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Majumdar D, Frontera A, Roy S, Sutradhar D. Experimental and Theoretical Survey of Intramolecular Spodium Bonds/σ/π-Holes and Noncovalent Interactions in Trinuclear Zn(II)-Salen Type Complex with OCN - Ions: A Holistic View in Crystal Engineering. ACS OMEGA 2024; 9:1786-1797. [PMID: 38222609 PMCID: PMC10785279 DOI: 10.1021/acsomega.3c08422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024]
Abstract
In this work, one new centrosymmetric trinuclear Zn(II) complex 1, [{(OCN)Zn(L)}2Zn], using a salen-type ligand (H2L) in the presence of OCN- was synthesized and characterized via elemental, spectral, SEM-EDX, and single-crystal X-ray diffraction (SCXRD) study. In 1, SCXRD reveals two different stereochemical environments of zinc metal ions; one terminal Zn(II) center adopts square pyramidal geometries with the Addison parameter (τ) 0.095, and the central Zn(II) is tetracoordinated tetrahedral geometry. This article provides evidence of the significance and presence of spodium bonds (SpBs) in solid-state crystal structures involving a pseudotetrahedral environment of the central Zn-atom. X-ray structures reveal intramolecular Zn···O SpBs caused by the methoxy (-OCH3) substituent O-atom adjacent to the coordinated phenoxy O-atom. These noncovalent interactions have been thoroughly studied using density functional theory calculations at the RI-BP86[2]-D3[3]/def2-TZVP level of theory that characterizes the nature of SpBs, including the Baders quantum theory of atoms-in-molecules "QTAIM", molecular electrostatic potential (MEP) surface, and noncovalent index plot (NCI). In addition, a unique complex-isomer-based theoretical model has been vividly employed to estimate the SpBs energy in the complex. Natural bond orbital (NBO) analysis also tries to establish the differentiation between σ-hole and π-hole SpBs' natures more authentically. The complex energy frameworks were used to investigate noncovalent interactions. To better understand the different intermolecular interactions, we conducted a Hirshfeld surface, which revealed N···H (15.4%) and O···H (9.1%) contacts and Zn···O (5.1%) (SpBs).
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Affiliation(s)
- Dhrubajyoti Majumdar
- Department
of Chemistry, Tamralipta Mahavidyalaya, Tamluk, West Bengal 721636, India
| | - Antonio Frontera
- Department
de Quimica, Universitat de les Illes Balears, Cra. de Valldemossa km 7.5, Palma de Mallorca (Baleares) 07122, Spain
| | - Sourav Roy
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bangalore 560012, India
| | - Dipankar Sutradhar
- School
of Advanced Sciences and Languages, VIT
Bhopal University, Kothrikalan, Sehore, Madhya Pradesh 466114, India
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Beckmann JL, Krieft J, Vishnevskiy YV, Neumann B, Stammler HG, Mitzel NW. A Bidentate Antimony Pnictogen Bonding Host System. Angew Chem Int Ed Engl 2023; 62:e202310439. [PMID: 37773008 DOI: 10.1002/anie.202310439] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023]
Abstract
A bidentate pnictogen bonding host-system based on 1,8-diethynylanthracene was synthesized by a selective tin-antimony exchange reaction and investigated regarding its ability to act as a Lewis acidic host component for the complexation of Lewis basic or anionic guests. In this work, the novel C≡C-Sb(C2 F5 )2 unit was established to study the potential of antimony(III) sites as representatives for the scarcely explored pnictogen bonding donors. The capability of this partly fluorinated host system was investigated towards halide anions (Cl- , Br- , I- ), dimethyl chalcogenides Me2 Y (Y=O, S, Se, Te), and nitrogen heterocycles (pyridine, pyrimidine). Insights into the adduct formation behavior as well as the bonding situation of such E⋅⋅⋅Sb-CF moieties were obtained in solution by means of NMR spectroscopy, in the solid state by X-ray diffraction, by elemental analyses, and by computational methods (DFT, QTAIM, IQA), respectively.
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Affiliation(s)
- J Louis Beckmann
- Chair of Inorganic and Structural Chemistry, Center for Molecular Materials CM2 Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Jonas Krieft
- Chair of Inorganic and Structural Chemistry, Center for Molecular Materials CM2 Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Yury V Vishnevskiy
- Chair of Inorganic and Structural Chemistry, Center for Molecular Materials CM2 Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Beate Neumann
- Chair of Inorganic and Structural Chemistry, Center for Molecular Materials CM2 Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Hans-Georg Stammler
- Chair of Inorganic and Structural Chemistry, Center for Molecular Materials CM2 Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Norbert W Mitzel
- Chair of Inorganic and Structural Chemistry, Center for Molecular Materials CM2 Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
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3
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Radiush EA, Wang H, Chulanova EA, Ponomareva YA, Li B, Wei QY, Salnikov GE, Petrakova SY, Semenov NA, Zibarev AV. Halide Complexes of 5,6-Dicyano-2,1,3-Benzoselenadiazole with 1 : 4 Stoichiometry: Cooperativity between Chalcogen and Hydrogen Bonding. Chempluschem 2023; 88:e202300523. [PMID: 37750466 DOI: 10.1002/cplu.202300523] [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: 09/19/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
The [M4 -Hal]- (M=the title compound; Hal=Cl, Br, and I) complexes were isolated in the form of salts of [Et4 N]+ cation and characterized by XRD, NMR, UV-Vis, DFT, QTAIM, EDD, and EDA. Their stoichiometry is caused by a cooperative interplay of σ-hole-driven chalcogen (ChB) and hydrogen (HB) bondings. In the crystal, [M4 -Hal]- are connected by the π-hole-driven ChB; overall, each [Hal]- is six-coordinated. In the ChB, the electrostatic interaction dominates over orbital and dispersion interactions. In UV-Vis spectra of the M+[Hal]- solutions, ChB-typical and [Hal]- -dependent charge-transfer bands are present; they reflect orbital interactions and allow identification of the individual [Hal]- . However, the structural situation in the solutions is not entirely clear. Particularly, the UV-Vis spectra of the solutions are different from the solid-state spectra of the [Et4 N]+ [M4 -Hal]- ; very tentatively, species in the solutions are assigned [M-Hal]- . It is supposed that the formation of the [M4 -Hal]- proceeds during the crystallization of the [Et4 N]+ [M4 -Hal]- . Overall, M can be considered as a chromogenic receptor and prototype sensor of [Hal]- . The findings are also useful for crystal engineering and supramolecular chemistry.
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Affiliation(s)
- Ekaterina A Radiush
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Hui Wang
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Elena A Chulanova
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Institute for Applied Physics, University of Tübingen, 72076, Tübingen, Germany
| | - Yana A Ponomareva
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Natural Sciences, National Research University - Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Bin Li
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Qiao Yu Wei
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Georgy E Salnikov
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Svetlana Yu Petrakova
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Nikolay A Semenov
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Andrey V Zibarev
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
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Zhang X, Wu J, Yan H, Chen H, Mao W, Dai G. Insight into the nature of the noncovalent interactions of furan, pyridine, and pyrazine with AtX. J Mol Model 2023; 29:13. [DOI: 10.1007/s00894-022-05411-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
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Varadwaj PR. Tetrel Bonding in Anion Recognition: A First Principles Investigation. Molecules 2022; 27:molecules27238449. [PMID: 36500544 PMCID: PMC9738195 DOI: 10.3390/molecules27238449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Twenty-five molecule-anion complex systems [I4Tt···X-] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I4Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I4C···X-] series and [I4Tt···X-] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from -3.0 to -112.2 kcal mol-1. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I4Tt···X-] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule-anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan; or
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
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6
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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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Feng W, Li D, Cheng L. Theoretical study on L-H +-L with identical donors: short strong hydrogen bond or not? J Chem Phys 2022; 157:094302. [DOI: 10.1063/5.0103228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Short strong hydrogen bonds (SSHBs) play crucial role in many chemical processes. Recently, as the representative of SSHBs, [F-H-F]- was experimentally observed. [F-H-F]- has a symmetric structure, which can be described as a H+ acid shared by two terminal F- donors (F--H+-F-). To explore whether two identical donors are bound to result in SSHBs, we performed theoretical studies on a series of compounds (L-H+-L) with two identical electron donors (L corresponds to donors containing group 14, 15, 16 and 17 elements). The results show that identical donors do not definitely lead to SSHBs. Instead, typical hydrogen bonds also exist. We found that both electronegativity and basicity contribute to the patterns of hydrogen bonds, where more electronegative and weaker donors benefit to SSHBs. Besides, it was found that zero-point energies also respond to the hydrogen bonding systems. This systemic work is expected to provide more insights into SSHBs.
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Affiliation(s)
- Wanwan Feng
- Anhui University Department of Chemistry, China
| | - Dan Li
- Anhui University - Qingyuan Campus, China
| | - Longjiu Cheng
- Department of Chemistry, Anhui University College of Chemistry and Chemical Engineering, China
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8
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Mahmoudi G, García-Santos I, Pittelkow M, Kamounah FS, Zangrando E, Babashkina MG, Frontera A, Safin DA. The tetrel bonding role in supramolecular aggregation of lead(II) acetate and a thiosemicarbazide derivative. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:685-694. [PMID: 35975834 DOI: 10.1107/s2052520622005789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
A new PbII coordination complex [PbL(OAc)], which was readily synthesized from a mixture of Pb(OAc)2·3H2O and 1-(pyridin-2-yl)benzylidene-4-phenylthiosemicarbazide (HL) is reported. The crystal structure analysis of [PbL(OAc)] showed that the PbII cation is N,N',S-chelated by the tridentate pincer-type ligand L and by the oxygen atoms of the acetate anion. In addition, the metal centre forms Pb...O and Pb...S tetrel bonds with an adjacent complex molecule, yielding a 1D zigzag polymeric chain, which is reinforced by N-H...O hydrogen bonds and π...π interactions. These chains are interlinked by C-H...py non-covalent interactions, realized between one of the acetate hydrogen atoms and the pyridine rings. According to the Hirshfeld surface analysis, the crystal packing is mainly characterized by intermolecular H...H, H...C and H...O contacts, followed by H...N, H...S, C...C, C...N, Pb...H, Pb...O and Pb...S contacts. The FTIR and 1H NMR spectra of [PbL(OAc)] testify to the deprotonation of the parent ligand HL, while the acetate ligand exhibits an anisobidentate coordination mode as established by means of single-crystal X-ray diffraction and FTIR spectroscopy. Lastly, theoretical calculations at the PBE0-D3/def2-TZVP level of theory have been used to analyze and characterize the Pb...O and Pb...S tetrel bonds observed in the crystal of [PbL(OAc)], using a combination of QTAIM (Quantum Theory of Atoms in Molecules) and NCIPlot (Non-Covalent Interaction Plot) computational tools.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, PO Box 55181-83111, Maragheh, Iran
| | - Isabel García-Santos
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Maria G Babashkina
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, 640020 Kurgan, Russian Federation
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca, Spain
| | - Damir A Safin
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, 640020 Kurgan, Russian Federation
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9
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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: 15] [Impact Index Per Article: 7.5] [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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10
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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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Yuan L, Jiang P, Hu J, Zeng H, Huo Y, Li Z, Zeng H. A highly active and selective chalcogen bond-mediated perchlorate channel. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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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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13
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Riel AMS, Decato DA, Sun J, Berryman OB. Halogen bonding organocatalysis enhanced through intramolecular hydrogen bonds. Chem Commun (Camb) 2022; 58:1378-1381. [PMID: 34989732 PMCID: PMC8919959 DOI: 10.1039/d1cc05475a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recent results indicate a halogen bond donor is strengthened through direct interaction with a hydrogen bond to the electron-rich belt of the halogen. Here, this Hydrogen Bond enhanced Halogen Bond (HBeXB) plays a clear role in a catalyst. Our HBeXB catalyst improves product conversion in a halide abstraction reaction over a traditional halogen bonding derivative.
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Affiliation(s)
| | - Daniel A. Decato
- Address University of Montana, 32 Campus Drive, Missoula, MT, USA
| | - Jiyu Sun
- Address University of Montana, 32 Campus Drive, Missoula, MT, USA
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Aliyarova IS, Tupikina EY, Ivanov DM, Kukushkin VY. Metal-Involving Halogen Bonding Including Gold(I) as a Nucleophilic Partner. The Case of Isomorphic Dichloroaurate(I)·Halomethane Cocrystals. Inorg Chem 2022; 61:2558-2567. [DOI: 10.1021/acs.inorgchem.1c03482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Irina S. Aliyarova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Elena Yu. Tupikina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Daniil M. Ivanov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, Barnaul 656049, Russian Federation
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15
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Radiush EA, Pritchina EA, Chulanova EA, Dmitriev AA, Bagryanskaya IY, Slawin AMZ, Woollins JD, Gritsan NP, Zibarev AV, Semenov NA. Chalcogen-bonded donor–acceptor complexes of 5,6-dicyano[1,2,5]selenadiazolo[3,4- b]pyrazine with halide ions. NEW J CHEM 2022. [DOI: 10.1039/d2nj02345h] [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
With halides X− (X = Cl, Br, I) 5,6-dicyano-[1,2,5]selenadiazolo[3,4-b]pyrazine 1 forms chalcogen-bonded complexes [1–X]− structurally defined by XRD. UV/Vis spectra of [1–X]− feature red-shifted charge-transfer bands in the Vis part.
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Affiliation(s)
- Ekaterina A. Radiush
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena A. Pritchina
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, National Research University – Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena A. Chulanova
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey A. Dmitriev
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, National Research University – Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | | | - J. Derek Woollins
- School of Chemistry, University of St. Andrews, St Andrews, Fife KY16 9ST, UK
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Nina P. Gritsan
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zibarev
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nikolay A. Semenov
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Karmakar M, Gomila RM, Frontera A, Chattopadhyay S. Large interaction energy for the homodimer and the heterodimer extracted from the supramolecular chain of a bent trinuclear zinc( ii) complex with a reduced Schiff base ligand. NEW J CHEM 2022. [DOI: 10.1039/d1nj03984a] [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 coordinated amino groups in a trinuclear zinc complex participate in strong H-bonding interactions that have been analysed. The dimerization energy is very large for both the homodimer and the heterodimer in the 1D supramolecular chain.
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Affiliation(s)
- Mainak Karmakar
- Department of Chemistry, Inorganic Section, Jadavpur University, Kolkata 700032, India
| | - Rosa M. Gomila
- Serveis Cientificotècnics, 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
| | - Shouvik Chattopadhyay
- Department of Chemistry, Inorganic Section, Jadavpur University, Kolkata 700032, India
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17
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Torubaev YV, Rozhkov AV, Skabitsky IV, Gomila RM, Frontera A, Kukushkin VY. Heterovalent chalcogen bonding: supramolecular assembly driven by the occurrence of a tellurium( ii)⋯Ch( i) (Ch = S, Se, Te) linkage. Inorg Chem Front 2022. [DOI: 10.1039/d2qi01420c] [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 revealed heterovalent TeII⋯ChI (Ch = S, Se, Te) chalcogen bonding was used for targeted noncovalent integration of two Ch centers in different oxidation states.
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Affiliation(s)
- Yury V. Torubaev
- N. S. Kurnakov Institute of General and Inorganic Chemistry of Russian Academy of Sciences, Moscow, 119991, Russian Federation
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anton V. Rozhkov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Ivan V. Skabitsky
- N. S. Kurnakov Institute of General and Inorganic Chemistry of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Rosa M. Gomila
- Department of Chemistry, Universitat de les Illes Balears, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, 07122 Palma de Mallorca, Baleares, Spain
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049 Barnaul, Russian Federation
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18
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Malenov DP, Zarić SD. New Type of Aromatic π-Systems for Anion Recognition: Strong Anion-π and C-H⋅⋅⋅Anion Interactions Between Halides and Aromatic Ligands in Half-Sandwich Compounds. Chemistry 2021; 27:17862-17872. [PMID: 34719802 DOI: 10.1002/chem.202102896] [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: 08/09/2021] [Indexed: 11/11/2022]
Abstract
Half-sandwich compounds of benzene, cyclopentadienyl, pentamethylcyclopentadienyl, and indenyl were studied as a new type of aromatic π-systems for interactions with halide anions. Although uncoordinated benzene forms only C-H⋅⋅⋅anion interactions, and hexafluorobenzene forms only anion-π interactions, aromatic ligands in half-sandwich compounds can form both types of interactions, because their entire electrostatic potential surface is positive. These aromatic ligands can form stronger anion-π interactions than organic aromatic molecules, as a consequence of more pronounced dispersion and induction energy components. Moreover, C-H⋅⋅⋅anion interactions of aromatic ligands are stronger than anion-π interactions, and significantly stronger than C-H⋅⋅⋅anion interactions of benzene. Our study shows that transition-metal coordination can make aromatic moieties suitable for strong interactions with anions, and gives insight into the design of new anion receptors.
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Affiliation(s)
- Dušan P Malenov
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia
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19
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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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20
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Biswal HS, Sahu AK, Galmés B, Frontera A, Chopra D. Se⋅⋅⋅O/S and S⋅⋅⋅O Chalcogen Bonds in Small Molecules and Proteins: A Combined CSD and PDB Study. Chembiochem 2021; 23:e202100498. [PMID: 34693623 PMCID: PMC9298333 DOI: 10.1002/cbic.202100498] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/23/2021] [Indexed: 12/13/2022]
Abstract
The importance of selenium-centered noncovalent chalcogen bonds represented as Se⋅⋅⋅A (A=O/S) has been explored for short directional contacts in small molecules and proteins. In addition, S⋅⋅⋅O centered contacts have been analyzed. Computational analyses involving the quantitative assessment of the associated energetics, the molecular electrostatic potentials (MEP), and electron density derived topological parameters, namely, quantum theory of atom in molecules (QTAIM) analyses, and NBO (natural bond orbital) based calculations, have been performed to unequivocally establish the strength, stability, and attractive role of chalcogen bonds in the solid-state. This investigation has been performed in molecules from both the Cambridge Structural Database (CSD) and Protein Data Bank (PDB). Thus futuristic materials may be designed keeping in mind the significance of these interactions, including their relevance in biology.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Bartomeu Galmés
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
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21
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Ivanov DM, Bokach NA, Yu Kukushkin V, Frontera A. Metal Centers as Nucleophiles: Oxymoron of Halogen Bond-Involving Crystal Engineering. Chemistry 2021; 28:e202103173. [PMID: 34623005 PMCID: PMC9298210 DOI: 10.1002/chem.202103173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 02/06/2023]
Abstract
This review highlights recent studies discovering unconventional halogen bonding (HaB) that involves positively charged metal centers. These centers provide their filled d‐orbitals for HaB, and thus behave as nucleophilic components toward the noncovalent interaction. This role of some electron‐rich transition metal centers can be considered an oxymoron in the sense that the metal is, in most cases, formally cationic; consequently, its electron donor function is unexpected. The importance of Ha⋅⋅⋅d‐[M] (Ha=halogen; M is Group 9 (Rh, Ir), 10 (Ni, Pd, Pt), or 11 (Cu, Au)) interactions in crystal engineering is emphasized by showing remarkable examples (reported and uncovered by our processing of the Cambridge Structural Database), where this Ha⋅⋅⋅d‐[M] directional interaction guides the formation of solid supramolecular assemblies of different dimensionalities.
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Affiliation(s)
- Daniil M Ivanov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Nadezhda A Bokach
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Vadim Yu Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation.,Institute of Chemistry and Pharmaceutical Technologies, Altai State University, Barnaul, 656049, Russian Federation
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Palma de Mallorca (Baleares), 07122, Spain
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22
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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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23
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24
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Efimenko ZM, Rozhkov AV, Suslonov VV, Kuznetsov ML, Kukushkin VY, Bokach NA. Copper(II)-Mediated Iodination of 1-Nitroso-2-naphthol. Molecules 2021; 26:molecules26185708. [PMID: 34577180 PMCID: PMC8465374 DOI: 10.3390/molecules26185708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
The 3-Iodo-1-nitrosonaphthalene-2-ol (I-NON) was obtained by the copper(II)-mediated iodination of 1-nitroso-2-naphthol (NON). The suitable reactants and optimized reaction conditions, providing 94% NMR yield of I-NON, included the usage of Cu(OAc)2·H2O and 1:2:8 CuII/NON/I2 molar ratio between the reactants. The obtained I-NON was characterized by elemental analyses (C, H, N), high-resolution ESI+-MS, 1H and 13C{1H} NMR, FTIR, UV-vis spectroscopy, TGA, and X-ray crystallography (XRD). The copper(II) complexes bearing deprotonated I-NON were prepared as follows: cis-[Cu(I-NON-H)(I-NON)](I3) (1) was obtained by the reaction between Cu(NON-H)2 and I2 in CHCl3/MeOH, while trans-[Cu(I-NON-H)2] (2) was synthesized from I-NON and Cu(OAc)2 in MeOH. Crystals of trans-[Cu(I-NON-H)2(THF)2] (3) and trans-[Cu(I-NON-H)2(Py)2] (4) were precipitated from solutions of 2 in CHCl3/THF and Py/CHCl3/MeOH mixtures, respectively. The structures of 1 and 3-4 were additionally verified by X-ray crystallography. The characteristic feature of the structures of 1 and 3 is the presence of intermolecular halogen bonds with the involvement of the iodine center of the metal-bound deprotonated I-NON. The nature of the I···I and I···O contacts in the structures of 1 and 3, correspondingly, were studied theoretically at the DFT (PBE0-D3BJ) level using the QTAIM, ESP, ELF, NBO, and IGM methods.
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Affiliation(s)
- Zarina M. Efimenko
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (Z.M.E.); (A.V.R.); (V.V.S.); (M.L.K.); (V.Y.K.)
| | - Anton V. Rozhkov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (Z.M.E.); (A.V.R.); (V.V.S.); (M.L.K.); (V.Y.K.)
| | - Vitalii V. Suslonov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (Z.M.E.); (A.V.R.); (V.V.S.); (M.L.K.); (V.Y.K.)
| | - Maxim L. Kuznetsov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (Z.M.E.); (A.V.R.); (V.V.S.); (M.L.K.); (V.Y.K.)
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (Z.M.E.); (A.V.R.); (V.V.S.); (M.L.K.); (V.Y.K.)
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049 Barnaul, Russia
| | - Nadezhda A. Bokach
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (Z.M.E.); (A.V.R.); (V.V.S.); (M.L.K.); (V.Y.K.)
- Correspondence:
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25
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Structural insights into coordination polymers based on 6s2 Pb(II) and Bi(III) centres connected via heteroaromatic carboxylate linkers and their potential applications. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213935] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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26
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Frontera A, Bauzá A. Biological halogen bonds in protein-ligand complexes: a combined QTAIM and NCIPlot study in four representative cases. Org Biomol Chem 2021; 19:6858-6864. [PMID: 34319314 DOI: 10.1039/d1ob01212f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, the PDB has been manually scrutinized by using a subset of all PDB entries containing organic iodinated ligands. Four structures exhibiting short IA halogen bonding (HaB) contacts (A stands for the σ-hole acceptor) have been selected and further analysed. In most hits, the sigma-hole acceptor corresponds to an O-atom of the amido group belonging to the protein backbone. In a minority of hits, the electron donors are O, S, Se or π-systems of the amino-acid side chains. A judicious selection of four PDB structures presenting all four types of HaB interactions (C-IA, A = O, S, Se, π) has been performed. For these selected structures, a comprehensive RI-MP2/def2-TZVP study has been carried out to evaluate the HaB energetically. Moreover, the interactions have been characterized by combining the quantum theory of "atoms-in-molecules" (QTAIM) and the noncovalent interaction plot (NCIPlot) and rationalized using the molecular electrostatic potential (MEP) surface.
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Affiliation(s)
- 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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27
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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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28
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Mahmoudi G, Zangrando E, Miroslaw B, Gurbanov AV, Babashkina MG, Frontera A, Safin DA. Spodium bonding and other non-covalent interactions assisted supramolecular aggregation in a new mercury(II) complex of a nicotinohydrazide derivative. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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29
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study. J Comput Chem 2021; 42:688-698. [PMID: 33543482 PMCID: PMC7986859 DOI: 10.1002/jcc.26489] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/27/2022]
Abstract
We have performed a hierarchical ab initio benchmark and DFT performance study of D2 Ch•••A- chalcogen bonds (Ch = S, Se; D, A = F, Cl). The ab initio benchmark study is based on a series of ZORA-relativistic quantum chemical methods [HF, MP2, CCSD, CCSD(T)], and all-electron relativistically contracted variants of Karlsruhe basis sets (ZORA-def2-SVP, ZORA-def2-TZVPP, ZORA-def2-QZVPP) with and without diffuse functions. The highest-level ZORA-CCSD(T)/ma-ZORA-def2-QZVPP counterpoise-corrected complexation energies (ΔECPC ) are converged within 1.1-3.4 kcal mol-1 and 1.5-3.1 kcal mol-1 with respect to the method and basis set, respectively. Next, we used the ZORA-CCSD(T)/ma-ZORA-def2-QZVPP (ΔECPC ) as reference data for analyzing the performance of 13 different ZORA-relativistic DFT approaches in combination with the Slater-type QZ4P basis set. We find that the three-best performing functionals are M06-2X, B3LYP, and M06, with mean absolute errors (MAE) of 4.1, 4.2, and 4.3 kcal mol-1 , respectively. The MAE for BLYP-D3(BJ) and PBE amount to 8.5 and 9.3 kcal mol-1 , respectively.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Institute for Molecules and MaterialsRadboud University NijmegenNijmegenNetherlands
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30
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de Azevedo Santos L, van der Lubbe SCC, Hamlin TA, Ramalho TC, Matthias Bickelhaupt F. A Quantitative Molecular Orbital Perspective of the Chalcogen Bond. ChemistryOpen 2021; 10:391-401. [PMID: 33594829 PMCID: PMC8015733 DOI: 10.1002/open.202000323] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO-LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A- to D2 Ch.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
| | - Stephanie C. C. van der Lubbe
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Teodorico C. Ramalho
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute for Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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31
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Tiekink ERT. Zero-, one-, two- and three-dimensional supramolecular architectures sustained by Se …O chalcogen bonding: A crystallographic survey. Coord Chem Rev 2021; 427:213586. [PMID: 33100367 PMCID: PMC7568495 DOI: 10.1016/j.ccr.2020.213586] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
The Cambridge Structural Database was evaluated for crystals containing Se…O chalcogen bonding interactions. These secondary bonding interactions are found to operate independently of complementary intermolecular interactions in about 13% of the structures they can potentially form. This number rises significantly when more specific interactions are considered, e.g. Se…O(carbonyl) interactions occur in 50% of cases where they can potentially form. In about 55% of cases, the supramolecular assemblies sustained by Se…O(oxygen) interactions are one-dimensional architectures, with the next most prominent being zero-dimensional assemblies, at 30%.
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Affiliation(s)
- Edward R T Tiekink
- Research Centre for Crystalline Materials, School of Science and Technology, 5 Jalan Universiti, Sunway University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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32
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Scheiner S. Comparison of Bifurcated Halogen with Hydrogen Bonds. Molecules 2021; 26:molecules26020350. [PMID: 33445461 PMCID: PMC7827642 DOI: 10.3390/molecules26020350] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 01/30/2023] Open
Abstract
Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH3 and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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Gomila RM, Bauzá A, Mooibroek TJ, Frontera A. Spodium bonding in five coordinated Zn(ii): a new player in crystal engineering? CrystEngComm 2021. [DOI: 10.1039/d1ce00221j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This highlight evidences the existence and importance of spodium bonds (SpB) in solid state structures involving five-coordinated square-pyramidal Zn(ii) spodium atom.
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Affiliation(s)
- Rosa M. Gomila
- Universitat de les Illes Balears
- Serveis Científico-Tècnics
- 07122 Palma de Mallorca
- Spain
| | - Antonio Bauzá
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- Netherlands
| | - Antonio Frontera
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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Torubaev YV, Skabitsky IV, Rozhkov AV, Galmés B, Frontera A, Kukushkin VY. Highly polar stacking interactions wrap inorganics in organics: lone-pair–π-hole interactions between the PdO 4 core and electron-deficient arenes. Inorg Chem Front 2021. [DOI: 10.1039/d1qi01067k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Each PdO4 plane of Pd3(OAc)6 behaved as a 5-center nucleophile (O lone pairs and the dz2-PdII orbital) that interacts with π-donating arenes to afford highly polar circular stacking, where organics wrapped inorganics.
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Affiliation(s)
- Yury V. Torubaev
- N. S. Kurnakov Institute of General and Inorganic Chemistry, of Russian Academy of Sciences, Moscow, 119991 Russian Federation
| | - Ivan V. Skabitsky
- N. S. Kurnakov Institute of General and Inorganic Chemistry, of Russian Academy of Sciences, Moscow, 119991 Russian Federation
| | - Anton V. Rozhkov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034 Russian Federation
| | - Bartomeu Galmés
- Department of Chemistry, Universitat de les IllesBalears, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les IllesBalears, 07122 Palma de Mallorca, Baleares, Spain
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034 Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049 Barnaul, Russian Federation
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Rana A, Galmés B, Frontera A, Biswal HS, Chopra D. Unravelling the electronic nature of C-FO-C non-covalent interaction in proteins and small molecules in the solid state. Phys Chem Chem Phys 2020; 22:25704-25711. [PMID: 33146185 DOI: 10.1039/d0cp05280a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The participation of organic fluorine as a halogen bond donor is rare and is sensitive to the electronic environment in the vicinity of the fluorine atom. The enhancement in the electropositive character (the σ-hole formalism) in fluorine is established by the presence of electron withdrawing groups and this has been examined in the solid-state structures in small molecules and proteins. Short, directional FO contacts have been observed and physical insights obtained, from quantum mechanical calculations, via the molecular electrostatic potential, an analysis of their topological features from atoms-in-molecules, and donor-acceptor characteristics from natural bond orbital analyses. It was observed that such contacts, cooperatively act in the presence of other interactions, and the formed aggregates are stabilizing in nature. In addition, the FO has a bonding character and is attractive in nature. The halogen bonding character of fluorine is relevant in supramolecular chemistry.
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Affiliation(s)
- Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, 752050, Bhubaneswar, India.
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Alashkar N, Arca M, Alnasr H, Lutter M, Lippolis V, Jurkschat K. Water‐Soluble Organotin Compounds – Syntheses, Structures and Reactivity towards Fluoride Anions in Water. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nour Alashkar
- Lehrstuhl für Anorganische Chemie II Technische Universität Dortmund 44221 Dortmund Germany
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche Università degli Studi di Cagliari S.S. 554 Bivio per Sestu 09042 Monserrato (CA) Italy
| | - Hazem Alnasr
- Lehrstuhl für Anorganische Chemie II Technische Universität Dortmund 44221 Dortmund Germany
| | - Michael Lutter
- Lehrstuhl für Anorganische Chemie II Technische Universität Dortmund 44221 Dortmund Germany
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche Università degli Studi di Cagliari S.S. 554 Bivio per Sestu 09042 Monserrato (CA) Italy
| | - Klaus Jurkschat
- Lehrstuhl für Anorganische Chemie II Technische Universität Dortmund 44221 Dortmund Germany
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McDowell SAC, Wang R, Li Q. Interactions in Model Ionic Dyads and Triads Containing Tetrel Atoms. Molecules 2020; 25:molecules25184197. [PMID: 32937741 PMCID: PMC7570900 DOI: 10.3390/molecules25184197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022] Open
Abstract
The interactions in model ionic YTX3···Z (Y = NC, F, Cl, Br; X = F, Cl, Br, Z = F-, Cl-, Br-, Li+) dyads containing the tetrel atoms, T = C, Si, Ge, were studied using ab initio computational methods, including an energy decomposition analysis, which found that the YTX3 molecules were stabilized by both anions (via tetrel bonding) and cations (via polarization). For the tetrel-bonded dyads, both the electrostatic and polarization forces make comparable contributions to the binding in the C-containing dyads, whereas, electrostatic forces are by far the largest contributor to the binding in the Si- and Ge-containing analogues. Model metastable Li+···NCTCl3···F- (T = C, Si, Ge) triads were found to be lower in energy than the combined energy of the Li+ + NCTCl3 + F- fragments. The pair energies and cooperative energies for these highly polar triads were also computed and discussed.
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Affiliation(s)
- Sean A. C. McDowell
- Department of Biological and Chemical Sciences, Cave Hill Campus, The University of the West Indies, P.O. Box 64, Bridgetown BB11000, Barbados
- Correspondence: (S.A.C.M.); (Q.L.)
| | - Ruijing Wang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
- Correspondence: (S.A.C.M.); (Q.L.)
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Lu J, Scheiner S. Relationships between Bond Strength and Spectroscopic Quantities in H-Bonds and Related Halogen, Chalcogen, and Pnicogen Bonds. J Phys Chem A 2020; 124:7716-7725. [DOI: 10.1021/acs.jpca.0c05936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jia Lu
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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Mahmoudi G, Abedi M, Lawrence SE, Zangrando E, Babashkina MG, Klein A, Frontera A, Safin DA. Tetrel Bonding and Other Non-Covalent Interactions Assisted Supramolecular Aggregation in a New Pb(II) Complex of an Isonicotinohydrazide. Molecules 2020; 25:molecules25184056. [PMID: 32899863 PMCID: PMC7571010 DOI: 10.3390/molecules25184056] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/31/2022] Open
Abstract
A new supramolecular Pb(II) complex [PbL(NO2)]n was synthesized from Pb(NO3)2, N’-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and NaNO2. [PbL(NO2)]n is constructed from discrete [PbL(NO2)] units with an almost ideal N2O3 square pyramidal coordination environment around Pb(II). The ligand L− is coordinated through the 2-pyridyl N-atom, one aza N-atom, and the carbonyl O-atom. The nitrite ligand binds in a κ2-O,O coordination mode through both O-atoms. The Pb(II) center exhibits a hemidirected coordination geometry with a pronounced coordination gap, which allows a close approach of two additional N-atoms arising from the N=C(O) N-atom of an adjacent molecule and from the 4-pyridyl N-atom from the another adjacent molecule, yielding a N4O3 coordination, constructed from two Pb–N and three Pb–O covalent bonds, and two Pb⋯N tetrel bonds. Dimeric units in the structure of [PbL(NO2)]n are formed by the Pb⋯N=C(O) tetrel bonds and intermolecular electrostatically enforced π+⋯π− stacking interactions between the 2- and 4-pyridyl rings and further stabilized by C–H⋯π intermolecular interactions, formed by one of the methyl H-atoms and the 4-pyridyl ring. These dimers are embedded in a 2D network representing a simplified uninodal 3-connected fes (Shubnikov plane net) topology defined by the point symbol (4∙82). The Hirshfeld surface analysis of [PbL(NO2)] revealed that the intermolecular H⋯X (X = H, C, N, O) contacts occupy an overwhelming majority of the molecular surface of the [PbL(NO2)] coordination unit. Furthermore, the structure is characterized by intermolecular C⋯C and C⋯N interactions, corresponding to the intermolecular π⋯π stacking interactions. Notably, intermolecular Pb⋯N and, most interestingly, Pb⋯H interactions are remarkable contributors to the molecular surface of [PbL(NO2)]. While the former contacts are due to the Pb⋯N tetrel bonds, the latter contacts are mainly due to the interaction with the methyl H-atoms in the π⋯π stacked [PbL(NO2)] molecules. Molecular electrostatic potential (MEP) surface calculations showed marked electrostatic contributions to both the Pb⋯N tetrel bonds and the dimer forming π+⋯π− stacking interactions. Quantum theory of atoms in molecules (QTAIM) analyses underlined the tetrel bonding character of the Pb⋯N interactions. The manifold non-covalent interactions found in this supramolecular assembly are the result of the proper combination of the polyfunctional multidentate pyridine-hydrazide ligand and the small nitrito auxiliary ligand.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh P.O. Box 55181-83111, Iran
- Correspondence: (G.M.); (A.K.); (D.A.S.)
| | - Marjan Abedi
- Department of Chemistry, Faculty of Science, University of Mohaghegh Ardabili, Ardabil P.O. Box 56199-11367, Iran;
| | - Simon E. Lawrence
- School of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, T12 K8AF Cork, Ireland;
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Maria G. Babashkina
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, D-50939 Köln, Germany;
| | - Axel Klein
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, D-50939 Köln, Germany;
- Correspondence: (G.M.); (A.K.); (D.A.S.)
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 5.7, 7122 Palma de Mallorca Baleares, Spain;
| | - Damir A. Safin
- Institute of Chemistry, University of Tyumen, Volodarskogo Str. 6, 625003 Tyumen, Russia
- West-Siberian Interregional Scientific and Educational Center, 625003 Tyumen, Russia
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B.N. Eltsin, Mira Str. 19, 620002 Ekaterinburg, Russia
- Correspondence: (G.M.); (A.K.); (D.A.S.)
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Mahmudov KT, Gurbanov AV, Aliyeva VA, Resnati G, Pombeiro AJ. Pnictogen bonding in coordination chemistry. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213381] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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: 103] [Impact Index Per Article: 25.8] [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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Ong WSY, Smaldone RA, Dodani SC. A neutral porous organic polymer host for the recognition of anionic dyes in water. Chem Sci 2020; 11:7716-7721. [PMID: 34094147 PMCID: PMC8159435 DOI: 10.1039/d0sc02941f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/19/2020] [Indexed: 11/21/2022] Open
Abstract
Neutral hosts for the recognition of anionic guests in water remain underdeveloped due to the inherent thermodynamic barrier for desolvation. To address this challenge, we have repurposed crosslinked porous organic polymers (POPs) as hosts. This polymer architecture affords a hydrophobic environment with a densely packed array of urea hydrogen bond donors to cooperatively promote anion desolvation and recognition in water. Using the principles of supramolecular design, we demonstrate through adsorption assays that the resulting Urea-POP-1 can recognize structurally different dyes containing phosphonate, sulfonate, and carboxylate anions in water. Moreover, when compared to Methyl-POP-1, a control POP lacking hydrogen bond donors, we find that the driving force for desolvation and adsorption of each dye is achieved through hydrophobic interactions with the POP backbone and, more importantly, cooperative hydrogen bonding interactions with the urea sidechains. This starting point sets the stage to exploit the modularity of our design to build a family of neutral polymer hosts with tunable pore sizes and anion preferences for fundamental investigations and targeted applications.
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Affiliation(s)
- Whitney S Y Ong
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA
| | - Ronald A Smaldone
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA
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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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Ananyev IV, Bokach NA, Kukushkin VY. Structure-directing sulfur...metal noncovalent semicoordination bonding. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:436-449. [PMID: 32831262 DOI: 10.1107/s2052520620005685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
The abundance and geometric features of nonbonding contacts between metal centers and `soft' sulfur atoms bound to a non-metal substituent R were analyzed by processing data from the Cambridge Structural Database. The angular arrangement of M, S and R atoms with ∠(R-S...M) down to 150° was a common feature of the late transition metal complexes exhibiting shortened R-S...M contacts. Several model nickel(II), palladium(II), platinum(II) and gold(I) complexes were chosen for a theoretical analysis of R-S...M interactions using the DFT method applied to (equilibrium) isolated systems. A combination of the real-space approaches, such as Quantum Theory of Atoms in Molecules (QTAIM), noncovalent interaction index (NCI), electron localization function (ELF) and Interacting Quantum Atoms (IQA), and orbital (Natural Bond Orbitals, NBO) methods was used to provide insights into the nature and energetics of R-S...M interactions with respect to the metal atom identity and its coordination environment. The explored features of the R-S...M interactions support the trends observed by inspecting the CSD statistics, and indicate a predominant contribution of semicoordination bonds between nucleophilic sites of the sulfur atom and electrophilic sites of the metal. A contribution of chalcogen bonding (that is formally opposite to semicoordination) was also recognized, although it was significantly smaller in magnitude. The analysis of R-S...M interaction strengths was performed and the structure-directing role of the intramolecular R-S...M interactions in stabilizing certain conformations of metal complexes was revealed.
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Affiliation(s)
- Ivan V Ananyev
- Laboratory of X-ray Structural Studies, Institute of Organoelement Compounds (INEOS) of RAS, Vavilova Str., 28, Moscow, 119991, Russian Federation
| | - Nadezhda A Bokach
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, Saint Petersburg, Russian Federation
| | - Vadim Yu Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, Saint Petersburg, Russian Federation
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Preorganization-enhanced halogen bonding via intramolecular hydrogen bonding: a theoretical study. Struct Chem 2020. [DOI: 10.1007/s11224-020-01559-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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48
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Katlenok EA, Haukka M, Levin OV, Frontera A, Kukushkin VY. Supramolecular Assembly of Metal Complexes by (Aryl)I⋅⋅⋅d[PtII] Halogen Bonds. Chemistry 2020; 26:7692-7701. [DOI: 10.1002/chem.202001196] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/31/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Eugene A. Katlenok
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Matti Haukka
- Department of ChemistryUniversity of Jyväskylä P.O. Box 35 40014 Jyväskylä Finland
| | - Oleg V. Levin
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Antonio Frontera
- Department de QuímicaUniversitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma, de Mallorca Baleares Spain
| | - Vadim Yu. Kukushkin
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
- South Ural State University Lenin Av. 76 454080 Chelyabinsk Russian Federation
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McDowell SA. A computational study of XCCl3 (X = NC, F, Cl, Br) interacting with model ions. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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50
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Mahmoudi G, Lawrence SE, Cisterna J, Cárdenas A, Brito I, Frontera A, Safin DA. A new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine. NEW J CHEM 2020. [DOI: 10.1039/d0nj04444j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this manuscript, the synthesis and X-ray characterization of a new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine are reported.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry
- Faculty of Science
- University of Maragheh
- Maragheh
- Iran
| | - Simon E. Lawrence
- School of Chemistry, Analytical and Biological Chemistry Research Facility
- Synthesis and Solid State Pharmaceutical Centre
- University College Cork
- Cork
- UK
| | - Jonathan Cisterna
- Departamento de Química
- Facultad de Ciencias Básicas
- Universidad de Antofagasta
- Antofagasta
- Chile
| | - Alejandro Cárdenas
- Departamento de Física
- Facultad de Ciencias Básicas
- Universidad de Antofagasta
- Antofagasta
- Chile
| | - Iván Brito
- Departamento de Química
- Facultad de Ciencias Básicas
- Universidad de Antofagasta
- Antofagasta
- Chile
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Damir A. Safin
- University of Tyumen
- 625003 Tyumen
- Russian Federation
- West-Siberian Interregional Scientific and Educational Center
- Russian Federation
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