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Gopakumar G, Unger I, Slavíček P, Hergenhahn U, Öhrwall G, Malerz S, Céolin D, Trinter F, Winter B, Wilkinson I, Caleman C, Muchová E, Björneholm O. Radiation damage by extensive local water ionization from two-step electron-transfer-mediated decay of solvated ions. Nat Chem 2023; 15:1408-1414. [PMID: 37620544 PMCID: PMC10533389 DOI: 10.1038/s41557-023-01302-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/21/2023] [Indexed: 08/26/2023]
Abstract
Biomolecular radiation damage is largely mediated by radicals and low-energy electrons formed by water ionization rather than by direct ionization of biomolecules. It was speculated that such an extensive, localized water ionization can be caused by ultrafast processes following excitation by core-level ionization of hydrated metal ions. In this model, ions relax via a cascade of local Auger-Meitner and, importantly, non-local charge- and energy-transfer processes involving the water environment. Here, we experimentally and theoretically show that, for solvated paradigmatic intermediate-mass Al3+ ions, electronic relaxation involves two sequential solute-solvent electron transfer-mediated decay processes. The electron transfer-mediated decay steps correspond to sequential relaxation from Al5+ to Al3+ accompanied by formation of four ionized water molecules and two low-energy electrons. Such charge multiplication and the generated highly reactive species are expected to initiate cascades of radical reactions.
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Affiliation(s)
- G Gopakumar
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - I Unger
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
- FS-BIG, DESY, Hamburg, Germany
| | - P Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - U Hergenhahn
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
| | - G Öhrwall
- MAX IV Laboratory, Lund University, Lund, Sweden
| | - S Malerz
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
| | - D Céolin
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Paris, France
| | - F Trinter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - B Winter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
| | - I Wilkinson
- Institute for Electronic Structure Dynamics, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - C Caleman
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - E Muchová
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic.
| | - O Björneholm
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden.
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2
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Fernando NK, Bostrom HLB, Murray CA, Owen RL, Thompson AL, Dickerson JL, Garman EF, Cairns AB, Regoutz A. Variability in X-ray induced effects in [Rh(COD)Cl] 2 with changing experimental parameters. Phys Chem Chem Phys 2022; 24:28444-28456. [PMID: 36399064 PMCID: PMC7614095 DOI: 10.1039/d2cp03928a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
X-ray characterisation methods have undoubtedly enabled cutting-edge advances in all aspects of materials research. Despite the enormous breadth of information that can be extracted from these techniques, the challenge of radiation-induced sample change and damage remains prevalent. This is largely due to the emergence of modern, high-intensity X-ray source technologies and the growing potential to carry out more complex, longer duration in situ or in operando studies. The tunability of synchrotron beamlines enables the routine application of photon energy-dependent experiments. This work explores the structural stability of [Rh(COD)Cl]2, a widely used catalyst and precursor in the chemical industry, across a range of beamline parameters that target X-ray energies of 8 keV, 15 keV, 18 keV and 25 keV, on a powder X-ray diffraction synchrotron beamline at room temperature. Structural changes are discussed with respect to absorbed X-ray dose at each experimental setting associated with the respective photon energy. In addition, the X-ray radiation hardness of the catalyst is discussed, by utilising the diffraction data collected at the different energies to determine a dose limit, which is often considered in protein crystallography and typically overlooked in small molecule crystallography. This work not only gives fundamental insight into how damage manifests in this organometallic catalyst, but will encourage careful consideration of experimental X-ray parameters before conducting diffraction on similar radiation-sensitive organometallic materials.
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Affiliation(s)
- Nathalie K. Fernando
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hanna L. B. Bostrom
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Claire A. Murray
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Amber L. Thompson
- Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Joshua L. Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Elspeth F. Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Andrew B. Cairns
- Department of Materials, Imperial College London, Royal School of Mines, Exhibition Road, SW7 2AZ, UK
| | - Anna Regoutz
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
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3
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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4
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Frank P, Carlson RMK, Carlson EJ, Hedman B, Hodgson KO. Biological sulfur in the blood cells of Ascidia ceratodes: XAS spectroscopy and a cellular-enzymatic hypothesis for vanadium reduction in the ascidians. J Inorg Biochem 2020; 205:110991. [PMID: 31945647 PMCID: PMC7033024 DOI: 10.1016/j.jinorgbio.2019.110991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/12/2019] [Accepted: 12/31/2019] [Indexed: 10/25/2022]
Abstract
Two samples of living blood cells and of cleared blood plasma from the Phlebobranch tunicate Ascidia ceratodes from Bodega Bay, California, and one of fresh Henze solution from A. ceratodes of Monterey Bay, California, have been examined using sulfur K-edge x-ray absorption spectroscopy (XAS). Biological sulfur included sulfate esters, sulfate and bisulfate ions, benzothiazole, thianthrene, epi-sulfide, thiol and disulfide. Glutathione dominated reduced sulfur, from which an average intracellular Voltage of -0.21 V was calculated. Sulfate-bisulfate ratios yielded blood cell pH values of 2.0 and 2.8. Total blood cell [sulfur] was 373±9 mM or 296±73 mM from BaSO4 gravimetry. Two plasma samples (pH 6.9 or 7.0; [S] = 33±6 mM or 26±4 mM) were dominated by sulfate and disulfide. Fresh Henze solution evidenced a sulfur inventory similar to blood cells, with calculated pH = 2.7. A V(III)-sulfonate fraction varied systematically with intracellular pH across six independent blood cell samples, implying a vanadium mobilization pathway. Bodega Bay and Monterey Bay A. ceratodes appear to maintain alternative suites of low-valent sulfur. The significance of the vanabins to vanadium metabolism is critically examined in terms of known protein - V(IV) biochemistry. Finally, a detailed hypothesis for the reduction of [VO4]3- to V(III) in ascidians is introduced. A vanadium oxido-reductase is proposed to span the signet ring membrane and to release V(III) into the inner acidic vacuole. The V(V) to V(III) reduction is predicted require an inner-sphere mechanism, a thiol reductant, 7-coordinate V(III), a biologically accessible Voltage, and proton-facilitated release of V(III).
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Affiliation(s)
- Patrick Frank
- Stanford Synchrotron Radiation laboratory, SLAC, Stanford University, Menlo Park, CA 94025, United States of America; Department of Chemistry, Stanford University, Stanford, CA 94305, United States of America.
| | - Robert M K Carlson
- Institute for Materials and Energy Sciences, SLAC, Stanford University, Menlo Park, CA 94025, United States of America
| | - Elaine J Carlson
- University of California, San Francisco, CA 94143, United States of America
| | - Britt Hedman
- Stanford Synchrotron Radiation laboratory, SLAC, Stanford University, Menlo Park, CA 94025, United States of America
| | - Keith O Hodgson
- Stanford Synchrotron Radiation laboratory, SLAC, Stanford University, Menlo Park, CA 94025, United States of America; Department of Chemistry, Stanford University, Stanford, CA 94305, United States of America
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5
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Montanha GS, Rodrigues ES, Marques JPR, de Almeida E, Dos Reis AR, Pereira de Carvalho HW. X-ray fluorescence spectroscopy (XRF) applied to plant science: challenges towards in vivo analysis of plants. Metallomics 2020; 12:183-192. [PMID: 31793600 DOI: 10.1039/c9mt00237e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
X-ray fluorescence spectroscopy (XRF) is an analytical tool used to determine the elemental composition in a myriad of sample matrices. Due to the XRF non-destructive feature, this technique may allow time-resolved plant tissue analyses under in vivo conditions, and additionally, the combination with other non-destructive techniques. In this study, we employed handheld and benchtop XRF to evaluate the elemental distribution changes in living plant tissues exposed to X-rays, as well as real-time uptake kinetics of Zn(aq) and Mn(aq) in soybean (Glycine max (L.) Merrill) stem and leaves, for 48 hours, combined with transpiration rate assessment on leaves by an infrared gas analyzer (IRGA). We found higher Zn content than Mn in stems. The latter micronutrient, in turn, presented higher concentration in leaf veins. Besides, both micronutrients were more concentrated in the first trifolium (i.e., youngest leaf) of soybean plants. Moreover, the transpiration rate was more influenced by circadian cycles than Zn and Mn uptake. Thus, XRF represents a convenient tool for in vivo nutritional studies in plants, and it can be coupled successfully to other analytical techniques.
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Affiliation(s)
- Gabriel Sgarbiero Montanha
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Avenida Centenário, 303, Piracicaba, SP 13416000, Brazil.
| | - Eduardo Santos Rodrigues
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Avenida Centenário, 303, Piracicaba, SP 13416000, Brazil.
| | - João Paulo Rodrigues Marques
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Avenida Centenário, 303, Piracicaba, SP 13416000, Brazil.
| | - Eduardo de Almeida
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Avenida Centenário, 303, Piracicaba, SP 13416000, Brazil.
| | | | - Hudson Wallace Pereira de Carvalho
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Avenida Centenário, 303, Piracicaba, SP 13416000, Brazil.
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6
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Wang P, McKenna BA, Menzies NW, Li C, Glover CJ, Zhao FJ, Kopittke PM. Minimizing experimental artefacts in synchrotron-based X-ray analyses of Fe speciation in tissues of rice plants. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1272-1279. [PMID: 31274454 DOI: 10.1107/s1600577519004351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
Iron (Fe) plays an important role within environmental systems. Synchrotron-based X-ray approaches, including X-ray absorption spectroscopy (XAS), provide powerful tools for in situ analyses of Fe speciation, but beam damage during analysis may alter Fe speciation during its measurement. XAS was used to examine whether experimental conditions affect the analysis of Fe speciation in plant tissues. Even when analyzed in a cryostat at 12 K, it was found that FeIII can rapidly (within 0.5-1 min) photoreduce to FeII, although the magnitude of photoreduction varied depending upon the hydration of the sample, the coordination chemistry of the Fe, as well as other properties. For example, photoreduction of FeIII was considerably higher for aqueous standard compounds than for hydrated plant-root tissues. The use of freeze-dried samples in the cryostat (12 K) markedly reduced the magnitude of this FeIII photoreduction, and there was no evidence that the freeze-drying process itself resulted in experimental artefacts under the current experimental conditions, such as through the oxidation of FeII, although some comparatively small differences were observed when comparing spectra of hydrated and freeze-dried FeII compounds. The results of this study have demonstrated that FeIII photoreduction can occur during X-ray analysis, and provides suitable conditions to preserve Fe speciation to minimize the extent of beam damage when analyzing environmental samples. All studies utilizing XAS are encouraged to include a preliminary experiment to determine if beam damage is occurring, and, where appropriate, to take the necessary steps (such as freeze drying) to overcome these issues.
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Affiliation(s)
- Peng Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Brigid A McKenna
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Neal W Menzies
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Cui Li
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Chris J Glover
- Australian Synchrotron ANSTO, Clayton, Victoria 3168, Australia
| | - Fang Jie Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
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7
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Frank P, Sarangi R, Hedman B, Hodgson KO. Synchrotron X-radiolysis of l-cysteine at the sulfur K-edge: Sulfurous products, experimental surprises, and dioxygen as an oxidoreductant. J Chem Phys 2019; 150:105101. [PMID: 30876351 PMCID: PMC7791807 DOI: 10.1063/1.5079419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/12/2019] [Indexed: 11/14/2022] Open
Abstract
In situ inventory of sulfurous products from the sulfur K-edge synchrotron X-radiolysis of l-cysteine in solid-phase and anaerobic (pH 5) and air-saturated (pH 5, 7, and 9) solutions without and with 40% glycerol is reported. Sequential K-edge X-ray Absorption Spectroscopic (XAS) spectra were acquired. l-cysteine degraded systematically in the X-ray beam. Radiolytic products were inventoried by fits using the XAS spectra of sulfur model compounds. Solid l-cysteine declined to 92% fraction after a single K-edge XAS scan. After six scans, 60% remained, accompanied by 14% cystine, 16% thioether, 5.4% elemental sulfur, and smaller fractions of more highly oxidized products. In air-saturated pH 5 solution, 73% of l-cysteine remained after ten scans, with 2% cystine and 19% elemental sulfur. Oxidation increased with 40% glycerol, yielding 67%, 5%, and 23% fractions, respectively, after ten scans. Higher pH solutions exhibited less radiolytic chemistry. All the reactivity followed first-order kinetics. The anaerobic experiment displayed two reaction phases, with sharp changes in kinetics and radiolytic chemistry. Unexpectedly, the radiolytic oxidation of l-cysteine was increased in anaerobic solution. After ten scans, only 60% of the l-cysteine remained, along with 17% cystine, 22% elemental sulfur, and traces of more highly oxidized products. A new aerobic reaction cycle is hypothesized, wherein dissolved dioxygen captures radiolytic H• or eaq -, enters HO2 •/O2 •-, reductively quenches cysteine thiyl radicals, and cycles back to O2. This cycle is suggested to suppress the radiolytic production of cystine in aerobic solution.
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Affiliation(s)
- Patrick Frank
- Author to whom correspondence should be addressed: . Tel.: 650-723-2479
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, USA
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8
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Kubin M, Kern J, Guo M, Källman E, Mitzner R, Yachandra VK, Lundberg M, Yano J, Wernet P. X-ray-induced sample damage at the Mn L-edge: a case study for soft X-ray spectroscopy of transition metal complexes in solution. Phys Chem Chem Phys 2018; 20:16817-16827. [PMID: 29888772 PMCID: PMC6011208 DOI: 10.1039/c8cp03094d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
X-ray induced sample damage can impede electronic and structural investigations of radiation-sensitive samples studied with X-rays. Here we quantify dose-dependent sample damage to the prototypical MnIII(acac)3 complex in solution and at room temperature for the soft X-ray range, using X-ray absorption spectroscopy at the Mn L-edge. We observe the appearance of a reduced MnII species as the X-ray dose is increased. We find a half-damage dose of 1.6 MGy and quantify a spectroscopically tolerable dose on the order of 0.3 MGy (1 Gy = 1 J kg-1), where 90% of MnIII(acac)3 are intact. Our dose-limit is around one order of magnitude lower than the Henderson limit (half-damage dose of 20 MGy) which is commonly employed for protein crystallography with hard X-rays. It is comparable, however, to the dose-limits obtained for collecting un-damaged Mn K-edge spectra of the photosystem II protein, using hard X-rays. The dose-dependent reduction of MnIII observed here for solution samples occurs at a dose limit that is two to four orders of magnitude smaller than the dose limits previously reported for soft X-ray spectroscopy of iron samples in the solid phase. We compare our measured to calculated spectra from ab initio restricted active space (RAS) theory and discuss possible mechanisms for the observed dose-dependent damage of MnIII(acac)3 in solution. On the basis of our results, we assess the influence of sample damage in other experimental studies with soft X-rays from storage-ring synchrotron radiation sources and X-ray free-electron lasers.
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Affiliation(s)
- Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
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9
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Ackerman CM, Lee S, Chang CJ. Analytical Methods for Imaging Metals in Biology: From Transition Metal Metabolism to Transition Metal Signaling. Anal Chem 2017; 89:22-41. [PMID: 27976855 PMCID: PMC5827935 DOI: 10.1021/acs.analchem.6b04631] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cheri M. Ackerman
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Sumin Lee
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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10
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James SA, Hare DJ, Jenkins NL, de Jonge MD, Bush AI, McColl G. φXANES: In vivo imaging of metal-protein coordination environments. Sci Rep 2016; 6:20350. [PMID: 26861174 PMCID: PMC4748213 DOI: 10.1038/srep20350] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/30/2015] [Indexed: 11/24/2022] Open
Abstract
We have developed an X-ray absorption near edge structure spectroscopy method using fluorescence detection for visualizing in vivo coordination environments of metals in biological specimens. This approach, which we term fluorescence imaging XANES (φXANES), allows us to spatially depict metal-protein associations in a native, hydrated state whilst avoiding intrinsic chemical damage from radiation. This method was validated using iron-challenged Caenorhabditis elegans to observe marked alterations in redox environment.
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Affiliation(s)
- Simon A James
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia.,Australian Synchrotron, Clayton, Victoria, 3168, Australia
| | - Dominic J Hare
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia.,Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - Nicole L Jenkins
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | | | - Ashley I Bush
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Gawain McColl
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
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11
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The role of metal ions in X-ray-induced photochemistry. Nat Chem 2016; 8:237-41. [DOI: 10.1038/nchem.2429] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/23/2015] [Indexed: 01/23/2023]
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12
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13
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Kuepper K, Derks C, Taubitz C, Prinz M, Joly L, Kappler JP, Postnikov A, Yang W, Kuznetsova TV, Wiedwald U, Ziemann P, Neumann M. Electronic structure and soft-X-ray-induced photoreduction studies of iron-based magnetic polyoxometalates of type {(M)M5}12FeIII30 (M = MoVI, WVI). Dalton Trans 2013; 42:7924-35. [DOI: 10.1039/c3dt32759k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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George GN, Pickering IJ, Pushie MJ, Nienaber K, Hackett MJ, Ascone I, Hedman B, Hodgson KO, Aitken JB, Levina A, Glover C, Lay PA. X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:875-86. [PMID: 23093745 PMCID: PMC3480274 DOI: 10.1107/s090904951203943x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 09/16/2012] [Indexed: 05/03/2023]
Abstract
As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts.
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Affiliation(s)
- Graham N. George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Ingrid J. Pickering
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - M. Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Kurt Nienaber
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Mark J. Hackett
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Isabella Ascone
- ENSCP Chimie ParisTech, LCF, CNRS, UMR 7223, 75005 Paris, France
| | - Britt Hedman
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jade B. Aitken
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Synchrotron, Clayton, VIC 3168, Australia
- Institute of Materials Structure Science, KEK, Tsukuba, Ibaraki 305-0801, Japan
| | - Aviva Levina
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Peter A. Lay
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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Shearer J, Callan PE, Masitas CA, Grapperhaus CA. Influence of sequential thiolate oxidation on a nitrile hydratase mimic probed by multiedge X-ray absorption spectroscopy. Inorg Chem 2012; 51:6032-45. [PMID: 22591049 DOI: 10.1021/ic202453c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nitrile hydratases (NHases) are Fe(III)- and Co(III)-containing hydrolytic enzymes that convert nitriles into amides. The metal-center is contained within an N(2)S(3) coordination motif with two post-translationally modified cysteinates contained in a cis arrangement, which have been converted into a sulfinate (R-SO(2)(-)) and a sulfenate (R-SO(-)) group. Herein, we utilize Ru L-edge and ligand (N-, S-, and P-) K-edge X-ray absorption spectroscopies to probe the influence that these modifications have on the electronic structure of a series of sequentially oxidized thiolate-coordinated Ru(II) complexes ((bmmp-TASN)RuPPh(3), (bmmp-O(2)-TASN)RuPPh(3), and (bmmp-O(3)-TASN)RuPPh(3)). Included is the use of N K-edge spectroscopy, which was used for the first time to extract N-metal covalency parameters. We find that upon oxygenation of the bis-thiolate compound (bmmp-TASN)RuPPh(3) to the sulfenato species (bmmp-O(2)-TASN)RuPPh(3) and then to the mixed sulfenato/sulfinato speices (bmmp-O(3)-TASN)RuPPh(3) the complexes become progressively more ionic, and hence the Ru(II) center becomes a harder Lewis acid. These findings are reinforced by hybrid DFT calculations (B(38HF)P86) using a large quadruple-ζ basis set. The biological implications of these findings in relation to the NHase catalytic cycle are discussed in terms of the creation of a harder Lewis acid, which aids in nitrile hydrolysis.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA.
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Leidel N, Popović-Bijelić A, Havelius KGV, Chernev P, Voevodskaya N, Gräslund A, Haumann M. High-valent [MnFe] and [FeFe] cofactors in ribonucleotide reductases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:430-44. [PMID: 22222354 DOI: 10.1016/j.bbabio.2011.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/13/2011] [Accepted: 12/16/2011] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNRs) are essential for DNA synthesis in most organisms. In class-Ic RNR from Chlamydia trachomatis (Ct), a MnFe cofactor in subunit R2 forms the site required for enzyme activity, instead of an FeFe cofactor plus a redox-active tyrosine in class-Ia RNRs, for example in mouse (Mus musculus, Mm). For R2 proteins from Ct and Mm, either grown in the presence of, or reconstituted with Mn and Fe ions, structural and electronic properties of higher valence MnFe and FeFe sites were determined by X-ray absorption spectroscopy and complementary techniques, in combination with bond-valence-sum and density functional theory calculations. At least ten different cofactor species could be tentatively distinguished. In Ct R2, two different Mn(IV)Fe(III) site configurations were assigned either L(4)Mn(IV)(μO)(2)Fe(III)L(4) (metal-metal distance of ~2.75Å, L = ligand) prevailing in metal-grown R2, or L(4)Mn(IV)(μO)(μOH)Fe(III)L(4) (~2.90Å) dominating in metal-reconstituted R2. Specific spectroscopic features were attributed to an Fe(IV)Fe(III) site (~2.55Å) with a L(4)Fe(IV)(μO)(2)Fe(III)L(3) core structure. Several Mn,Fe(III)Fe(III) (~2.9-3.1Å) and Mn,Fe(III)Fe(II) species (~3.3-3.4Å) likely showed 5-coordinated Mn(III) or Fe(III). Rapid X-ray photoreduction of iron and shorter metal-metal distances in the high-valent states suggested radiation-induced modifications in most crystal structures of R2. The actual configuration of the MnFe and FeFe cofactors seems to depend on assembly sequences, bound metal type, valence state, and previous catalytic activity involving subunit R1. In Ct R2, the protonation of a bridging oxide in the Mn(IV)(μO)(μOH)Fe(III) core may be important for preventing premature site reduction and initiation of the radical chemistry in R1.
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Affiliation(s)
- Nils Leidel
- Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
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Johnson PS, Cook PL, Liu X, Yang W, Bai Y, Abbott NL, Himpsel FJ. Universal mechanism for breaking amide bonds by ionizing radiation. J Chem Phys 2011; 135:044702. [DOI: 10.1063/1.3613638] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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de Serrano VS, Davis MF, Gaff JF, Zhang Q, Chen Z, D'Antonio EL, Bowden EF, Rose R, Franzen S. X-ray structure of the metcyano form of dehaloperoxidase fromAmphitrite ornata: evidence for photoreductive dissociation of the iron–cyanide bond. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:770-82. [DOI: 10.1107/s0907444910014605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 04/20/2010] [Indexed: 11/11/2022]
Abstract
X-ray crystal structures of the metcyano form of dehaloperoxidase-hemoglobin (DHP A) fromAmphitrite ornata(DHPCN) and the C73S mutant of DHP A (C73SCN) were determined using synchrotron radiation in order to further investigate the geometry of diatomic ligands coordinated to the heme iron. The DHPCN structure was also determined using a rotating-anode source. The structures show evidence of photoreduction of the iron accompanied by dissociation of bound cyanide ion (CN−) that depend on the intensity of the X-ray radiation and the exposure time. The electron density is consistent with diatomic molecules located in two sites in the distal pocket of DHPCN. However, the identities of the diatomic ligands at these two sites are not uniquely determined by the electron-density map. Consequently, density functional theory calculations were conducted in order to determine whether the bond lengths, angles and dissociation energies are consistent with bound CN−or O2in the iron-bound site. In addition, molecular-dynamics simulations were carried out in order to determine whether the dynamics are consistent with trapped CN−or O2in the second site of the distal pocket. Based on these calculations and comparison with a previously determined X-ray crystal structure of the C73S–O2form of DHP [de Serranoet al.(2007),Acta Cryst.D63, 1094–1101], it is concluded that CN−is gradually replaced by O2as crystalline DHP is photoreduced at 100 K. The ease of photoreduction of DHP A is consistent with the reduction potential, but suggests an alternative activation mechanism for DHP A compared with other peroxidases, which typically have reduction potentials that are 0.5 V more negative. The lability of CN−at 100 K suggests that the distal pocket of DHP A has greater flexibility than most other hemoglobins.
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Smolentsev G, Soldatov AV, Messinger J, Merz K, Weyhermüller T, Bergmann U, Pushkar Y, Yano J, Yachandra VK, Glatzel P. X-ray emission spectroscopy to study ligand valence orbitals in Mn coordination complexes. J Am Chem Soc 2010; 131:13161-7. [PMID: 19663435 DOI: 10.1021/ja808526m] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We discuss a spectroscopic method to determine the character of chemical bonding and for the identification of metal ligands in coordination and bioinorganic chemistry. It is based on the analysis of satellite lines in X-ray emission spectra that arise from transitions between valence orbitals and the metal ion 1s level (valence-to-core XES). The spectra, in connection with calculations based on density functional theory (DFT), provide information that is complementary to other spectroscopic techniques, in particular X-ray absorption (XANES and EXAFS). The spectral shape is sensitive to protonation of ligands and allows ligands, which differ only slightly in atomic number (e.g., C, N, O...), to be distinguished. A theoretical discussion of the main spectral features is presented in terms of molecular orbitals for a series of Mn model systems: [Mn(H(2)O)(6)](2+), [Mn(H(2)O)(5)OH](+), and [Mn(H(2)O)(5)NH(3)](2+). An application of the method, with comparison between theory and experiment, is presented for the solvated Mn(2+) ion in water and three Mn coordination complexes, namely [LMn(acac)N(3)]BPh(4), [LMn(B(2)O(3)Ph(2))(ClO(4))], and [LMn(acac)N]BPh(4), where L represents 1,4,7-trimethyl-1,4,7-triazacyclononane, acac stands for the 2,4-pentanedionate anion, and B(2)O(3)Ph(2) represents the 1,3-diphenyl-1,3-dibora-2-oxapropane-1,3-diolato dianion.
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Affiliation(s)
- Grigory Smolentsev
- Faculty of Physics and Research Center for Nanoscale Structure of Matter, Southern Federal University, 344090 Rostov-on-Don, Russia.
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Cook PL, Johnson PS, Liu X, Chin AL, Himpsel FJ. Radiation damage in biomimetic dye molecules for solar cells. J Chem Phys 2009; 131:214702. [DOI: 10.1063/1.3267849] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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