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Grödler D, Burguera S, Frontera A, Strub E. Investigating Recurrent Matere Bonds in Pertechnetate Compounds. Chemistry 2024; 30:e202400100. [PMID: 38385852 DOI: 10.1002/chem.202400100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
In this manuscript we evaluate the X-ray structure of five new pertechnetate derivatives of general formula [M(H2O)4(TcO4)2], M=Mg, Co, Ni, Cu, Zn (compounds 1-5) and one perrhenate compound Zn(H2O)4(ReO4)2 (6). In these complexes the metal center exhibits an octahedral coordination with the pertechnetate units as axial ligands. All compounds exhibit the formation of directional Tc⋅⋅⋅O Matere bonds (MaBs) that propagate the [M(H2O)4(TcO4)2], into 1D supramolecular polymers in the solid state. Such 1D polymers are linked, generating 2D layers, by combining additional MaBs and hydrogen bonds (HBs). Such concurrent motifs have been analyzed theoretically, suggesting the noncovalent σ-hole nature of the MaBs. The interaction energies range from weak (~ -2 kcal/mol) for the MaBs to strong (~ -30 kcal/mol) for the MaB+HB assemblies, where HB dominates. In case of M=Zn, the corresponding perrhenate Zn(H2O)4(ReO4)2 complex, has been also synthesized for comparison purposes, resulting in the formation of an isostructural X-ray structure, corroborating the structure-directing role of Matere bonds.
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Affiliation(s)
- Dennis Grödler
- Department of Chemistry, Division of Nuclear Chemistry, University of Cologne, Zülpicher Str. 45, 50674, Cologne, Germany
| | - Sergi Burguera
- Departament de Química, Universitat de les Illes Balears, Crta. De Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), SPAIN
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. De Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), SPAIN
| | - Erik Strub
- Department of Chemistry, Division of Nuclear Chemistry, University of Cologne, Zülpicher Str. 45, 50674, Cologne, Germany
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2
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Topić NB, Bedeković N, Poljanić L, Stilinović V, Cinčić D. Evaluation of Concomitant Halogen and Pnictogen Bonds in Cocrystals of Imines Derived from 2-Nitrobenzaldehyde and 4-Haloaniline. CRYSTAL GROWTH & DESIGN 2024; 24:3010-3020. [PMID: 38585379 PMCID: PMC10996288 DOI: 10.1021/acs.cgd.4c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/09/2024]
Abstract
Three imines have been prepared by condensation of 2-nitrobenzaldehyde and 4-haloanilines (halo = Cl, Br, and I) with functionalities that enabled them to act as both halogen and pnictogen bond donors; however, both interactions were found to be absent in the solid state. The prepared imines were further cocrystallized with 1,3-diiodotetrafluorobenzene and 1,3,5-triiodotetrafluorobenzene as halogen bond donors. Six novel cocrystals were prepared by means of liquid-assisted mechanochemical synthesis and by crystallization from solution. All six cocrystals were of 1:1 stoichiometry and comprised a N···I halogen bond between an iodine atom of the perhalogenated halogen bond donor and the imino nitrogen atom of the imine acting as an acceptor. Additionally, in all six cocrystals, the imine molecules were interconnected by NO2···NO2 pnictogen bonding interactions. Computational analysis has shown that the NO2···NO2 exhibits bond critical point electron densities in the region (4.897-8.306) × 10-3 e Å-3 and interaction energies of 23.6-27.7 kJ mol-1, whereas the N···I halogen bonds generally have higher critical point electron densities ((1.795-1.937) × 10-2 e Å-3), but the corresponding total interaction energies are lower (19.4-20.4 kJ mol-1). Statistical analysis of the appearance of NO2···NO2 contacts concomitantly with halogen or hydrogen bonds seems to indicate that there is a positive correlation between the presence of NO2···NO2 pnictogen bonding interactions and other directional interactions in crystal structures.
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Affiliation(s)
- Nea Baus Topić
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb 10000, Croatia
| | - Nikola Bedeković
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb 10000, Croatia
| | | | - Vladimir Stilinović
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb 10000, Croatia
| | - Dominik Cinčić
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb 10000, Croatia
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3
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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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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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Burguera S, Frontera A, Bauza A. Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications. Inorg Chem 2023; 62:6740-6750. [PMID: 37083254 PMCID: PMC10155183 DOI: 10.1021/acs.inorgchem.3c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium-π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal-DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.
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Affiliation(s)
- Sergi Burguera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Bauza
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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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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7
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Metal Coordination Enhances Chalcogen Bonds: CSD Survey and Theoretical Calculations. Int J Mol Sci 2022; 23:ijms23084188. [PMID: 35457005 PMCID: PMC9030556 DOI: 10.3390/ijms23084188] [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: 02/21/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 12/03/2022] Open
Abstract
In this study the ability of metal coordinated Chalcogen (Ch) atoms to undergo Chalcogen bonding (ChB) interactions has been evaluated at the PBE0-D3/def2-TZVP level of theory. An initial CSD (Cambridge Structural Database) inspection revealed the presence of square planar Pd/Pt coordination complexes where divalent Ch atoms (Se/Te) were used as ligands. Interestingly, the coordination to the metal center enhanced the σ-hole donor ability of the Ch atom, which participates in ChBs with neighboring units present in the X-ray crystal structure, therefore dictating the solid state architecture. The X-ray analyses were complemented with a computational study (PBE0-D3/def2-TZVP level of theory), which shed light into the strength and directionality of the ChBs studied herein. Owing to the new possibilities that metal coordination offers to enhance or modulate the σ-hole donor ability of Chs, we believe that the findings presented herein are of remarkable importance for supramolecular chemists as well as for those scientists working in the field of solid state chemistry.
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8
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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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9
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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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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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11
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On the Importance of Pnictogen and Chalcogen Bonding Interactions in Supramolecular Catalysis. Int J Mol Sci 2021; 22:ijms222212550. [PMID: 34830432 PMCID: PMC8623369 DOI: 10.3390/ijms222212550] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
In this review, several examples of the application of pnictogen (Pn) (group 15) and chalcogen (Ch) bonding (group 16) interactions in organocatalytic processes are gathered, backed up with Molecular Electrostatic Potential surfaces of model systems. Despite the fact that the use of catalysts based on pnictogen and chalcogen bonding interactions is taking its first steps, it should be considered and used by the scientific community as a novel, promising tool in the field of organocatalysis.
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Abstract
Elements from groups 14–18 and periods 3–6 commonly behave as Lewis acids, which are involved in directional noncovalent interactions (NCI) with electron-rich species (lone pair donors), π systems (aromatic rings, triple and double bonds) as well as nonnucleophilic anions (BF4−, PF6−, ClO4−, etc.). Moreover, elements of groups 15 to 17 are also able to act as Lewis bases (from one to three available lone pairs, respectively), thus presenting a dual character. These emerging NCIs where the main group element behaves as Lewis base, belong to the σ–hole family of interactions. Particularly (i) tetrel bonding for elements belonging to group 14, (ii) pnictogen bonding for group 15, (iii) chalcogen bonding for group 16, (iv) halogen bonding for group 17, and (v) noble gas bondings for group 18. In general, σ–hole interactions exhibit different features when moving along the same group (offering larger and more positive σ–holes) or the same row (presenting a different number of available σ–holes and directionality) of the periodic table. This is illustrated in this review by using several examples retrieved from the Cambridge Structural Database (CSD), especially focused on σ–hole interactions, complemented with molecular electrostatic potential surfaces of model systems.
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Sruthi P, Ramanathan N, Sundararajan K. Pentavalent P…N phosphorus bonding in the heterodimers of POCl3…nitrogen bases: Evidence from matrix isolation infrared spectroscopy and Ab initio computations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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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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16
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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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17
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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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18
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Mooibroek TJ. DFT and IsoStar Analyses to Assess the Utility of σ- and π-Hole Interactions for Crystal Engineering. Chemphyschem 2021; 22:141-153. [PMID: 33241585 PMCID: PMC7898519 DOI: 10.1002/cphc.202000927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/25/2020] [Indexed: 11/25/2022]
Abstract
The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.
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Affiliation(s)
- Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van Amsterdam, Science Park 9041098 XHAmsterdamThe Netherlands
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19
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Suryaprasad B, Chandra S, Ramanathan N, Sundararajan K. Pentavalent P…π phosphorus bonding with associated Cl…π halogen bonding in influencing the geometry of POCl3-Phenylacetylene heterodimers: Evidence from matrix isolation infrared spectroscopy and ab initio computations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Nemec V, Lisac K, Bedeković N, Fotović L, Stilinović V, Cinčić D. Crystal engineering strategies towards halogen-bonded metal–organic multi-component solids: salts, cocrystals and salt cocrystals. CrystEngComm 2021. [DOI: 10.1039/d1ce00158b] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This highlight presents an overview of the current advances in the preparation of halogen bonded metal–organic multi-component solids, including salts and cocrystals comprising neutral and ionic constituents.
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Affiliation(s)
- Vinko Nemec
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Katarina Lisac
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Nikola Bedeković
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Luka Fotović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Vladimir Stilinović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Dominik Cinčić
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
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21
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Rouco L, Sánchez-González Á, Alvariño R, Alfonso A, Vázquez-López EM, García-Martínez E, Maneiro M. Combined Effect of Caspase-Dependent and Caspase-Independent Apoptosis in the Anticancer Activity of Gold Complexes with Phosphine and Benzimidazole Derivatives. Pharmaceuticals (Basel) 2020; 14:10. [PMID: 33374177 PMCID: PMC7824672 DOI: 10.3390/ph14010010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/28/2022] Open
Abstract
Since the potential anticancer activity of auranofin was discovered, gold compounds have attracted interest with a view to developing anticancer agents that follow cytotoxic mechanisms other than cisplatin. Two benzimidazole gold(I) derivatives containing triphenylphosphine (Au(pben)(PPh3)) (1) or triethylphosphine (Au(pben)(PEt3)) (2) were prepared and characterized by standard techniques. X-ray crystal structures for 1 and 2 were solved. The cytotoxicity of 1 and 2 was tested in human neuroblastoma SH-SY5Y cells. Cells were incubated with compounds for 24 h with concentrations ranging from 10 µM to 1 nM, and the half-maximal inhibitory concentration (IC50) was determined. 1 and 2 showed an IC50 of 2.7 and 1.6 µM, respectively. In order to better understand the type of cell death induced by compounds, neuroblastoma cells were stained with Annexin-FITC and propidium iodide. The fluorescence analysis revealed that compounds were inducing apoptosis; however, pre-treatment with the caspase inhibitor Z-VAD did not reduce cell death. Analysis of compound effects on caspase-3 activity and reactive oxygen species (ROS) production in SH-SY5Y cells revealed an antiproliferative ability mediated through oxidative stress and both caspase-dependent and caspase-independent mechanisms.
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Grants
- 2017 GRC GI-1682 (ED431C 2017/01), 2018 GRC-1584 (ED431C 2018/13), MetalBIO network (ED431D 2017/01) Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia
- CTQ2015-65707-C2-2-P, AGL2016-78728-R (AEI/FEDER, UE), ISCIII/PI16/01830, RTC-2016-5507-2, ITC-20161072 Ministerio de Economía, Industria y Competitividad
- POPTEP 0161-Nanoeaters-1-E-1, Interreg AlertoxNet EAPA-317-2016, Interreg Agritox EAPA-998-2018, H2020 778069-EMERTOX European Union
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Affiliation(s)
- Lara Rouco
- Departamento de Química Inorgánica, Facultade de Ciencias, Universidade de Santiago de Compostela, 27002 Lugo, Spain;
| | - Ángeles Sánchez-González
- Departamento de Química Inorgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rebeca Alvariño
- Departamento de Farmacología, Facultade de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain;
| | - Amparo Alfonso
- Departamento de Farmacología, Facultade de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain;
| | - Ezequiel M. Vázquez-López
- Departamento de Química Inorgánica, Facultade de Química, Campus Universitario Lagoas-Marcosende, Universidade de Vigo, 36310 Vigo, Spain; (E.M.V.-L.); (E.G.-M.)
| | - Emilia García-Martínez
- Departamento de Química Inorgánica, Facultade de Química, Campus Universitario Lagoas-Marcosende, Universidade de Vigo, 36310 Vigo, Spain; (E.M.V.-L.); (E.G.-M.)
| | - Marcelino Maneiro
- Departamento de Química Inorgánica, Facultade de Ciencias, Universidade de Santiago de Compostela, 27002 Lugo, Spain;
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22
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Abstract
The regium-π interaction is an attractive noncovalent force between group 11 elements (Cu, Ag, and Au) acting as Lewis acids and aromatic surfaces. Herein, we report for the first time experimental (Protein Data Bank analysis) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of regium-π bonds involving Au(I) and aromatic amino acids (Phe, Tyr, Trp, and His). These findings might be important in the field of drug design and for retrospectively understanding the role of gold in proteins.
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Affiliation(s)
- María de Las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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23
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Chandra S, Suryaprasad B, Ramanathan N, Sundararajan K. Dominance of unique Pπ phosphorus bonding with π donors: evidence using matrix isolation infrared spectroscopy and computational methodology. Phys Chem Chem Phys 2020; 22:20771-20791. [PMID: 32909555 DOI: 10.1039/d0cp02880k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albeit the first account of hypervalentπ interactions has been reported with halogenπ interactions, the feasibility of their extension to other hypervalent atoms as possible Lewis acids is still open. In this work, the role of phosphorus as an acceptor from the π electron cloud (Pπ pnicogen or phosphorus bonding) in PCl3-C2H2 and PCl3-C2H4 heterodimers is explored, by combining matrix isolation infrared spectroscopy with ab initio and DFT computational methodologies. The respective potential energy surfaces of the PCl3-C2H2 and PCl3-C2H4 heterodimers reveal unique minima stabilized by a concert of reasonably strong to weak interactions, of which Pπ phosphorus bonding was energetically dominant. Heterodimers, trimers and tetramers bound primarily by this unique phosphorus bond were generated at low temperatures. The dominance of phosphorus bonding in the PCl3-C2H2 and PCl3-C2H4 heterodimers over other interactions (such as Hπ, HCl, HP, Clπ and lone pair-π interactions) was confirmed and substantiated using extended quantum theory of atoms in molecules, natural bond orbital, electrostatic potential mapping and energy decomposition analyses. The following inferences in correlation with results from non-covalent-interaction analysis offer a complete understanding of the nature of the Pπ phosphorus bonding interactions. The significance of electrostatic forces kinetically favoring the formation of phosphorus bonded heterodimers, in addition to thermodynamic stabilization, is demonstrated experimentally.
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Affiliation(s)
- Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - B Suryaprasad
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
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24
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Galmés B, Adrover J, Terraneo G, Frontera A, Resnati G. Radicalradical chalcogen bonds: CSD analysis and DFT calculations. Phys Chem Chem Phys 2020; 22:12757-12765. [PMID: 32463046 DOI: 10.1039/d0cp01643h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This manuscript reports a combination of crystallographic analysis (Cambridge Structural Database) and theoretical DFT calculations in chalcogen bonding interactions involving radicals in both the Ch bond (ChB) donor and acceptor. As a radical ChB acceptor (nucleophile) we have used benzodithiazolyl radical (BDTA) and as Ch bond donors (electrophile) we have used dithiadiazolyl and diselenadiazolyl radicals of the general formula p-X-C6F4-CNChChN (Ch = S, and Se). We have evaluated how the para substituent (X) affects the interaction energy, spin density and charge/spin transfer from the electron rich BDTA radical to the electron poor dichalcogenadiazolyl ring. The ability of the latter rings to form ChBs in the solid state has been examined by a comprehensive search in the CSD; several cases are used to exemplify the preferred geometric features of the complexes and they are compared with the theory. The molecular surface electrostatic potentials calculated for these ChB donors allow for a very precise rationalization of the self-assembly motifs most frequently adopted in the crystalline state and of their relative robustness.
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Affiliation(s)
- Bartomeu Galmés
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Jaume Adrover
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Giancarlo Terraneo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy.
| | - Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Giuseppe Resnati
- Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy.
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25
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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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