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Alhimidi SRH, Al-Ibadi MAM, Jabbar ML. QTAIM analysis of the bonding in anionic group 6 carbonyl selenide clusters: [Se 2M 3(CO) 10] 2- (M=Cr, Mo, W). J Mol Model 2024; 30:230. [PMID: 38922351 DOI: 10.1007/s00894-024-06031-x] [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: 05/29/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
CONTEXT This research aims to offer a deeper understanding of the bonding interactions between M-Se and M-CO and how these interactions change across the group 6 transition metal series: [Se2M3(CO)10]2- (M = Cr, Mo, W). It also seeks to explore the impact of carbonyl groups on M-M interactions within the clusters. Seven criteria, which are based on QTAIM properties, have been considered and compared with the corresponding criteria in other transition metal clusters. The results confirm that no such bond critical points or bond baths occur between transition metals, which instead have 5c-7e bonding interactions delocalized over their five-membered M3(μ-Se)2 ring, as evidenced by the non-negligible nonbonding delocalization indices. The topological properties of three bond clusters, Cr-Se, Mo-Se, and W-Se, resemble those of "intermediate closed shell characters," which combine covalent and electrostatic properties. Source function calculations indicated that the bonded Se atom contributed the most to each Cr-Se and Mo-Se bcp. The OCO atoms and nonbonded Se atoms also contributed to some extent. However, metal atoms act as sinks rather than as sources of electron density. In contrast, the majority of the metal atoms, both bonded and nonbonded, contribute to Cr-W bcps. Analysis of the delocalization indices δ(M…O) in the three clusters indicates that CO significantly contributes to Cr π-back donation in cluster 1. In contrast, no π-back donation occurs from CO to Mo or W in clusters 2 or 3, respectively. METHODS The B3P86 hybrid functional was used for computations in the Gaussian 09 software. The LanL2DZ basis set was employed for Cr, Mo, and W, while the 6-31G (d, p) basis set was used for C, O, and Se atoms. We performed QTAIM analysis using the AIM2000 and Multiwfn packages, incorporating B3P86/WTBS for Cr, Mo, and W atoms. The 6-311++G(3df,3pd) basis set was used for C, O, and Se atoms. Additionally, we utilized the ELF and SF.
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Affiliation(s)
| | - Muhsen Abood Muhsen Al-Ibadi
- Department of Chemistry, College of Science, University of Kufa, Najaf, Iraq.
- Department of Medical Techniques Analysis, College of Medical Techniques, The Islamic University, Najaf, Iraq.
| | - Mohammed L Jabbar
- Department of Physics, College of Science, Thi-Qar University, Nasiriyah, Iraq
- Medical physics Department, Hilla University College, Babylon, Iraq
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Varadwaj PR. Tetrel Bonding in Anion Recognition: A First Principles Investigation. Molecules 2022; 27:molecules27238449. [PMID: 36500544 PMCID: PMC9738195 DOI: 10.3390/molecules27238449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Twenty-five molecule-anion complex systems [I4Tt···X-] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I4Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I4C···X-] series and [I4Tt···X-] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from -3.0 to -112.2 kcal mol-1. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I4Tt···X-] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule-anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan; or
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
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Theoretical Analysis of Polynuclear Zinc Complexes Isolobally Related to Hydrocarbons. Int J Mol Sci 2022; 23:ijms232314858. [PMID: 36499186 PMCID: PMC9736195 DOI: 10.3390/ijms232314858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Based on the isolobal analogy of ZnCp (Cp = η5-C5H5) and ZnR (R = alkyl or aryl group) fragments with hydrogen atom and fragment [Zn(CO)2] with a CH2 carbene, the following complexes [(ZnCp)2{µ-Zn(CO)2}], 1, [(ZnPh)2{µ-Zn(CO)2}], 2, [(ZnPh){µ-Zn(CO)2}(ZnCp)], 3, [(ZnCp)2{µ-Zn2(CO)4}], 4, [(ZnPh)2{µ-Zn2(CO)4}], 5, [(ZnPh){µ-Zn(CO)2}2(ZnCp)], 6, [Zn3(CO)6], 7 and [Zn5(CO)10], 8, were built. These polynuclear zinc compounds are isolobally related to simple hydrocarbons (methane, ethane, cyclopropane and cyclopentane). They have been studied by density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) to compare the nature and topology of the Zn-Zn bond with previous studies. There are bond critical points (BCPs) between each pair of adjacent Zn centers in complexes 1-8 with Zn-Zn distances within the range 2.37-2.50 Å. The nature of the Zn-Zn bond in these complexes can be described as polar rather than pure covalent bonds. Although in a subtle way, the presence of different ligands and zinc oxidation states introduces asymmetry and polarity in the Zn-Zn bond. In addition, the Zn-Zn bond is delocalized in nature in complex 7 whereas it can be described as a localized bond for the remaining zinc complexes here studied.
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Attia AS, Alfallous KA, El-Shahat M. A novel quinoxalinedione-bicapped tri-ruthenium carbonyl cluster [Ru3(μ-H)2(CO)6(μ3-HDCQX)2]: synthesis, characterization, anticancer activity and theoretical investigation of Ru–Ru and Ru–Ligand bonding interactions. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cleaves PA, Ayres AJ, Vondung L, Stewart JC, Cobb PJ, Wooles AJ, Liddle ST. Bridged and Unbridged Nickel–Nickel Bonds Supported by Cyclopentadienyl and Phosphine Ligand Sets. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Peter A. Cleaves
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Alexander J. Ayres
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Lisa Vondung
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - John C. Stewart
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Philip J. Cobb
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Ashley J. Wooles
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Stephen T. Liddle
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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Van der Maelen JF, Ceroni M, Ruiz J. The X-ray constrained wavefunction of the [Mn(CO) 4{(C 6H 5) 2P-S-C(Br 2)-P(C 6H 5) 2}]Br complex: a theoretical and experimental study of dihalogen bonds and other noncovalent interactions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:802-814. [PMID: 33017314 DOI: 10.1107/s2052520620009889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
The synthesis and X-ray structure determination of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex (1) are described. The C-Br...Br dihalogen bond present in 1 has been characterized by means of topological studies of the electron density. Both the quantum theory of atoms in molecules and the electron localization function approaches have been applied to several theoretically calculated wavefunctions as well as to an X-ray constrained wavefunction. In addition, a number of theoretical techniques, such as the source function, the reduced density gradient method and the interacting quantum atoms approach, among others, have been used to analyse the dihalogen bond as well as several intramolecular interactions of the type C-H...Br-C which have also been detected in 1. The results show clearly that while bonding in the latter interactions are dominated by electrostatic components, the former has a high degree of covalency.
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Affiliation(s)
- Juan F Van der Maelen
- Dept. Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
| | - Mario Ceroni
- Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Javier Ruiz
- Dept. Química Orgánica e Inorgánica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
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Joy J, Danovich D, Kaupp M, Shaik S. Covalent vs Charge-Shift Nature of the Metal-Metal Bond in Transition Metal Complexes: A Unified Understanding. J Am Chem Soc 2020; 142:12277-12287. [PMID: 32571021 DOI: 10.1021/jacs.0c03957] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present here a general conceptualization of the nature of metal-metal (M-M) bonding in transition-metal (TM) complexes across the periods of TM elements, by use of ab initio valence-bond theory. The calculations reveal a dual-trend: For M-M bonds in groups 7 and 9, the 3d-series forms charge-shift bonds (CSB), while upon moving down to the 5d-series, the bonds become gradually covalent. In contrast, M-M bonds of metals having filled d-orbitals (groups 11 and 12) behave oppositely; initially the M-M bond is covalent, but upon moving down the Periodic Table, the CSB character increases. These trends originate in the radial-distribution-functions of the atomic orbitals, which determine the compactness of the valence-orbitals vis-à-vis the filled semicore orbitals. Key factors that gauge this compactness are the presence/absence of a radial-node in the valence-orbital and relativistic contraction/expansion of the valence/semicore orbitals. Whenever these orbital-types are spatially coincident, the covalent bond-pairing is weakened by Pauli-repulsion with the semicore electrons, and CSB takes over. Thus, for groups 3-10, which possess (n - 1)s2(n - 1)p6 semicores, this spatial-coincidence is maximal at the 3d-transition-metals which consequently form charge-shift M-M bonds. However, in groups 11 and 12, the relativistic effects maximize spatial-coincidence in the third series, wherein the 5d10 core approaches the valence 6s orbital, and the respective Pauli repulsion generates M-M bonds with CSB character. These considerations create a generalized paradigm for M-M bonding in the transition-elements periods, and Pauli repulsion emerges as the factor that unifies CSB over the periods of main-group and transition elements.
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Affiliation(s)
- Jyothish Joy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - David Danovich
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie - Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Two octahedral σ-borane metal (MnI and RuII) complexes containing a tripod κ3N,H,H-ligand: Synthesis, structural characterization, and theoretical topological study of the charge density. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Van der Maelen JF. Topological Analysis of the Electron Density in the Carbonyl Complexes M(CO)8 (M = Ca, Sr, Ba). Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan F. Van der Maelen
- Departamento de Química Física y Analítica, Universidad de Oviedo, E-33006 Oviedo, Spain
- Centro de Investigación en Nanomateriales y Nanotecnología (CINN-CSIC), E-33940 El Entrego, Spain
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Dehghani N, Ghalami-Choobar B, Arabieh M, Dezhampanah H. Theoretical insight to the complexation of some transition metals with cryptand. Struct Chem 2019. [DOI: 10.1007/s11224-018-1268-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ruiz J, Sol D, García L, Mateo MA, Vivanco M, Van der Maelen JF. Generation and Tunable Cyclization of Formamidinate Ligands in Carbonyl Complexes of Mn(I): An Experimental and Theoretical Study. Organometallics 2019. [DOI: 10.1021/acs.organomet.8b00898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Shedding light on the electronic structure of [Ru(η6-C16H16)(NH3)3]2+ complex: a computational insight. J Mol Model 2019; 25:11. [DOI: 10.1007/s00894-018-3882-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/25/2018] [Indexed: 01/19/2023]
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Menacer R, May A, Belkhiri L, Mousser A. Electronic structure and bonding of the dinuclear metal M 2(CO) 10 decacarbonyls: applications of natural orbitals for chemical valence. J Mol Model 2017; 23:358. [PMID: 29185066 DOI: 10.1007/s00894-017-3523-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
The nature of the chemical metal-metal bond in M2(CO)10 (M = Mn, Re, Tc) dinuclear decacarbonyls complexes was investigated for the first time using the natural orbital chemical valence (NOCV) approach combined with the extended transition state (ETS) for energy decomposition analysis (EDA). The optimized geometries carried out at different levels of theory BP86, BLYP, BLYPD and BP86D, showed that the latter method, i.e., BP86D, led to the best agreement with X-ray experimental measurements. The BP86D/TZP results revealed that the computed covalent contribution to the metal-metal bond are 60.5%, 54.1% and 52.0% for Mn-Mn, Re-Re and Tc-Tc, respectively. The computed total interaction energies resulting from attractive terms (ΔE orb and ΔE eles), correspond well to experimental predictions, based on bond lengths and energy interaction analysis for the studied complexes.
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Affiliation(s)
- Rafik Menacer
- Laboratoire de Physicochimie Analytique et Cristallochimie des Matériaux Organométalliques et Biomoléculaires LPACMOB, Département de Chimie, Université Frères Mentouri, 25017, Constantine, Algeria.,Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques CRAPC, BP 384, Zone Industrielle, Bou-ismail, Tipaza, RP 42004, Algeria
| | - Abdelghani May
- Département de Chimie, Université Frères Mentouri, Route de Ain El Bey, 25017, Constantine, Algeria
| | - Lotfi Belkhiri
- URCHEMS, Département de Chimie, Université Frères Mentouri, Route de Ain El Bey, 25017, Constantine, Algeria.
| | - Abdelhamid Mousser
- Laboratoire de Physicochimie Analytique et Cristallochimie des Matériaux Organométalliques et Biomoléculaires LPACMOB, Département de Chimie, Université Frères Mentouri, 25017, Constantine, Algeria
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Tsipis AC. RETRACTED: DFT challenge of intermetallic interactions: From metallophilicity and metallaromaticity to sextuple bonding. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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16
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Lepetit C, Fau P, Fajerwerg K, Kahn ML, Silvi B. Topological analysis of the metal-metal bond: A tutorial review. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Brugos J, Cabeza JA, García-Álvarez P, Pérez-Carreño E, Van der Maelen JF. Octahedral manganese(i) and ruthenium(ii) complexes containing 2-(methylamido)pyridine–borane as a tripod κ3N,H,H-ligand. Dalton Trans 2017; 46:4009-4017. [DOI: 10.1039/c7dt00378a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The borane adduct of the 2-(methylamido)pyridine anion has been incorporated into octahedral metal (Mn, Ru) complexes and their bonding has been studied by theoretical methods (DFT, QTAIM).
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Affiliation(s)
- Javier Brugos
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Departamento de Química Orgánica e Inorgánica-IUQOEM
- Universidad de Oviedo-CSIC
- 33071 Oviedo
- Spain
| | - Javier A. Cabeza
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Departamento de Química Orgánica e Inorgánica-IUQOEM
- Universidad de Oviedo-CSIC
- 33071 Oviedo
- Spain
| | - Pablo García-Álvarez
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Departamento de Química Orgánica e Inorgánica-IUQOEM
- Universidad de Oviedo-CSIC
- 33071 Oviedo
- Spain
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Brugos J, Cabeza JA, García-Álvarez P, Kennedy AR, Pérez-Carreño E, Van der Maelen JF. 2-(Methylamido)pyridine–Borane: A Tripod κ3-N,H,H Ligand in Trigonal Bipyramidal Rhodium(I) and Iridium(I) Complexes with an Asymmetric Coordination of Its BH3 Group. Inorg Chem 2016; 55:8905-12. [DOI: 10.1021/acs.inorgchem.6b01427] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javier Brugos
- Departamento de Química Orgánica e Inorgánica-IUQOEM,
Centro de Innovación en Química Avanzada ORFEO-CINQA, Universidad de Oviedo-CSIC, E-33071 Oviedo, Spain
| | - Javier A. Cabeza
- Departamento de Química Orgánica e Inorgánica-IUQOEM,
Centro de Innovación en Química Avanzada ORFEO-CINQA, Universidad de Oviedo-CSIC, E-33071 Oviedo, Spain
| | - Pablo García-Álvarez
- Departamento de Química Orgánica e Inorgánica-IUQOEM,
Centro de Innovación en Química Avanzada ORFEO-CINQA, Universidad de Oviedo-CSIC, E-33071 Oviedo, Spain
| | - Alan R. Kennedy
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, U. K
| | - Enrique Pérez-Carreño
- Departamento de Química Física y Analítica, Universidad de Oviedo, E-33071 Oviedo, Spain
| | - Juan F. Van der Maelen
- Departamento de Química Física y Analítica, Universidad de Oviedo, E-33071 Oviedo, Spain
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