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Silveira CM, Zuccarello L, Barbosa C, Caserta G, Zebger I, Hildebrandt P, Todorovic S. Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies. Molecules 2021; 26:4852. [PMID: 34443440 PMCID: PMC8398457 DOI: 10.3390/molecules26164852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
Abstract
Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.
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Affiliation(s)
- Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Giorgio Caserta
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Ingo Zebger
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Peter Hildebrandt
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
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Capitanio G, Palese LL, Papa F, Papa S. Allosteric Cooperativity in Proton Energy Conversion in A1-Type Cytochrome c Oxidase. J Mol Biol 2019; 432:534-551. [PMID: 31626808 DOI: 10.1016/j.jmb.2019.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/06/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022]
Abstract
Cytochrome c oxidase (CcO), the CuA, heme a, heme a3, CuB enzyme of respiratory chain, converts the free energy released by aerobic cytochrome c oxidation into a membrane electrochemical proton gradient (ΔμH+). ΔμH+ derives from the membrane anisotropic arrangement of dioxygen reduction to two water molecules and transmembrane proton pumping from a negative (N) space to a positive (P) space separated by the membrane. Spectroscopic, potentiometric, and X-ray crystallographic analyses characterize allosteric cooperativity of dioxygen binding and reduction with protonmotive conformational states of CcO. These studies show that allosteric cooperativity stabilizes the favorable conformational state for conversion of redox energy into a transmembrane ΔμH+.
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Affiliation(s)
- Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luigi Leonardo Palese
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy.
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Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:103-108. [PMID: 27810193 DOI: 10.1016/j.bbabio.2016.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/18/2016] [Accepted: 10/28/2016] [Indexed: 12/16/2022]
Abstract
Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (CcO) is still an open problem. The propionic acids of heme a3 have been proposed to act as a proton loading site (PLS) in the proton pumping pathway, yet this proposal could not be verified by experimental data so far. We have set up an experiment where the redox states of the two hemes in CcO can be controlled via external electrical potential. Surface enhanced resonance Raman (SERR) spectroscopy was applied to simultaneously monitor the redox state of the hemes and the protonation state of the heme propionates. Simulated spectra based on QM/MM calculations were used to assign the resonant enhanced CH2 twisting modes of the propionates to the protonation state of the individual heme a and heme a3 propionates respectively. The comparison between calculated and measured H2OD2O difference spectra allowed a sound band assignment. In the fully reduced enzyme at least three of the four heme propionates were found to be protonated whereas in the presence of a reduced heme a and an oxidized heme a3 only protonation of one heme a3 propionates was observed. Our data supports the postulated scenario where the heme a3 propionates are involved in the proton pathway.
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Yoshikawa S, Shimada A, Shinzawa-Itoh K. Respiratory conservation of energy with dioxygen: cytochrome C oxidase. Met Ions Life Sci 2015; 15:89-130. [PMID: 25707467 DOI: 10.1007/978-3-319-12415-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Cytochrome c oxidase (CcO) is the terminal oxidase of cell respiration which reduces molecular oxygen (O₂) to H2O coupled with the proton pump. For elucidation of the mechanism of CcO, the three-dimensional location and chemical reactivity of each atom composing the functional sites have been extensively studied by various techniques, such as crystallography, vibrational and time-resolved electronic spectroscopy, since the X-ray structures (2.8 Å resolution) of bovine and bacterial CcO have been published in 1995.X-ray structures of bovine CcO in different oxidation and ligand binding states showed that the O₂reduction site, which is composed of Fe (heme a 3) and Cu (CuB), drives a non-sequential four-electron transfer for reduction of O₂to water without releasing any reactive oxygen species. These data provide the crucial structural basis to solve a long-standing problem, the mechanism of the O₂reduction.Time-resolved resonance Raman and charge translocation analyses revealed the mechanism for coupling between O₂reduction and the proton pump: O₂is received by the O₂reduction site where both metals are in the reduced state (R-intermediate), giving the O₂-bound form (A-intermediate). This is spontaneously converted to the P-intermediate, with the bound O₂fully reduced to 2 O²⁻. Hereafter the P-intermediate receives four electron equivalents from the second Fe site (heme a), one at a time, to form the three intermediates, F, O, and E to regenerate the R-intermediate. Each electron transfer step from heme a to the O₂reduction site is coupled with the proton pump.X-ray structural and mutational analyses of bovine CcO show three possible proton transfer pathways which can transfer pump protons (H) and chemical (water-forming) protons (K and D). The structure of the H-pathway of bovine CcO indicates that the driving force of the proton pump is the electrostatic repulsion between the protons on the H-pathway and positive charges of heme a, created upon oxidation to donate electrons to the O₂reduction site. On the other hand, mutational and time-resolved electrometric findings for the bacterial CcO strongly suggest that the D-pathway transfers both pump and chemical protons. However, the structure for the proton-gating system in the D-pathway has not been experimentally identified. The structural and functional diversities in CcO from various species suggest a basic proton pumping mechanism in which heme a pumps protons while heme a 3 reduces O₂as proposed in 1978.
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan,
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
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Ishigami I, Hikita M, Egawa T, Yeh SR, Rousseau DL. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:98-108. [PMID: 25268561 DOI: 10.1016/j.bbabio.2014.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/11/2014] [Accepted: 09/20/2014] [Indexed: 11/19/2022]
Abstract
Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLoS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Masahide Hikita
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Denis L Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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7
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Weidinger IM. Analysis of structure-function relationships in cytochrome c oxidase and its biomimetic analogs via resonance Raman and surface enhanced resonance Raman spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:119-25. [PMID: 25223590 DOI: 10.1016/j.bbabio.2014.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 01/08/2023]
Abstract
Cytochrome c oxidase (CcO) catalyzes the four electron reduction of molecular oxygen to water while avoiding the formation of toxic peroxide; a quality that is of high relevance for the development of oxygen-reducing catalysts. Resonance Raman spectroscopy has been used since many years as a technique to identify electron transfer pathways in cytochrome c oxidase and to identify the key intermediates in the catalytic cycle. This information can be compared to artificial systems such as modified heme-copper enzymes, molecular heme-copper catalysts or CcO/electrode complexes in order to shed light into the reaction mechanism of these non-natural systems. Understanding the structural commonalities and differences of CcO with its non-natural analogs is of great value for designing efficient oxygen-reducing catalysts. In this review therefore Raman spectroscopic measurements on artificial heme-copper enzymes and model complexes are summarized and compared to the natural enzyme cytochrome c oxidase. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Inez M Weidinger
- Department of Chemistry PC 14, Technische Universitaet Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
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Nakashima S, Ogura T, Kitagawa T. Infrared and Raman spectroscopic investigation of the reaction mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:86-97. [PMID: 25135480 DOI: 10.1016/j.bbabio.2014.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/07/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Recent progress in studies on the proton-pumping and O₂reduction mechanisms of cytochrome c oxidase (CcO) elucidated by infrared (IR) and resonance Raman (rR) spectroscopy, is reviewed. CcO is the terminal enzyme of the respiratory chain and its O₂reduction reaction is coupled with H⁺ pumping activity across the inner mitochondrial membrane. The former is catalyzed by heme a3 and its mechanism has been determined using a rR technique, while the latter used the protein moiety and has been investigated with an IR technique. The number of H⁺ relative to e⁻ transferred in the reaction is 1:1, and their coupling is presumably performed by heme a and nearby residues. To perform this function, different parts of the protein need to cooperate with each other spontaneously and sequentially. It is the purpose of this article to describe the structural details on the coupling on the basis of the vibrational spectra of certain specified residues and chromophores involved in the reaction. Recent developments in time-resolved IR and Raman technology concomitant with protein manipulation methods have yielded profound insights into such structural changes. In particular, the new IR techniques that yielded the breakthrough are reviewed and assessed in detail. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Satoru Nakashima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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9
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IR signatures of the metal centres of bovine cytochrome c oxidase: assignments and redox-linkage. Biochem Soc Trans 2014; 41:1242-8. [PMID: 24059514 DOI: 10.1042/bst20130087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Assignments of IR bands of reduced minus oxidized IR difference spectra of bovine and related cytochrome c oxidases are reviewed and their linkages to specific metal centres are assessed. To aid this, redox-poised difference spectra in the presence of cyanide or carbon monoxide are presented. These ligands fix the redox states of either haem a3 alone or haem a3 and CuB respectively, while allowing redox cycling of the remaining centres.
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10
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Redox-controlled proton gating in bovine cytochrome c oxidase. PLoS One 2013; 8:e63669. [PMID: 23696843 PMCID: PMC3656056 DOI: 10.1371/journal.pone.0063669] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/04/2013] [Indexed: 11/19/2022] Open
Abstract
Cytochrome c oxidase is the terminal enzyme in the electron transfer chain of essentially all organisms that utilize oxygen to generate energy. It reduces oxygen to water and harnesses the energy to pump protons across the mitochondrial membrane in eukaryotes and the plasma membrane in prokaryotes. The mechanism by which proton pumping is coupled to the oxygen reduction reaction remains unresolved, owing to the difficulty of visualizing proton movement within the massive membrane-associated protein matrix. Here, with a novel hydrogen/deuterium exchange resonance Raman spectroscopy method, we have identified two critical elements of the proton pump: a proton loading site near the propionate groups of heme a, which is capable of transiently storing protons uploaded from the negative-side of the membrane prior to their release into the positive side of the membrane and a conformational gate that controls proton translocation in response to the change in the redox state of heme a. These findings form the basis for a postulated molecular model describing a detailed mechanism by which unidirectional proton translocation is coupled to electron transfer from heme a to heme a 3, associated with the oxygen chemistry occurring in the heme a 3 site, during enzymatic turnover.
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Weinberg DR, Gagliardi CJ, Hull JF, Murphy CF, Kent CA, Westlake BC, Paul A, Ess DH, McCafferty DG, Meyer TJ. Proton-Coupled Electron Transfer. Chem Rev 2012; 112:4016-93. [DOI: 10.1021/cr200177j] [Citation(s) in RCA: 1125] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David R. Weinberg
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
- Department of Physical and Environmental
Sciences, Colorado Mesa University, 1100 North Avenue, Grand Junction,
Colorado 81501-3122, United States
| | - Christopher J. Gagliardi
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Jonathan F. Hull
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Christine Fecenko Murphy
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Caleb A. Kent
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Brittany C. Westlake
- The American Chemical Society,
1155 Sixteenth Street NW, Washington, District of Columbia 20036,
United States
| | - Amit Paul
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Daniel H. Ess
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Dewey Granville McCafferty
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Thomas J. Meyer
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
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Pavlou A, Soulimane T, Pinakoulaki E. Evidence for the Presence of Two Conformations of the Heme a3-CuB Pocket of Cytochrome caa3 from Thermus thermophilus. J Phys Chem B 2011; 115:11455-61. [DOI: 10.1021/jp2033356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Pavlou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Sciences Department and Materials & Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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13
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Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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