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Tran VA, Teucher M, Galazzo L, Sharma B, Pongratz T, Kast SM, Marx D, Bordignon E, Schnegg A, Neese F. Dissecting the Molecular Origin of g-Tensor Heterogeneity and Strain in Nitroxide Radicals in Water: Electron Paramagnetic Resonance Experiment versus Theory. J Phys Chem A 2023; 127:6447-6466. [PMID: 37524058 PMCID: PMC10424240 DOI: 10.1021/acs.jpca.3c02879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/01/2023] [Indexed: 08/02/2023]
Abstract
Nitroxides are common EPR sensors of microenvironmental properties such as polarity, numbers of H-bonds, pH, and so forth. Their solvation in an aqueous environment is facilitated by their high propensity to form H-bonds with the surrounding water molecules. Their g- and A-tensor elements are key parameters to extracting the properties of their microenvironment. In particular, the gxx value of nitroxides is rich in information. It is known to be characterized by discrete values representing nitroxide populations previously assigned to have different H-bonds with the surrounding waters. Additionally, there is a large g-strain, that is, a broadening of g-values associated with it, which is generally correlated with environmental and structural micro-heterogeneities. The g-strain is responsible for the frequency dependence of the apparent line width of the EPR spectra, which becomes evident at high field/frequency. Here, we address the molecular origin of the gxx heterogeneity and of the g-strain of a nitroxide moiety (HMI: 2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water. To treat the solvation effect on the g-strain, we combined a multi-frequency experimental approach with ab initio molecular dynamics simulations for structural sampling and quantum chemical EPR property calculations at the highest realistically affordable level, including an explicitly micro-solvated HMI ensemble and the embedded cluster reference interaction site model. We could clearly identify the distinct populations of the H-bonded nitroxides responsible for the gxx heterogeneity experimentally observed, and we dissected the role of the solvation shell, H-bond formation, and structural deformation of the nitroxide in the creation of the g-strain associated with each nitroxide subensemble. Two contributions to the g-strain were identified in this study. The first contribution depends on the number of hydrogen bonds formed between the nitroxide and the solvent because this has a large and well-understood effect on the gxx-shift. This contribution can only be resolved at high resonance frequencies, where it leads to distinct peaks in the gxx region. The second contribution arises from configurational fluctuations of the nitroxide that necessarily lead to g-shift heterogeneity. These contributions cannot be resolved experimentally as distinct resonances but add to the line broadening. They can be quantitatively analyzed by studying the apparent line width as a function of microwave frequency. Interestingly, both theory and experiment confirm that this contribution is independent of the number of H-bonds. Perhaps even more surprisingly, the theoretical analysis suggests that the configurational fluctuation broadening is not induced by the solvent but is inherently present even in the gas phase. Moreover, the calculations predict that this broadening decreases upon solvation of the nitroxide.
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Affiliation(s)
- Van Anh Tran
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Markus Teucher
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laura Galazzo
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
- Faculty
of Chemistry and Biochemistry, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Bikramjit Sharma
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Tim Pongratz
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Stefan M. Kast
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Dominik Marx
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Enrica Bordignon
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
- Faculty
of Chemistry and Biochemistry, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Alexander Schnegg
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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Soetbeer J, Gast P, Walish JJ, Zhao Y, George C, Yang C, Swager TM, Griffin RG, Mathies G. Conformation of bis-nitroxide polarizing agents by multi-frequency EPR spectroscopy. Phys Chem Chem Phys 2018; 20:25506-25517. [PMID: 30277229 PMCID: PMC7256712 DOI: 10.1039/c8cp05236k] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The chemical structure of polarizing agents critically determines the efficiency of dynamic nuclear polarization (DNP). For cross-effect DNP, biradicals are the polarizing agents of choice and the interaction and relative orientation of the two unpaired electrons should be optimal. Both parameters are affected by the molecular structure of the biradical in the frozen glassy matrix that is typically used for DNP/MAS NMR and likely differs from the structure observed with X-ray crystallography. We have determined the conformations of six bis-nitroxide polarizing agents, including the highly efficient AMUPol, in their DNP matrix with EPR spectroscopy at 9.7 GHz, 140 GHz, and 275 GHz. The multi-frequency approach in combination with an advanced fitting routine allows us to reliably extract the interaction and relative orientation of the nitroxide moieties. We compare the structures of six bis-nitroxides to their DNP performance at 500 MHz/330 GHz.
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Affiliation(s)
- Janne Soetbeer
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter Gast
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Joseph J Walish
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yanchuan Zhao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christy George
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chen Yang
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Timothy M Swager
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert G Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guinevere Mathies
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Biller JR, Barnes R, Han S. Perspective of Overhauser dynamic nuclear polarization for the study of soft materials. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Möbius K, Lubitz W, Savitsky A. Jim Hyde and the ENDOR Connection: A Personal Account. APPLIED MAGNETIC RESONANCE 2017; 48:1149-1183. [PMID: 29151676 PMCID: PMC5668355 DOI: 10.1007/s00723-017-0959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Indexed: 06/07/2023]
Abstract
In this minireview, we report on our year-long EPR work, such as electron-nuclear double resonance (ENDOR), pulse electron double resonance (PELDOR) and ELDOR-detected NMR (EDNMR) at X-band and W-band microwave frequencies and magnetic fields. This report is dedicated to James S. Hyde and honors his pioneering contributions to the measurement of spin interactions in large (bio)molecules. From these interactions, detailed information is revealed on structure and dynamics of macromolecules embedded in liquid-solution or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultra-fast electronics for signal data handling and processing have pushed the limits of EPR spectroscopy and its multi-frequency extensions to new horizons concerning sensitivity of detection, selectivity of molecular interactions and time resolution. Among the most important advances is the upgrading of EPR to high magnetic fields, very much in analogy to what happened in NMR. The ongoing progress in EPR spectroscopy is exemplified by reviewing various multi-frequency electron-nuclear double-resonance experiments on organic radicals, light-generated donor-acceptor radical pairs in photosynthesis, and site-specifically nitroxide spin-labeled bacteriorhodopsin, the light-driven proton pump, as well as EDNMR and ENDOR on nitroxides. Signal and resolution enhancements are particularly spectacular for ENDOR, EDNMR and PELDOR on frozen-solution samples at high Zeeman fields. They provide orientation selection for disordered samples approaching single-crystal resolution at canonical g-tensor orientations-even for molecules with small g-anisotropies. Dramatic improvements of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Thus, unique structural and dynamic information is revealed that can hardly be obtained by other analytical techniques. Micromolar concentrations of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems-offering exciting applications for physicists, chemists, biochemists and molecular biologists.
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Affiliation(s)
- Klaus Möbius
- Department of Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
- Max-Planck-Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Anton Savitsky
- Max-Planck-Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
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Consentius P, Loll B, Gohlke U, Alings C, Müller C, Müller R, Teutloff C, Heinemann U, Kaupp M, Wahl MC, Risse T. Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins. J Phys Chem Lett 2017; 8:1113-1117. [PMID: 28221042 DOI: 10.1021/acs.jpclett.6b02971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.
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Affiliation(s)
- Philipp Consentius
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
| | - Bernhard Loll
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
| | - Ulrich Gohlke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Claudia Alings
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
| | - Carsten Müller
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
| | - Robert Müller
- Institute of Chemistry, Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin , Arnimallee 14, D-14195 Berlin, Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin , 14195 Berlin, Germany
| | - Udo Heinemann
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Martin Kaupp
- Institute of Chemistry, Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography , Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Thomas Risse
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin , 14195 Berlin, Germany
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Nalepa A, Malferrari M, Lubitz W, Venturoli G, Möbius K, Savitsky A. Local water sensing: water exchange in bacterial photosynthetic reaction centers embedded in a trehalose glass studied using multiresonance EPR. Phys Chem Chem Phys 2017; 19:28388-28400. [DOI: 10.1039/c7cp03942e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pulsed EPR spectroscopies and isotope labeled water are applied to detect and quantify the local water in a bacterial reaction center embedded into a trehalose glass.
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Affiliation(s)
- Anna Nalepa
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Marco Malferrari
- Laboratorio di Biochimica e Biofisica
- Dipartimento di Farmacia e Biotecnologie
- FaBiT
- Università di Bologna
- I-40126 Bologna
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica
- Dipartimento di Farmacia e Biotecnologie
- FaBiT
- Università di Bologna
- I-40126 Bologna
| | - Klaus Möbius
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
- Department of Physics
- Free University Berlin
| | - Anton Savitsky
- Max-Planck-Institut für Chemische Energiekonversion
- D-45470 Mülheim an der Ruhr
- Germany
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8
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Malferrari M, Savitsky A, Lubitz W, Möbius K, Venturoli G. Protein Immobilization Capabilities of Sucrose and Trehalose Glasses: The Effect of Protein/Sugar Concentration Unraveled by High-Field EPR. J Phys Chem Lett 2016; 7:4871-4877. [PMID: 27934049 DOI: 10.1021/acs.jpclett.6b02449] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Disaccharide glasses are increasingly used to immobilize proteins at room temperature for structural/functional studies and long-term preservation. To unravel the molecular basis of protein immobilization, we studied the effect of sugar/protein concentration ratios in trehalose or sucrose matrixes, in which the bacterial photosynthetic reaction center (RC) was embedded as a model protein. The structural, dynamical, and H-bonding characteristics of the sugar-protein systems were probed by high-field W-band EPR of a matrix-dissolved nitroxide radical. We discovered that RC immobilization and thermal stabilization, being independent of the protein concentration in trehalose, occur in sucrose only at sufficiently low sugar/protein ratios. EPR reveals that only under such conditions does sucrose form a microscopically homogeneous matrix that immobilizes, via H-bonds, the nitroxide probe. We conclude that the protein immobilization capability depends critically on the propensity of the glass-forming sugar to create intermolecular H-bond networks, thus establishing long-range, homogeneous connectivity within the matrix.
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Affiliation(s)
- Marco Malferrari
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna , I-40126 Bologna, Italy
| | - Anton Savitsky
- Max-Planck-Institut für Chemische Energiekonversion , D-45470 Mülheim (Ruhr), Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , D-45470 Mülheim (Ruhr), Germany
| | - Klaus Möbius
- Max-Planck-Institut für Chemische Energiekonversion , D-45470 Mülheim (Ruhr), Germany
- Fachbereich Physik, Freie Universität Berlin , D-14195 Berlin, Germany
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna , I-40126 Bologna, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM) , c/o Dipartimento di Fisica e Astronomia (DIFA), I-40126 Bologna, Italy
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9
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Abdullin D, Hagelueken G, Schiemann O. Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography. Phys Chem Chem Phys 2016; 18:10428-37. [DOI: 10.1039/c6cp01307d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PELDOR is used to unravel the position and orientation of MTSSL in six singly-labelled azurin mutants. A comparison with X-ray structures of the mutants shows good agreement with respect to the position and orientation of the nitroxide group.
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Affiliation(s)
- D. Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - G. Hagelueken
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - O. Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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Bordignon E, Nalepa AI, Savitsky A, Braun L, Jeschke G. Changes in the Microenvironment of Nitroxide Radicals around the Glass Transition Temperature. J Phys Chem B 2015; 119:13797-806. [DOI: 10.1021/acs.jpcb.5b04104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Enrica Bordignon
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
- Berlin
Joint EPR Laboratories, Department of Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Anna I. Nalepa
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Lukas Braun
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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