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Savastano M. Ye Olde supramolecular chemistry, its modern rebranding and overarching trends in chemistry. Dalton Trans 2024; 53:1373-1392. [PMID: 38180341 DOI: 10.1039/d3dt03686c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
We can describe current contingency of supramolecular chemistry as "post-halogen bonding", with clear reference to the success of the σ-hole model and the halogen bond concepts. This phase is characterized by a strong push towards a new nomenclature for non-covalent interactions, a group-by-group one focusing on the electrophile. As such nomenclature increasingly meets IUPAC endorsement, its proposers report resistances to such ideas, especially in the inorganic and coordination chemistry communities. The whole issue has been generating considerable debate in the last decade. Herein we fully embrace such discussion in the hope of involving a larger share of the relevant communities. Alternative descriptions are here reevaluated, novel views reconnected with older ones, and it is ultimately questioned whether the introduction of such a nomenclature and its subtending ideas would be beneficial. The themes of appreciation of general trends in chemistry, of counterintuitive interactions, of positioning of novel nomenclature with respect to existing ones, and of the extension of group-by-group naming from main block to d-block elements - as key and currently unresolved issues - are discussed. Equivalent, alternative and arguably more comprehensive descriptions are tentatively given, in the hope to overcome controversies together in the pursuit of higher rewards: a comprehensive shared view of supramolecular forces and a common language to express it.
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Affiliation(s)
- Matteo Savastano
- Department of Human Sciences for the Promotion of Quality of Life, University San Raffaele Roma, via di Val Cannuta 247, 00166, Rome, Italy.
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2
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Yan J, Zeng Y, Meng L, Li X, Zhang X. Gold(III) derivatives as the noncovalent interaction donors: theoretical study of the π-hole regium bonds. Phys Chem Chem Phys 2023; 25:29155-29164. [PMID: 37870082 DOI: 10.1039/d3cp04354a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Except for the well-known σ-hole regium bonds formed by metal nanoparticles and M(I) (M = Cu, Ag, and Au) derivatives, the existence of π-hole regions located above and below the Au atom in gold(III) derivatives suggests that gold(III) also functions as an efficient electrophilic site. In this study, a comprehensive analysis was conducted on the electrophilicity of trichloro-(p-toluonitrilo-N)-gold(III) derivatives AuL3(NCC6H4X) (L = Cl, Br, CN; X = NH2, CH3, CF3, NC, and CN) and the nature of π-hole regium bonds in the AuL3(NCC6H4X)⋯LB (LB = NH3, N(NH3)3, CH2O, C2H2, C2H4, C6H6) and (AuCl3(NCC6H4Y))n (Y = Cl, CN, NC, NO2; n = 2, 3)) complexes. The characteristics of the π-hole regium bonds were studied with respect to the influence of ligands and substituents, the strength of intermolecular interactions between Au(III) derivatives and Lewis bases, and those in the polymers. In the case of the AuL3(NCC6H4X)⋯NH3 complexes, the strength of the regium bonds increases gradually in the order of L = Cl < Br < CN and X = NH2 < CH3 < CF3 ≈ NC < CN. The ligands (L) attached to the Au atom exert a significant effect on the strength of the π-hole regium bonds in comparison to the substituents (X) on the benzene ring. The regium bonds are primarily dominated by electrostatic interaction, accompanied by moderate contribution from polarization. Linear relationships were identified between the electrostatic energies and the local most positive potentials over the Au atom, as well as between the polarization energies and the amount of charge transfer. Most of the π-hole regium bonds in the AuL3(NCC6H4X)⋯LB complexes exhibit the characters of closed shell noncovalent interactions. In the polymers (AuCl3(NCC6H4Y))n, weak face-to-face π-π stacking interactions are also present, in addition to regium bonds. The trimers displayed a slightly negative cooperativity in comparison to the dimers.
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Affiliation(s)
- Jiajing Yan
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China.
| | - Yanli Zeng
- Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Lingpeng Meng
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China.
| | - Xiaoyan Li
- Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China.
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Das A, Arunan E. Unified classification of non-covalent bonds formed by main group elements: a bridge to chemical bonding. Phys Chem Chem Phys 2023; 25:22583-22594. [PMID: 37435670 DOI: 10.1039/d3cp00370a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Using correlation plots of binding energy and electron density at the bond critical point, we investigated the nature of intermolecular non-covalent bonds (D-X⋯A, where D = O/S/F/Cl/Br/H, mostly, X = main group elements (except noble gases), A = H2O, NH3, H2S, PH3, HCHO, C2H4, HCN, CO, CH3OH, and CH3OCH3). The binding energies were calculated at the MP2 level of theory, followed by Atoms in Molecules (AIM) analysis of the ab initio wave functions to obtain the electron density at the bond critical point (BCP). For each non-covalent bond, the slopes of the binding energy versus electron density plot have been determined. Based on their slopes, non-covalent bonds are classified as non-covalent bond closed-shell (NCB-C) or non-covalent bond shared-shell (NCB-S). Intriguingly, extrapolating the slopes of the NCB-C and NCB-S cases leads to intramolecular "ionic" and "covalent" bonding regimes, establishing a link between such intermolecular non-covalent and intramolecular chemical bonds. With this new classification, hydrogen bonds and other non-covalent bonds formed by a main-group atom in a covalent molecule are classified as NCB-S. Atoms found in ionic molecules generally form NCB-C type bonds, with the exception of carbon which also forms NCB-C type bonds. Molecules with a tetravalent carbon do behave like ions in ionic molecules such as NaCl and interact with other molecules through NCB-C type bonds. As with the chemical bonds, there are some non-covalent bonds that are intermediate cases.
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Affiliation(s)
- Arijit Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Elangannan Arunan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
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4
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Song J, Wang M, Xu X, Shao Q, Zhao Y, Zhang G, Sun N. Charge-Shift Bonding Propensity in Halogen-Bonded BXY (B Is a Small Lewis Base H 2O or NH 3; X and Y Are Halogen Atoms) Complexes: An NBO/NRT/AIM Investigation. Molecules 2023; 28:6212. [PMID: 37687041 PMCID: PMC10489069 DOI: 10.3390/molecules28176212] [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: 07/26/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Charge-shift (CS) bonding is a new bonding paradigm in the field of chemical bonds. Our recent study has revealed that certain Cu/Ag/Au-bonds display both CS bonding and ω-bonding characters. In this investigation, we extend our study to halogen bonding. Our focus is on scrutinizing the CS bonding in halogen-bonded BXY (B is a small Lewis base H2O or NH3; X and Y are halogen atoms) complexes by using natural bond orbital (NBO) analysis, natural resonance theory (NRT), and atoms in molecules (AIM) methods. The primary objective is to establish a connection between halogen bonding (B-X) in BXY and CS bonding in free XY (di-halogens). The calculations indicate that the studied BXY can be classified into two types. One type with a weak halogen bond shows closed-shell interaction. The other type with a stronger B-X interaction exhibits both CS bonding and ω-bonding characters (as seen in NH3ClF, NH3BrF, and NH3IF). Another interesting finding is a novel propensity that the CS bonding in free XY tends to carry over the halogen bonding in BXY, and the same propensity is found in Cu/Ag/Au ω-bonded species. The present study may offer an approach to probe CS bonding in many more 3c/4e ω-bonded molecules.
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Affiliation(s)
- Junjie Song
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Mengyang Wang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiaocheng Xu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qinghao Shao
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Ying Zhao
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Guiqiu Zhang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Nan Sun
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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5
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Khera M, Anchal, Goel N. Ligand and Substituent Effect on Regium-π Bonding in Cu and Ag π-Conjugated Complexes: A Density Functional Study. J Phys Chem A 2023; 127:6953-6961. [PMID: 37558247 DOI: 10.1021/acs.jpca.3c04110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Density functional theory investigation of regium (Rg)-π bonding using the RgL-X model system, where Rg = Cu and Ag; L = CN, NO2, and OH; X = π-conjugated system (benzene, cyanobenzene, benzoic acid, pyridine, 2-methoxy aniline, 1,4-dimethoxy benzene, and cyclophane), has been performed. Conclusive evidence of the Rg-π bond has been provided by analysis of molecular electrostatic potential surfaces, Rg-π bond length, interaction energy (ΔE), second-order perturbation energy (E2), charge transfer (Δq), quantum theory of atom in molecules, and noncovalent interaction plots for 42 structural arrangements with varying ligands and the substituted aromatic ring. The Rg-π bond length in the optimized model systems varies from 2.03 to 2.12 Å in Cu complexes (1-21) and from 2.26 to 2.38 Å in Ag complexes (22-42) at the PBE0-D3 functional. While the ligand (L) attached to the Rg metal has a bargaining effect on the strength of the Rg-π bond (in the order of -OH > -CN = -NO2), the π-conjugated systems have a diminutive effect. Two X-ray crystal structures (CUCSOI and AHIDQU) having the Rg-π bond, accessed from Cambridge Crystallographic Data Centre (CCDC), are discussed here to signify the influence of Rg-π bonding on the crystal structure.
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Affiliation(s)
- Mayank Khera
- Computational and Theoretical Chemistry Group, Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Anchal
- Computational and Theoretical Chemistry Group, Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Neetu Goel
- Computational and Theoretical Chemistry Group, Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
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6
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Song J, Fu L, Li H, Su Y, Wang Q, Zhang G, Wang J. Equivalent and Complement of the ω-Bonding Model and Charge-Shift Bonding Model: A Natural Bond Orbital/Natural Resonance Theory/Atoms in Molecules Investigation via Cu/Ag/Au Bonding in BMX (B = H 2O, H 2S, NH 3, and PH 3; M = Cu, Ag, and Au; and X = F, Cl, Br, and I). J Phys Chem Lett 2023:5226-5233. [PMID: 37261929 DOI: 10.1021/acs.jpclett.3c01217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Chemical bonding is the language of logic for chemists. Two new resonance bonding models, ω-bonding and charge-shift (CS) bonding, are gaining popularity among chemists. This study investigated the Cu/Ag/Au bonding in BMX (B = H2O, H2S, NH3, and PH3; M = Cu, Ag, and Au; and X = F, Cl, Br, and I) complexes using natural bond orbital (NBO) analysis, natural resonance theory (NRT), and atoms in molecules (AIM) method. The main aim is to reveal the relation between ω-bonding model and CS bonding model via Cu/Ag/Au bonding. Our studies demonstrate that the Cu/Ag/Au bonds exhibit the characteristics of both ω-bonding and CS bonding. Further studies found that ω-bonding and CS bonding models are equivalent and complement each other in understanding the studied Cu/Ag/Au bonding. Another interesting finding is the implication of the omega symbol in the ω-bonding model. These findings could help to promote the communication and CS bonding understanding of many more similar ω-bonded complexes.
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Affiliation(s)
- Junjie Song
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China
| | - Lei Fu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Hong Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China
| | - Yue Su
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Qiong Wang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Guiqiu Zhang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Jin Wang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
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7
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Andreo L, Gomila RM, Priola E, Giordana A, Pantaleone S, Diana E, Mahmoudi G, Frontera A. Anion···Anion [AuI 4] -···[AuI 2] - Complex Trapped in the Solid State by Tetramethylammonium Cations. CRYSTAL GROWTH & DESIGN 2022; 22:6539-6544. [PMID: 36345385 PMCID: PMC9635596 DOI: 10.1021/acs.cgd.2c00749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/01/2022] [Indexed: 05/24/2023]
Abstract
A discrete π-hole···σ-hole dimer is synthesized and X-ray characterized. It presents a perfect thumbtack geometry where the σ-hole of the linear [AuI2]- anion points to the π-hole located above the central Au-atom of the [AuI4]- anion. Such discrete π-hole···σ-hole dimers are unprecedented in literature, since all mixed-valence gold(I/III) iodide compounds reported to date form infinite ···([AuI4]-···[AuI2]-) n ·· chains in the solid state. If an excess of iodine is used for the synthesis, triiodide [I3]- ions are partially incorporated into the [AuI2]- sites, forming infinite chains. The nature of the anion···anion interaction has been studied considering two possibilities: (i) a π-hole coinage bond or (ii) σ-hole halogen bond using high-level density functional theory calculations, the quantum theory of atoms in molecules, and the noncovalent interaction plot index.
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Affiliation(s)
- Luca Andreo
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Emanuele Priola
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Alessia Giordana
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Stefano Pantaleone
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Eliano Diana
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh 83111-55181, Iran
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
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8
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de Las Nieves Piña M, Mooibroek TJ, Frontera A, Bauzá A. Importance of Cu and Ag regium-π bonds in supramolecular chemistry and biology: a combined crystallographic and ab initio study. Phys Chem Chem Phys 2022; 24:24983-24991. [PMID: 36214369 DOI: 10.1039/d2cp03874a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Identifying and characterizing new binding events between electron donor and acceptor counterparts represents a crucial step to complete the molecular recognition and aggregation picture, which is key to chemistry and biology. In this study we interrogated both the PDB (Protein Data Bank) and CSD (Cambridge Structural Database) for the presence of Cu and Ag regium-π (Rg-π) bonds (an attractive noncovalent force between elements from group 11 and π-systems). Concretely, we found evidence of the plausible biological role of the interaction in protein-DNA systems, bacterial Ag extrusion processes and Heme group redox functionality. Furthermore, we also highlighted the implications of Rg-π bonds in the crystal packing of two host-guest systems, where this interaction is key for the binding and recognition of small organic molecules as well as for the encapsulation of organometallic complexes. Theoretical models were used to analyse the strength of the interaction (RI-MP2/def2-TZVP level of theory) together with QTAIM (Quantum Theory of Atoms in Molecules), NBO (Natural Bonding Orbital) and NCIplot (Non Covalent Interactions plot) analyses, which further assisted in the characterization of the regium-π interactions described herein. We expect the results from this study will be useful to attract the attention of chemical biologists as well as to expand the potential of the interaction to the supramolecular chemistry and crystal engineering communities.
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Affiliation(s)
- María de Las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Ctra de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
| | - Tiddo J Mooibroek
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park A, 904, E1.26, 1098 XH Amsterdam, The Netherlands.
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Ctra de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Ctra de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
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Nag T, Ovens JS, Bryce DL. 77Se and 125Te solid-state NMR and X-ray diffraction structural study of chalcogen-bonded 3,4-dicyano-1,2,5-chalcogenodiazole cocrystals. Acta Crystallogr C Struct Chem 2022; 78:517-523. [PMID: 36196784 DOI: 10.1107/s2053229622008518] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Three novel chalcogen-bonded cocrystals featuring 3,4-dicyano-1,2,5-selenodiazole (C4N4Se) or 3,4-dicyano-1,2,5-tellurodiazole (C4N4Te) as chalcogen-bond donors and hydroquinone (C6H6O2), tetraphenylphosphonium chloride (C24H20P+·Cl-) or tetraethylphosphonium chloride (C8H20P+·Cl-) as chalcogen-bond acceptors have been prepared and characterized by single-crystal X-ray diffraction (XRD), powder X-ray diffraction and 77Se/125Te magic-angle spinning solid-state NMR spectroscopy. The single-crystal XRD results show that the chalcogenodiazole molecules interact with the electron donors through two σ-holes on each of the chalcogen atoms, which results in highly directional and moderately strong chalcogen bonds. Powder XRD confirms that the crystalline phases are preserved upon moderate grinding of the samples for solid-state NMR experiments. Measurement of 77Se and 125Te chemical shift tensors via magic-angle spinning solid-state NMR spectroscopy confirms the number of magnetically unique chalcogen sites in each asymmetric unit and reveals the impact of chalcogen-bond formation on the local electronic structure. These NMR data are further assessed in the context of analogous data for a wider range of crystalline chalcogen-bonded systems.
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Affiliation(s)
- Tamali Nag
- Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5, Canada
| | - Jeffrey S Ovens
- Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5, Canada
| | - David L Bryce
- Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5, Canada
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10
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Abstract
Osme bonds have been recently defined as the attractive interaction between an element of group 8 acting as an electrophile and any atom or group of atoms acting as a nucleophile. To date, the known examples of osme bonds in X-ray structures involve mostly the highly reactive OsO4 and amines and amine oxides. In this work, evidence supporting the existence of osme bonds in osmium(VI) derivatives is reported. In particular, nitrido-osmium(VI) complexes that present square-pyramidal geometries are well disposed to participate in osme bonds opposite to the Os≡N bond. By using a combination of experimental and theoretical results, the existence and importance of this new class of σ-hole interactions is demonstrated in the solid state of several nitrido-osmium(VI) derivatives.
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11
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12
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Peluso P, Mamane V. Stereoselective Processes Based on σ-Hole Interactions. Molecules 2022; 27:molecules27144625. [PMID: 35889497 PMCID: PMC9323542 DOI: 10.3390/molecules27144625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/01/2023] Open
Abstract
The σ-hole interaction represents a noncovalent interaction between atoms with σ-hole(s) on their surface (such as halogens and chalcogens) and negative sites. Over the last decade, significant developments have emerged in applications where the σ-hole interaction was demonstrated to play a key role in the control over chirality. The aim of this review is to give a comprehensive overview of the current advancements in the use of σ-hole interactions in stereoselective processes, such as formation of chiral supramolecular assemblies, separation of enantiomers, enantioselective complexation and asymmetric catalysis.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede Secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy
- Correspondence: (P.P.); (V.M.)
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR CNRS 7177, Equipe LASYROC, 1 Rue Blaise Pascal, 67008 Strasbourg, France
- Correspondence: (P.P.); (V.M.)
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13
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Bauzá A, Frontera A. Noncovalent Interactions Involving Group 6 in Biological Systems: The Case of Molybdopterin and Tungstopterin Cofactors. Chemistry 2022; 28:e202201660. [PMID: 35670547 PMCID: PMC9545818 DOI: 10.1002/chem.202201660] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 12/14/2022]
Abstract
In this study we propose to coin the term Wolfium bond (WfB) to refer to a net attractive force (noncovalent interaction) between any element of group 6 and electron donor atoms (neutral molecules or anions) and to differentiate it from a coordination bond (metal‐ligand interaction). We provide evidence of the existence of this interaction by inspecting the X‐ray crystal structure of proteins containing Molybdopterin and Tungstopterin cofactors from the Protein Data Bank (PDB). The plausible biological role of the interaction as well as its physical nature (antibonding Wf‐Ligand orbital involved) are also analyzed by means of ab initio calculations (RI‐MP2/def2‐TZVP level of theory), Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Noncovalent Interactions plot (NCIplot) analyses.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
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14
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Ward JS, Gomila RM, Frontera A, Rissanen K. Iodine(i) complexes incorporating sterically bulky 2-substituted pyridines. RSC Adv 2022; 12:8674-8682. [PMID: 35424827 PMCID: PMC8984907 DOI: 10.1039/d2ra01390h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 11/21/2022] Open
Abstract
The silver(i) and iodine(i) complexes of the 2-substituted pyridines 2-(diphenylmethyl)pyridine (1) and 2-(1,1-diphenylethyl)pyridine (2), along with their potential protonated side products, were synthesised to investigate the steric limitations of iodine(i) complex formation. The complexes were characterised by 1H and 1H–15N HMBC NMR, X-ray crystallography, and DFT calculations. The solid-state structures for the silver(i) and iodine(i) complexes were extensively compared to the literature and analysed by DFT to examine the influence of the sterically bulky pyridines and their anions. The silver(i) and iodine(i) complexes of two sterically bulky 2-substituted pyridines, along with their potential protonated side products, were synthesised to investigate the steric limitations of iodine(i) ion formation.![]()
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Affiliation(s)
- Jas S Ward
- University of Jyvaskyla, Department of Chemistry Jyväskylä 40014 Finland
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears Crts de Valldemossa km 7.6 07122 Palma de Mallorca Baleares Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears Crts de Valldemossa km 7.6 07122 Palma de Mallorca Baleares Spain
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry Jyväskylä 40014 Finland
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15
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Piña MDLN, Burguera S, Buils J, Crespí MÀ, Morales JE, Pons J, Bauzá A, Frontera A. Substituent effects in π-hole regium bonding interactions between Au(p-X-Py)2 complexes and Lewis bases: an ab initio study. Chemphyschem 2022; 23:e202200010. [PMID: 35191571 DOI: 10.1002/cphc.202200010] [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: 01/06/2022] [Revised: 02/09/2022] [Indexed: 11/10/2022]
Abstract
For the first time, long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated. The Au(I) atom is coordinated to two para -substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of "atoms-in-molecules" has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide some experimental support to the existence of regium π-hole bonding in [Au(Py) 2 ] + derivatives.
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Affiliation(s)
| | | | - Jordi Buils
- Universitat de les Illes Balears, Chemistry, SPAIN
| | | | | | - Jordi Pons
- Universitat de les Illes Balears, Chemistry, SPAIN
| | | | - Antonio Frontera
- Universitat Illes Balears, Chemistry, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, SPAIN
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16
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Malonaldehyde-like Systems: BeF2 Clusters—A Subtle Balance between Hydrogen Bonds, Beryllium Bonds, and Resonance. SCI 2022. [DOI: 10.3390/sci4010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, this work explores at the high level ab initio G4 level of theory the effect of including this non-covalent interaction in the system through its association with BeF2. Although malonaldehyde follows the expected trends, where the formation of a pseudocyclic form is favored also when IMHB and Be bonds are present, the subtle balance between both non-covalent interactions leads to some surprising results when other heteroatoms are involved, to the point that interaction energies can be much larger than expected or even cyclization is not favored. A complete analysis using different computational tools gives an answer to those cases escaping the predictable trends.
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17
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Shan A, Li X, Zeng Y, Meng L, Zhang X. Theoretical investigation on the nature of substituted benzene⋯AuX interactions: covalent or noncovalent? NEW J CHEM 2022. [DOI: 10.1039/d1nj05328k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of interactions between AuX (X = F, Cl, Br, CN, NO2, CH3) and aromatic moieties with different electronic properties has been investigated for possible tuning of coinage–metal bonds by varying the substituents.
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Affiliation(s)
- Aiting Shan
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Xiaoyan Li
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Yanli Zeng
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Lingpeng Meng
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Xueying Zhang
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
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18
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Pizzi A, Calabrese M, Daolio A, Ursini M, Frontera A, Resnati G. Expanding the toolbox of coinage bond: Adducts involving new gold(III) derivatives and bioactive molecules. CrystEngComm 2022. [DOI: 10.1039/d2ce00446a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray analyses of a small library of adducts between AuX3 (X=Cl, Br) and several pyridine derivatives indicate the systematic presence of quite short π -holes coinage bonds; computational studies reveal...
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19
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Alkorta I, Legon A. A reduced electrophilicity for simple Lewis acids A involved in non-covalent interactions with Lewis bases B. Phys Chem Chem Phys 2022; 24:6856-6865. [DOI: 10.1039/d2cp00779g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Dissociation energies De for B⋯A = B +A can be written De = c′NBEA, where NB and EA are the nucleophilicities and electrophilicities of the Lewis base B and the Lewis acid A, respectively.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Anthony Legon
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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20
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Priola E, Giordana A, Mazzeo PP, Mahmoudi G, Gomila RM, Zubkov FI, Pokazeev KM, Valchuk KS, Bacchi A, Zangrando E, Frontera A. On the nature of recurrent Au⋯π motifs in tris(2,2'-bipyridine)M(II) (M = Fe, Co and Ni) dicyanoaurate(I) salts: X-ray analysis and theoretical rationalization. Dalton Trans 2021; 50:16954-16960. [PMID: 34617941 DOI: 10.1039/d1dt02632a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This manuscript reports the synthesis, X-ray characterization and DFT study of three new [M(bipy)3]2[Au(CN)2]3(X) (M = Fe, Co, and Ni; bipy = 2,2'-bipyridine; X = anion) ionic compounds. These salts are composed of [M(bipy)3]2+ dications and [Au(CN)2]- anions in a 2 : 3 ratio. The positive charge is compensated by X = Cl- anions in compounds 1 (M = Fe) and 2 (M = Co) and X = OH- in 3 (M = Ni). The three tridentate bipyridine ligands define the coordination of the M2+ cation, resulting in a nearly octahedral coordination sphere. The linear dicyanoaurate(I) anions are completely surrounded by a cradle of aromatic rings with Au-ring centroid distances below the sum of van der Waals radii, evidencing the existence of a specific Au⋯π attraction. This interaction has been analyzed in terms of the role of the Au-atom (Lewis acid or Lewis base) using DFT calculations combined with the quantum theory of atoms in molecules (QTAIM), noncovalent interaction plot index (NCIplot) and natural bond orbital (NBO) computational tools. The NBO suggests that the Au⋯π interaction is an example of a coinage bond in spite of the anionic nature of the acceptor and the cationic nature of the donor.
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Affiliation(s)
- Emanuele Priola
- Department of Chemistry, University of Turin, Via Pietro Giuria 7, 10125 Turin, Italy
| | - Alessia Giordana
- Department of Chemistry, University of Turin, Via Pietro Giuria 7, 10125 Turin, Italy
| | - Paolo P Mazzeo
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy.,Biopharmanet-TEC, Università degli studi di Parma, via Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, P.O. Box 55181-83111, Maragheh, Iran.
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | - Fedor I Zubkov
- Faculty of Science, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russian Federation
| | - Kuzma M Pokazeev
- Faculty of Science, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russian Federation
| | - Karina S Valchuk
- Faculty of Science, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russian Federation
| | - Alessia Bacchi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy.,Biopharmanet-TEC, Università degli studi di Parma, via Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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21
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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22
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Daolio A, Pizzi A, Calabrese M, Terraneo G, Bordignon S, Frontera A, Resnati G. Molecular Electrostatic Potential and Noncovalent Interactions in Derivatives of Group 8 Elements. Angew Chem Int Ed Engl 2021; 60:20723-20727. [PMID: 34260810 PMCID: PMC8519081 DOI: 10.1002/anie.202107978] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/14/2021] [Indexed: 12/15/2022]
Abstract
This communication reports experimental and theoretical evidences of σ‐hole interactions in adducts between nitrogen or oxygen nucleophiles and tetroxides of osmium or other group 8 elements. Cocrystals between pyridine or pyridine N‐oxide derivatives and osmium tetroxide are characterized through various techniques and rationalized as σ‐hole interactions using DFT calculations and several other computational tools. We propose the term “osme bond” (OmB, Om=Fe, Ru, Os, (Hs)) for naming the noncovalent interactions wherein group 8 elements have the role of the electrophile. The word osme is the transcription of ὀσμή, the ancient Greek word for smell that was used to name the heaviest group 8 element in relation to the smoky odor of its tetroxide.
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Affiliation(s)
- Andrea Daolio
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, 20131, Milano, Italy
| | - Andrea Pizzi
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, 20131, Milano, Italy
| | - Miriam Calabrese
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, 20131, Milano, Italy
| | - Giancarlo Terraneo
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, 20131, Milano, Italy
| | | | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa, 07122, Palma, de Mallorca (Baleares, Spain
| | - Giuseppe Resnati
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, 20131, Milano, Italy
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23
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Daolio A, Pizzi A, Calabrese M, Terraneo G, Bordignon S, Frontera A, Resnati G. Molecular Electrostatic Potential and Noncovalent Interactions in Derivatives of Group 8 Elements. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andrea Daolio
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via Mancinelli 7 20131 Milano Italy
| | - Andrea Pizzi
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via Mancinelli 7 20131 Milano Italy
| | - Miriam Calabrese
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via Mancinelli 7 20131 Milano Italy
| | - Giancarlo Terraneo
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via Mancinelli 7 20131 Milano Italy
| | | | - Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears Crta. de Valldemossa 07122 Palma de Mallorca (Baleares Spain
| | - Giuseppe Resnati
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via Mancinelli 7 20131 Milano Italy
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24
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Mahmudov KT, Huseynov FE, Aliyeva VA, Guedes da Silva MFC, Pombeiro AJL. Noncovalent Interactions at Lanthanide Complexes. Chemistry 2021; 27:14370-14389. [PMID: 34363268 DOI: 10.1002/chem.202102245] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Lanthanide complexes have attracted a widespread attention due to their structural diversity, as well as multifunctional and tunable properties. The development of lanthanide based functional materials has often relied on the design of the secondary coordination sphere of the corresponding lanthanide complexes. For instance, usually simple lanthanide salts (solvento complexes) do not catalyze effectively organic reactions or provide low yield of the expected product, whereas the presence of a suitable organic ligand with a noncovalent bond donor or acceptor centre (secondary coordination sphere) modifies the symmetry around the metal centre in lanthanide complexes which then successfully can act as catalysts in both homogenous and heterogenous catalysis. In this minireview, we discuss several relevant examples, based on X-ray crystal structure analyses, in which the hydrogen, halogen, chalcogen, pnictogen, tetrel and rare-earth bonds, as well as cation-π, anion-π, lone pair-π, π-π and pancake interactions, are used as a synthon in the decoration of the secondary coordination sphere of lanthanide complexes.
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Affiliation(s)
- Kamran T Mahmudov
- University of Lisbon Higher Technical Institute: Universidade de Lisboa Instituto Superior Tecnico, CQE, R., 1009 - 001, Lisbon, PORTUGAL
| | - Fatali E Huseynov
- Baku State University, Department of Ecology and Soil Sciences, AZERBAIJAN
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25
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Calabrese C, Temelso B, Usabiaga I, Seifert NA, Basterretxea FJ, Prampolini G, Shields GC, Pate BH, Evangelisti L, Cocinero EJ. The Role of Non-Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane. Angew Chem Int Ed Engl 2021; 60:16894-16899. [PMID: 34028158 PMCID: PMC8362204 DOI: 10.1002/anie.202103900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Indexed: 01/30/2023]
Abstract
The role of non-covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and a plethora of weak donor/acceptor partners. This work illustrates the potential of chirped-pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs' in the molecular self-aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.
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Affiliation(s)
- Camilla Calabrese
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)48940LeioaSpain
| | - Berhane Temelso
- George Mason UniversityInformation Technology ServicesFairfaxVA22030USA
| | - Imanol Usabiaga
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bolognavia S. Alberto 16348100RavennaItaly
| | - Nathan A. Seifert
- Department of ChemistryUniversity of VirginiaMcCormick RoadCharlottesvilleVA22903USA
| | - Francisco J. Basterretxea
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)Area della Ricercavia G. Moruzzi 156124PisaItaly
| | | | - Brooks H. Pate
- Department of ChemistryUniversity of VirginiaMcCormick RoadCharlottesvilleVA22903USA
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bolognavia S. Alberto 16348100RavennaItaly
| | - Emilio J. Cocinero
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
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26
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Calabrese C, Temelso B, Usabiaga I, Seifert NA, Basterretxea FJ, Prampolini G, Shields GC, Pate BH, Evangelisti L, Cocinero EJ. The Role of Non‐Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Camilla Calabrese
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) 48940 Leioa Spain
| | - Berhane Temelso
- George Mason University Information Technology Services Fairfax VA 22030 USA
| | - Imanol Usabiaga
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
- Dipartimento di Chimica “Giacomo Ciamician” Università degli Studi di Bologna via S. Alberto 163 48100 Ravenna Italy
| | - Nathan A. Seifert
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22903 USA
| | - Francisco J. Basterretxea
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) Area della Ricerca via G. Moruzzi 1 56124 Pisa Italy
| | | | - Brooks H. Pate
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22903 USA
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician” Università degli Studi di Bologna via S. Alberto 163 48100 Ravenna Italy
| | - Emilio J. Cocinero
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
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27
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Zhao C, Lin H, Shan A, Guo S, Li X, Zhang X. Theoretical study on the noncovalent interactions involving triplet diphenylcarbene. J Mol Model 2021; 27:224. [PMID: 34244865 DOI: 10.1007/s00894-021-04838-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/23/2021] [Indexed: 11/27/2022]
Abstract
The properties of some types of noncovalent interactions formed by triplet diphenylcarbene (DPC3) have been investigated by means of density functional theory (DFT) calculations and quantum theory of atoms in molecule (QTAIM) studies. The DPC3···LA (LA = AlF3, SiF4, PF5, SF2, ClF) complexes have been analyzed from their equilibrium geometries, binding energies, and properties of electron density. The triel bond in the DPC3···AlF3 complex exhibits a partially covalent nature, with the binding energy - 65.7 kJ/mol. The tetrel bond, pnicogen bond, chalcogen bond, and halogen bond in the DPC3···LA (LA = SiF4, PF5, SF2, ClF) complexes show the character of a weak closed-shell noncovalent interaction. Polarization plays an important role in the formation of the studied complexes. The strength of intermolecular interaction decreases in the order LA = AlF3 > ClF > SF2 > SiF4 > PF5. The electron spin density transfers from the radical DPC3 to ClF and SF2 in the formation of halogen bond and chalcogen bond, but for the DPC3···AlF3/SiF4/PF5 complexes, the transfer of electron spin density is minimal.
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Affiliation(s)
- Chunhong Zhao
- Huihua College of Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Hui Lin
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Aiting Shan
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Shaofu Guo
- Huihua College of Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Xiaoyan Li
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China.
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28
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Priola E, Mahmoudi G, Andreo J, Frontera A. Unprecedented [d 9]Cu[d 10]Au coinage bonding interactions in {Cu(NH 3) 4[Au(CN) 2]} +[Au(CN) 2] - salt. Chem Commun (Camb) 2021; 57:7268-7271. [PMID: 34195712 DOI: 10.1039/d1cc02709c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The X-ray structure of the {Cu(NH3)4[Au(CN)2]}+[Au(CN)2]- salt is reported showing an unprecedented [d9]Cu[d10]Au coinage bond. The physical nature of the interaction has been studied using DFT calculations, including the quantum theory of atoms-in-molecules, the noncovalent interaction plot and the natural bond orbital analysis, revealing the nucleophilic role of the [d10]Au metal and the electrophilic role of [d9]Cu metal.
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Affiliation(s)
- Emanuele Priola
- Department of Chemistry, Universitá di Torino, Via Pietro Giuria 7, Torino 10125, Italy
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Daolio A, Pizzi A, Terraneo G, Ursini M, Frontera A, Resnati G. Anion⋅⋅⋅Anion Coinage Bonds: The Case of Tetrachloridoaurate. Angew Chem Int Ed Engl 2021; 60:14385-14389. [PMID: 33872450 PMCID: PMC8251892 DOI: 10.1002/anie.202104592] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Indexed: 01/13/2023]
Abstract
Interactions in crystalline tetrachloridoaurates of acetylcholine and dimethylpropiothetine are characterized by Au⋅⋅⋅Cl and Au⋅⋅⋅O short contacts. The former interactions assemble the AuCl4 - units into supramolecular anionic polymers, while the latter interactions append the acetylcholine and propiothetine units to the polymer. The distorted octahedral geometry of the bonding pattern around the gold center is rationalized on the basis of the anisotropic distribution of the electron density, which enables gold to behave as an electrophile (π-hole coinage-bond donor). Computational studies prove that gold atoms in negatively charged species can function as acceptors of electron density. The attractive nature of the Au⋅⋅⋅Cl/O interactions described here complement the known aurophilic bonds involved in gold-centered interactions.
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Affiliation(s)
- Andrea Daolio
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milanovia L. Mancinelli 720131MilanoItaly
| | - Andrea Pizzi
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milanovia L. Mancinelli 720131MilanoItaly
| | - Giancarlo Terraneo
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milanovia L. Mancinelli 720131MilanoItaly
| | - Maurizio Ursini
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milanovia L. Mancinelli 720131MilanoItaly
| | - Antonio Frontera
- Dept. ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma de Mallorca (Baleares)Spain
| | - Giuseppe Resnati
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milanovia L. Mancinelli 720131MilanoItaly
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Daolio A, Pizzi A, Terraneo G, Ursini M, Frontera A, Resnati G. Anion⋅⋅⋅Anion Coinage Bonds: The Case of Tetrachloridoaurate. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Andrea Daolio
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via L. Mancinelli 7 20131 Milano Italy
| | - Andrea Pizzi
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via L. Mancinelli 7 20131 Milano Italy
| | - Giancarlo Terraneo
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via L. Mancinelli 7 20131 Milano Italy
| | - Maurizio Ursini
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via L. Mancinelli 7 20131 Milano Italy
| | - Antonio Frontera
- Dept. Chemistry Universitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Giuseppe Resnati
- NFMLab, Dept- Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano via L. Mancinelli 7 20131 Milano Italy
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31
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Shen S, Jing X, Zhang X, Li X, Zeng Y. The competition and cooperativity of hydrogen/halogen bond and π-hole bond involving the heteronuclear ethylene analogues. J Comput Chem 2021; 42:908-916. [PMID: 33729600 DOI: 10.1002/jcc.26513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/07/2021] [Accepted: 03/01/2021] [Indexed: 11/08/2022]
Abstract
The noncovalent interactions involving heteronuclear ethylene analogues H2 CEH2 (E = Si, Ge and Sn) have been studied by the Møller-Plesset perturbation theory to investigate the competition and cooperativity between the hydrogen/halogen bond and π-hole bond. H2 CEH2 has a dual role of being a Lewis base and acid with the region of π-electron accumulation above the carbon atom and the region of π-electron depletion (π-hole) above the E atom to participate in the NCX···CE (X = H and Cl) hydrogen/halogen bond and CE···NCY (Y = H, Cl, Li and Na) π-hole bond, respectively. When HCN/ClCN interacts with H2 CEH2 by two sites, the strength of hydrogen bond/halogen bond is stronger than that of π-hole bond. The π-hole bond becomes obviously stronger when the metal substituent of YCN (Y = Li and Na) interacting with H2 CEH2 , showing the character of partial covalent, its strength is much greater than that of hydrogen/halogen bond. In the ternary complexes, both hydrogen/halogen bond and π-hole bond are simultaneously strengthened compared to those in the binary complexes, especially in the systems containing alkali metal.
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Affiliation(s)
- Shaojie Shen
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Xinyue Jing
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Xiaoyan Li
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Yanli Zeng
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, China
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32
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Jabłoński M. Study of Beryllium, Magnesium, and Spodium Bonds to Carbenes and Carbodiphosphoranes. Molecules 2021; 26:2275. [PMID: 33920004 PMCID: PMC8071025 DOI: 10.3390/molecules26082275] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this article is to present results of theoretical study on the properties of C⋯M bonds, where C is either a carbene or carbodiphosphorane carbon atom and M is an acidic center of MX2 (M = Be, Mg, Zn). Due to the rarity of theoretical data regarding the C⋯Zn bond (i.e., the zinc bond), the main focus is placed on comparing the characteristics of this interaction with C⋯Be (beryllium bond) and C⋯Mg (magnesium bond). For this purpose, theoretical studies (ωB97X-D/6-311++G(2df,2p)) have been performed for a large group of dimers formed by MX2 (X = H, F, Cl, Br, Me) and either a carbene ((NH2)2C, imidazol-2-ylidene, imidazolidin-2-ylidene, tetrahydropyrymid-2-ylidene, cyclopropenylidene) or carbodiphosphorane ((PH3)2C, (NH3)2C) molecule. The investigated dimers are characterized by a very strong charge transfer effect from either the carbene or carbodiphosphorane molecule to the MX2 one. This may even be over six times as strong as in the water dimer. According to the QTAIM and NCI method, the zinc bond is not very different than the beryllium bond, with both featuring a significant covalent contribution. However, the zinc bond should be definitely stronger if delocalization index is considered.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland
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Ciancaleoni G, Rocchigiani L. Assessing the Orbital Contribution in the "Spodium Bond" by Natural Orbital for Chemical Valence-Charge Displacement Analysis. Inorg Chem 2021; 60:4683-4692. [PMID: 33760600 DOI: 10.1021/acs.inorgchem.0c03650] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The term "spodium bond" (SpB) has been recently proposed to describe the noncoordinative interaction that can be established between a polarized group 12 metal and a mild Lewis base (LB). Most of the systems showing short metal-donor distances compatible with SpB are characterized by the coexistence of multiple weak interactions, including hydrogen and halogen bonding, making the assessment of real importance of SpB difficult. Here, we show that the relative importance of each contribution can be probed by dissecting the orbital component of the interaction through the extended transition state-natural orbital for chemical valence-charge displacement analysis (ETS-NOCV-CD). The latter gives useful information about relative energies and electrons involved, for model systems ([(thiourea)2MX2]···LB; M = Zn, Cd, and Hg; X = Cl and I; and LB = CH2S, CH2O, CH3CN, and CO) and a variety of structures extracted from experimentally characterized adducts, allowing us to demonstrate the lack of a direct correlation between a favorable metal-base distance and the presence of an orbital contribution for the SpB.
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Affiliation(s)
- Gianluca Ciancaleoni
- Università degli Studi di Pisa, Dipartimento di Chimica e Chimica Industriale, via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Luca Rocchigiani
- School of Chemistry, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, U.K
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Savastano M. Words in supramolecular chemistry: the ineffable advances of polyiodide chemistry. Dalton Trans 2021; 50:1142-1165. [PMID: 33496303 DOI: 10.1039/d0dt04091f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Polyiodide chemistry has a rich history deeply intertwined with the development of supramolecular chemistry. Technological and theoretical interest in polyiodides has not diminished in the last decade, quite the contrary; yet the advances this perspective intends to cover are muddled by the involution of supramolecular vocabulary, preventing their unbiased discussion. Herein we discuss the pressing necessity of ordering the current babel of novel - and less so - supramolecular terms. Shared decisions at the community level might be required to shape the field into a harmonious body of knowledge, dominated by concepts rather than words. Secondary, σ-hole and halogen bonding schools of thought are all addressed here, together with their respective impact on the field. Then, on the basis of a shared vocabulary, a discussion of polyiodide chemistry is presented, starting with a revisited view of triiodide. The contemporary fields of supramolecular caging and polyiodide networks are then discussed, with emphasis on how the terms we choose to use deeply affect scientific progress.
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Affiliation(s)
- Matteo Savastano
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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35
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Non-Covalent Interactions of the Lewis Acids Cu–X, Ag–X, and Au–X (X = F and Cl) with Nine Simple Lewis Bases B: A Systematic Investigation of Coinage–Metal Bonds by Ab Initio Calculations. INORGANICS 2021. [DOI: 10.3390/inorganics9020013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The equilibrium geometry and two measures (the equilibrium dissociation energy in the complete basis set limit, De(CBS) and the intermolecular stretching force constant kσ) of the strength of the non-covalent interaction of each of six Lewis acids M–X (M = Cu, Ag, Au) with each of nine simple Lewis bases B (B = N2, CO, HCCH, CH2CH2, H2S, PH3, HCN, H2O, and NH3) have been calculated at the CCSD(T)/aug-cc-pVTZ level of theory in a systematic investigation of the coinage–metal bond. Unlike the corresponding series of hydrogen-bonded B⋯HX and halogen-bonded B⋯XY complexes (and other series involving non-covalent interactions), De is not directly proportional to kσ. Nevertheless, as for the other series, it has been possible to express De in terms of the equation De = cNB.EMX, where NB and EMX are the nucleophilicities of the Lewis bases B and the electrophilicities of the Lewis acids M–X, respectively. The order of the EMX is determined to be EAuF > EAuCl > ECuF > ECuCl > EAgF ≈ EAgCl. A reduced electrophilicity defined as (EMX/σmax) is introduced, where σmax is the maximum positive value of the molecular electrostatic surface potential on the 0.001 e/bohr3 iso-surface. This quantity is, in good approximation, independent of whether F or Cl is attached to M.
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36
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Alkorta I, Elguero J, Oliva-Enrich JM, Yáñez M, Mó O, Montero-Campillo MM. The Importance of Strain (Preorganization) in Beryllium Bonds. Molecules 2020; 25:molecules25245876. [PMID: 33322617 PMCID: PMC7763456 DOI: 10.3390/molecules25245876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022] Open
Abstract
In order to explore the angular strain role on the ability of Be to form strong beryllium bonds, a theoretical study of the complexes of four beryllium derivatives of orthocloso-carboranes with eight molecules (CO, N2, NCH, CNH, OH2, SH2, NH3, and PH3) acting as Lewis bases has been carried out at the G4 computational level. The results for these complexes, which contain besides Be other electron-deficient elements, such as B, have been compared with the analogous ones formed by three beryllium salts (BeCl2, CO3Be and SO4Be) with the same set of Lewis bases. The results show the presence of large and positive values of the electrostatic potential associated to the beryllium atoms in the isolated four beryllium derivatives of ortho-carboranes, evidencing an intrinsically strong acidic nature. In addition, the LUMO orbital in these systems is also associated to the beryllium atom. These features led to short intermolecular distances and large dissociation energies in the complexes of the beryllium derivatives of ortho-carboranes with the Lewis bases. Notably, as a consequence of the special framework provided by the ortho-carboranes, some of these dissociation energies are larger than the corresponding beryllium bonds in the already strongly bound SO4Be complexes, in particular for N2 and CO bases. The localized molecular orbital energy decomposition analysis (LMOEDA) shows that among the attractive terms associated with the dissociation energy, the electrostatic term is the most important one, except for the complexes with the two previously mentioned weakest bases (N2 and CO), where the polarization term dominates. Hence, these results contribute to further confirm the importance of bending on the beryllium environment leading to strong interactions through the formation of beryllium bonds.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain;
- Correspondence: (I.A.); (J.M.O.-E.); (M.Y.)
| | - José Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - Josep M. Oliva-Enrich
- Instituto de Química-Física “Rocasolano” (CSIC), Serrano, 119, E-28006 Madrid, Spain
- Correspondence: (I.A.); (J.M.O.-E.); (M.Y.)
| | - Manuel Yáñez
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain; (O.M.); (M.M.M.-C.)
- Correspondence: (I.A.); (J.M.O.-E.); (M.Y.)
| | - Otilia Mó
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain; (O.M.); (M.M.M.-C.)
| | - M. Merced Montero-Campillo
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain; (O.M.); (M.M.M.-C.)
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Alkorta I, Elguero J, Trujillo C, Sánchez-Sanz G. Interaction between Trinuclear Regium Complexes of Pyrazolate and Anions, a Computational Study. Int J Mol Sci 2020; 21:E8036. [PMID: 33126636 PMCID: PMC7663457 DOI: 10.3390/ijms21218036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/27/2023] Open
Abstract
The geometry, energy and electron density properties of the 1:1, 1:2 and 1:3 complexes between cyclic (Py-M)3 (M = Au, Ag and Cu) and halide ions (F-, Cl- and Br-) were studied using Møller Plesset (MP2) computational methods. Three different configurations were explored. In two of them, the anions interact with the metal atoms in planar and apical dispositions, while in the last configuration, the anions interact with the CH(4) group of the pyrazole. The energetic results for the 1:2 and 1:3 complexes are a combination of the specific strength of the interaction plus a repulsive component due to the charge:charge coulombic term. However, stable minima structures with dissociation barriers for the anions indicate that those complexes are stable and (Py-M)3 can hold up to three anions simultaneously. A search in the CSD confirmed the presence of (Pyrazole-Cu)3 systems with two anions interacting in apical disposition.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, Trinity Dublin College, D02 R590 Dublin 2, Ireland;
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland
- School of Chemistry, University College Dublin, Belfield, D02 HP83 Dublin 4, Ireland
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Rivalry between Regium and Hydrogen Bonds Established within Diatomic Coinage Molecules and Lewis Acids/Bases. Chemphyschem 2020; 21:2557-2563. [PMID: 32893396 DOI: 10.1002/cphc.202000704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/04/2020] [Indexed: 11/09/2022]
Abstract
A theoretical study of the complexes formed by Ag2 and Cu2 with different molecules, XH (FH, ClH, OH2 , SH2 , HCN, HNC, HCCH, NH3 and PH3 ) that can act as hydrogen-bond donors (Lewis acids) or regium-bond acceptors (Lewis bases) was carried out at the CCSD(T)/CBS computational level. The heteronuclear diatomic coinage molecules (AuAg, AuCu, and AgCu) have also been considered. With the exception of some of the hydrogen-bonded complexes with FH, the regium-bonded binary complexes are more stable. The AuAg and AuCu molecules show large dipole moments that weaken the regium bond (RB) with Au and favour those through the Ag and Cu atoms, respectively.
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Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin, D2, Ireland & School of Chemistry, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin, D2, Ireland
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
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Wang R, Wang Z, Yu X, Li Q. Synergistic and Diminutive Effects between Regium and Aerogen Bonds. Chemphyschem 2020; 21:2426-2431. [PMID: 32889745 DOI: 10.1002/cphc.202000720] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/03/2020] [Indexed: 11/07/2022]
Abstract
The aerogen bond is formed in complexes of HCN-XeF2 O and C2 H4 -XeF2 O. The lone pair on the N atom of HCN is a better electron donor in the aerogen bond than the π electron on the C=C bond of C2 H4 . The coinage substitution strengthens the aerogen bond in MCN-XeF2 O (M=Cu, Ag, and Au) and its enhancing effect becomes larger in the Au<Cu<Ag pattern. The aerogen bond is further enhanced by the regium bond in C2 H2 -MCN-XeF2 O and C2 H4 -MCN-XeF2 O, but is weakened by the regium bond in MCN-C2 H4 -XeF2 O and C2 (CN)4 -MCN-XeF2 O. Simultaneously, the regium bond is also strengthened or weakened in these triads. The synergistic and diminutive effects between regium and aerogen bonds have been explained by means of charge transfer and electrostatic potentials.
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Affiliation(s)
- Ruijing Wang
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Zheng Wang
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Xuefang Yu
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
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40
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Fekete C, Barrett J, Benkő Z, Heift D. Dibismuthates as Linking Units for Bis-Zwitterions and Coordination Polymers. Inorg Chem 2020; 59:13270-13280. [PMID: 32897714 PMCID: PMC7509842 DOI: 10.1021/acs.inorgchem.0c01619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Adducts of bismuth
trihalides BiX3 (X = Cl, Br, I) and the PS3 ligand (PS3 = P(C6H4-o-CH2SCH3)3) react with HCl to form inorganic/organic
hybrids with the general formula [HPS3BiX4]2. On the basis of their solid-state
structures determined by single-crystal X-ray diffraction, these compounds
exhibit discrete bis-zwitterionic assemblies consisting of two phosphonium
units [HPS3]+ linked
to a central dibismuthate core [Bi2X8]2– via S→Bi dative interactions. Remarkably, the phosphorus
center of the PS3 ligand undergoes
protonation with hydrochloric acid. This is in stark contrast to the
protonation of phosphines commonly observed with hydrogen halides
resulting in equilibrium. To understand the important factors in this
protonation reaction, 31P NMR experiments and DFT computations
have been performed. Furthermore, the dibismuthate linker was utilized
to obtain the coordination polymer {[AgPS3BiCl3(OTf)]2(CH3CN)2}∞, in which dicationic [Ag(PS3)]22+ macrocycles containing
five-coordinate silver centers connect the dianionic [Bi2Cl6(OTf)2]2– dibismuthate
fragments. The bonding situation in these dibismuthates has been investigated
by single-crystal X-ray diffraction and DFT calculations (NBO analysis,
AIM analysis, charge distribution). The potential
of dibismuthates [Bi2X8]2− as building blocks for the synthesis of bis-zwitterions and coordination
polymers has been shown. The structures of these compounds and the
bonding in the dibismuthate linkers have been studied by single-crystal
X-ray diffraction and DFT calculations.
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Affiliation(s)
- Csilla Fekete
- Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Jamie Barrett
- Department of Chemistry, Durham University, DH1 3LE Durham, United Kingdom
| | - Zoltán Benkő
- Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Dominikus Heift
- Department of Chemistry, Durham University, DH1 3LE Durham, United Kingdom
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41
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Burevschi E, Alonso ER, Sanz ME. Binding Site Switch by Dispersion Interactions: Rotational Signatures of Fenchone-Phenol and Fenchone-Benzene Complexes. Chemistry 2020; 26:11327-11333. [PMID: 32428270 PMCID: PMC7497235 DOI: 10.1002/chem.202001713] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Indexed: 12/15/2022]
Abstract
Non-covalent interactions between molecules determine molecular recognition and the outcome of chemical and biological processes. Characterising how non-covalent interactions influence binding preferences is of crucial importance in advancing our understanding of these events. Here, we analyse the interactions involved in smell and specifically the effect of changing the balance between hydrogen-bonding and dispersion interactions by examining the complexes of the common odorant fenchone with phenol and benzene, mimics of tyrosine and phenylalanine residues, respectively. Using rotational spectroscopy and quantum chemistry, two isomers of each complex have been identified. Our results show that the increased weight of dispersion interactions in these complexes changes the preferred binding site in fenchone and sets the basis for a better understanding of the effect of different residues in molecular recognition and binding events.
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Trujillo C, Sánchez-Sanz G, Elguero J, Alkorta I. The Lewis acidities of gold(I) and gold(III) derivatives: a theoretical study of complexes of AuCl and AuCl3. Struct Chem 2020. [DOI: 10.1007/s11224-020-01590-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Alkorta I, Hill JG, Legon AC. An ab initio investigation of alkali-metal non-covalent bonds BLiR and BNaR (R = F, H or CH 3) formed with simple Lewis bases B: the relative inductive effects of F, H and CH 3. Phys Chem Chem Phys 2020; 22:16421-16430. [PMID: 32658222 DOI: 10.1039/d0cp02697b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The alkali-metal bonds formed by simple molecules LiR and NaR (R = F, H or CH3) with each of the six Lewis bases B = OC, HCN, H2O, H3N, H2S and H3P were investigated by ab initio calculations at the CCSD(T)/AVTZ and CCSD(T)/awCVTZ levels of theory with the aim of characterising this type of non-covalent interaction. In some complexes, two minima were discovered, especially for those involving the NaR. The higher-energy minimum (referred to as Type I) for a given B was found to have geometry that is isomorphous with that of the corresponding hydrogen-bonded analogue BHF. The lower-energy minimum (when two were present) showed evidence of a significant secondary interaction of R with the main electrophilic region of B (Type II complexes). Energies DCBSe for dissociation of the complexes into separate components were found to be directly proportional to the intermolecular stretching force constant kσ The value of DCBSe could be partitioned into a nucleophilicity of B and an electrophilicity of LiR or NaR, with the order ELiH ⪆ ELiF = ELiCH3 for the LiR and ENaF > ENaH ≈ ENaCH3 for the NaR. For a given B, the order of the electrophilicities is ELiR > ENaR, which presumably reflects the fact that Li+ is smaller than Na+ and can approach the Lewis base more closely. A SAPT analysis revealed that the complexes BLiR and BNaR have larger electrostatic contributions to De than do the hydrogen- and halogen-bonded counterparts BHCl and BClF.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain.
| | - J Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
| | - Anthony C Legon
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8 1TS, UK.
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Bauzá A, Alkorta I, Elguero J, Mooibroek TJ, Frontera A. Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007814] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Antonio Bauzá
- Departament de Química Universitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares Spain
| | - Ibon Alkorta
- Instituto de Química Médica Juan de la Cierva, 3 28006- Madrid Spain
| | - José Elguero
- Instituto de Química Médica Juan de la Cierva, 3 28006- Madrid Spain
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park A, 904, E1.26 1098 XH Amsterdam The Netherlands
| | - Antonio Frontera
- Departament de Química Universitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares Spain
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Bauzá A, Alkorta I, Elguero J, Mooibroek TJ, Frontera A. Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements. Angew Chem Int Ed Engl 2020; 59:17482-17487. [PMID: 32542948 DOI: 10.1002/anie.202007814] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Indexed: 02/06/2023]
Abstract
The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma, de Mallorca (Baleares, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, Juan de la Cierva, 3, 28006-, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, Juan de la Cierva, 3, 28006-, Madrid, Spain
| | - Tiddo J Mooibroek
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park A, 904, E1.26, 1098 XH, Amsterdam, The Netherlands
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma, de Mallorca (Baleares, Spain
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Wang R, Li Q, Scheiner S. Complexes of HArF and AuX (X = F, Cl, Br, I). Comparison of H‐bonds, halogen bonds, F‐shared bonds and covalent bonds. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ruijing Wang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering Yantai University Yantai 264005 People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering Yantai University Yantai 264005 People's Republic of China
| | - Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan UT 84322‐0300 USA
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Alikhani ME. Beryllium bonding: insights from the σ- and π-hole analysis. J Mol Model 2020; 26:94. [PMID: 32248314 DOI: 10.1007/s00894-020-4348-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Abstract
Beryllium bonding is actually a subclass of secondary bonding. Similar to the case of halogen bonding, the σ- and π-holes on the Be atom of the monomers give in zeroth approximation the direction of electrophilic attack favorable to the formation of beryllium bonds. The nature of beryllium bonding is purely electrostatic so that the symmetry-adapted perturbation theory energy decomposition perfectly explains the relevance of the polarization and dispersion contribution on the formation of the beryllium bond.
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Affiliation(s)
- M Esmaïl Alikhani
- Sorbonne Université, CNRS, UMR 8233, MONARIS, Case Courrier 49, 4 Place Jussieu, F-75005, Paris, France.
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Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
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Towards an unified chemical model of secondary bonding. J Mol Model 2020; 26:62. [DOI: 10.1007/s00894-019-4283-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/19/2019] [Indexed: 11/27/2022]
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