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Niu Z, McDowell SAC, Li Q. The Tetrel Bonds of Hypervalent Halogen Compounds. Molecules 2023; 28:7087. [PMID: 37894566 PMCID: PMC10609133 DOI: 10.3390/molecules28207087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/26/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The tetrel bond between PhXF2Y(TF3) (T = C and Si; X = Cl, Br, and I; Y = F and Cl) and the electron donor MCN (M = Li and Na) was investigated at the M06-2X/aug-cc-pVDZ level of theory. As the electronegativity of the halogen atom X increases, the strength of the tetrel bond also increases, but as the electronegativity of the halogen atom Y increases, the strength of the tetrel bond decreases. The magnitude of the interaction energy in most -CF3 complexes was found to be less than 10 kcal/mol, but to exceed 11 kcal/mol for PhClF2Cl(CF3)⋯NCNa. The tetrel bond is greatly enhanced when the -SiF3 group interacts with LiCN or NaCN, with the largest interaction energy approaching 100 kcal/mol and displaying a covalent Si⋯N interaction. Along with this enhancement, the Si⋯N distance was found to be less than the X-Si bond length, the -SiF3 group to be closer to the N atom, and in most -SiF3 systems, the X-Si-F angle to be less than 90°; the -SiF3 group therefore undergoes inversion and complete transfer in some systems.
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Affiliation(s)
- Zhihao Niu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
| | - Sean A. C. McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
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2
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Liyanage S, Ovens JS, Bryce DL. Tetrel bond in the triphenyltin(IV) chloride-cyclo-hexyl-diphenyl-phosphane oxide (1/1) cocrystal. IUCrdata 2023; 8:x230637. [PMID: 37693789 PMCID: PMC10483546 DOI: 10.1107/s2414314623006375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/21/2023] [Indexed: 09/12/2023] Open
Abstract
The single-crystal X-ray diffraction structure of the title compound, [SnCl(C6H5)3]·C18H21OP, is reported. The 1:1 cocrystal features a short and directional tetrel bond between tin and oxygen. The tin-oxygen distance is 2.346 (4) Å, representing 62% of the sum of the van der Waals radii of Sn and O. The Cl-Sn⋯O angle is 174.0 (1)° and this nearly linear arrangement is consistent with a tetrel bond formed via a σ-hole opposite the tin-chlorine covalent bond. Some weak C-H⋯Cl inter-actions are noted between adjacent mol-ecules.
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Affiliation(s)
- Sachin Liyanage
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N6N5, Canada
| | - Jeffrey S. Ovens
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N6N5, Canada
| | - David L. Bryce
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N6N5, Canada
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3
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. Methylammonium Tetrel Halide Perovskite Ion Pairs and Their Dimers: The Interplay between the Hydrogen-, Pnictogen- and Tetrel-Bonding Interactions. Int J Mol Sci 2023; 24:10554. [PMID: 37445738 DOI: 10.3390/ijms241310554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The structural stability of the extensively studied organic-inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX3 (MA = CH3NH3+; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH3NH3+) and an inorganic anion (TtX3-). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N-H···X and C-H···X hydrogen bonds but also the C-N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX3 in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX3-) together. We have demonstrated that each Tt in each [CH3NH3+•TtX3-] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX3- units, thus causing the emergence of an infinite array of 3D TtX64- octahedra in the crystalline phase. The TtX44- octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions.
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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
- School of Chemistry, Molecular Sciences Institute, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
| | - Helder M Marques
- School of Chemistry, Molecular Sciences Institute, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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4
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Brammer L, Peuronen A, Roseveare TM. Halogen bonds, chalcogen bonds, pnictogen bonds, tetrel bonds and other σ-hole interactions: a snapshot of current progress. Acta Crystallogr C Struct Chem 2023:S2053229623004072. [PMID: 37212787 DOI: 10.1107/s2053229623004072] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
We report here on the status of research on halogen bonds and other σ-hole interactions involving p-block elements in Lewis acidic roles, such as chalcogen bonds, pnictogen bonds and tetrel bonds. A brief overview of the available literature in this area is provided via a survey of the many review articles that address this field. Our focus has been to collect together most review articles published since 2013 to provide an easy entry into the extensive literature in this area. A snapshot of current research in the area is provided by an introduction to the virtual special issue compiled in this journal, comprising 11 articles and entitled `Halogen, chalcogen, pnictogen and tetrel bonds: structural chemistry and beyond.'
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Affiliation(s)
- Lee Brammer
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, United Kingdom
| | - Anssi Peuronen
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, United Kingdom
| | - Thomas M Roseveare
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, United Kingdom
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5
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Walker MG, Mendez CG, Ho PS. Non-classical Non-covalent σ-Hole Interactions in Protein Structure and Function: Concepts for Potential Protein Engineering Applications. Chem Asian J 2023; 18:e202300026. [PMID: 36764929 DOI: 10.1002/asia.202300026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/12/2023]
Abstract
The structures and associated functions of biological molecules are driven by noncovalent interactions, which have classically been dominated by the hydrogen bond (H-bond). Introduction of the σ-hole concept to describe the anisotropic distribution of electrostatic potential of covalently bonded elements from across the periodic table has opened a broad range of nonclassical noncovalent (ncNC) interactions for applications in chemistry and biochemistry. Here, we review how halogen bonds, chalcogen bonds and tetrel bonds, as they are found naturally or introduced synthetically, affect the structures, assemblies, and potential functions of peptides and proteins. This review intentionally focuses on examples that introduce or support principles of stability, assembly and catalysis that can potentially guide the design of new functional proteins. These three types of ncNC interactions have energies that are comparable to the H-bond and, therefore, are now significant concepts in molecular recognition and design. However, the recently described H-bond enhanced X-bond shows how synergism among ncNC interactions can be exploited as potential means to broaden the range of their applications to affect protein structures and functions.
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Affiliation(s)
- Margaret G Walker
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - C Gustavo Mendez
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO, 80523-1870, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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 Crystallogr B Struct Sci Cryst Eng Mater 2022; 78:685-694. [PMID: 35975834 DOI: 10.1107/s2052520622005789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Zierkiewicz W, Michalczyk M, Mahmoudi G, García-Santos I, Castiñeiras A, Zangrando E, Scheiner S. Experimental and Theoretical Evidence of a Pb⋅⋅⋅Pb Di tetrel Bond Without a σ-Hole. Chemphyschem 2022; 23:e202200306. [PMID: 35638192 DOI: 10.1002/cphc.202200306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 11/07/2022]
Abstract
The crystal structure of a newly synthesized compound, [PbL(Ac)]2 , (where L=2 (amino(pyrazin-2-yl) methylene) hydrazinecarbothioamide, Ac=acetate anion) exhibits a close contact between pairs of Pb atoms, suggesting a ditetrel bond, in addition to two Pb⋅⋅⋅O tetrel bonds, and two C-H⋅⋅⋅O H-bonds. The presence of this ditetrel bond as an attractive component is confirmed by various quantum chemical methods. This novelty of this particular bond is its existence even in the absence of a σ-hole on the Pb atom, which is typically considered a prerequisite for a bond of this type. From a wider perspective, a survey of the Cambridge Structural Database suggests this bond may be more common than was hitherto thought, with 44 examples of Pb⋅⋅⋅Pb contacts amongst a total number of 219 examples of T⋅⋅⋅T interactions in general (T=Si, Ge, Sn, Pb).
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, P.O. Box 55136-83111, Maragheh, Iran
| | - Isabel García-Santos
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Alfonso Castiñeiras
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, United States
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Bhattarai S, Sutradhar D, Chandra AK. Strongly Bound π-Hole Tetrel Bonded Complexes between H2SiO and Substituted Pyridines. Influence of Substituents. Chemphyschem 2022; 23:e202200146. [PMID: 35362233 DOI: 10.1002/cphc.202200146] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/21/2022] [Indexed: 11/08/2022]
Abstract
Ab initio calculation at the MP2/aug-cc-pVTZ level has been performed on the π-hole based N … Si tetrel bonded complexes between substituted pyridines and H 2 SiO. The primary aim of the study is to find out the effect of substitution on the strength and nature of this tetrel bond, and its similarity/difference with the N … C tetrel bond. Correlation between the strength of the N … Si bond and several molecular properties of the Lewis acid (H 2 SiO) and base (pyridines) are explored. The properties of the tetrel bond are analyzed using AIM, NBO, and symmetry-adapted perturbation theory calculations. The complexes are characterized with short N … Si intermolecular distances and high binding energies ranging between -142.72 and -115.37 kJ/mol. The high value of deformation energy indicates significant geometrical distortion of the monomer units. The AIM and NBO analysis reveal significant coordinate covalent bond character of the N … Si π-hole bond. Sharp differences are also noticed in the orbital interactions present in the N … Si and N … C tetrel bonds.
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Affiliation(s)
- Sumitra Bhattarai
- North-Eastern Hill University, Chemistry, Mawlai, 793022, Shillong, INDIA
| | - Dipankar Sutradhar
- VIT University, School of Advanced Science & Language, 466114, Bhopal, INDIA
| | - Asit K Chandra
- North Eastern Hill University, Chemistry, Umshing, 793022, Shillong, INDIA
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10
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Brzeski J. The influence of tetrel bonds on the acidities of group 14 tetrafluoride - inorganic acid complexes. J Comput Chem 2022; 43:611-618. [PMID: 35147239 DOI: 10.1002/jcc.26822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Ab initio methods were used to determine the influence of tetrel bond formation on the acidity. The systems composed of inorganic acids and tetrafluorides of 14 group elements have been tested - HA/EF4 , where HA = H2 O, NH3 , HF, HCN, HNC, HCNO, HOCN and E = C, Si, Ge, Sn or Pb. It turns out that the electron density flow involved with formation of tetrel bond to carbon-based systems leads to negligible increase in acidity. In the case of the acceptor compounds based on the remaining 14 group elements however, the effect is much more apparent, as most of those compounds may be considered a Brønsted superacids. The electronic stability of anions formed after the deprotonation of aforementioned complexes has been investigated. Vast majority of the anions were found to exhibit significant electron binding energies.
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Affiliation(s)
- Jakub Brzeski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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11
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Scheiner S. Maximal occupation by bases of π-hole bands surrounding linear molecules. J Comput Chem 2021; 43:319-330. [PMID: 34859910 DOI: 10.1002/jcc.26792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/19/2022]
Abstract
Linear molecules such as CO2 contain a positive π-hole ring that surrounds C on the molecule's equator. Quantum calculations examine the question as to how many bases can simultaneously bind to this ring. Linear molecules examined are TO2 , where T = C, Si, Ge, Sn; bases are NCH and NH3 . CO2 engages in the weakest of the tetrel bonds, and can bind up to three NCH and two NH3 . Unlike σ-hole tetrel bonds, Si forms the strongest tetrel bonds, with interaction energies as high as 43 kcal/mol with NH3 . But like GeO2 , SiO2 can sustain only two bases in its equatorial ring. The π-hole ring of SnO2 can engage in up to four tetrel bonds with either NCH or NH3 , even though these bonds are weaker than those with GeO2 or SiO2 . As all of these complexes cast TO2 in the role of multiple electron acceptor, the resulting negative cooperativity makes each successive bond weaker than its predecessor as bases are added, as well as reducing the magnitude of the central molecule's π-hole.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
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12
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Liu N, Xie X, Li Q, Scheiner S. Enhancement of the Tetrel Bond by the Effects of Substituents, Cooperativity, and Electric Field: Transition from Noncovalent to Covalent Bond. Chemphyschem 2021; 22:2305-2312. [PMID: 34436816 DOI: 10.1002/cphc.202100612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 12/14/2022]
Abstract
The T⋅⋅⋅N tetrel bond (TB) formed between TX3 OH (T=C, Si, Ge; X=H, F) and the Lewis base N≡CM (M=H, Li, Na) is studied by ab initio calculations at the MP2/aug-cc-pVTZ level. Complexes involving TH3 OH contain a conventional TB with interaction energy less than 10 kcal/mol. This bond is substantially strengthened, approaching 35 kcal/mol and covalent character, when fluorosubstituted TF3 OH is combined with NCLi or NCNa. Along with this enhanced binding comes a near equalization of the TB T⋅⋅⋅N and the internal T-O bond lengths, and the associated structure acquires a trigonal bipyramidal shape, despite a high internal deformation energy. This structural transformation becomes more complete, and the TB is further strengthened upon adding an electron acceptor BeCl2 to the Lewis acid and a base to the NCM unit. This same TB strengthening can be accomplished also by imposition of an external electric field.
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Affiliation(s)
- Na Liu
- Laboratory of Theoretical and Computational Chemistry and, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Xiaoying Xie
- Laboratory of Theoretical and Computational Chemistry and, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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13
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Zierkiewicz W, Michalczyk M, Scheiner S. Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons. Molecules 2021; 26:molecules26061740. [PMID: 33804617 PMCID: PMC8003638 DOI: 10.3390/molecules26061740] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/21/2023] Open
Abstract
Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA;
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Cheng W, Zheng Y, Herbers S, Zheng H, Gou Q. Conformational Equilibria of 2-Methoxypyridine⋅⋅⋅CO 2 : Cooperative and Competitive Tetrel and Weak Hydrogen Bonds. Chemphyschem 2021; 22:154-159. [PMID: 33315294 DOI: 10.1002/cphc.202000910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/16/2020] [Indexed: 11/11/2022]
Abstract
The rotational spectrum of 2-methoxypyridine⋅⋅⋅CO2 was recorded and analysed employing a cavity-based Fourier transform microwave spectrometer, complemented with quantum chemical calculations which predicted three possible isomers within energies less than 1000 cm-1 . The two most stable isomers were observed in the pulsed jet, which are stabilized by a network of C⋅⋅⋅N/O tetrel and C-H⋅⋅⋅O weak hydrogen bonds. The relative population ratio of the two detected isomers was estimated to be NI /NII ≈2.5. The competition and cooperation of the present non-covalent interactions in both isomers are discussed within the framework of Bader's quantum theory of atoms in molecules and Johnson's non-covalent interaction analyses. The study shows, that when looking for CO2 adsorbents, one might prefer candidates with multiple interactions in one site over candidates with few but strong interactions.
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Affiliation(s)
- Wanying Cheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
| | - Sven Herbers
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
| | - Huaili Zheng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, State Ministry of Education, Chongqing University, No.83 Shabei Str., Shapingba, 400045, Chongqing, China
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
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Grabowski SJ. Hydrogen Bond and Other Lewis Acid-Lewis Base Interactions as Preliminary Stages of Chemical Reactions. Molecules 2020; 25:E4668. [PMID: 33066201 PMCID: PMC7587390 DOI: 10.3390/molecules25204668] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 01/21/2023] Open
Abstract
Various Lewis acid-Lewis base interactions are discussed as initiating chemical reactions and processes. For example, the hydrogen bond is often a preliminary stage of the proton transfer process or the tetrel and pnicogen bonds lead sometimes to the SN2 reactions. There are numerous characteristics of interactions being first stages of reactions; one can observe a meaningful electron charge transfer from the Lewis base unit to the Lewis acid; such interactions possess at least partly covalent character, one can mention other features. The results of different methods and approaches that are applied in numerous studies to describe the character of interactions are presented here. These are, for example, the results of the Quantum Theory of Atoms in Molecules, of the decomposition of the energy of interaction or of the structure-correlation method.
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Affiliation(s)
- Sławomir J. Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Euskadi, Spain; ; Tel.: +34-943-018-187
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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16
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Abstract
Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH3 base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature of the bonding varies a bit from one complex to the next but typically contains a tetrel bond to the C atoms of the cyano groups or the C atoms of the linkage connecting the C≡N substituents. The placement of the cyano groups on a cyclic system like cyclopropane or cyclobutane has a mild weakening effect upon the binding. Although F is comparable to C≡N in terms of electron-withdrawing power, the replacement of cyano by F substituents substantially weakens the binding with NH3.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Bartashevich E, Matveychuk Y, Tsirelson V. Identification of the Tetrel Bonds between Halide Anions and Carbon Atom of Methyl Groups Using Electronic Criterion. Molecules 2019; 24:E1083. [PMID: 30893831 PMCID: PMC6471983 DOI: 10.3390/molecules24061083] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 11/17/2022] Open
Abstract
The consideration of the disposition of minima of electron density and electrostatic potential along the line between non-covalently bound atoms in systems with Hal-···CH₃⁻Y (Hal- = Cl, Br; Y = N, O) fragments allowed to prove that the carbon atom in methyl group serves as an electrophilic site provider. These interactions between halide anion and carbon in methyl group can be categorized as the typical tetrel bonds. Statistics of geometrical parameters for such tetrel bonds in CSD is analyzed. It is established that the binding energy in molecular complexes with tetrel bonds correlate with the potential acting on an electron in molecule (PAEM). The PAEM barriers for tetrel bonds show a similar behavior for both sets of complexes with Br- and Cl- electron donors.
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Affiliation(s)
- Ekaterina Bartashevich
- Research Laboratory of Multiscale Modelling of Multicomponent Functional Materials, REC Nanotechnology, South Ural State University, 454080 Chelyabinsk, Russia.
| | - Yury Matveychuk
- Research Laboratory of Multiscale Modelling of Multicomponent Functional Materials, REC Nanotechnology, South Ural State University, 454080 Chelyabinsk, Russia.
| | - Vladimir Tsirelson
- Research Laboratory of Multiscale Modelling of Multicomponent Functional Materials, REC Nanotechnology, South Ural State University, 454080 Chelyabinsk, Russia.
- Quantum Chemistry Department, D.I. Mendeleev University of Chemical Technology, 125047 Moscow, Russia.
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20
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Shukla R, Ruzié C, Schweicher G, Kennedy AR, Geerts YH, Chopra D, Chattopadhyay B. Insight from electron density and energy framework analysis on the structural features of F x-TCNQ (x = 0, 2, 4) family of molecules. Acta Crystallogr B Struct Sci Cryst Eng Mater 2019; 75:71-78. [PMID: 32830780 DOI: 10.1107/s2052520618017109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 12/02/2018] [Indexed: 06/11/2023]
Abstract
In this study, the nature and characteristics of the intramolecular and intermolecular interactions in crystal structures of the fluoro-substituted 7,7,8,8-tetracyanoquinodimethane (TCNQ) family of molecules, i.e. Fx-TCNQ (x = 0, 2, 4), are explored. The molecular geometry of the reported crystal structures is directly dependent on the degree of fluorination in the molecule, which consequently also results in the presence of an intramolecular N[triple-bond]C...F-C π-hole tetrel bond. Apart from this, the energy framework analysis performed along the respective transport planes provides new insights into the energetic distribution in this class of molecules.
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Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhopal, Madhya Pradesh, India 462066
| | - Christian Ruzié
- Laboratoire de Chimie des Polymères, CP 206/01, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Guillaume Schweicher
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Alan R Kennedy
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Yves H Geerts
- Laboratoire de Chimie des Polymères, CP 206/01, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhopal, Madhya Pradesh, India 462066
| | - Basab Chattopadhyay
- Laboratoire de Chimie des Polymères, CP 206/01, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
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21
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Trievel RC, Scheiner S. Crystallographic and Computational Characterization of Methyl Tetrel Bonding in S-Adenosylmethionine-Dependent Methyltransferases. Molecules 2018; 23:E2965. [PMID: 30428636 DOI: 10.3390/molecules23112965] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 11/17/2022] Open
Abstract
Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in SN2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the SN2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered multiple instances of carbon tetrel bonding between the methyl group of the substrate S-adenosylmethionine (AdoMet) and electronegative atoms of small molecule inhibitors, ions, and solvent molecules. The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. The discovery of methyl tetrel bonding offers new insights into the mechanism underlying the SN2 reaction catalyzed by AdoMet-dependent methyltransferases. These findings highlight the potential of exploiting these interactions in developing new methyltransferase inhibitors.
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22
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Abstract
Tetrel bonds are noncovalent interactions formed by tetrel atoms (as σ-hole carriers) with a Lewis base. Here, we present a computational and molecular orbital study on the effect of the geometry of the substituents around the tetrel atom on the σ-hole and on the binding strengths. We show that changing the angles between substituents can dramatically increase bond strength. In addition, our findings suggest that the established Sn > Ge > Si order of binding strength can be changed in sufficiently distorted molecules due to the enhancement of the charge transfer component, making silicon the strongest tetrel donor.
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Affiliation(s)
- Ephrath Solel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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23
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Dong W, Li Q, Scheiner S. Comparative Strengths of Tetrel, Pnicogen, Chalcogen, and Halogen Bonds and Contributing Factors. Molecules 2018; 23:E1681. [PMID: 29996528 PMCID: PMC6100607 DOI: 10.3390/molecules23071681] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/20/2022] Open
Abstract
Ab initio calculations are employed to assess the relative strengths of various noncovalent bonds. Tetrel, pnicogen, chalcogen, and halogen atoms are represented by third-row atoms Ge, As, Se, and Br, respectively. Each atom was placed in a series of molecular bonding situations, beginning with all H atoms, then progressing to methyl substitutions, and F substituents placed in various locations around the central atom. Each Lewis acid was allowed to engage in a complex with NH₃ as a common nucleophile, and the strength and other aspects of the dimer were assessed. In the context of fully hydrogenated acids, the strengths of the various bonds varied in the pattern of chalcogen > halogen > pnicogen ≈ tetrel. Methyl substitution weakened all bonds, but not in a uniform manner, resulting in a greatly weakened halogen bond. Fluorosubstitution strengthened the interactions, increasing its effect as the number of F atoms rises. The effect was strongest when the F atom lay directly opposite the base, resulting in a halogen > chalcogen > pnicogen > tetrel order of bond strength. Replacing third-row atoms by their second-row counterparts weakened the bonds, but not uniformly. Tetrel bonds were weakest for the fully hydrogenated acids and surpassed pnicogen bonds when F had been added to the acid.
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Affiliation(s)
- Wenbo Dong
- 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.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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24
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Grabowski SJ. Tetrel Bonds with π-Electrons Acting as Lewis Bases-Theoretical Results and Experimental Evidences. Molecules 2018; 23:molecules23051183. [PMID: 29762534 PMCID: PMC6100247 DOI: 10.3390/molecules23051183] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022] Open
Abstract
MP2/aug-cc-pVTZ calculations were carried out for the ZFH₃-B complexes (Z = C, Si, Ge, Sn and Pb; B = C₂H₂, C₂H₄, C₆H₆ and C₅H₅⁻; relativistic effects were taken into account for Ge, Sn and Pb elements). These calculations are supported by other approaches; the decomposition of the energy of interaction, Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) method. The results show that tetrel bonds with π-electrons as Lewis bases are classified as Z···C links between single centers (C is an atom of the π-electron system) or as Z···π interactions where F‒Z bond is directed to the mid-point (or nearly so) of the CC bond of the Lewis base. The analogous systems with Z···C/π interactions were found in the Cambridge Structural Database (CSD). It was found that the strength of interaction increases with the increase of the atomic number of the tetrel element and that for heavier tetrel elements the ZFH₃ tetrahedral structure is more deformed towards the structure with the planar ZH₃ fragment. The results of calculations show that the tetrel bond is sometimes accompanied by the Z-H···C hydrogen bond or even sometimes the ZFH₃-B complexes are linked only by the hydrogen bond interaction.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Spain.
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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25
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Del Bene JE, Elguero J, Alkorta I. Complexes of CO₂ with the Azoles: Tetrel Bonds, Hydrogen Bonds and Other Secondary Interactions. Molecules 2018; 23:E906. [PMID: 29662005 DOI: 10.3390/molecules23040906] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 02/07/2023] Open
Abstract
Ab initio MP2/aug’-cc-pVTZ calculations have been performed to investigate the complexes of CO2 with the azoles pyrrole, pyrazole, imidazole, 1,2,3- and 1,2,4-triazole, tetrazole and pentazole. Three types of complexes have been found on the CO2:azole potential surfaces. These include ten complexes stabilized by tetrel bonds that have the azole molecule in the symmetry plane of the complex; seven tetrel-bonded complexes in which the CO2 molecule is perpendicular to the symmetry plane; and four hydrogen-bonded complexes. Eight of the planar complexes are stabilized by Nx···C tetrel bonds and by a secondary interaction involving an adjacent Ny-H bond and an O atom of CO2. The seven perpendicular CO2:azole complexes form between CO2 and two adjacent N atoms of the ring, both of which are electron-pair donors. In three of the four hydrogen-bonded complexes, the proton-donor Nz-H bond of the ring is bonded to two C-H bonds, thereby precluding the planar and perpendicular complexes. The fourth hydrogen-bonded complex forms with the strongest acid pentazole. Binding energies, charge-transfer energies and changes in CO2 stretching and bending frequencies upon complex formation provide consistent descriptions of these complexes. Coupling constants across tetrel bonds are negligibly small, but 2hJ(Ny-C) across Nz-H···C hydrogen bonds are larger and increase as the number of N atoms in the ring increases.
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26
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Scheiner S. Comparison of Various Means of Evaluating Molecular Electrostatic Potentials for Noncovalent Interactions. J Comput Chem 2017; 39:500-510. [PMID: 29083034 DOI: 10.1002/jcc.25085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/22/2017] [Accepted: 09/29/2017] [Indexed: 01/12/2023]
Abstract
The various heterodimers formed by a series of Lewis acids with NH3 as Lewis base are identified. Lewis acids include those that can form chalcogen (HSF and HSBr), pnicogen (H2 PF and H2 PBr), and tetrel (H3 SiF and H3 SiBr) bonds, as well as H-bonds and halogen bonds. The molecular electrostatic potential (MEP) of each Lewis acid is considered in a number of ways. Pictorial versions show broad regions of positive and negative MEP, on surfaces that vary with respect to either the value of the chosen isopotential, or their distance from the nuclei. Specific points are identified where the MEP reaches a maximum on a particular isodensity surface (Vs,max ). The locations and values of Vs,max were evaluated on different isodensity surfaces, and compared to the stabilities of the various equilibrium geometries. As the chosen isodensity is decreased, and the MEP maxima drift away from the molecule, some points maintain their angular positions with respect to the molecule, whereas others undergo a reorientation. The lowering isodensity also causes some of the maxima to disappear. In general, there is a fairly good correlation between the energetic ordering of the equilibrium structures and the values of Vs,max . A number of possible Lewis acid sites on the heteroaromatic imidazole ring were also considered and presents some cautions about application of Vs,max as the principal criterion for predicting equilibrium geometries. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300
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