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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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Bankiewicz B, Kupfer S, Matczak P. Tuning the metal-ligand bond in the σ-complexes of stannylenes and azabenzenes. J Comput Chem 2021; 42:2103-2115. [PMID: 34420225 DOI: 10.1002/jcc.26741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/01/2021] [Accepted: 07/26/2021] [Indexed: 11/10/2022]
Abstract
The metal-ligand bond in a set of 60 σ-complexes has been investigated by electronic structure computations. These σ-complexes originate from the unique combination of 12 stannylenes (SnX2 ) with five azabenzene ligands (pyridine, pyrazine, pyrimidine, pyridazine, and s-triazine), where the nitrogen center of the ligand acts as σ-donor and the tin(II) center as σ-acceptor in a 1:1 fashion. The Sn ← N bond and the total interaction between the stannylene and azabenzene moieties of the σ-complexes are characterized in depth to relate the Sn ← N strength to the substitution pattern at SnX2 and to the number and the positioning of N atoms in the azabenzenes. Such X substituents as (iso)cyano and trifluoromethyl groups enhance the interaction strength, while the presence of alkyl, phenyl, and silyl substituents in SnX2 diminishes the stability of σ-complexes. A gradual weakening of the total interaction is associated with the growing number of N atoms in the azabenzenes, while the N-atom positioning in pyridazine is particularly effective in strengthening the interaction with stannylenes. Variations in the Sn ← N bond strength usually follow those in the total interaction between the moieties but the interacting quantum atoms picture of Sn ← N reveals certain intriguing exceptions.
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Affiliation(s)
| | - Stephan Kupfer
- Institute of Physical Chemistry, Friedrich-Schiller University Jena, Jena, Germany
| | - Piotr Matczak
- Faculty of Chemistry, University of Łódź, Lodz, Poland
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Synthesis, structural characterization, electronic structure calculation, molecular docking study and biological activity of triorganotin(IV) complexes of schiff base (E)-4-amino-3-(2-(2-hydroxybenzylidene)hydrazinyl)-1H-1,2,4-triazole-5(4H)-thione). J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Electronic Structure Explanation for the Structure and Reactivity of di-n-Butyltin(IV) Derivative of Glycylphenylalanine. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2019. [DOI: 10.1007/s40010-018-0582-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Joshi R, Kumari A, Singh K, Mishra H, Pokharia S. New diorganotin(IV) complexes of Schiff base derived from 4‐amino‐3‐hydrazino‐5‐mercapto‐4H‐1,2,4‐triazole: Synthesis, structural characterization, density functional theory studies, atoms‐in‐molecules analysis and antifungal activity. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rachana Joshi
- Chemistry Section, MMVBanaras Hindu University (BHU) Varanasi 221005 India
| | - Ankita Kumari
- Zoology Section, MMVBanaras Hindu University (BHU) Varanasi 221005 India
| | - Karuna Singh
- Zoology Section, MMVBanaras Hindu University (BHU) Varanasi 221005 India
| | - Hirdyesh Mishra
- Physics Section, MMVBanaras Hindu University (BHU) Varanasi 221005 India
| | - Sandeep Pokharia
- Chemistry Section, MMVBanaras Hindu University (BHU) Varanasi 221005 India
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Michalczyk M, Zierkiewicz W, Wysokiński R, Scheiner S. Hexacoordinated Tetrel‐Bonded Complexes between TF4(T=Si, Ge, Sn, Pb) and NCH: Competition between σ‐ and π‐Holes. Chemphyschem 2019; 20:959-966. [DOI: 10.1002/cphc.201900072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 02/15/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Mariusz Michalczyk
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże, Wyspiańskiego 27 50-370 Wrocław Poland
| | - Wiktor Zierkiewicz
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże, Wyspiańskiego 27 50-370 Wrocław Poland
| | - Rafał Wysokiński
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże, Wyspiańskiego 27 50-370 Wrocław Poland
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State University Logan, Utah 84322-0300 United States
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Matczak P. N → Sn coordination in the complexes of tin halides with pyridine: A comparison between Sn(II) and Sn(IV). Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4811] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Piotr Matczak
- Department of Physical Chemistry, Faculty of Chemistry; University of Łódź; Pomorska 163/165 90-236 Lodz Poland
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Scheiner S. Ability of IR and NMR Spectral Data to Distinguish between a Tetrel Bond and a Hydrogen Bond. J Phys Chem A 2018; 122:7852-7862. [DOI: 10.1021/acs.jpca.8b07631] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Joshi R, Yadav SK, Pandey N, Mishra H, Tilak R, Pokharia S. Combined experimental and theoretical studies on the diorganotin(IV) complexes of sparfloxacin: Synthesis, spectroscopic and DFT studies, and biological activity. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Joshi R, Pandey N, Tilak R, Yadav SK, Mishra H, Pokharia S. New triorganotin(IV) complexes of quinolone antibacterial drug sparfloxacin: Synthesis, structural characterization, DFT studies and biological activity. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4324] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rachana Joshi
- Organometallics and Molecular Modelling Group, Chemistry Section, M.M.V; Banaras Hindu University (B.H.U.); Varanasi -221005 India
| | - Nidhi Pandey
- Department of Microbiology, Institute of Medical Science; Banaras Hindu University (B.H.U.); Varanasi -221005 India
| | - Ragini Tilak
- Department of Microbiology, Institute of Medical Science; Banaras Hindu University (B.H.U.); Varanasi -221005 India
| | | | - Hirdyesh Mishra
- Physics Section, M.M.V; Banaras Hindu University (B.H.U.); Varanasi -221005 India
| | - Sandeep Pokharia
- Organometallics and Molecular Modelling Group, Chemistry Section, M.M.V; Banaras Hindu University (B.H.U.); Varanasi -221005 India
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Scheiner S. Systematic Elucidation of Factors That Influence the Strength of Tetrel Bonds. J Phys Chem A 2017; 121:5561-5568. [DOI: 10.1021/acs.jpca.7b05300] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Scheiner S. Highly Selective Halide Receptors Based on Chalcogen, Pnicogen, and Tetrel Bonds. Chemistry 2016; 22:18850-18858. [PMID: 27740702 DOI: 10.1002/chem.201603891] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 11/09/2022]
Abstract
The interactions of halides with a number of bipodal receptors were examined by quantum chemical methods. The receptors were based on a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms were replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms were added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride bound the most strongly, followed by Cl- , Br- , and I- , respectively. Replacing S by the pnicogen bonds of P strengthened the binding, as did moving down to As in the third row of the periodic table. A further large increment is associated with the switch to the tetrel bonds of Ge. Even though the thiophene S atom is remote from the binding site, each additional O atom added to it raises the binding energy, which can be quite large, as much as 63 kcal mol-1 for the Ge⋅⋅⋅F- interaction. The receptors have a pronounced selectivity for F- over the other halides, as high as 27 orders of magnitude. The data suggest that incorporation of tetrel atoms may lead to new and more powerful halide receptors.
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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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Interplay of thermochemistry and Structural Chemistry, the journal (Volume 26, 2015, Issues 1–2) and the discipline. Struct Chem 2016. [DOI: 10.1007/s11224-016-0751-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Matczak P, Domagała M, Domagała S. Conformers of diheteroaryl ketones and thioketones: a quantum chemical study of their properties and fundamental intramolecular energetic effects. Struct Chem 2015. [DOI: 10.1007/s11224-015-0643-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Matczak P, Wojtulewski S. Performance of Møller-Plesset second-order perturbation theory and density functional theory in predicting the interaction between stannylenes and aromatic molecules. J Mol Model 2015; 21:41. [PMID: 25677452 PMCID: PMC4326664 DOI: 10.1007/s00894-015-2589-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 11/21/2022]
Abstract
The performances of Møller-Plesset second-order perturbation theory (MP2) and density functional theory (DFT) have been assessed for the purposes of investigating the interaction between stannylenes and aromatic molecules. The complexes between SnX2 (where X = H, F, Cl, Br, and I) and benzene or pyridine are considered. Structural and energetic properties of such complexes are calculated using six MP2-type and 14 DFT methods. The assessment of the above-mentioned methods is based on the comparison of the structures and interaction energies predicted by these methods with reference computational data. A very detailed analysis of the performances of the MP2-type and DFT methods is carried out for two complexes, namely SnH2-benzene and SnH2-pyridine. Of the MP2-type methods, the reference structure of SnH2-benzene is reproduced best by SOS-MP2, whereas SCS-MP2 is capable of mimicking the reference structure of SnH2-pyridine with the greatest accuracy. The latter method performs best in predicting the interaction energy between SnH2 and benzene or pyridine. Among the DFT methods, ωB97X provides the structures and interaction energies of the SnH2-benzene and SnH2-pyridine complexes with good accuracy. However, this density functional is not as effective in reproducing the reference data for the two complexes as the best performing MP2-type methods. Next, the DFT methods are evaluated using the full test set of SnX2-benzene and SnX2-pyridine complexes. It is found that the range-separated hybrid or dispersion-corrected density functionals should be used for describing the interaction in such complexes with reasonable accuracy.
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Affiliation(s)
- Piotr Matczak
- Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź, Pomorska 163/165, 90-236, Lodz, Poland,
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Assessment of various density functionals for intermolecular N→Sn interactions: The test case of poly(trimethyltin cyanide). COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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