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Wiechers H, Kehl A, Hiller M, Eltzner B, Huckemann SF, Meyer A, Tkach I, Bennati M, Pokern Y. Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107491. [PMID: 37301045 DOI: 10.1016/j.jmr.2023.107491] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
ENDOR spectroscopy is a fundamental method to detect nuclear spins in the vicinity of paramagnetic centers and their mutual hyperfine interaction. Recently, site-selective introduction of 19F as nuclear labels has been proposed as a tool for ENDOR-based distance determination in biomolecules, complementing pulsed dipolar spectroscopy in the range of angstrom to nanometer. Nevertheless, one main challenge of ENDOR still consists of its spectral analysis, which is aggravated by a large parameter space and broad resonances from hyperfine interactions. Additionally, at high EPR frequencies and fields (⩾94 GHz/3.4 Tesla), chemical shift anisotropy might contribute to broadening and asymmetry in the spectra. Here, we use two nitroxide-fluorine model systems to examine a statistical approach to finding the best parameter fit to experimental 263 GHz 19F ENDOR spectra. We propose Bayesian optimization for a rapid, global parameter search with little prior knowledge, followed by a refinement by more standard gradient-based fitting procedures. Indeed, the latter suffer from finding local rather than global minima of a suitably defined loss function. Using a new and accelerated simulation procedure, results for the semi-rigid nitroxide-fluorine two and three spin systems lead to physically reasonable solutions, if minima of similar loss can be distinguished by DFT predictions. The approach also delivers the stochastic error of the obtained parameter estimates. Future developments and perspectives are discussed.
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Affiliation(s)
- H Wiechers
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - B Eltzner
- Research Group Computational Biomolecular Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - S F Huckemann
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany
| | - I Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany.
| | - Y Pokern
- Department of Statistical Science, University College London, WC1E 6BT, United Kingdom.
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2
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Schleicher E, Rein S, Illarionov B, Lehmann A, Al Said T, Kacprzak S, Bittl R, Bacher A, Fischer M, Weber S. Selective 13C labelling reveals the electronic structure of flavocoenzyme radicals. Sci Rep 2021; 11:18234. [PMID: 34521887 PMCID: PMC8440535 DOI: 10.1038/s41598-021-97588-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Flavocoenzymes are nearly ubiquitous cofactors that are involved in the catalysis and regulation of a wide range of biological processes including some light-induced ones, such as the photolyase-mediated DNA repair, magnetoreception of migratory birds, and the blue-light driven phototropism in plants. One of the factors that enable versatile flavin-coenzyme biochemistry and biophysics is the fine-tuning of the cofactor's frontier orbital by interactions with the protein environment. Probing the singly-occupied molecular orbital (SOMO) of the intermediate radical state of flavins is therefore a prerequisite for a thorough understanding of the diverse functions of the flavoprotein family. This may be ultimately achieved by unravelling the hyperfine structure of a flavin by electron paramagnetic resonance. In this contribution we present a rigorous approach to obtaining a hyperfine map of the flavin's chromophoric 7,8-dimethyl isoalloxazine unit at an as yet unprecedented level of resolution and accuracy. We combine powerful high-microwave-frequency/high-magnetic-field electron-nuclear double resonance (ENDOR) with 13C isotopologue editing as well as spectral simulations and density functional theory calculations to measure and analyse 13C hyperfine couplings of the flavin cofactor in DNA photolyase. Our data will provide the basis for electronic structure considerations for a number of flavin radical intermediates occurring in blue-light photoreceptor proteins.
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Affiliation(s)
- Erik Schleicher
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Stephan Rein
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Boris Illarionov
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Ariane Lehmann
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Tarek Al Said
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Sylwia Kacprzak
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany ,grid.423218.ePresent Address: Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Robert Bittl
- grid.14095.390000 0000 9116 4836Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Adelbert Bacher
- grid.6936.a0000000123222966Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Markus Fischer
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Stefan Weber
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
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Chiesa M, Giamello E. On the Role and Applications of Electron Magnetic Resonance Techniques in Surface Chemistry and Heterogeneous Catalysis. Catal Letters 2021. [DOI: 10.1007/s10562-021-03576-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
Some relevant aspects of Electron Paramagnetic Resonance (EPR) applied to the fields of surface chemistry and heterogeneous catalysis are illustrated in this perspective paper that aims to show the potential of these techniques in describing critical features of surface structures and reactivity. Selected examples are employed covering distinct aspects of catalytic science from morphological analysis of surfaces to detailed descriptions of chemical bonding and catalytic sites topology. In conclusions the pros and cons related to the acquisition of EPR instrumentations in an advanced laboratory of surface chemistry and heterogeneous catalysis are briefly considered.
Graphic Abstract
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Kim J, Park S, Go YK, Jin K, Kim Y, Nam KT, Kim SH. Probing the Structure and Binding Mode of EDTA on the Surface of Mn 3O 4 Nanoparticles for Water Oxidation by Advanced Electron Paramagnetic Resonance Spectroscopy. Inorg Chem 2020; 59:8846-8854. [PMID: 32501692 DOI: 10.1021/acs.inorgchem.0c00611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identification of the surface structure of nanoparticles is important for understanding the catalytic mechanism and improving the properties of the particles. Here, we provide a detailed description of the coordination modes of ethylenediaminetetraacetate (EDTA) on Mn3O4 nanoparticles at the atomic level, as obtained by advanced electron paramagnetic resonance (EPR) spectroscopy. Binding of EDTA to Mn3O4 leads to dramatic changes in the EPR spectrum, with a 5-fold increase in the axial zero-field splitting parameter of Mn(II). This indicates significant changes in the coordination environment of the Mn(II) site; hence, the binding of EDTA causes a profound change in the electronic structure of the manganese site. Furthermore, the electron spin echo envelope modulation results reveal that two 14N atoms of EDTA are directly coordinated to the Mn site and a water molecule is coordinated to the surface of the nanoparticles. An Fourier transform infrared spectroscopy study shows that the Ca(II) ion is coordinated to the carboxylic ligands via the pseudobridging mode. The EPR spectroscopic results provide an atomic picture of surface-modified Mn3O4 nanoparticles for the first time. These results can enhance our understanding of the rational design of catalysts, for example, for the water oxidation reaction.
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Affiliation(s)
- Jin Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea
| | - Sunghak Park
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoo Kyung Go
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea
| | - Kyoungsuk Jin
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yujeong Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea.,Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun Hee Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea.,Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
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Morra E, Signorile M, Salvadori E, Bordiga S, Giamello E, Chiesa M. Nature and Topology of Metal-Oxygen Binding Sites in Zeolite Materials: 17 O High-Resolution EPR Spectroscopy of Metal-Loaded ZSM-5. Angew Chem Int Ed Engl 2019; 58:12398-12403. [PMID: 31294524 DOI: 10.1002/anie.201906488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Indexed: 11/05/2022]
Abstract
Determining structural models is pivotal to the rational understanding and development of heterogeneous catalytic systems. A paradigmatic case is represented by open-shell metals supported on oxides, where the catalytic properties crucially depend on the nature of the metal-oxygen bonds and the extent of charge and spin transfer. Through a combination of selective 17 O isotopic enrichment and the unique properties of open-shell s-state monovalent Group 12 cations, we derive a site-specific topological description of active sites in an MFI zeolite. We show that just a few selected sites out of all possible are populated and that the relative occupancies depend on the specific properties of the metal, and we provide maps of charge and spin transfer at the metal-oxygen interface. This approach is not restricted to zeotype materials, rather it is applicable to any catalysts supported on oxygen-containing materials.
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Affiliation(s)
- Elena Morra
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Matteo Signorile
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Enrico Salvadori
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Silvia Bordiga
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Elio Giamello
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
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Morra E, Signorile M, Salvadori E, Bordiga S, Giamello E, Chiesa M. Nature and Topology of Metal–Oxygen Binding Sites in Zeolite Materials:
17
O High‐Resolution EPR Spectroscopy of Metal‐Loaded ZSM‐5. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elena Morra
- Department of ChemistryUniversity of Torino Via Giuria, 7 10125 Torino Italy
| | - Matteo Signorile
- Department of ChemistryUniversity of Torino Via Giuria, 7 10125 Torino Italy
| | - Enrico Salvadori
- Department of ChemistryUniversity of Torino Via Giuria, 7 10125 Torino Italy
| | - Silvia Bordiga
- Department of ChemistryUniversity of Torino Via Giuria, 7 10125 Torino Italy
| | - Elio Giamello
- Department of ChemistryUniversity of Torino Via Giuria, 7 10125 Torino Italy
| | - Mario Chiesa
- Department of ChemistryUniversity of Torino Via Giuria, 7 10125 Torino Italy
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Tkach I, Bejenke I, Hecker F, Kehl A, Kasanmascheff M, Gromov I, Prisecaru I, Höfer P, Hiller M, Bennati M. 1H high field electron-nuclear double resonance spectroscopy at 263 GHz/9.4 T. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 303:17-27. [PMID: 30991287 DOI: 10.1016/j.jmr.2019.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
We present and discuss the performance of 1H electron-nuclear double resonance (ENDOR) at 263 GHz/9.4 T by employing a prototype, commercial quasi optical spectrometer. Basic instrumental features of the setup are described alongside a comprehensive characterization of the new ENDOR probe head design. The performance of three different ENDOR pulse sequences (Davies, Mims and CP-ENDOR) is evaluated using the 1H BDPA radical. A key feature of 263 GHz spectroscopy - the increase in orientation selectivity in comparison with 94 GHz experiments - is discussed in detail. For this purpose, the resolution of 1H ENDOR spectra at 263 GHz is verified using a representative protein sample containing approximately 15 picomoles of a tyrosyl radical. Davies ENDOR spectra recorded at 5 K reveal previously obscured spectral features, which are interpreted by spectral simulations aided by DFT calculations. Our analysis shows that seven internal proton couplings are detectable for this specific radical if sufficient orientation selectivity is achieved. The results prove the fidelity of 263 GHz experiments in reporting orientation-selected 1H ENDOR spectra and demonstrate that new significant information can be uncovered in complex molecular systems, owing to the enhanced resolution combined with high absolute sensitivity and no compromise in acquisition time.
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Affiliation(s)
- Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Isabel Bejenke
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Fabian Hecker
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Annemarie Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Department of Chemistry, Georg-August University of Göttingen, Tammannstr. 2, Göttingen, Germany
| | - Müge Kasanmascheff
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Igor Gromov
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Ion Prisecaru
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Peter Höfer
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Markus Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marina Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Department of Chemistry, Georg-August University of Göttingen, Tammannstr. 2, Göttingen, Germany.
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8
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Roessler MM, Salvadori E. Principles and applications of EPR spectroscopy in the chemical sciences. Chem Soc Rev 2018; 47:2534-2553. [PMID: 29498718 DOI: 10.1039/c6cs00565a] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Electron spins permeate every aspect of science and influence numerous chemical processes: they underpin transition metal chemistry and biochemistry, mediate photosynthesis and photovoltaics and are paramount in the field of quantum information, to name but a few. Electron paramagnetic resonance (EPR) spectroscopy detects unpaired electrons and provides detailed information on structure and bonding of paramagnetic species. In this tutorial review, aimed at non-specialists, we provide a theoretical framework and examples to illustrate the vast scope of the technique in chemical research. Case studies were chosen to exemplify systematically the different interactions that characterize a paramagnetic centre and to illustrate how EPR spectroscopy may be used to derive chemical information.
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Affiliation(s)
- Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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Kim J, Kim Y, Sinha I, Park K, Kim SH, Lee Y. The unusual hydridicity of a cobalt bound Si–H moiety. Chem Commun (Camb) 2016; 52:9367-70. [DOI: 10.1039/c6cc03983a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A paramagnetic cobalt–SiH intermediate possessing the Co–(η1-H–Si) moiety shows unusual Si–H bond activation studied by ENDOR, XRD and DFT.
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Affiliation(s)
- Jin Kim
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 34141
- Republic of Korea
| | - Yujeong Kim
- Western Seoul Centre
- Korea Basic Science Institute
- Seoul 03759
- Republic of Korea
- Department of Chemistry and Nano Science
| | - Indranil Sinha
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 34141
- Republic of Korea
- Centre for Catalytic Hydrocarbon Functionalizations
| | - Koeun Park
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 34141
- Republic of Korea
| | - Sun Hee Kim
- Western Seoul Centre
- Korea Basic Science Institute
- Seoul 03759
- Republic of Korea
- Department of Chemistry and Nano Science
| | - Yunho Lee
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 34141
- Republic of Korea
- Centre for Catalytic Hydrocarbon Functionalizations
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Liu L, Mayo DJ, Sahu ID, Zhou A, Zhang R, McCarrick RM, Lorigan GA. Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. Methods Enzymol 2015; 564:289-313. [PMID: 26477255 DOI: 10.1016/bs.mie.2015.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Revealing detailed structural and dynamic information of membrane embedded or associated proteins is challenging due to their hydrophobic nature which makes NMR and X-ray crystallographic studies challenging or impossible. Electron paramagnetic resonance (EPR) has emerged as a powerful technique to provide essential structural and dynamic information for membrane proteins with no size limitations in membrane systems which mimic their natural lipid bilayer environment. Therefore, tremendous efforts have been devoted toward the development and application of EPR spectroscopic techniques to study the structure of biological systems such as membrane proteins and peptides. This chapter introduces a novel approach established and developed in the Lorigan lab to investigate membrane protein and peptide local secondary structures utilizing the pulsed EPR technique electron spin echo envelope modulation (ESEEM) spectroscopy. Detailed sample preparation strategies in model membrane protein systems and the experimental setup are described. Also, the ability of this approach to identify local secondary structure of membrane proteins and peptides with unprecedented efficiency is demonstrated in model systems. Finally, applications and further developments of this ESEEM approach for probing larger size membrane proteins produced by overexpression systems are discussed.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.
| | - Daniel J Mayo
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Andy Zhou
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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Manck S, Sarkar B. Use of EPR Spectroscopy to Unravel Reaction Mechanisms in (Catalytic) Bond Activation Reactions: Some Selected Examples. Top Catal 2015. [DOI: 10.1007/s11244-015-0416-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Morra E, Maurelli S, Chiesa M, Giamello E. Rational Design of Engineered Multifunctional Heterogeneous Catalysts. The Role of Advanced EPR Techniques. Top Catal 2015. [DOI: 10.1007/s11244-015-0418-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Abstract
Electron-nuclear double resonance (ENDOR) is a method that probes the local structure of paramagnetic centers via their hyperfine interactions with nearby magnetic nuclei. Here we describe the use of this technique to structurally characterize the ATPase active site of the RNA helicase DbpA, where Mg(2+)-ATP binds. This is achieved by substituting the EPR (electron paramagnetic resonance) silent Mg(2+) ion with paramagnetic, EPR active, Mn(2+) ion. (31)P ENDOR provides the interaction of the Mn(2+) with the nucleotide (ADP, ATP and its analogs) through the phosphates. The ENDOR spectra clearly distinguish between ATP- and ADP-binding modes. In addition, by preparing (13)C-enriched DbpA, (13)C ENDOR is used to probe the interaction of the Mn(2+) with protein residues. This combination allows tracking structural changes in the Mn(2+) coordination shell, in the ATPase site, in different states of the protein, namely with and without RNA and with different ATP analogs. Here, a detailed description of sample preparation and the ENDOR measurement methodology is provided, focusing on measurements at W-band (95 GHz) where sensitivity is high and spectral interpretations are relatively simple.
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Morra E, Giamello E, Chiesa M. Probing the redox chemistry of titanium silicalite-1: formation of tetrahedral Ti3+ centers by reaction with triethylaluminum. Chemistry 2014; 20:7381-8. [PMID: 24824439 DOI: 10.1002/chem.201304139] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 11/21/2013] [Indexed: 11/10/2022]
Abstract
Transition-metal ions with open-shell configurations hold promise in the development of novel coordination chemistry and potentially unprecedented redox catalysis. Framework-substituted Ti(3+) ions with tetrahedral coordination are generated by reductive activation of titanium silicalite-1 with triethylaluminum, an indispensable co-catalyst for heterogeneous Ziegler-Natta polymerization catalysts. Continuous-wave and pulse electron paramagnetic resonance methods are applied to unravel details on the local environment of the reduced transition metal-ions, which are shown to be part of the silica framework by detection of (29)Si hyperfine interactions. The chemical accessibility of the reduced sites is probed using ammonia as probe molecule. Evidence is found for the coordination of a single ammonia molecule. Comparison to similar systems, such as TiAlPO-5, reveals clear differences in the coordination chemistry of the reduced Ti sites in the two solids, which may be understood considering the different electronic properties of the solid frameworks.
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Affiliation(s)
- Elena Morra
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125 Torino (Italy), Fax: (+39) 0116707855; Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven (The Netherlands)
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15
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Fittipaldi M, Gatteschi D, Fornasiero P. The power of EPR techniques in revealing active sites in heterogeneous photocatalysis: The case of anion doped TiO2. Catal Today 2013. [DOI: 10.1016/j.cattod.2012.04.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Continuous Wave EPR of Radicals in Solids. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/978-94-007-4893-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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18
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Sala LF, González JC, García SI, Frascaroli MI, Van Doorslaer S. Detection and structural characterization of oxo-chromium(V)-sugar complexes by electron paramagnetic resonance. Adv Carbohydr Chem Biochem 2011; 66:69-120. [PMID: 22123188 DOI: 10.1016/b978-0-12-385518-3.00002-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article describes the detection and characterization of oxo-Cr(V)-saccharide coordination compounds, produced during chromic oxidation of carbohydrates by Cr(VI) and Cr(V), using electron paramagnetic resonance (EPR) spectroscopy. After an introduction into the main importance of chromium (bio)chemistry, and more specifically the oxo-chromium(V)-sugar complexes, a general overview is given of the current state-of-the-art EPR techniques. The next step reviews which types of EPR spectroscopy are currently applied to oxo-Cr(V) complexes, and what information about these systems can be gained from such experiments. The advantages and pitfalls of the different approaches are discussed, and it is shown that the potential of high-field and pulsed EPR techniques is as yet still largely unexploited in the field of oxo-Cr(V) complexes. Subsequently, the discussion focuses on the analysis of oxo-Cr(V) complexes of different types of sugars and the implications of the results in terms of understanding chromium (bio)chemistry.
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Affiliation(s)
- Luis F Sala
- Departamento de Químico Física-Área Química General, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
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Schleicher E, Wenzel R, Ahmad M, Batschauer A, Essen LO, Hitomi K, Getzoff ED, Bittl R, Weber S, Okafuji A. The Electronic State of Flavoproteins: Investigations with Proton Electron-Nuclear Double Resonance. APPLIED MAGNETIC RESONANCE 2010; 37:339-352. [PMID: 26089595 PMCID: PMC4469238 DOI: 10.1007/s00723-009-0101-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Electron-nuclear double resonance (ENDOR) spectroscopy provides useful information on hyperfine interactions between nuclear magnetic moments and the magnetic moment of an unpaired electron spin. Because the hyperfine coupling constant reacts quite sensitively to polarity changes in the direct vicinity of the nucleus under consideration, ENDOR spectroscopy can be favorably used for the detection of subtle protein-cofactor interactions. A number of pulsed ENDOR studies on flavoproteins have been published during the past few years; most of them were designed to characterize the flavin cofactor by means of its protonation state, or to detect individual protein-cofactor interactions. The aim of this study is to compare the pulsed ENDOR spectra from different flavoproteins in terms of variations of characteristic proton hyperfine values. The general concept is to observe limits of possible influences on the cofactor's electronic state by surrounding amino acids. Furthermore, we compare ENDOR data obtained from in vivo experiments with in vitro data to emphasize the potential of the method for gaining molecular information in complex media.
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Affiliation(s)
- Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Ringo Wenzel
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Alfred Batschauer
- Fachbereich Biologie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Kenichi Hitomi
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth D Getzoff
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Bittl
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Asako Okafuji
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
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Schleicher E, Bittl R, Weber S. New roles of flavoproteins in molecular cell biology: Blue-light active flavoproteins studied by electron paramagnetic resonance. FEBS J 2009; 276:4290-303. [DOI: 10.1111/j.1742-4658.2009.07141.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Van Doorslaer S, Caretti I, Fallis I, Murphy D. The power of electron paramagnetic resonance to study asymmetric homogeneous catalysts based on transition-metal complexes. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2008.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Goldfarb D, Lipkin Y, Potapov A, Gorodetsky Y, Epel B, Raitsimring AM, Radoul M, Kaminker I. HYSCORE and DEER with an upgraded 95GHz pulse EPR spectrometer. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:8-15. [PMID: 18571956 DOI: 10.1016/j.jmr.2008.05.019] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 05/18/2008] [Accepted: 05/19/2008] [Indexed: 05/26/2023]
Abstract
The set-up of a new microwave bridge for a 95 GHz pulse EPR spectrometer is described. The virtues of the bridge are its simple and flexible design and its relatively high output power (0.7 W) that generates pi pulses of 25 ns and a microwave field, B(1)=0.71 mT. Such a high B(1) enhances considerably the sensitivity of high field double electron-electron resonance (DEER) measurements for distance determination, as we demonstrate on a nitroxide biradical with an interspin distance of 3.6 nm. Moreover, it allowed us to carry out HYSCORE (hyperfine sublevel-correlation) experiments at 95 GHz, observing nuclear modulation frequencies of 14N and 17O as high as 40 MHz. This opens a new window for the observation of relatively large hyperfine couplings, yet not resolved in the EPR spectrum, that are difficult to observe with HYSCORE carried out at conventional X-band frequencies. The correlations provided by the HYSCORE spectra are most important for signal assignment, and the improved resolution due to the two dimensional character of the experiment provides 14N quadrupolar splittings.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel.
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24
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Van Doorslaer S, Desmet F. The power of using continuous-wave and pulsed electron paramagnetic resonance methods for the structure analysis of ferric forms and nitric oxide-ligated ferrous forms of globins. Methods Enzymol 2008; 437:287-310. [PMID: 18433634 DOI: 10.1016/s0076-6879(07)37015-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
For several decades now, electron paramagnetic resonance (EPR) has been a valuable spectroscopic tool for the characterization of globin proteins. In the early years, the majority of EPR studies were performed using standard continuous-wave EPR techniques at conventional microwave frequencies. In the last years, the field of EPR has known tremendous technological developments, including the introduction of advanced pulsed EPR and high-frequency EPR techniques. After a short overview of the basics of EPR and recent advances in the field, we will illustrate how these different EPR methods can provide information about the dynamics and geometric and electronic structures of heme proteins. Although the main focus of this chapter lies on the EPR analysis of nitric oxide-ligated ferrous heme proteins and ferric heme systems, we also briefly outline the possibility of site-directed spin labeling of heme proteins. The last section highlights the future potential and challenges in using this magnetic resonance technique in globin research.
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Affiliation(s)
- Sabine Van Doorslaer
- University of Antwerp, Department of Physics, SIBAC Laboratory, Antwerp, Belgium
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25
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Yeagle GJ, Gilchrist ML, Walker LM, Debus RJ, Britt RD. Multifrequency electron spin-echo envelope modulation studies of nitrogen ligation to the manganese cluster of photosystem II. Philos Trans R Soc Lond B Biol Sci 2008; 363:1157-66; discussion 1166. [PMID: 17954435 DOI: 10.1098/rstb.2007.2211] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The CalEPR Center at UC-Davis (http://brittepr.ucdavis.edu) is equipped with five research grade electron paramagnetic resonance (EPR) instruments operating at various excitation frequencies between 8 and 130GHz. Of particular note for this RSC meeting are two pulsed EPR spectrometers working at the intermediate microwave frequencies of 31 and 35GHz. Previous lower frequency electron spin-echo envelope modulation (ESEEM) studies indicated that histidine nitrogen is electronically coupled to the Mn cluster in the S2 state of photosystem II (PSII). However, the amplitude and resolution of the spectra were relatively poor at these low frequencies, precluding any in-depth analysis of the electronic structure properties of this closely associated nitrogen nucleus. With the intermediate frequency instruments, we are much closer to the 'exact cancellation' limit, which optimizes ESEEM spectra for hyperfine-coupled nuclei such as 14N and 15N. Herein, we report the results from ESEEM studies of both 14N- and 15N-labelled PSII at these two frequencies. Spectral simulations were constrained by both isotope datasets at both frequencies, with a focus on high-resolution spectral examination of the histidine ligation to the Mn cluster in the S2 state.
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Affiliation(s)
- Gregory J Yeagle
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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26
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Okafuji A, Schnegg A, Schleicher E, Möbius K, Weber S. G-tensors of the flavin adenine dinucleotide radicals in glucose oxidase: a comparative multifrequency electron paramagnetic resonance and electron-nuclear double resonance study. J Phys Chem B 2008; 112:3568-74. [PMID: 18302360 DOI: 10.1021/jp077170j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The flavin adenine dinucleotide (FAD) cofactor of Aspergillus niger glucose oxidase (GO) in its anionic (FAD*-) and neutral (FADH*) radical form was investigated by electron paramagnetic resonance (EPR) at high microwave frequencies (93.9 and 360 GHz) and correspondingly high magnetic fields and by pulsed electron-nuclear double resonance (ENDOR) spectroscopy at 9.7 GHz. Because of the high spectral resolution of the frozen-solution continuous-wave EPR spectrum recorded at 360 GHz, the anisotropy of the g-tensor of FAD*- could be fully resolved. By least-squares fittings of spectral simulations to experimental data, the principal values of g have been established with high precision: gX=2.00429(3), gY=2.00389(3), gZ=2.00216(3) (X, Y, and Z are the principal axes of g) yielding giso=2.00345(3). The gY-component of FAD*- from GO is moderately shifted upon deprotonation of FADH*, rendering the g-tensor of FAD*- slightly more axially symmetric as compared to that of FADH*. In contrast, significantly altered proton hyperfine couplings were observed by ENDOR upon transforming the neutral FADH* radical into the anionic FAD*- radical by pH titration of GO. That the g-principal values of both protonation forms remain largely identical demonstrates the robustness of g against local changes in the electron-spin density distribution of flavins. Thus, in flavins, the g-tensor reflects more global changes in the electronic structure and, therefore, appears to be ideally suited to identify chemically different flavin radicals.
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Affiliation(s)
- Asako Okafuji
- Freie Universität Berlin, Fachbereich Physik, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany
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Stoll S, Epel B, Vega S, Goldfarb D. Ligand protons in a frozen solution of copper histidine relax via a T1e -driven three-spin mechanism. J Chem Phys 2008; 127:164511. [PMID: 17979364 DOI: 10.1063/1.2794329] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Davies electron-nuclear double resonance spectra can exhibit strong asymmetries for long mixing times, short repetition times, and large thermal polarizations. These asymmetries can be used to determine nuclear relaxation rates in paramagnetic systems. Measurements of frozen solutions of copper(L-histidine)(2) reveal a strong field dependence of the relaxation rates of the protons in the histidine ligand, increasing from low (g( parallel)) to high (g( perpendicular)) field. It is shown that this can be attributed to a concentration-dependent T(1e)-driven relaxation process involving strongly mixed states of three spins: the histidine proton, the Cu(II) electron spin of the same complex, and another distant electron spin with a resonance frequency differing from the spectrometer frequency approximately by the proton Larmor frequency. The protons relax more efficiently in the g( perpendicular) region, since the number of distant electrons able to participate in this relaxation mechanism is higher than in the g( parallel) region. Analytical expressions for the associated nuclear polarization decay rate Tau(een) (-1) are developed and Monte Carlo simulations are carried out, reproducing both the field and the concentration dependences of the nuclear relaxation.
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Affiliation(s)
- S Stoll
- Physical Chemistry Laboratory, ETH Zurich, 8093 Zurich, Switzerland.
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28
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Weber S, Bittl R. Studies of Organic Protein Cofactors Using Electron Paramagnetic Resonance. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Van Doorslaer S, Vinck E. The strength of EPR and ENDOR techniques in revealing structure-function relationships in metalloproteins. Phys Chem Chem Phys 2007; 9:4620-38. [PMID: 17700864 DOI: 10.1039/b701568b] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent technological and methodological advances have strongly increased the potential of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) techniques to characterize the structure and dynamics of metalloproteins. These developments include the introduction of powerful pulsed EPR/ENDOR methodologies and the development of spectrometers operating at very high microwave frequencies and high magnetic fields. This overview focuses on how valuable information about metalloprotein structure-function relations can be obtained using a combination of EPR and ENDOR techniques. After an overview of the historical development and a limited theoretical description of some of the key EPR and ENDOR techniques, their potential will be highlighted using selected examples of applications to iron-, nickel-, cobalt-, and copper-containing proteins. We will end with an outlook of future developments.
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Affiliation(s)
- Sabine Van Doorslaer
- SIBAC Laboratory, University of Antwerp, Universiteitsplein 1, B-2160, Wilrijk-Antwerp, Belgium.
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30
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Otero Areán C, Nachtigallová D, Nachtigall P, Garrone E, Rodríguez Delgado M. Thermodynamics of reversible gas adsorption on alkali-metal exchanged zeolites—the interplay of infrared spectroscopy and theoretical calculations. Phys Chem Chem Phys 2007; 9:1421-37. [PMID: 17356750 DOI: 10.1039/b615535a] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Detailed understanding of weak solid-gas interactions giving rise to reversible gas adsorption on zeolites and related materials is relevant to both, fundamental studies on gas adsorption and potential improvement on a number of (adsorption based) technological processes. Combination of variable-temperature infrared spectroscopy with theoretical calculations constitutes a fruitful approach towards both of these aims. Such an approach is demonstrated here (mainly) by reviewing recent studies on hydrogen and carbon monoxide adsorption (at a low temperature) on alkali-metal exchanged ferrierite. However, the methodology discussed, which involves the interplay of experimental measurements and theoretical calculations at the periodic DFT level, should be equally valid for many other gas-solid systems. Specific aspects considered are the identification of gas adsorption complexes and thermodynamic studies related to standard adsorption enthalpy and entropy.
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Affiliation(s)
- C Otero Areán
- Departamento de Química, Universidad de las Islas Baleares, E-07122 Palma de Mallorca, Spain.
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