1
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Gupta R, Singha S, Mani D. Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH 3CN/CH 3NC···HX Trimers (ZY = H 2O, H 2S, HF, HCl, HBr, NH 3, and H 2CO; HX = HF, HCl, and HBr). J Phys Chem A 2024; 128:4605-4622. [PMID: 38598527 DOI: 10.1021/acs.jpca.4c00911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order Mo̷ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.
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Affiliation(s)
- Riya Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Sujan Singha
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Devendra Mani
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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2
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Amonov A, Scheiner S. Competition between Binding to Various Sites of Substituted Imidazoliums. J Phys Chem A 2023. [PMID: 37490696 DOI: 10.1021/acs.jpca.3c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH3 base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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3
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Li J, Wang C, Mo Y. Selectivity Rule of Cryptands for Anions: Molecular Rigidity and Bonding Site. Chemistry 2023; 29:e202203558. [PMID: 36538660 DOI: 10.1002/chem.202203558] [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: 11/15/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Cryptands utilize inside CH or NH groups as hydrogen bond (H-bond) donors to capture anions such as halides. In this work, the nature and selectivity of confined hydrogen bonds inside cryptands were computationally analyzed with the energy decomposition scheme based on the block-localized wavefunction method (BLW-ED), aiming at an elucidation of governing factors in the binding between cryptands and anions. It was revealed that the intrinsic strengths of inward hydrogen bonds are dominated by the electrostatic attraction, while the anion preferences (selectivity) of inner CH and NH hydrogen bonds are governed by the Pauli exchange repulsion and electrostatic interaction, respectively. Typical conformers of cages are classified into two groups, including the C3(h) -symmetrical conformers, in which all halide anions are located near the centroids of cages, and the "semi-open" conformers, which exhibit shifted bonding sites for different halide anions. Accordingly, the difference in governing factors of selectivity is attributed to either the rigidity of cages or the binding site of anions for these two groups. In details, the C3 conformers of NH cryptands can be enlarged more remarkably than the C3(h) -symmetrical conformers of CH cryptands as the size of anion (ionic radius) increases, resulting in the relaxation of the Pauli repulsion and a dramatic reduction in electrostatic attraction, which eventually rules the selectivity of NH cryptands for halide anions. By contrary, the CH cryptands are more rigid and cannot effectively reduce the Pauli repulsion, which subsequently governs the anion preference. Unlike C3 conformers whose rigidity determines the selectivity, semi-open conformers exhibit different binding sites for different anions. From F- to I- , the bonding site shifts toward the outside end of the pocket inside the semi-open NH cryptand, leading to the significant reduction of the electrostatic interaction that dominates the anion preference. Differently, binding sites are much less affected by the size of anion inside the semi-open CH cryptand, in which the Pauli exchange repulsion remains the key factor for the selectivity of inner hydrogen bonds.
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Affiliation(s)
- Jiayao Li
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience & Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA
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4
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Liu N, Wu Q, Li Q, Scheiner S. Promotion of TH 3 (T = Si and Ge) group transfer within a tetrel bond by a cation-π interaction. Phys Chem Chem Phys 2022; 24:1113-1119. [PMID: 34927648 DOI: 10.1039/d1cp05323j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The possibility of the transfer of the TH3 group across a tetrel bond is considered by ab initio calculations. The TB is constructed by pairing PhTH3 (Ph = phenyl; T = Si and Ge) with bases NH3, NHCH2, and the C3N2H4 carbene. The TH3 moves toward the base but only by a small amount in these dimers. However, when a Be2+ or Mg2+ dication is placed above the phenyl ring, the tetrel bond strength is greatly magnified reaching up to nearly 100 kcal mol-1. This dication also induces a much higher degree of transfer which can be best categorized as half-transfer for the two N-bases and a near complete transfer for the carbene.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Qiaozhuo Wu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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5
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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] [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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6
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Yang Q, Zhang X, Li Q. Comparison for Electron Donor Capability of Carbon-Bound Halogens in Tetrel Bonds. ACS OMEGA 2021; 6:29037-29044. [PMID: 34746592 PMCID: PMC8567400 DOI: 10.1021/acsomega.1c04085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The tetrel bond formed by HC≡CX, H2C=CHX, and H3CCH2X (X=F, Cl, Br, I) as an electron donor and TH3F (T=C, Si, Ge) was explored by ab initio calculations. The tetrel bond formed by H3CCH2X is the strongest, as high as -3.45 kcal/mol for the H3CCH2F···GeH3F dimer, followed by H2C=CHX, and the weakest bond is from HC≡CX, where the tetrel bond can be as small as -0.8 kcal/mol. The strength of the tetrel bond increases in the order of C < Si < Ge. For the H3CCH2X and HC≡CX complexes, the tetrel bond strength shows a similar increasing tendency with the decrease of the electronegativity of the halogen atom. Electrostatic interaction plays the largest role in the stronger tetrel bonds, while dispersion interaction makes an important contribution to the H2C=CHX complexes.
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Affiliation(s)
- Qingqing Yang
- The Laboratory of Theoretical
and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
| | - Xiaolong Zhang
- The Laboratory of Theoretical
and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical
and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
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7
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Sitha S. Tetrel bonding in the realm of transition states favors silicon over Carbon: Role of water as a tetrel spectator in the formation of silaformamide. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Wang X, Li B, Li Y, Wang H, Ni Y, Wang H. The influence of monomer deformation on triel and tetrel bonds between TrR3/TR4 (Tr = Al, Ga, In; T = Si, Ge, Sn) and N-base (N-base = HCN, NH3, CN−). COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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Iribarren I, Sánchez-Sanz G, Alkorta I, Elguero J, Trujillo C. Evaluation of Electron Density Shifts in Noncovalent Interactions. J Phys Chem A 2021; 125:4741-4749. [PMID: 34061527 PMCID: PMC8279648 DOI: 10.1021/acs.jpca.1c00830] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Indexed: 12/12/2022]
Abstract
In the present paper, we report the quantitative evaluation of the electron density shift (EDS) maps within different complexes. Values associated with the total EDS maps exhibited good correlation with different quantities such as interaction energies, Eint, intermolecular distances, bond critical points, and LMOEDA energy decomposition terms. Besides, EDS maps at different cutoffs were also evaluated and related with the interaction energies values. Finally, EDS maps and their corresponding values are found to correlate with Eint within systems with cooperative effects. To our knowledge, this is the first time that the EDS has been quanitatively evaluated.
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Affiliation(s)
- Iñigo Iribarren
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish
Centre For High-End Computing, 7 Floor, The Tower, Grand Canal Quay, Dublin 2 D02 HP83, Ireland
| | - Ibon Alkorta
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Cristina Trujillo
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
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10
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Zierkiewicz W, Grabarz A, Michalczyk M, Scheiner S. Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey. Chemphyschem 2021; 22:924-934. [PMID: 33876515 DOI: 10.1002/cphc.202100157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Indexed: 01/02/2023]
Abstract
Crystal structures document the ability of a TF3 group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN- anionic base can approach the T either along the extension of a T-C or T-F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and 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
| | - Anna Grabarz
- 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
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah, 84322-0300, USA
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11
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Liu N, Liu J, Li Q, Scheiner S. Noncovalent bond between tetrel π-hole and hydride. Phys Chem Chem Phys 2021; 23:10536-10544. [PMID: 33899891 DOI: 10.1039/d1cp01245b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The π-hole above the plane of the X2T'Y molecule (T' = Si, Ge, Sn; X = F, Cl, H; Y = O, S) was allowed to interact with the TH hydride of TH(CH3)3 (T = Si, Ge, Sn). The resulting THT' tetrel bond is quite strong, with interaction energies exceeding 30 kcal mol-1. F2T'O engages in the strongest such bonds, as compared to F2T'S, Cl2T'O, or Cl2T'S. The bond weakens as T' grows larger as in Si > Ge > Sn, despite the opposite trend in the depth of the π-hole. The reverse pattern of stronger tetrel bond with larger T is observed for the Lewis base TH(CH3)3, even though the minimum in the electrostatic potential around the H is nearly independent of T. The THT' arrangement is nonlinear which can be understood on the basis of the positions of the extrema in the molecular electrostatic potentials of the monomers. The tetrel bond is weakened when H2O forms an OT' tetrel bond with the second π-hole of F2T'O, and strengthened if H2O participates in an OHO H-bond.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Jiaxing Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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12
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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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13
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Abstract
The tetrel bond (TB) recruits an element drawn from the C, Si, Ge, Sn, Pb family as electron acceptor in an interaction with a partner Lewis base. The underlying principles that explain this attractive interaction are described in terms of occupied and vacant orbitals, total electron density, and electrostatic potential. These principles facilitate a delineation of the factors that feed into a strong TB. The geometric deformation that occurs within the tetrel-bearing Lewis acid monomer is a particularly important issue, with both primary and secondary effects. As a first-row atom of low polarizability, C is a reluctant participant in TBs, but its preponderance in organic and biochemistry make it extremely important that its potential in this regard be thoroughly understood. The IR and NMR manifestations of tetrel bonding are explored as spectroscopy offers a bridge to experimental examination of this phenomenon. In addition to the most common σ-hole type TBs, discussion is provided of π-hole interactions which are a result of a common alternate covalent bonding pattern of tetrel atoms.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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15
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Zhang Z, Lu T, Ding L, Wang G, Wang Z, Zheng B, Liu Y, Ding XL. Cooperativity effects between regium-bonding and pnicogen-bonding interactions in ternary MF···PH3O···MF (M = Cu, Ag, Au): an ab initio study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1784478] [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]
Affiliation(s)
- Zan Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing, People’s Republic of China
| | - Luyang Ding
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Guanyu Wang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Zhaoxu Wang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Baishu Zheng
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Yuan Liu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Xun Lei Ding
- Institute of Clusters and Low Dimensional Nanomaterials, School of Mathematics and Physics, North China Electric Power University, Beijing, People’s Republic of China
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Liu N, Li Q, McDowell SAC. Reliable Comparison of Pnicogen, Chalcogen, and Halogen Bonds in Complexes of 6-OXF 2-Fulvene (X = As, Sb, Se, Te, Be, I) With Three Electron Donors. Front Chem 2020; 8:608486. [PMID: 33425859 PMCID: PMC7793776 DOI: 10.3389/fchem.2020.608486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/27/2020] [Indexed: 01/03/2023] Open
Abstract
The pnicogen, chalcogen, and halogen bonds between 6-OXF2-fulvene (X = As, Sb, Se, Te, Br, and I) and three nitrogen-containing bases (FCN, HCN, and NH3) are compared. For each nitrogen base, the halogen bond is strongest, followed by the pnicogen bond, and the chalcogen bond is weakest. For each type of bond, the binding increases in the FCN < HCN < NH3 pattern. Both FCN and HCN engage in a bond with comparable strengths and the interaction energies of most bonds are < -6 kcal/mol. However, the strongest base NH3 forms a much more stable complex, particularly for the halogen bond with the interaction energy going up to -18 kcal/mol. For the same type of interaction, its strength increases as the mass of the central X atom increases. These bonds are different in strength, but all of them are dominated by the electrostatic interaction, with the polarization contribution important for the stronger interaction. The presence of these bonds changes the geometries of 6-OXF2-fulvene, particularly for the halogen bond formed by NH3, where the F-X-F arrangement is almost vertical to the fulvene ring.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, China
| | - Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Cave Hill, Barbados
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17
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Grabarz A, Michalczyk M, Zierkiewicz W, Scheiner S. Noncovalent Bonds between Tetrel Atoms. Chemphyschem 2020; 21:1934-1944. [DOI: 10.1002/cphc.202000444] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/07/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Anna Grabarz
- 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
| | - Wiktor Zierkiewicz
- Faculty of Chemistry Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan Utah 84322-0300 United States
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18
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Röther A, Kretschmer R. Syntheses of Bis(N-heterocyclic carbene)s and their application in main-group chemistry. J Organomet Chem 2020. [DOI: 10.1016/j.jorganchem.2020.121289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Muya JT, Isamura BK, Patouossa I, Nguyen MT. Interplay between σ Holes, Anion···H-C, and Cation-π Interactions in Dibromo[2,2]paracyclophane Complexes. J Phys Chem A 2020; 124:4379-4389. [PMID: 32364383 DOI: 10.1021/acs.jpca.9b09879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Theoretical calculations were performed to investigate the interplay between σ-hole, anion-HC and cation-π interactions in the complexes of dibromo[2,2]paracyclophane (DBr[2,2]PCP) with alkali (Li+, Na+, K+), alkaline earth metal cations (Be2+, Mg2+, and Ca2+), and halogen anions (F-, Cl-, and Br-) using the wave function (MP2) and density functional theory (M06-2X and B3LYP) methods with the 6-311++G(d,p) basis set. The study reveals that DBr[2,2]PCP behaves as amphoteric molecule with a predominance of basic character. It prefers to interact with hard cations and hard anions such as Be2+ and F- through cation-π and anion···HC interactions, respectively. Substitution of Br by F and Cl atoms in DBr[2,2]PCP decreases slightly the interaction energies of DX[2,2]PCP-halogen complexes (X = F, Cl, and Br) by 2.0 and 0.3 kcal/mol (M06-2X), respectively. The anion-HC interactions in DBr[2,2]PCP complexes are ∼10 kcal/mol stronger (B3LYP; ∼15 kcal/mol at M06-2X and 7 kcal/mol at MP2) than the σ-hole interactions.
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Affiliation(s)
- Jules Tshishimbi Muya
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, DR Congo.,Department of Chemistry, Faculty of Science, University of Kinshasa, P.O. Box 190 Kinshasa XI, DR Congo.,Department of Chemistry and Research Institute for Natural Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Bienfait Kabuyaya Isamura
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, DR Congo.,Department of Chemistry, Faculty of Science, University of Kinshasa, P.O. Box 190 Kinshasa XI, DR Congo
| | - Issofa Patouossa
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, DR Congo.,Laboratory of Physical and Theoretical Chemistry, Faculty of Sciences, University of Yaoundé, P.O. Box 812, Yaoundé I, Cameroon
| | - Minh Tho Nguyen
- Computational Chemistry Research Group and Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
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20
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Wysokiński R, Zierkiewicz W, Michalczyk M, Scheiner S. How Many Pnicogen Bonds can be Formed to a Central Atom Simultaneously? J Phys Chem A 2020; 124:2046-2056. [PMID: 32052970 PMCID: PMC7590972 DOI: 10.1021/acs.jpca.0c00257] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
A central ZF3 molecule (Z = P, As, Sb, Bi) is allowed
to interact with a number of nucleophiles exemplified by NCH, NH3, and NC– anion. The Z···N
pnicogen bond (ZB) to a single base grows stronger for heavier Z atom:
P < A < Sb < Bi and follows the NCH < NH3 <
NC– order for the three bases. The maximum number
of ZBs depends on both the nature of the base and pnicogen atom. PF3 and AsF3 can pnicogen bond with only a single
CN–; SbF3 and BiF3 can interact
with two anions but only weakly. The weak NCH nucleophile can engage
in a maximum of two ZBs, while three ZBs occur for NH3.
The latter NH3 maximum can be extended to four ZBs but
only for BiF3. The fourth ZB is somewhat longer and weaker
than the others, and the entire (H3N)4···BiF3 complex relies partially on secondary interactions for its
stability.
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Affiliation(s)
- Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - 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
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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21
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Iribarren I, Sánchez-Sanz G, Trujillo C. Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds. Molecules 2020; 25:E798. [PMID: 32059506 PMCID: PMC7070532 DOI: 10.3390/molecules25040798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 11/30/2022] Open
Abstract
A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X···I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.
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Affiliation(s)
- Iñigo Iribarren
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, D02 R590 Dublin 2, Ireland;
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of Chemistry, University College Dublin, Belfield, D02 HP83 Dublin 4, Ireland;
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, D02 R590 Dublin 2, Ireland;
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22
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Structures and energetics of clusters surrounding diatomic anions stabilized by hydrogen, halogen, and other noncovalent bonds. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Scheiner S, Michalczyk M, Zierkiewicz W. Coordination of anions by noncovalently bonded σ-hole ligands. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213136] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Aakeroy CB, Bryce DL, Desiraju GR, Frontera A, Legon AC, Nicotra F, Rissanen K, Scheiner S, Terraneo G, Metrangolo P, Resnati G. Definition of the chalcogen bond (IUPAC Recommendations 2019). PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-0713] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
This recommendation proposes a definition for the term “chalcogen bond”; it is recommended the term is used to designate the specific subset of inter- and intramolecular interactions formed by chalcogen atoms wherein the Group 16 element is the electrophilic site.
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Affiliation(s)
- Christer B. Aakeroy
- Department of Chemistry , Kansas State University , 1212 Mid-Campus Dr. North , Manhattan, KS 66506-0401 , USA
| | - David L. Bryce
- Department of Chemistry and Biomolecular Sciences and Centre for Catalysis Research and Innovation , University of Ottawa , 10 Marie Curie Private, Ottawa , Ontario K1N 6N5 , Canada
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bangalore 560 012 , India
| | - Antonio Frontera
- Departament de Quımica , Universitat de les Illes Balears , Crta de Valldemossa km 7.5 , 07122 Palma de Mallorca (Baleares) , Spain
| | - Anthony C. Legon
- School of Chemistry, University of Bristol , Bristol BS8 1TS , Avon , UK
| | - Francesco Nicotra
- Department of Biotechnologies and Biosciences , University of Milano Bicocca , Piazza della Scienza 2 , I-20126 Milano , Italy
| | - Kari Rissanen
- Department of Chemistry, Nanoscience Centre , University of Jyväskylä , POB 34 , Jyväskylä 40014 , Finland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry , Utah State University , Logan, UT 84322-0300 , USA
| | - Giancarlo Terraneo
- SBNLab, Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” , Politecnico di Milano, via Mancinelli 7 , I-20131 Milano , Italy
| | - Pierangelo Metrangolo
- SBNLab, Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” , Politecnico di Milano, via Mancinelli 7 , I-20131 Milano , Italy
| | - Giuseppe Resnati
- NFMLab, Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” , Politecnico di Milano, via Mancinelli 7 , I-20131 Milano , Italy
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26
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Lu J, Scheiner S. Effects of Halogen, Chalcogen, Pnicogen, and Tetrel Bonds on IR and NMR Spectra. Molecules 2019; 24:E2822. [PMID: 31382402 PMCID: PMC6696224 DOI: 10.3390/molecules24152822] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 11/22/2022] Open
Abstract
Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A-F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This shift varies from 42 to 175 cm-1 and is largest for the halogen bonds, followed by chalcogen, tetrel, and then pnicogen. The shift also decreases as the central A atom is enlarged. The NMR chemical shielding of the A atom is increased while that of the F and electron donor N atom are lowered. Unlike the IR frequency shifts, it is the third-row A atoms that undergo the largest change in NMR shielding. The change in shielding of A is highly variable, ranging from negligible for FSnH3 all the way up to 1675 ppm for FBr, while those of the F atom lie in the 55-422 ppm range. Although smaller in magnitude, the changes in the N shielding are still easily detectable, between 7 and 27 ppm.
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Affiliation(s)
- Jia Lu
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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27
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Scheiner S, Michalczyk M, Zierkiewicz W. Structures of clusters surrounding ions stabilized by hydrogen, halogen, chalcogen, and pnicogen bonds. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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28
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29
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Chipanina NN, Lazareva NF, Oznobikhina LP, Shainyan BA. Tetrel Bonding along the Pathways of Transsilylation and Alkylation of N-Trimethylsilyl-N-methylacetamide with Bifunctional (Chloromethyl)fluorosilanes. J Phys Chem A 2019; 123:5178-5189. [DOI: 10.1021/acs.jpca.9b03876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nina N. Chipanina
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
| | - Nataliya F. Lazareva
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
| | - Larisa P. Oznobikhina
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
| | - Bagrat A. Shainyan
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
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30
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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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31
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Dual Geometry Schemes in Tetrel Bonds: Complexes between TF₄ (T = Si, Ge, Sn) and Pyridine Derivatives. Molecules 2019; 24:molecules24020376. [PMID: 30669688 PMCID: PMC6359171 DOI: 10.3390/molecules24020376] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
When an N-base approaches the tetrel atom of TF4 (T = Si, Ge, Sn) the latter molecule deforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situate itself at either an axial or equatorial position, leading to two different equilibrium geometries. The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol, which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform the tetrahedral monomer into the equatorial structure is much higher than the equivalent deformation energy in the axial dimer. When these two opposite trends are combined, it is the axial geometry which is somewhat more stable than the equatorial, yielding binding energies in the 8–34 kcal/mol range. There is a clear trend of increasing interaction energy as the tetrel atom grows larger: Si < Ge < Sn, a pattern which is accentuated for the binding energies.
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32
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Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions. Molecules 2019; 24:molecules24020227. [PMID: 30634503 PMCID: PMC6358819 DOI: 10.3390/molecules24020227] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/05/2019] [Accepted: 01/05/2019] [Indexed: 11/22/2022] Open
Abstract
Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl− was thus compared to that of HCOO−, HSO4−, and H2PO4− with a wide variety of bidentate receptors. A pair of SnFH2 groups, as strong tetrel-binding agents, were first added to a phenyl ring in ortho, meta, and para arrangements. These same groups were also added in 1,3 and 1,4 positions of an aliphatic cyclohexyl ring. The tetrel-bonding groups were placed at the termini of (-C≡C-)n (n = 1,2) extending arms so as to further separate the two Sn atoms. Finally, the Sn atoms were incorporated directly into an eight-membered ring, rather than as appendages. The ordering of the binding energetics follows the HCO2− > Cl− > H2PO4− > HSO4− general pattern, with some variations in selected systems. The tetrel bonding is strong enough that in most cases, it engenders internal deformations within the receptors that allow them to engage in bidentate bonding, even for the monatomic chloride, which mutes any effects of a long Sn···Sn distance within the receptor.
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33
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Wysokiński R, Michalczyk M, Zierkiewicz W, Scheiner S. Influence of monomer deformation on the competition between two types of σ-holes in tetrel bonds. Phys Chem Chem Phys 2019; 21:10336-10346. [DOI: 10.1039/c9cp01759c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Competition between two competing sites on a tetrel atom is explained by balance between structural deformation and σ-hole intensity.
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Affiliation(s)
- Rafał Wysokiński
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
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34
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Caballero-García G, Mondragón-Solórzano G, Torres-Cadena R, Díaz-García M, Sandoval-Lira J, Barroso-Flores J. Calculation of VS,max and Its Use as a Descriptor for the Theoretical Calculation of p Ka Values for Carboxylic Acids. Molecules 2018; 24:molecules24010079. [PMID: 30587832 PMCID: PMC6337188 DOI: 10.3390/molecules24010079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/21/2018] [Accepted: 12/25/2018] [Indexed: 01/30/2023] Open
Abstract
The theoretical calculation of pKa values for Brønsted acids is a challenging task that involves sophisticated and time-consuming methods. Therefore, heuristic approaches are efficient and appealing methodologies to approximate these values. Herein, we used the maximum surface electrostatic potential (VS,max) on the acidic hydrogen atoms of carboxylic acids to describe the H-bond interaction with water (the same descriptor that is used to characterize σ-bonded complexes) and correlate the results with experimental pKa values to obtain a predictive model for other carboxylic acids. We benchmarked six different methods, all including an implicit solvation model (water): Five density functionals and the Møller–Plesset second order perturbation theory in combination with six different basis sets for a total of thirty-six levels of theory. The ωB97X-D/cc-pVDZ level of theory stood out as the best one for consistently reproducing the reported pKa values, with a predictive power of 98% correlation in a test set of ten other carboxylic acids.
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Affiliation(s)
- Guillermo Caballero-García
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Unidad San Cayetano, Carretera Toluca⁻Atlacomulco km 14.5, Personal de la UNAM, Toluca 50200, Mexico.
| | - Gustavo Mondragón-Solórzano
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Unidad San Cayetano, Carretera Toluca⁻Atlacomulco km 14.5, Personal de la UNAM, Toluca 50200, Mexico.
| | - Raúl Torres-Cadena
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Unidad San Cayetano, Carretera Toluca⁻Atlacomulco km 14.5, Personal de la UNAM, Toluca 50200, Mexico.
| | - Marco Díaz-García
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Unidad San Cayetano, Carretera Toluca⁻Atlacomulco km 14.5, Personal de la UNAM, Toluca 50200, Mexico.
| | - Jacinto Sandoval-Lira
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Unidad San Cayetano, Carretera Toluca⁻Atlacomulco km 14.5, Personal de la UNAM, Toluca 50200, Mexico.
| | - Joaquín Barroso-Flores
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Unidad San Cayetano, Carretera Toluca⁻Atlacomulco km 14.5, Personal de la UNAM, Toluca 50200, Mexico.
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Tetrel Bond between 6-OTX₃-Fulvene and NH₃: Substituents and Aromaticity. Molecules 2018; 24:molecules24010010. [PMID: 30577501 PMCID: PMC6337681 DOI: 10.3390/molecules24010010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 11/24/2022] Open
Abstract
Carbon bonding is a weak interaction, particularly when a neutral molecule acts as an electron donor. Thus, there is an interesting question of how to enhance carbon bonding. In this paper, we found that the –OCH3 group at the exocyclic carbon of fulvene can form a moderate carbon bond with NH3 with an interaction energy of about −10 kJ/mol. The –OSiH3 group engages in a stronger tetrel bond than does the –OGeH3 group, while a reverse result is found for both –OSiF3 and –OGeF3 groups. The abnormal order in the former is mainly due to the stronger orbital interaction in the –OSiH3 complex, which has a larger deformation energy. The cyano groups adjoined to the fulvene ring not only cause a change in the interaction type, from vdW interactions in the unsubstituted system of –OCF3 to carbon bonding, but also greatly strengthen tetrel bonding. The formation of tetrel bonding has an enhancing effect on the aromaticity of the fulvene ring.
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36
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Crystallographic and Computational Characterization of Methyl Tetrel Bonding in S-Adenosylmethionine-Dependent Methyltransferases. Molecules 2018; 23:molecules23112965. [PMID: 30428636 PMCID: PMC6278250 DOI: 10.3390/molecules23112965] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [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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37
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Esrafili MD, Mousavian P. Strong Tetrel Bonds: Theoretical Aspects and Experimental Evidence. Molecules 2018; 23:E2642. [PMID: 30326582 PMCID: PMC6222713 DOI: 10.3390/molecules23102642] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years, noncovalent interactions involving group-14 elements of the periodic table acting as a Lewis acid center (or tetrel-bonding interactions) have attracted considerable attention due to their potential applications in supramolecular chemistry, material science and so on. The aim of the present study is to characterize the geometry, strength and bonding properties of strong tetrel-bond interactions in some charge-assisted tetrel-bonded complexes. Ab initio calculations are performed, and the results are supported by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) approaches. The interaction energies of the anionic tetrel-bonded complexes formed between XF₃M molecule (X=F, CN; M=Si, Ge and Sn) and A- anions (A-=F-, Cl-, Br-, CN-, NC- and N₃-) vary between -16.35 and -96.30 kcal/mol. The M atom in these complexes is generally characterized by pentavalency, i.e., is hypervalent. Moreover, the QTAIM analysis confirms that the anionic tetrel-bonding interaction in these systems could be classified as a strong interaction with some covalent character. On the other hand, it is found that the tetrel-bond interactions in cationic tetrel-bonded [p-NH₃(C₆H₄)MH₃]⁺···Z and [p-NH₃(C₆F₄)MH₃]⁺···Z complexes (M=Si, Ge, Sn and Z=NH₃, NH₂CH₃, NH₂OH and NH₂NH₂) are characterized by a strong orbital interaction between the filled lone-pair orbital of the Lewis base and empty BD*M-C orbital of the Lewis base. The substitution of the F atoms in the benzene ring provides a strong orbital interaction, and hence improved tetrel-bond interaction. For all charge-assisted tetrel-bonded complexes, it is seen that the formation of tetrel-bond interaction is accompanied bysignificant electron density redistribution over the interacting subunits. Finally, we provide some experimental evidence for the existence of such charge-assisted tetrel-bond interactions in crystalline phase.
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Affiliation(s)
- Mehdi D Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh 5513864596, Iran.
| | - Parisasadat Mousavian
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh 5513864596, Iran.
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38
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Sengupta A, Liu Y, Flood AH, Raghavachari K. Anion‐Binding Macrocycles Operate Beyond the Electrostatic Regime: Interaction Distances Matter. Chemistry 2018; 24:14409-14417. [PMID: 30036449 DOI: 10.1002/chem.201802657] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Arkajyoti Sengupta
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
- Current Address: Department of Chemistry Michigan State University East Lansing Michigan 48824 USA
| | - Yun Liu
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
- Current Address: Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Amar H. Flood
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
| | - Krishnan Raghavachari
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
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39
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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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40
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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] [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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41
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Esrafili MD, Mousavian P, Mohammadian-Sabet F. Tuning of pnicogen and chalcogen bonds by an aerogen-bonding interaction: a comparative ab initio study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1492746] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Parisasadat Mousavian
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Fariba Mohammadian-Sabet
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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42
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Scheiner S. Tetrel Bonding as a Vehicle for Strong and Selective Anion Binding. Molecules 2018; 23:E1147. [PMID: 29751608 PMCID: PMC6100077 DOI: 10.3390/molecules23051147] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/22/2023] Open
Abstract
Tetrel atoms T (T = Si, Ge, Sn, and Pb) can engage in very strong noncovalent interactions with nucleophiles, which are commonly referred to as tetrel bonds. The ability of such bonds to bind various anions is assessed with a goal of designing an optimal receptor. The Sn atom seems to form the strongest bonds within the tetrel family. It is most effective in the context of a -SnF₃ group and a further enhancement is observed when a positive charge is placed on the receptor. Connection of the -SnF₃ group to either an imidazolium or triazolium provides a strong halide receptor, which can be improved if its point of attachment is changed from the C to an N atom of either ring. Aromaticity of the ring offers no advantage nor is a cyclic system superior to a simple alkyl amine of any chain length. Placing a pair of -SnF₃ groups on a single molecule to form a bipodal dicationic receptor with two tetrel bonds enhances the binding, but falls short of a simple doubling. These two tetrel groups can be placed on opposite ends of an alkyl diamine chain of any length although SnF₃⁺NH₂(CH₂)nNH₂SnF₃⁺ with n between 2 and 4 seems to offer the strongest halide binding. Of the various anions tested, OH− binds most strongly: OH− > F− > Cl− > Br− > I−. The binding energy of the larger NO₃− and HCO₃− anions is more dependent upon the charge of the receptor. This pattern translates into very strong selectivity of binding one anion over another. The tetrel-bonding receptors bind far more strongly to each anion than an equivalent number of K⁺ counterions, which leads to equilibrium ratios in favor of the former of many orders of magnitude.
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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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44
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Esrafili MD, Sadr-Mousavi A. A computational study on the strength and nature of bifurcated aerogen bonds. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.066] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Dong W, Yang X, Cheng J, Li W, Li Q. Comparison for σ-hole and π-hole tetrel-bonded complexes involving F 2 C CFTF 3 (T C, Si, and Ge): Substitution, hybridization, and solvation effects. J Fluor Chem 2018. [DOI: 10.1016/j.jfluchem.2018.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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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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47
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Wei Y, Li Q, Scheiner S. The π-Tetrel Bond and its Influence on Hydrogen Bonding and Proton Transfer. Chemphyschem 2018; 19:736-743. [DOI: 10.1002/cphc.201701136] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/27/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Yuanxin Wei
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
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48
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Zierkiewicz W, Michalczyk M, Scheiner S. Implications of monomer deformation for tetrel and pnicogen bonds. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00430g] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Monomer rearrangement raises the interaction energy by up to 20 kcal mol−1and intensifies its σ-hole by a factor of 1.5–2.9.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
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49
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Del Bene JE, Alkorta I, Elguero J. Carbon–Carbon Bonding between Nitrogen Heterocyclic Carbenes and CO2. J Phys Chem A 2017; 121:8136-8146. [DOI: 10.1021/acs.jpca.7b08393] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janet E. Del Bene
- Department
of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
| | - Ibon Alkorta
- Instituto
de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
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50
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Halogen Bonds Formed between Substituted Imidazoliums and N Bases of Varying N-Hybridization. Molecules 2017; 22:molecules22101634. [PMID: 28961202 PMCID: PMC6151534 DOI: 10.3390/molecules22101634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 12/16/2022] Open
Abstract
Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp³, sp² and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution.
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