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Yue J, Yang H, Liu C, Wang S, Wang L. Unraveling the pyridinic nitrogen vacancy in carbon nitride for photo-self Fenton-like purification of organic contaminants. J Colloid Interface Sci 2024; 673:475-485. [PMID: 38879989 DOI: 10.1016/j.jcis.2024.06.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
This work reports a carbon nitride with pyridinic nitrogen-vacancy (N2CV-CN), which purifies organic contaminants via an in-situ photo-self Fenton-like reaction. Experiments and calculations demonstrated that the nitrogen-vacancy induces lone-paired (LP) and symmetry-unpaired electrons, promoting the formation of low-energy LP-π hybridized orbitals and helping to overcome the pairing energy required for oxygen to accept electrons. Furthermore, the nitrogen-vacancy accelerates film and intra-particle diffusion rates of organic contaminants on N2CV-CN, creating beneficial conditions for reactive oxide species to mineralize organic contaminants. Under sunlight and atmospheric oxygen, a photo-self Fenton-like reaction involving proton-coupled electron transfer occurred on the surface of N2CV-CN. Furthermore, by integrating photocatalysis with flocculation, about 99.1 % suspended substance, 45.5 % chemical oxygen demand, and 38.4 % biological oxygen demand were reduced from polluted river-water. Constructing N2CV-CN and understanding its crucial role offer theoretical and methodological insights into the in-situ purification of contaminated water bodies.
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Affiliation(s)
- Junpeng Yue
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Hanpei Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Chen Liu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Shi Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Lina Wang
- College of Civil Engineering and Architecture, Quzhou University, Quzhou 324000, China
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2
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Rymbai LD, Klausmeyer KK, Farmer PJ. The case for an oxidopyrylium intermediate in the mechanism of quercetin dioxygenases. J Inorg Biochem 2023; 247:112343. [PMID: 37549474 DOI: 10.1016/j.jinorgbio.2023.112343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/22/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
The quercetin dioxygenases (QDOs) are unusual metalloenzymes in that they display ring-opening dioxygenase activity with several different first-row transition metal ions which do not undergo redox changes during turnover. The QDOs are also unique in that the substrate binds as an η1-flavonolate rather than the η2 -bidentate mode seen in all reported model complexes. The flavonol substrates were early examples of excited state intramolecular proton transfer (ESIPT) phenomena, in which photoexcitation causes an H-atom exchange between the adjacent hydroxyl and ketone, generating an oxidopyrylium emissive state. These oxidopyryliums undergo ring-opening dioxygenations analogous to the enzymatic reactions. Our hypothesis is that lability of the divalent metal ion may allow access to a reactive oxidopyrylium intermediate via coordination switching from the oxy to ketone position, which allows reaction with O2. In this report, we use a straight-forward methylation strategy to generate a panel of flavonol and thioflavonol derivatives modeling several η1- and η2-coordination modes. Methylation of 3-hydroxythioflavone generates an air stable η1 hydroxopyrylium salt, which undergoes rapid ring-opening dioxygenation by deprotonation or photoexcitation. By comparison, the η1-methoxyflavonol does not react with O2 under any condition. We find that any of the studied flavonol derivatives, η1 or η2, which demonstrates ESIPT-like oxidopyrylium emissions undergo QDO-like ring-opening reactions with dioxygen. The implications of these results concerning the mechanism of QDOs and related dioxygenases is discussed.
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Affiliation(s)
- Lasien D Rymbai
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States of America
| | - Kevin K Klausmeyer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States of America
| | - Patrick J Farmer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, United States of America.
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3
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Ortega P, Gil-Guerrero S, González-Sánchez L, Sanz-Sanz C, Jambrina PG. Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates-Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid. Int J Mol Sci 2023; 24:ijms24087424. [PMID: 37108586 PMCID: PMC10138960 DOI: 10.3390/ijms24087424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O2 to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. Nevertheless, the spin-forbidden addition of O2 to uncharged ligands has also been observed in the laboratory, and the detailed mechanism of how the system circumvents the spin-forbiddenness of the reaction is still unknown. One of these examples is the cofactorless peroxidation of 2-methyl-3,4-dihydro-1-naphthol, which will be studied computationally using single and multi-reference electronic structure calculations. Our results show that the preferred mechanism is that in which O2 picks a proton from the substrate in the triplet state, and subsequently hops to the singlet state in which the product is stable. For this reaction, the formation of the radical pair is associated with a higher barrier than that associated with the intersystem crossing, even though the absence of the negative charge leads to relatively small values of the spin-orbit coupling.
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Affiliation(s)
- Pablo Ortega
- Departamento de Química-Física, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Sara Gil-Guerrero
- Departamento de Química-Física, Universidad de Salamanca, 37008 Salamanca, Spain
- CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Cristina Sanz-Sanz
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Pablo G Jambrina
- Departamento de Química-Física, Universidad de Salamanca, 37008 Salamanca, Spain
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4
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Zhang QY, Li X, Luo J, Li X, Song J, Wei D. Cofactor-Free Dioxygenases-Catalyzed Reaction Pathway via Proton-Coupled Electron Transfer. J Phys Chem B 2023; 127:95-103. [PMID: 36525303 DOI: 10.1021/acs.jpcb.2c03161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the general mechanism of the metal-free and cofactor-free oxidases and oxygenases catalyzed activation of triplet O2 is one of the most challenging questions in the field of enzymatic catalysis. Herein, we have performed Quantum Mechanics/Molecular Mechanics (QM/MM) multiscale simulations to reveal the detailed mechanism of the HOD catalyzed (i.e., 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase from Arthrobacter nitroguajacolicus Rü61a) decomposition of N-heteroaromatic compounds. The complete catalytic mechanism includes four steps: (1) proton transfer from 1-H-3-hydroxy-4-oxoquinaldine (QND) substrate to His251 residue coupled with an electron transfer from QND to triplet O2 (i.e., PCET), (2) formation of C-O bond via an open-shell singlet diradical recombination pathway, (3) ring-closure to form a bicyclic ring, and (4) dissociation of CO. The dissociation of CO is determined as the rate-limiting step, and its calculated energy barrier of 14.9 kcal/mol is consistent with the 15.5 kcal/mol barrier derived from experimental kinetic data. The mechanistic profile is not only valuable for understanding the fundamental pathway of cofactor-free oxidases and oxygenases-catalyzed reactions involving the triplet O2 activation but also discloses a new pathway that undergoes the processes of PCET and open-shell singlet transition state.
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Affiliation(s)
- Qiao-Yu Zhang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Xing Li
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong510280, China
| | - Jing Luo
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Xue Li
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials and Engineering, Henan University, Kaifeng475001, China
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Donghui Wei
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
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5
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Lushchak VI, Duszenko M, Gospodaryov DV, Garaschuk O. Oxidative Stress and Energy Metabolism in the Brain: Midlife as a Turning Point. Antioxidants (Basel) 2021; 10:1715. [PMID: 34829586 PMCID: PMC8614699 DOI: 10.3390/antiox10111715] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 01/10/2023] Open
Abstract
Neural tissue is one of the main oxygen consumers in the mammalian body, and a plentitude of metabolic as well as signaling processes within the brain is accompanied by the generation of reactive oxygen (ROS) and nitrogen (RNS) species. Besides the important signaling roles, both ROS and RNS can damage/modify the self-derived cellular components thus promoting neuroinflammation and oxidative stress. While previously, the latter processes were thought to progress linearly with age, newer data point to midlife as a critical turning point. Here, we describe (i) the main pathways leading to ROS/RNS generation within the brain, (ii) the main defense systems for their neutralization and (iii) summarize the recent literature about considerable changes in the energy/ROS homeostasis as well as activation state of the brain's immune system at midlife. Finally, we discuss the role of calorie restriction as a readily available and cost-efficient antiaging and antioxidant lifestyle intervention.
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Affiliation(s)
- Volodymyr I. Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., 76018 Ivano-Frankivsk, Ukraine; (V.I.L.); (D.V.G.)
- Department of Medical Biochemistry, I. Horbachevsky Ternopil National Medical University, 46002 Ternopil, Ukraine
- Research and Development University, 13a Shota Rustaveli Str., 76018 Ivano-Frankivsk, Ukraine
| | - Michael Duszenko
- Department of Neurophysiology, Institute of Physiology, University of Tübingen, 72074 Tübingen, Germany;
| | - Dmytro V. Gospodaryov
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., 76018 Ivano-Frankivsk, Ukraine; (V.I.L.); (D.V.G.)
| | - Olga Garaschuk
- Department of Neurophysiology, Institute of Physiology, University of Tübingen, 72074 Tübingen, Germany;
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6
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Sigmund LM, Ehlert C, Enders M, Graf J, Gryn'ova G, Greb L. Disauerstoffaktivierung und Pyrrol‐α‐Spaltung mit Calix[4]pyrrolatoaluminaten: Enzymmodell durch strukturellen Zwang. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lukas Maximilian Sigmund
- Anorganisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
| | - Christopher Ehlert
- Heidelberger Institut für Theoretische Studien (HITS gGmbH) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Deutschland
- Interdisziplinäres Zentrum für wissenschaftliches Rechnen (IWR) Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 205 69120 Heidelberg Deutschland
| | - Markus Enders
- Anorganisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
| | - Jürgen Graf
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
| | - Ganna Gryn'ova
- Heidelberger Institut für Theoretische Studien (HITS gGmbH) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Deutschland
- Interdisziplinäres Zentrum für wissenschaftliches Rechnen (IWR) Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 205 69120 Heidelberg Deutschland
| | - Lutz Greb
- Anorganisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
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7
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Sigmund LM, Ehlert C, Enders M, Graf J, Gryn'ova G, Greb L. Dioxygen Activation and Pyrrole α-Cleavage with Calix[4]pyrrolato Aluminates: Enzyme Model by Structural Constraint. Angew Chem Int Ed Engl 2021; 60:15632-15640. [PMID: 33955154 PMCID: PMC8362023 DOI: 10.1002/anie.202104916] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Indexed: 01/30/2023]
Abstract
The present work describes the reaction of triplet dioxygen with the porphyrinogenic calix[4]pyrrolato aluminates to alkylperoxido aluminates in high selectivity. Multiconfigurational quantum chemical computations disclose the mechanism for this spin‐forbidden process. Despite a negligible spin–orbit coupling constant, the intersystem crossing (ISC) is facilitated by singlet and triplet state degeneracy and spin–vibronic coupling. The formed peroxides are stable toward external substrates but undergo an unprecedented oxidative pyrrole α‐cleavage by ligand aromatization/dearomatization‐initiated O−O σ‐bond scission. A detailed comparison of the calix[4]pyrrolato aluminates with dioxygen‐related enzymology provides insights into the ISC of metal‐ or cofactor‐free enzymes. It substantiates the importance of structural constraint and element–ligand cooperativity for the functions of aerobic life.
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Affiliation(s)
- Lukas Maximilian Sigmund
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Christopher Ehlert
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 205, 69120, Heidelberg, Germany
| | - Markus Enders
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Jürgen Graf
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Ganna Gryn'ova
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 205, 69120, Heidelberg, Germany
| | - Lutz Greb
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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8
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Ortega P, Gil-Guerrero S, Veselinova A, Zanchet A, González-Sánchez L, Jambrina PG, Sanz-Sanz C. Multi- and single-reference methods for the analysis of multi-state peroxidation of enolates. J Chem Phys 2021; 154:144303. [PMID: 33858147 DOI: 10.1063/5.0046906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In spite of being spin-forbidden, some enzymes are capable of catalyzing the incorporation of O2(Σg-3) to organic substrates without needing any cofactor. It has been established that the process followed by these enzymes starts with the deprotonation of the substrate forming an enolate. In a second stage, the peroxidation of the enolate formation occurs, a process in which the system changes its spin multiplicity from a triplet state to a singlet state. In this article, we study the addition of O2 to enolates using state-of-the-art multi-reference and single-reference methods. Our results confirm that intersystem crossing is promoted by stabilization of the singlet state along the reaction path. When multi-reference methods are used, large active spaces are required, and in this situation, semistochastic heat-bath configuration interaction emerges as a powerful method to study these multi-configurational systems and is in good agreement with PNO-LCCSD(T) when the system is well-represented by a single-configuration.
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Affiliation(s)
- P Ortega
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - S Gil-Guerrero
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - A Veselinova
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - A Zanchet
- Instituto de Física Fundamental (CSIC), Madrid 28006, Spain
| | - L González-Sánchez
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - P G Jambrina
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - C Sanz-Sanz
- Departamento de Química Física Aplicada. Universidad Autónoma de Madrid, Madrid 28049, Spain
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9
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Ortega P, Zanchet A, Sanz-Sanz C, Gómez-Carrasco S, González-Sánchez L, Jambrina PG. DpgC-Catalyzed Peroxidation of 3,5-Dihydroxyphenylacetyl-CoA (DPA-CoA): Insights into the Spin-Forbidden Transition and Charge Transfer Mechanisms*. Chemistry 2020; 27:1700-1712. [PMID: 32975323 DOI: 10.1002/chem.202002993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Indexed: 11/06/2022]
Abstract
Despite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O2 at room temperature because O2 is a diradical whereas most organic molecules are closed-shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non-relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet-singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical-pair between dioxygen and enolate is enough to promote spin-forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.
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Affiliation(s)
- Pablo Ortega
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
| | - Alexandre Zanchet
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain.,Instituto de Física Fundamental (CSIC), Madrid, 28006, Spain
| | - Cristina Sanz-Sanz
- Departamento de Química Física Aplicada, University Autónoma de Madrid, Madrid, 28049, Spain
| | | | | | - Pablo G Jambrina
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
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