1
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Giraudon--Colas G, Devineau S, Marichal L, Barruet E, Zitolo A, Renault JP, Pin S. How Nanoparticles Modify Adsorbed Proteins: Impact of Silica Nanoparticles on the Hemoglobin Active Site. Int J Mol Sci 2023; 24:3659. [PMID: 36835069 PMCID: PMC9967434 DOI: 10.3390/ijms24043659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The adsorption of proteins on surfaces has been studied for a long time, but the relationship between the structural and functional properties of the adsorbed protein and the adsorption mechanism remains unclear. Using hemoglobin adsorbed on silica nanoparticles, we have previously shown that hemoglobin's affinity towards oxygen increases with adsorption. Nevertheless, it was also shown that there were no significant changes in the quaternary and secondary structures. In order to understand the change in activity, we decided in this work to focus on the active sites of hemoglobin, the heme and its iron. After measuring adsorption isotherms of porcine hemoglobin on Ludox silica nanoparticles, we analyzed the structural modifications of adsorbed hemoglobin by X-ray absorption spectroscopy and circular dichroism spectra in the Soret region. It was found that upon adsorption, there were modifications in the heme pocket environment due to changes in the angles of the heme vinyl functions. These alterations can explain the greater affinity observed.
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Affiliation(s)
| | - Stéphanie Devineau
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Elodie Barruet
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Andrea Zitolo
- Synchrotron SOLEIL, L’Orme des Merisiers, BP 48 Saint Aubin, 91192 Gif-sur-Yvette, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
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2
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Ovalle S, Malardier-Jugroot C. Choice of Functional for Iron Porphirin Density Functional Theory Studies: Geometry, Spin-State, and Binding Energy Analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Wu Y, Wen J, Xu W, Huang J, Jiao L, Tang Y, Chen Y, Yan H, Cao S, Zheng L, Gu W, Hu L, Zhang L, Zhu C. Defect-Engineered Nanozyme-Linked Receptors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101907. [PMID: 34227222 DOI: 10.1002/smll.202101907] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/08/2021] [Indexed: 06/13/2023]
Abstract
Though nanozymes are successfully applied in various areas, the increasing demands facilitate the exploitation of nanozymes possessing higher activity and more functions. Natural enzyme-linked receptors (ELRs) are critical components for signal transductions in vivo by expressing activity variations after binding with ligands. Inspired by this, the defect-engineered carbon nitrides (DCN) are reported to serve as nanozyme-linked receptors (NLRs). For one thing, cyano defects increase the enzyme-like activity by a factor of 109.5. For another, DCN-based NLRs are constructed by employing cyano groups as receptors, and variable outputs are ensued upon the addition of ion ligands. Significantly, both the cascade effect and electronic effect are demonstrated to contribute to this phenomenon. Finally, NLRs are used for pattern recognition of metal ions, indicating the signal transduction ability of NLRs as well. This work not only provides great promise of defect engineering in nanozymes, but also contributes to the design of artificial ELRs.
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Affiliation(s)
- Yu Wu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Jing Wen
- School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Weiqing Xu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Jiajia Huang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Lei Jiao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Yinjun Tang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Yifeng Chen
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Hongye Yan
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Shiyu Cao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wenling Gu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Liuyong Hu
- School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Lizhi Zhang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Chengzhou Zhu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
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4
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Samajdar RN, Bhattacharyya AJ. Structure-Redox Response Correlation in a Few Select Heme Systems Using X-ray Absorption Spectroelectrochemistry. J Phys Chem B 2021; 125:5258-5264. [PMID: 33983739 DOI: 10.1021/acs.jpcb.1c02180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme based biomolecules control some of the most crucial life processes, such as oxygen and electron transport during respiration and energy metabolism, respectively. The active site of the heme, viz., the metal center, plays a key role and attributes functionality to these biomolecules. During the oxygen binding and debinding processes, it is important to note that the oxidation state of iron in hemoglobin (+II in the native form) does not undergo any change. However, the spin states of the metal center change. We present here a comprehensive study of the redox response of such molecules, based on the electronic structure of the active site. The local electronic structure of heme in a few selective molecular systems is studied in operando via synchrotron X-ray absorption spectroscopy (Fe K-edge) and cyclic voltammetry. Our objective is to identify the electronic structural parameters that can effectively be correlated with the redox reversibility. Evolution in these parameters can be followed to trace the overall changes in redox state of the system. Our data indicate that axial coordination and spin state of the iron center are two such parameters that are intimately connected with the redox response.
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Affiliation(s)
- Rudra N Samajdar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aninda J Bhattacharyya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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5
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Migliorati V, Fazio G, Pollastri S, Gentili A, Tomai P, Tavani F, D'Angelo P. Solubilization properties and structural characterization of dissociated HgO and HgCl2 in deep eutectic solvents. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115505] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Tavani F, Capocasa G, Martini A, Sessa F, Di Stefano S, Lanzalunga O, D'Angelo P. Activation of C-H bonds by a nonheme iron(IV)-oxo complex: mechanistic evidence through a coupled EDXAS/UV-Vis multivariate analysis. Phys Chem Chem Phys 2021; 23:1188-1196. [PMID: 33355324 DOI: 10.1039/d0cp04304d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The understanding of reactive processes involving organic substrates is crucial to chemical knowledge and requires multidisciplinary efforts for its advancement. Herein, we apply a combined multivariate, statistical and theoretical analysis of coupled time-resolved X-ray absorption (XAS)/UV-Vis data to obtain detailed mechanistic information for on the C-H bond activation of 9,10-dihydroanthracene (DHA) and diphenylmethane (Ph2CH2) by the nonheme FeIV-oxo complex [N4Py·FeIV(O)]2+ (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) in CH3CN at room temperature. Within this approach, we determine the number of key chemical species present in the reaction mixtures and derive spectral and concentration profiles for the reaction intermediates. From the quantitative analysis of the XAS spectra the transient intermediate species are structurally determined. As a result, it is suggested that, while DHA is oxidized by [N4Py·FeIV(O)]2+ with a hydrogen atom transfer-electron transfer (HAT-ET) mechanism, Ph2CH2 is oxidized by the nonheme iron-oxo complex through a HAT-radical dissociation pathway. In the latter process, we prove that the intermediate FeIII complex [N4Py·FeIII(OH)]2+ is not able to oxidize the diphenylmethyl radical and we provide its structural characterization in solution. The employed combined experimental and theoretical strategy is promising for the spectroscopic characterization of transient intermediates as well as for the mechanistic investigation of redox chemical transformations on the second to millisecond time scales.
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Affiliation(s)
- Francesco Tavani
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.
| | - Giorgio Capocasa
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.
| | - Andrea Martini
- Dipartimento di Chimica, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy and The Smart Materials Research Institute, Southern Federal University, 344090 Sladkova 178/24 Rostov-on-Don, Russia
| | - Francesco Sessa
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.
| | - Stefano Di Stefano
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.
| | - Osvaldo Lanzalunga
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.
| | - Paola D'Angelo
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.
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7
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Tavani F, Capocasa G, Martini A, Sessa F, Di Stefano S, Lanzalunga O, D'Angelo P. Direct structural and mechanistic insights into fast bimolecular chemical reactions in solution through a coupled XAS/UV–Vis multivariate statistical analysis. Dalton Trans 2021; 50:131-142. [DOI: 10.1039/d0dt03083j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined multivariate and theoretical analysis of coupled XAS/UV–Vis data was proven to be an innovative method to obtain direct structural and mechanistic evidence for bimolecular reactions in solution involving organic substrates.
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Affiliation(s)
- Francesco Tavani
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Giorgio Capocasa
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Andrea Martini
- Dipartimento di Chimica
- Università degli Studi di Torino
- 10125 Torino
- Italy
- The Smart Materials Research Institute
| | - Francesco Sessa
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | | | | | - Paola D'Angelo
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
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8
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Gericke R, Doyle LM, Farquhar ER, McDonald AR. Oxo-Free Hydrocarbon Oxidation by an Iron(III)-Isoporphyrin Complex. Inorg Chem 2020; 59:13952-13961. [PMID: 32955871 DOI: 10.1021/acs.inorgchem.0c01618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal-halides that perform proton coupled electron-transfer (PCET) oxidation are an important new class of high-valent oxidant. In investigating metal-dihalides, we reacted [FeIII(Cl)(T(OMe)PP)] (1, T(OMe)PP = meso-tetra(4-methoxyphenyl)porphyrinyl) with (dichloroiodo)benzene. An FeIII-meso-chloro-isoporphyrin complex [FeIII(Cl)2(T(OMe)PP-Cl)] (2) was obtained. 2 was characterized by electronic absorption, 1H NMR, EPR, and X-ray absorption spectroscopies and mass spectrometry with support from computational analyses. 2 was reacted with a series of hydrocarbon substrates. The measured kinetic data exhibited a nonlinear behavior, whereby the oxidation followed a hydrogen-atom-transfer (HAT) PCET mechanism. The meso-chlorine atom was identified as the HAT agent. In one case, a halogenated product was identified by mass spectrometry. Our findings demonstrate that oxo-free hydrocarbon oxidation with heme systems is possible and show the potential for iron-dihalides in oxidative hydrocarbon halogenation.
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Affiliation(s)
- Robert Gericke
- School of Chemistry, College Green, Trinity College Dublin, The University of Dublin, Dublin 2 D02 PN40, Ireland
| | - Lorna M Doyle
- School of Chemistry, College Green, Trinity College Dublin, The University of Dublin, Dublin 2 D02 PN40, Ireland
| | - Erik R Farquhar
- National Synchrotron Light Source II, Brookhaven National Laboratory, Case Western Reserve University Center for Synchrotron Biosciences, Upton, New York 11973, United States
| | - Aidan R McDonald
- School of Chemistry, College Green, Trinity College Dublin, The University of Dublin, Dublin 2 D02 PN40, Ireland
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9
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Tavani F, Martini A, Capocasa G, Di Stefano S, Lanzalunga O, D'Angelo P. Direct Mechanistic Evidence for a Nonheme Complex Reaction through a Multivariate XAS Analysis. Inorg Chem 2020; 59:9979-9989. [PMID: 32598841 PMCID: PMC8008396 DOI: 10.1021/acs.inorgchem.0c01132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
In
this work, we propose a method to directly determine the mechanism
of the reaction between the nonheme complex FeII(tris(2-pyridylmethyl)amine)
([FeII(TPA)(CH3CN)2]2+) and peracetic acid (AcOOH) in CH3CN, working at room
temperature. A multivariate analysis is applied to the time-resolved
coupled energy-dispersive X-ray absorption spectroscopy (EDXAS) reaction
data, from which a set of spectral and concentration profiles for
the reaction key species is derived. These “pure” extracted
EDXAS spectra are then quantitatively characterized by full multiple
scattering (MS) calculations. As a result, structural information
for the elusive reaction intermediates [FeIII(TPA)(κ2-OOAc)]2+ and [FeIV(TPA)(O)(X)]+/2+ is obtained, and it is suggested that X = AcO– in opposition to X = CH3CN. The employed strategy is
promising both for the spectroscopic characterization of reaction
intermediates that are labile or silent to the conventional spectroscopic
techniques, as well as for the mechanistic understanding of complex
redox reactions involving organic substrates. A combined multivariate and theoretical XAS analysis was
proven to be a powerful method to obtain direct evidence for the mechanism
of the reaction between the nonheme complex FeII(tris(2-pyridymethyl)amine)
([FeII(TPA)(CH3CN)2]2+) and peroxyacetic acid. This approach allowed to determine the time
evolution of the concentration profiles for all reaction intermediates
and to quantitatively characterize their structures, suggesting the
sixth coordinating ligand of the nonheme oxo complex [FeIV(TPA)(O)(X)]+/2+ is X = AcO− in
opposition to X = CH3CN.
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Affiliation(s)
- Francesco Tavani
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Andrea Martini
- Dipartimento di Chimica, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy.,The Smart Materials Research Institute, Southern Federal University, Sladkova 178/24, 344090 Rostov-on-Don, Russia
| | - Giorgio Capocasa
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Osvaldo Lanzalunga
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Paola D'Angelo
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
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10
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Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prangé T, Brunori M, Colloc’h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCRJ 2019; 6:832-842. [PMID: 31576217 PMCID: PMC6760443 DOI: 10.1107/s2052252519008157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Life and Environmental Sciences, New York–Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli–IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Avella
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy
| | - Cécile Exertier
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thierry Prangé
- CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France
| | - Maurizio Brunori
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nathalie Colloc’h
- ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France
| | - Beatrice Vallone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
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11
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Spezia R, Migliorati V, D’Angelo P. Response to “Comment on ‘On the development of polarizable and Lennard-Jones force fields to study hydration structure and dynamics of actinide(III) ions based on effective ionic radii’” [J. Chem. Phys. 150, 097101 (2019)]. J Chem Phys 2019; 150:097102. [DOI: 10.1063/1.5087193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Riccardo Spezia
- LAMBE, Université d’Evry Val d’Essonne, CEA, CNRS, Université Paris Saclay, F-91025 Evry, France
| | | | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Roma, Italy
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12
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Soldatov MA, Martini A, Bugaev AL, Pankin I, Medvedev PV, Guda AA, Aboraia AM, Podkovyrina YS, Budnyk AP, Soldatov AA, Lamberti C. The insights from X-ray absorption spectroscopy into the local atomic structure and chemical bonding of Metal–organic frameworks. Polyhedron 2018. [DOI: 10.1016/j.poly.2018.08.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Sessa F, Migliorati V, Serva A, Lapi A, Aquilanti G, Mancini G, D'Angelo P. On the coordination of Zn2+ ion in Tf2N− based ionic liquids: structural and dynamic properties depending on the nature of the organic cation. Phys Chem Chem Phys 2018; 20:2662-2675. [DOI: 10.1039/c7cp07497b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Zn2+ coordination structure changes when the Zn(Tf2N)2 salt is dissolved in ionic liquids resulting in more favorable interactions among solvent cations and anions.
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Affiliation(s)
- Francesco Sessa
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | | | - Alessandra Serva
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Andrea Lapi
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
- Istituto CNR di Metodologie Chimiche-IMC
| | | | | | - Paola D'Angelo
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
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14
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Migliorati V, Filipponi A, Di Cicco A, De Panfilis S, D’Angelo P. Structure of Water in Zn2+ Aqueous Solutions from Ambient Conditions up to the Gigapascal Pressure Range: A XANES and Molecular Dynamics Study. Inorg Chem 2017; 56:14013-14022. [DOI: 10.1021/acs.inorgchem.7b02151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di
Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
| | - Adriano Filipponi
- Dipartimento di Scienze
Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio, 67100 L’Aquila, Italy
| | - Andrea Di Cicco
- Sezione di Fisica,
Scuola di Scienze e Tecnologie, Università di Camerino, 62032 Camerino (MC), Italy
| | - Simone De Panfilis
- Centre
for Life Nano Science - IIT@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161 Rome, Italy
| | - Paola D’Angelo
- Dipartimento di
Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
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15
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Spezia R, Migliorati V, D’Angelo P. On the development of polarizable and Lennard-Jones force fields to study hydration structure and dynamics of actinide(III) ions based on effective ionic radii. J Chem Phys 2017; 147:161707. [DOI: 10.1063/1.4989969] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Migliorati V, Serva A, Terenzio FM, D’Angelo P. Development of Lennard-Jones and Buckingham Potentials for Lanthanoid Ions in Water. Inorg Chem 2017; 56:6214-6224. [DOI: 10.1021/acs.inorgchem.7b00207] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessandra Serva
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Filippo Maria Terenzio
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
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17
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Serva A, Migliorati V, Spezia R, D'Angelo P. How Does CeIII
Nitrate Dissolve in a Protic Ionic Liquid? A Combined Molecular Dynamics and EXAFS Study. Chemistry 2017; 23:8424-8433. [DOI: 10.1002/chem.201604889] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Alessandra Serva
- Dipartimento di Chimica; Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Valentina Migliorati
- Dipartimento di Chimica; Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Riccardo Spezia
- LAMBE CEA, CNRS; Université Paris Saclay; 91025 Evry Cedex France
- LAMBE Université d'Evry; 91025 Evry Cedex France
| | - Paola D'Angelo
- Dipartimento di Chimica; Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
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18
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Persson I, D'Angelo P, Lundberg D. Hydrated and Solvated Tin(II) Ions in Solution and the Solid State, and a Coordination Chemistry Overview of the d 10 s 2 Metal Ions. Chemistry 2016; 22:18583-18592. [PMID: 27862415 DOI: 10.1002/chem.201603904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/19/2016] [Indexed: 11/10/2022]
Abstract
The coordination chemistry of d10 s2 metal ions is strongly affected by an (at least partially) occupied d10 s2 metal ion-ligand atom antibonding orbital, which may cause a void in the coordination sphere due to repulsion between the electrons in the antibonding orbital on the metal ion and those on the ligands. The character of the formed d10 s2 metal ion-ligand atom bond plays an important role in the electron density in the antibonding orbital and thereby also in the coordination chemistry. The hydrated tin(II) ion, [Sn(H2 O)3 ]2+ , and the trihydroxidostannate ion, [Sn(OH)3 ]- , have very different mean Sn-O bond lengths (2.21 and 2.08 Å, respectively) and O-Sn-O angles (ca. 78 and 90°, respectively) both in the solid state and in solution. On increasing the covalency of the tin(II)-ligand bonds, the repulsion decreases and higher coordination numbers are obtained, as seen in the dimethylsulfoxide- and N,N-dimethylthioformamide-solvated tin(II) ions, both of which are five-coordinate with square-pyramidal structures.
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Affiliation(s)
- Ingmar Persson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07, Uppsala, Sweden
| | - Paola D'Angelo
- Dipartimento di Chimica, Universitá di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Daniel Lundberg
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07, Uppsala, Sweden
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19
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D’Angelo P, Migliorati V, Sessa F, Mancini G, Persson I. XANES Reveals the Flexible Nature of Hydrated Strontium in Aqueous Solution. J Phys Chem B 2016; 120:4114-24. [DOI: 10.1021/acs.jpcb.6b01054] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paola D’Angelo
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Valentina Migliorati
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Sessa
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, 56126 Pisa, Italy
| | - Ingmar Persson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences (SLU), SE-750 07 Uppsala, Sweden
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20
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Rossi G, d'Acapito F, Amidani L, Boscherini F, Pedio M. Local environment of metal ions in phthalocyanines: K-edge X-ray absorption spectra. Phys Chem Chem Phys 2016; 18:23686-94. [DOI: 10.1039/c6cp04022e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We describe a model for interpreting XAFS spectra of metal phthalocyanines. The near edge spectra are reproduced in a full potential approach.
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Affiliation(s)
- G. Rossi
- Department of Physics and Astronomy
- University of Bologna
- 40127 Bologna
- Italy
| | - F. d'Acapito
- Consiglio Nazionale delle Ricerche – Istituto Officina dei Materiali – Operative Group in Grenoble
- c/o ESRF – The European Synchrotron
- CS 40220
- 38043 Grenoble Cedex 9
- France
| | - L. Amidani
- Department of Physics and Astronomy
- University of Bologna
- 40127 Bologna
- Italy
| | - F. Boscherini
- Department of Physics and Astronomy
- University of Bologna
- 40127 Bologna
- Italy
- Consiglio Nazionale delle Ricerche – Istituto Officina dei Materiali – Operative Group in Grenoble
| | - M. Pedio
- Consiglio Nazionale delle Ricerche – Istituto Officina dei Materiali
- Laboratorio TASC
- 34149 Trieste
- Italy
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21
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Zitolo A, Goellner V, Armel V, Sougrati MT, Mineva T, Stievano L, Fonda E, Jaouen F. Identification of catalytic sites for oxygen reduction in iron- and nitrogen-doped graphene materials. NATURE MATERIALS 2015; 14:937-42. [PMID: 26259106 DOI: 10.1038/nmat4367] [Citation(s) in RCA: 896] [Impact Index Per Article: 99.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 06/05/2015] [Indexed: 05/22/2023]
Abstract
While platinum has hitherto been the element of choice for catalysing oxygen electroreduction in acidic polymer fuel cells, tremendous progress has been reported for pyrolysed Fe-N-C materials. However, the structure of their active sites has remained elusive, delaying further advance. Here, we synthesized Fe-N-C materials quasi-free of crystallographic iron structures after argon or ammonia pyrolysis. These materials exhibit nearly identical Mössbauer spectra and identical X-ray absorption near-edge spectroscopy (XANES) spectra, revealing the same Fe-centred moieties. However, the much higher activity and basicity of NH3-pyrolysed Fe-N-C materials demonstrates that the turnover frequency of Fe-centred moieties depends on the physico-chemical properties of the support. Following a thorough XANES analysis, the detailed structures of two FeN4 porphyrinic architectures with different O2 adsorption modes were then identified. These porphyrinic moieties are not easily integrated in graphene sheets, in contrast with Fe-centred moieties assumed hitherto for pyrolysed Fe-N-C materials. These new insights open the path to bottom-up synthesis approaches and studies on site-support interactions.
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Affiliation(s)
- Andrea Zitolo
- Synchrotron SOLEIL, L'orme des Merisiers, BP 48 Saint Aubin, 91192 Gif-sur-Yvette, France
| | - Vincent Goellner
- Institut Charles Gerhardt Montpellier, UMR 5253, CNRS, Université Montpellier, 34095 Montpellier, France
| | - Vanessa Armel
- Institut Charles Gerhardt Montpellier, UMR 5253, CNRS, Université Montpellier, 34095 Montpellier, France
| | - Moulay-Tahar Sougrati
- Institut Charles Gerhardt Montpellier, UMR 5253, CNRS, Université Montpellier, 34095 Montpellier, France
| | - Tzonka Mineva
- Institut Charles Gerhardt Montpellier, UMR 5253, CNRS, Université Montpellier, 34095 Montpellier, France
| | - Lorenzo Stievano
- Institut Charles Gerhardt Montpellier, UMR 5253, CNRS, Université Montpellier, 34095 Montpellier, France
| | - Emiliano Fonda
- Synchrotron SOLEIL, L'orme des Merisiers, BP 48 Saint Aubin, 91192 Gif-sur-Yvette, France
| | - Frédéric Jaouen
- Institut Charles Gerhardt Montpellier, UMR 5253, CNRS, Université Montpellier, 34095 Montpellier, France
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22
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Guda SA, Guda AA, Soldatov MA, Lomachenko KA, Bugaev AL, Lamberti C, Gawelda W, Bressler C, Smolentsev G, Soldatov AV, Joly Y. Optimized Finite Difference Method for the Full-Potential XANES Simulations: Application to Molecular Adsorption Geometries in MOFs and Metal-Ligand Intersystem Crossing Transients. J Chem Theory Comput 2015; 11:4512-21. [PMID: 26575941 DOI: 10.1021/acs.jctc.5b00327] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate modeling of the X-ray absorption near-edge spectra (XANES) is required to unravel the local structure of metal sites in complex systems and their structural changes upon chemical or light stimuli. Two relevant examples are reported here concerning the following: (i) the effect of molecular adsorption on 3d metals hosted inside metal-organic frameworks and (ii) light induced dynamics of spin crossover in metal-organic complexes. In both cases, the amount of structural models for simulation can reach a hundred, depending on the number of structural parameters. Thus, the choice of an accurate but computationally demanding finite difference method for the ab initio X-ray absorption simulations severely restricts the range of molecular systems that can be analyzed by personal computers. Employing the FDMNES code [Phys. Rev. B, 2001, 63, 125120] we show that this problem can be handled if a proper diagonalization scheme is applied. Due to the use of dedicated solvers for sparse matrices, the calculation time was reduced by more than 1 order of magnitude compared to the standard Gaussian method, while the amount of required RAM was halved. Ni K-edge XANES simulations performed by the accelerated version of the code allowed analyzing the coordination geometry of CO and NO on the Ni active sites in CPO-27-Ni MOF. The Ni-CO configuration was found to be linear, while Ni-NO was bent by almost 90°. Modeling of the Fe K-edge XANES of photoexcited aqueous [Fe(bpy)3](2+) with a 100 ps delay we identified the Fe-N distance elongation and bipyridine rotation upon transition from the initial low-spin to the final high-spin state. Subsequently, the X-ray absorption spectrum for the intermediate triplet state with expected 100 fs lifetime was theoretically predicted.
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Affiliation(s)
| | | | | | - Kirill A Lomachenko
- Department of Chemistry, NIS and CrisDi Centers, Turin University and INSTM Reference Center , 10125 Turin, Turin, Italy
| | | | - Carlo Lamberti
- Department of Chemistry, NIS and CrisDi Centers, Turin University and INSTM Reference Center , 10125 Turin, Turin, Italy
| | | | - Christian Bressler
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg , Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | | | - Yves Joly
- Inst NEEL, Université Grenoble Alpes , 38042 Grenoble, France.,Institut NEEL, CNRS , 38042 Grenoble, France
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23
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Tierney DL, Schenk G. X-ray absorption spectroscopy of dinuclear metallohydrolases. Biophys J 2015; 107:1263-72. [PMID: 25229134 DOI: 10.1016/j.bpj.2014.07.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/14/2014] [Accepted: 07/24/2014] [Indexed: 12/26/2022] Open
Abstract
In this mini-review, we briefly discuss the physical origin of x-ray absorption spectroscopy (XAS) before illustrating its application using dinuclear metallohydrolases as exemplary systems. The systems we have selected for illustrative purposes present a challenging problem for XAS, one that is ideal to demonstrate the potential of this methodology for structure/function studies of metalloenzymes in general. When the metal ion is redox active, XAS provides a sensitive measure of oxidation-state-dependent differences. When the metal ion is zinc, XAS is the only spectroscopic method that will provide easily accessible structural information in solution. In the case of heterodimetallic sites, XAS has the unique ability to interrogate each metal site independently in the same sample. One of the strongest advantages of XAS is its ability to examine metal ion site structures with crystallographic precision, without the need for a crystal. This is key for studying flexible metal ion sites, such as those described in the selected examples, because it allows one to monitor structural changes that occur during substrate turnover.
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Affiliation(s)
- David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
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24
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Hunter SC, Smith BA, Hoffmann CM, Wang X, Chen YS, McIntyre GJ, Xue ZL. Intermolecular Interactions in Solid-State Metalloporphyrins and Their Impacts on Crystal and Molecular Structures. Inorg Chem 2014; 53:11552-62. [DOI: 10.1021/ic5015835] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Seth C. Hunter
- Department of Chemistry, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Brenda A. Smith
- Department of Chemistry, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Christina M. Hoffmann
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Xiaoping Wang
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Yu-Sheng Chen
- ChemMatCARS,
Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois 60439, United States
| | | | - Zi-Ling Xue
- Department of Chemistry, The University of Tennessee, Knoxville, Tennessee 37996, United States
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25
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Shelby ML, Mara MW, Chen LX. New insight into metalloporphyrin excited state structures and axial ligand binding from X-ray transient absorption spectroscopic studies. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.05.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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26
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Lima FA, Penfold TJ, van der Veen RM, Reinhard M, Abela R, Tavernelli I, Rothlisberger U, Benfatto M, Milne CJ, Chergui M. Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy. Phys Chem Chem Phys 2014; 16:1617-31. [PMID: 24317683 DOI: 10.1039/c3cp53683a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.
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Affiliation(s)
- Frederico A Lima
- École Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, CH, Switzerland.
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27
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Xu W, Dziedzic-Kocurek K, Yu M, Wu Z, Marcelli A. Spectroscopic study and electronic structure of prototypical iron porphyrins and their μ-oxo-dimer derivatives with different functional configurations. RSC Adv 2014. [DOI: 10.1039/c4ra04685d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The electronic structures and the charge dynamics of prototypical porphyrins and their μ-oxo-dimer derivatives have been investigated to provide insight into their molecular biophysical mechanisms.
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Affiliation(s)
- Wei Xu
- Beijing Synchrotron Radiation Facility
- Institute of High Energy Physics
- Beijing, China
| | | | - Meijuan Yu
- Beijing Synchrotron Radiation Facility
- Institute of High Energy Physics
- Beijing, China
| | - Ziyu Wu
- Beijing Synchrotron Radiation Facility
- Institute of High Energy Physics
- Beijing, China
- NSRL
- University of Science and Technology of China
| | - Augusto Marcelli
- NSRL
- University of Science and Technology of China
- Hefei 230026, China
- INFN - Laboratori Nazionali di Frascati
- Frascati, Italy
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28
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Mara MW, Shelby M, Stickrath A, Harpham M, Huang J, Zhang X, Hoffman BM, Chen LX. Electronic and Nuclear Structural Snapshots in Ligand Dissociation and Recombination Processes of Iron Porphyrin in Solution: A Combined Optical/X-ray Approach. J Phys Chem B 2013; 117:14089-98. [DOI: 10.1021/jp407094u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael W. Mara
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | - Megan Shelby
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | | | | | | | | | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | - Lin X. Chen
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
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29
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D'Angelo P, Migliorati V, Spezia R, De Panfilis S, Persson I, Zitolo A. K-edge XANES investigation of octakis(DMSO)lanthanoid(III) complexes in DMSO solution and solid iodides. Phys Chem Chem Phys 2013; 15:8684-91. [PMID: 23657739 DOI: 10.1039/c3cp50842k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential of high energy XANES (X-ray absorption near edge structure) as a tool for the structural analysis of lanthanoid-containing systems has been explored. The K-edge XANES spectra of La(3+), Gd(3+), and Lu(3+) ions both in DMSO solution and solid octakis(DMSO)lanthanoid(III) iodides have been analysed. Although the K-edges of lanthanoids cover the energy range of 38 (La) to 65 (Lu) keV, the large widths of the core hole states do not appreciably reduce the potential structural information of the XANES data. We show that, for lanthanoid compounds, accurate structural parameters are obtained from the analysis of K-edge XANES signals if a deconvolution procedure is carried out. We found that in solid octakis(DMSO)lanthanoid(III) iodides the Ln(3+) ions are coordinated by eight DMSO ligands arranged in a quite symmetric fashion. In DMSO solution the Ln(3+) ions retain a regular eight-coordination structure and the coordination number does not change along the series. In contrast to when in water the second coordination shell has been found to provide a negligible contribution to the XANES spectra of Ln(3+) ions in DMSO solution.
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Affiliation(s)
- Paola D'Angelo
- Dipartimento di Chimica, Università di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy.
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30
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Stickrath AB, Mara MW, Lockard JV, Harpham MR, Huang J, Zhang X, Attenkofer K, Chen LX. Detailed Transient Heme Structures of Mb-CO in Solution after CO Dissociation: An X-ray Transient Absorption Spectroscopic Study. J Phys Chem B 2012; 117:4705-12. [DOI: 10.1021/jp3086705] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew B. Stickrath
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Michael W. Mara
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Jenny V. Lockard
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Michael R. Harpham
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Jier Huang
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Xiaoyi Zhang
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Klaus Attenkofer
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Lin X. Chen
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
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31
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D'Angelo P, Della Longa S, Arcovito A, Mancini G, Zitolo A, Chillemi G, Giachin G, Legname G, Benetti F. Effects of the pathological Q212P mutation on human prion protein non-octarepeat copper-binding site. Biochemistry 2012; 51:6068-79. [PMID: 22788868 DOI: 10.1021/bi300233n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Prion diseases are a class of fatal neurodegenerative disorders characterized by brain spongiosis, synaptic degeneration, microglia and astrocytes activation, neuronal loss and altered redox control. These maladies can be sporadic, iatrogenic and genetic. The etiological agent is the prion, a misfolded form of the cellular prion protein, PrP(C). PrP(C) interacts with metal ions, in particular copper and zinc, through the octarepeat and non-octarepeat binding sites. The physiological implication of this interaction is still unclear, as is the role of metals in the conversion. Since prion diseases present metal dyshomeostasis and increased oxidative stress, we described the copper-binding site located in the human C-terminal domain of PrP-HuPrP(90-231), both in the wild-type protein and in the protein carrying the pathological mutation Q212P. We used the synchrotron-based X-ray absorption fine structure technique to study the Cu(II) and Cu(I) coordination geometries in the mutant, and we compared them with those obtained using the wild-type protein. By analyzing the extended X-ray absorption fine structure and the X-ray absorption near-edge structure, we highlighted changes in copper coordination induced by the point mutation Q212P in both oxidation states. While in the wild-type protein the copper-binding site has the same structure for both Cu(II) and Cu(I), in the mutant the coordination site changes drastically from the oxidized to the reduced form of the copper ion. Copper-binding sites in the mutant resemble those obtained using peptides, confirming the loss of short- and long-range interactions. These changes probably cause alterations in copper homeostasis and, consequently, in redox control.
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Affiliation(s)
- Paola D'Angelo
- Department of Chemistry, University of Rome La Sapienza, P.le Aldo Moro 5, I-00185 Rome, Italy.
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32
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Chillemi G, De Santis S, Falconi M, Mancini G, Migliorati V, Battistoni A, Pacello F, Desideri A, D'Angelo P. Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase from Haemophilus ducreyi: in silico and in vitro evidences. J Biomol Struct Dyn 2012; 30:269-79. [PMID: 22686457 DOI: 10.1080/07391102.2012.680028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations have been jointly applied to the study of the Cu,Zn superoxide dismutase from Haemophilus ducreyi (HdSOD) in interaction with the carbon monoxide molecule. The configurational flexibility of the Fe(II)-heme group, intercalated between the two subunits, has been sampled by MD simulations and included in the XANES data analysis without optimization in the structural parameter space. Our results provide an interpretation of the observed discrepancy in the Fe-heme distances as detected by extended X-ray absorption fine structure (EXAFS) spectroscopy and the classical XANES analysis, in which the structural parameters are optimized in a unique structure. Moreover, binding of the CO molecule to the heme induces a long range effect on the Cu,Zn active site, as evidenced by both MD simulations and in vitro experiments. MD simulation of the CO bound system, in fact, highlighted a structural rearrangement of the protein-protein hydrogen bond network in the region of the Cu,Zn active site, correlated with an increase in water accessibility at short distance from the copper atom. In line, in vitro experiments evidenced an increase of copper accessibility to a chelating agent when the CO molecule binds to the heme group, as compared to a heme deprived HdSOD. Altogether, our results support the hypothesis that the HdSOD is a heme-sensor protein, in which binding to small gaseous molecules modulates the enzyme superoxide activity as an adaptive response to the bacterial environment.
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Arcovito A, della Longa S. Local structure and dynamics of hemeproteins by X-ray absorption near edge structure spectroscopy. J Inorg Biochem 2012; 112:93-9. [PMID: 22541673 DOI: 10.1016/j.jinorgbio.2012.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 03/28/2012] [Accepted: 03/29/2012] [Indexed: 11/19/2022]
Abstract
X-ray absorption near edge structure (XANES) spectroscopy is a synchrotron radiation technique sensitive to the local structure and dynamics around the metal site of a heme containing protein. Advances in detection techniques and theoretical/computational platforms in the last 15 years allowed the use of XANES as a quantitative probe of the key structural determinants driving functional changes, both in a concerted way with protein crystallography and EXAFS (extended X-ray absorption fine structure), or as a stand-alone method to apply in the crystal state as well as in solution. Moreover, the local dynamics of the heme site has been deeply investigated, on one hand, coupling XANES to classical photolysis experiments at cryogenic temperatures; on the other hand, the intrinsic property of the synchrotron radiation to induce radiolysis events, has been exploited to investigate specific cryotrapped intermediates, using X-rays both as a pump and a probe. Insights on the XANES method and some specific examples are presented to illustrate these topics.
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Affiliation(s)
- Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Roma, Italy.
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Probing the local electronic and geometric properties of the heme iron center in a H-NOX domain. J Inorg Biochem 2011; 105:784-92. [PMID: 21497576 DOI: 10.1016/j.jinorgbio.2011.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/03/2011] [Accepted: 03/04/2011] [Indexed: 11/23/2022]
Abstract
Heme-Nitric oxide and/or OXygen binding (H-NOX) proteins are a family of diatomic gas binding hemoproteins that have attracted intense research interest. Here we employ X-ray absorption near-edge structure (XANES) spectroscopy to study the nitric oxide (NO) binding site of H-NOX. This is the first time this technique has been utilized to examine the NO/H-NOX signaling pathway. XANES spectra of wildtype and a point mutant (proline 115 to alanine, P115A) of the H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) were obtained and analyzed for ferrous and ferric complexes of the protein. This work provides specific structural characterization of the solution state of several Tt H-NOX ferrous complexes (-unligated, -NO, and -CO) that were previously unavailable. Our iron K-edges indicate effective charge on the iron center in the various complexes and report on the electronic environment of heme iron. We analyzed the ligand field indicator ratio (LFIR), which is extracted from XANES spectra, for each complex, providing an understanding of ligand field strength, spin state of the central iron, movement of the iron atom upon ligation, and ligand binding properties. In particular, our LFIRs indicate that the heme iron is dramatically displaced towards the distal pocket during ligand binding. Based on these results, we propose that iron displacement towards the distal heme pocket is an essential step in signal initiation in H-NOX proteins. This provides a mechanistic link between ligand binding and the changes in heme and protein conformation that have been observed for H-NOX family members during signaling.
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D’Angelo P, Della Longa S, Arcovito A, Anselmi M, Di Nola A, Chillemi G. Dynamic Investigation of Protein Metal Active Sites: Interplay of XANES and Molecular Dynamics Simulations. J Am Chem Soc 2010; 132:14901-9. [DOI: 10.1021/ja1056533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paola D’Angelo
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Stefano Della Longa
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Alessandro Arcovito
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Massimiliano Anselmi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Alfredo Di Nola
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Giovanni Chillemi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
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Arcovito A, Ardiccioni C, Cianci M, D’Angelo P, Vallone B, Della Longa S. Polarized X-ray Absorption Near-Edge Structure Spectroscopy of Neuroglobin and Myoglobin Single Crystals. J Phys Chem B 2010; 114:13223-31. [DOI: 10.1021/jp104395g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Chiara Ardiccioni
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Michele Cianci
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Paola D’Angelo
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Beatrice Vallone
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Stefano Della Longa
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
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D’Angelo P, Zitolo A, Pacello F, Mancini G, Proux O, Hazemann JL, Desideri A, Battistoni A. Fe-heme structure in Cu,Zn superoxide dismutase from Haemophilus ducreyi by X-ray Absorption Spectroscopy. Arch Biochem Biophys 2010; 498:43-9. [DOI: 10.1016/j.abb.2010.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 03/19/2010] [Accepted: 03/20/2010] [Indexed: 11/29/2022]
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Borghi E, Casella L. X-Ray absorption spectroscopy quantitative analysis of biomimetic copper(II) complexes with tridentate nitrogen ligands mimicking the tris(imidazole) array of protein centres. Phys Chem Chem Phys 2010; 12:1525-34. [PMID: 20126765 DOI: 10.1039/b921769j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study copper(ii) complexes with the tridentate nitrogen ligand bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-BB) are considered as model compounds for the Cu-tris(imidazole) array found in several copper proteins. 2-BB chelates copper(ii) forming two six-membered rings and the complexes contain methanol, nitrite, azide and water as ancillary ligands; both the coordination numbers and stereochemistries differ in these complexes. Their key structural features were investigated by using full multiple-scattering theoretical analysis of the copper K-edge X-ray absorption spectrum with the MXAN code. We showed that using cluster sizes large enough to include all atoms of the ligand, the analysis of the XANES region can give both a structural model of the metal centre and map the structure of the 2-BB complexes. Complex [Cu(2-BB)(N(3))](+) provided a critical test through the comparison of the XANES simulation results with crystallographic data, thus permitting the extension of the method to the complex [Cu(2-BB)(H(2)O)(n)](+) (n = 1 or 2), for which crystallographic data are not available but is expected to bear a five-coordinated Cu(3N)(2O) core (n = 2). The structural data of [Cu(2-BB)(MeOH)(ClO(4))](+) and [Cu(2-BB)(NO(2))](+), both with a Cu(3N)(2O) core but with a different stereochemistry, were used as the starting parameters for two independent simulations of the XANES region of the [Cu(2-BB)(H(2)O)(2)](+) cation. The two structural models generated by simulation converge towards a structure for the aqua-cation with a lower coordination number. New calculations, where four-coordinated Cu(3N)(O) cores were considered as the starting structures, validated that the structure of the aqua-complex in the powder state has a copper(ii) centre with a four-coordinated Cu(3N)(O) core and a molecular formula [Cu(2-BB)(H(2)O)](ClO(4)).(H(2)O). A water solvation molecule, presumed to be disordered from the simulations with the two Cu(3N)(2O) cores, is present. The successful treatment of this Cu-2-BB complex system allows the extension of the method to other biomimetic compounds when a structural characterization is lacking.
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Affiliation(s)
- Elena Borghi
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy.
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Aitken JB, Carter EA, Eastgate H, Hackett MJ, Harris HH, Levina A, Lee YC, Chen CI, Lai B, Vogt S, Lay PA. Biomedical applications of X-ray absorption and vibrational spectroscopic microscopies in obtaining structural information from complex systems. Radiat Phys Chem Oxf Engl 1993 2010. [DOI: 10.1016/j.radphyschem.2009.03.068] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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D'Angelo P, Zitolo A, Migliorati V, Persson I. Analysis of the Detailed Configuration of Hydrated Lanthanoid(III) Ions in Aqueous Solution and Crystalline Salts by Using K- and L3-Edge XANES Spectroscopy. Chemistry 2010; 16:684-92. [DOI: 10.1002/chem.200900122] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Giorgetti M, Pellei M, Lobbia GG, Santini C. XAFS studies on copper(I) complexes containing scorpionate ligands. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/190/1/012146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wellenreuther G, Cianci M, Tucoulou R, Meyer-Klaucke W, Haase H. The ligand environment of zinc stored in vesicles. Biochem Biophys Res Commun 2009; 380:198-203. [PMID: 19171119 DOI: 10.1016/j.bbrc.2009.01.074] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 01/14/2009] [Indexed: 11/28/2022]
Abstract
Zinc serves regulatory functions in cells and thus, several mechanisms exist for tight control of its homeostasis. One mechanism is storage in and retrieval from vesicles, so-called zincosomes, but the chemical speciation of zincosomal zinc has remained enigmatic. Here, we determine the intravesicular zinc-coordination in isolated zincosomes in comparison to intact RAW264.7 murine macrophage cells. In elemental maps of a cell monolayer, generated by microbeam X-ray fluorescence, zincosomes were identified as spots of high zinc accumulation. A fingerprint for the binding motif obtained by muXANES (X-ray absorption near edge structure) matches the XANES from isolated vesicles; zinc is not free, but present as a complexed form (average coordination; 1.0 sulfur, 2,5 histidines 30 and 1.0 oxygen), resembling regulatory or catalytic zinc sites in proteins. Such coordination enables reversible binding, acting as a 'zinc sink', facilitating the accumulation of high amounts of zinc against a concentration gradient.
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Affiliation(s)
- Gerd Wellenreuther
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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