resolved X-ray scattering community. Our theory is supported by numerical simulations and experiment and paves the way for establishing quantitative methods to determine the atomic structures of small molecules in solution with resolution approaching that of crystallography.
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Affiliation(s)
- Niklas B. Thompson
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 USA
| | - Karen L. Mulfort
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 USA
| | - David M. Tiede
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 USA
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7
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Eng J, Rankine CD, Penfold TJ. The photochemistry of Rydberg-excited cyclobutanone: Photoinduced processes and ground state dynamics. J Chem Phys 2024; 160:154301. [PMID: 38619456 DOI: 10.1063/5.0203597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/28/2024] [Indexed: 04/16/2024] Open
Abstract
Owing to ring strain, cyclic ketones exhibit complex excited state dynamics with multiple competing photochemical channels active on the ultrafast timescale. While the excited state dynamics of cyclobutanone after π* ← n excitation into the lowest-energy excited singlet (S1) state has been extensively studied, the dynamics following 3s ← n excitation into the higher-lying singlet Rydberg (S2) state are less well understood. Herein, we employ fully quantum multiconfigurational time-dependent Hartree (MCTDH) simulations using a model Hamiltonian as well as "on-the-fly" trajectory-based surface-hopping dynamics (TSHD) simulations to study the relaxation dynamics of cyclobutanone following 3s ← n excitation and to predict the ultrafast electron diffraction scattering signature of these relaxation dynamics. Our MCTDH and TSHD simulations indicate that relaxation from the initially-populated singlet Rydberg (S2) state occurs on the timescale of a few hundreds of femtoseconds to a picosecond, consistent with the symmetry-forbidden nature of the state-to-state transition involved. There is no obvious involvement of excited triplet states within the timeframe of our simulations (<2 ps). After non-radiative relaxation to the electronic ground state (S0), vibrationally hot cyclobutanone has sufficient internal energy to form multiple fragmented products including C2H4 + CH2CO (C2; 20%) and C3H6 + CO (C3; 2.5%). We discuss the limitations of our MCTDH and TSHD simulations, how these may influence the excited state dynamics we observe, and-ultimately-the predictive power of the simulated experimental observable.
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Affiliation(s)
- J Eng
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - C D Rankine
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - T J Penfold
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
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8
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Mortensen JJ, Larsen AH, Kuisma M, Ivanov AV, Taghizadeh A, Peterson A, Haldar A, Dohn AO, Schäfer C, Jónsson EÖ, Hermes ED, Nilsson FA, Kastlunger G, Levi G, Jónsson H, Häkkinen H, Fojt J, Kangsabanik J, Sødequist J, Lehtomäki J, Heske J, Enkovaara J, Winther KT, Dulak M, Melander MM, Ovesen M, Louhivuori M, Walter M, Gjerding M, Lopez-Acevedo O, Erhart P, Warmbier R, Würdemann R, Kaappa S, Latini S, Boland TM, Bligaard T, Skovhus T, Susi T, Maxson T, Rossi T, Chen X, Schmerwitz YLA, Schiøtz J, Olsen T, Jacobsen KW, Thygesen KS. GPAW: An open Python package for electronic structure calculations. J Chem Phys 2024; 160:092503. [PMID: 38450733 DOI: 10.1063/5.0182685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 03/08/2024] Open
Abstract
We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.
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Affiliation(s)
- Jens Jørgen Mortensen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ask Hjorth Larsen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mikael Kuisma
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Aleksei V Ivanov
- Riverlane Ltd., St Andrews House, 59 St Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Alireza Taghizadeh
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andrew Peterson
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Anubhab Haldar
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Asmus Ougaard Dohn
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark and Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, Reykjavík 107, Iceland
| | - Christian Schäfer
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Eric D Hermes
- Quantum-Si, 29 Business Park Drive, Branford, Connecticut 06405, USA
| | | | - Georg Kastlunger
- CatTheory, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Gianluca Levi
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Hannu Häkkinen
- Departments of Physics and Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Jakub Fojt
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jiban Kangsabanik
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Joachim Sødequist
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jouko Lehtomäki
- Department of Applied Physics, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
| | - Julian Heske
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jussi Enkovaara
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Kirsten Trøstrup Winther
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marcin Dulak
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Marko M Melander
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Martin Ovesen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Martti Louhivuori
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Michael Walter
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Morten Gjerding
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Olga Lopez-Acevedo
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia
| | - Paul Erhart
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Robert Warmbier
- School of Physics and Mandelstam Institute for Theoretical Physics, University of the Witwatersrand, 1 Jan Smuts Avenue, 2001 Johannesburg, South Africa
| | - Rolf Würdemann
- Freiburger Materialforschungszentrum, Universität Freiburg, Stefan-Meier-Straße 21, D-79104 Freiburg, Germany
| | - Sami Kaappa
- Computational Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Simone Latini
- Nanomade, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tara Maria Boland
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Bligaard
- Department of Energy Conversion and Storage, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Thorbjørn Skovhus
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Toma Susi
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Tristan Maxson
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Tuomas Rossi
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Xi Chen
- School of Physical Science and Technology, Lanzhou University, Lanzhou, Gansu 730000, China
| | | | - Jakob Schiøtz
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Olsen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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9
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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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10
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Dohn AO, Markmann V, Nimmrich A, Haldrup K, Møller KB, Nielsen MM. Eliminating finite-size effects on the calculation of x-ray scattering from molecular dynamics simulations. J Chem Phys 2023; 159:124115. [PMID: 38127395 DOI: 10.1063/5.0164365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/01/2023] [Indexed: 12/23/2023] Open
Abstract
Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus toward describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell. To eliminate this error, we derive a new scheme to renormalize the sampled RDFs based on a model of the excluded volume of the particle-pairs they were sampled from, to emulate sampling from an infinite system. We compare this new correction method to two previous RDF-correction methods, developed for Kirkwood-Buff theory applications. We present a quantitative test to assess the reliability of the simulated low-q scattering signal and show that our RDF-correction successfully recovers the correct q = 0 limit for neat water. We investigate the effect of MD-sampling time on the RDF-corrections, before advancing to a molecular example system, comprised of a transition metal complex solvated in a series of water cells with varying densities. We show that our correction recovers the correct q = 0 behavior for all densities. Furthermore, we employ a simple continuum scattering model to dissect the total scattering signal from the solvent-solvent structural correlations in a solute-solvent model system to find two distinct contributions: a non-local density-contribution from the finite, fixed cell size in NVT simulations, and a local contribution from the solvent shell. We show how the second contribution can be approximated without also including the finite-size contribution. Finally, we provide a "best-practices"-checklist for experimentalists planning to incorporate explicit solvation MD simulations in future work, offering guidance for improving the accuracy and reliability of structural studies using x-ray scattering methods in solution.
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Affiliation(s)
- A O Dohn
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, Reykjavík 107, Iceland
| | - V Markmann
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - A Nimmrich
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - K Haldrup
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - K B Møller
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - M M Nielsen
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
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11
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Appleby MV, Cowin RA, Ivalo II, Peralta-Arriaga SL, Robertson CC, Bartlett S, Fitzpatrick A, Dent A, Karras G, Diaz-Moreno S, Chekulaev D, Weinstein JA. Ultrafast electronic, infrared, and X-ray absorption spectroscopy study of Cu(I) phosphine diimine complexes. Faraday Discuss 2023; 244:391-410. [PMID: 37415486 DOI: 10.1039/d3fd00027c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The study aims to understand the role of the transient bonding in the interplay between the structural and electronic changes in heteroleptic Cu(I) diimine diphosphine complexes. This is an emerging class of photosensitisers which absorb in the red region of the spectrum, whilst retaining a sufficiently long excited state lifetime. Here, the dynamics of these complexes are explored by transient absorption (TA) and time-resolved infrared (TRIR) spectroscopy, which reveal ultrafast intersystem crossing and structural distortion occurring. Two potential mechanisms affecting excited state decay in these complexes involve a transient formation of a solvent adduct, made possible by the opening up of the Cu coordination centre in the excited state due to structural distortion, and by a transient coordination of the O-atom of the phosphine ligand to the copper center. X-ray absorption studies of the ground electronic state have been conducted as a prerequisite for the upcoming X-ray spectroscopy studies which will directly determine structural dynamics. The potential for these complexes to be used in bimolecular applications is confirmed by a significant yield of singlet oxygen production.
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Affiliation(s)
- Martin V Appleby
- Department of Chemistry, The University of Sheffield, Sheffield, S3 7HF, UK.
| | - Rory A Cowin
- Department of Chemistry, The University of Sheffield, Sheffield, S3 7HF, UK.
| | - Iona I Ivalo
- Department of Chemistry, The University of Sheffield, Sheffield, S3 7HF, UK.
| | | | - Craig C Robertson
- Department of Chemistry, The University of Sheffield, Sheffield, S3 7HF, UK.
| | - Stuart Bartlett
- Diamond Light Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Ann Fitzpatrick
- Diamond Light Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Andrew Dent
- Diamond Light Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Gabriel Karras
- Diamond Light Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Sofia Diaz-Moreno
- Diamond Light Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Dimitri Chekulaev
- Department of Chemistry, The University of Sheffield, Sheffield, S3 7HF, UK.
| | - Julia A Weinstein
- Department of Chemistry, The University of Sheffield, Sheffield, S3 7HF, UK.
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12
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Nimmrich A, Panman MR, Berntsson O, Biasin E, Niebling S, Petersson J, Hoernke M, Björling A, Gustavsson E, van Driel TB, Dohn AO, Laursen M, Zederkof DB, Tono K, Katayama T, Owada S, Nielsen MM, Davidsson J, Uhlig J, Hub JS, Haldrup K, Westenhoff S. Solvent-Dependent Structural Dynamics in the Ultrafast Photodissociation Reaction of Triiodide Observed with Time-Resolved X-ray Solution Scattering. J Am Chem Soc 2023. [PMID: 37163700 PMCID: PMC10375522 DOI: 10.1021/jacs.3c00484] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Resolving the structural dynamics of bond breaking, bond formation, and solvation is required for a deeper understanding of solution-phase chemical reactions. In this work, we investigate the photodissociation of triiodide in four solvents using femtosecond time-resolved X-ray solution scattering following 400 nm photoexcitation. Structural analysis of the scattering data resolves the solvent-dependent structural evolution during the bond cleavage, internal rearrangements, solvent-cage escape, and bond reformation in real time. The nature and structure of the reaction intermediates during the recombination are determined, elucidating the full mechanism of photodissociation and recombination on ultrafast time scales. We resolve the structure of the precursor state for recombination as a geminate pair. Further, we determine the size of the solvent cages from the refined structures of the radical pair. The observed structural dynamics present a comprehensive picture of the solvent influence on structure and dynamics of dissociation reactions.
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Affiliation(s)
- Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Matthijs R Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Oskar Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Elisa Biasin
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Stephan Niebling
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Jonas Petersson
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Maria Hoernke
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Alexander Björling
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Tim B van Driel
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Asmus O Dohn
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
- Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Mads Laursen
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Diana B Zederkof
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Martin M Nielsen
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jan Davidsson
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Jens Uhlig
- Department of Chemical Physics, Lund University, Box 124, 22100 Lund, Sweden
| | - Jochen S Hub
- Georg-August-Universität Göttingen, Institute for Microbiology and Genetics, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Kristoffer Haldrup
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- Department of Chemical Physics, Lund University, Box 124, 22100 Lund, Sweden
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