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Ibrahim MAA, Abuelliel HAA, Moussa NAM, Rady ASSM, Sayed SRM, El-Tayeb MA, Ahmed MN, Abd El-Rahman MK, Shoeib T. σ-Hole, lone-pair-hole, and π-hole site-based interactions in aerogen-comprising complexes: a comparative study. RSC Adv 2024; 14:22408-22417. [PMID: 39010916 PMCID: PMC11248570 DOI: 10.1039/d4ra03614j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024] Open
Abstract
Herein, the potential of ZO3 and ZF2 aerogen-comprising molecules (where Z = Ar, Kr, and Xe) to engage in σ-, lp-, and π-hole site-based interactions was comparatively studied using various ab initio computations. For the first time, a premier in-depth elucidation of the external electric field (EEF) influence on the strength of the σ-, lp-, and π-hole site-based interactions within the ZO3/ZF2⋯NH3 and ⋯NCH complexes was addressed using oriented EEF with disparate magnitude. Upon the energetic features, σ-hole site-based interactions were noticed with the most prominent preferability in comparison to lp- and π-hole analogs. This finding was ensured by the negative interaction energy values of -11.65, -3.50, and -2.74 kcal mol-1 in the case of σ-, lp-, and π-hole site-based interactions within the XeO3⋯ and XeF2⋯NH3 complexes, respectively. Detailedly, the strength of the σ- and lp-hole site-based interactions directly correlated with the atomic size of the aerogen atoms and the magnitude of the positively oriented EEF. Unexpectedly, an irregular correlation was noticed for the interaction energies of the π-hole site-based interactions with the size of the π-hole. Interestingly, the π-hole site-based interactions within Kr-comprising complexes exhibited higher negative interaction energies than the Ar- and Xe-comprising counterparts. Notwithstanding, a direct proportion between the interaction energies of the π-hole site-based interactions and π-hole size was obtained by employing EEF along the positive orientation with high strength. The present outcomes would be a fundamental basis for forthcoming progress in studying the σ-, lp-, and π-hole site-based interactions within aerogen-comprising complexes and their pertinent applications in materials science and crystal engineering.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
- School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4000 South Africa
| | - Hassan A A Abuelliel
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
- Basic and Clinical Medical Science Department, Faculty of Dentistry, Deraya University New Minya 61768 Egypt
| | - Al-Shimaa S M Rady
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Shaban R M Sayed
- Department of Botany and Microbiology, College of Science, King Saud University P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Mohamed A El-Tayeb
- Department of Botany and Microbiology, College of Science, King Saud University P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Muhammad Naeem Ahmed
- Department of Chemistry, The University of Azad Jammu and Kashmir Muzaffarabad 13100 Pakistan
| | | | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo New Cairo 11835 Egypt
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2
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Niu Z, McDowell SAC, Li Q. Triel Bonds with Au Atoms as Electron Donors. Chemphyschem 2023; 24:e202200748. [PMID: 36448371 DOI: 10.1002/cphc.202200748] [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: 10/10/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The novel triel bonds of BX3 (X=H, F, Cl, Br, and I) and C5 H5 B as electron acceptors and AuR2 (R=Cl and CH3 ) as an electron donor were explored. The triel bond is a primary driving force for most complexes, while the contribution from a halogen-chlorine interaction in BX3 -AuCl2 (X=Cl, Br, and I) and an iodine-Au interaction in BI3 -Au(CH3 )3 is also very important. Interestingly, the positively charged Au atom of AuCl2 can attractively bind with the holes of BX3 and C5 H5 B. The interaction energy lies in the range of 1 and 80 kcal/mol, in the order X=F<H<Cl<Br<I. In most cases, the triel bond of C5 H5 B is stronger than the triel bond of BX3 . In the formation of B-Au triel bond, electrostatic energy is not dominant, while polarization energy including orbital interaction has the largest contribution for the strongly bonded complexes and dispersion energy for the weak triel bond.
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Affiliation(s)
- Zhihao Niu
- Laboratory of Theoretical and Computational Chemistry and 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, Barbados
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
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3
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Tabernero V, Teresa Muñoz M, Palenzuela M, Gomila RM, Frontera A, Mosquera MEG. σ-Hole triel bonds in aluminium derivatives. Dalton Trans 2023; 52:551-555. [PMID: 36594397 DOI: 10.1039/d2dt03581b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This communication reports the synthesis and X-ray characterization of a new mononuclear aluminium compound exhibiting an intramolecular σ-hole triel bonding interaction. It is compared with a dinuclear aluminium compound, previously reported by us, where the aluminium atoms participate in two concurrent σ-hole triel bonding interactions. To our knowledge, such behaviour has not been previously described in the literature.
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Affiliation(s)
- Vanessa Tabernero
- Department of Organic and Inorganic Chemistry, Institute of Chemical Research "Andrés M. del Río" (IQAR), Universidad de Alcalá, Campus Universitario, 28871 Madrid, Spain.
| | - M Teresa Muñoz
- Department of Organic and Inorganic Chemistry, Institute of Chemical Research "Andrés M. del Río" (IQAR), Universidad de Alcalá, Campus Universitario, 28871 Madrid, Spain.
| | - Miguel Palenzuela
- Department of Organic and Inorganic Chemistry, Institute of Chemical Research "Andrés M. del Río" (IQAR), Universidad de Alcalá, Campus Universitario, 28871 Madrid, Spain.
| | - Rosa M Gomila
- Departament de Química, Universitat de les Illes Balears, Crts. De Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crts. De Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | - Marta E G Mosquera
- Department of Organic and Inorganic Chemistry, Institute of Chemical Research "Andrés M. del Río" (IQAR), Universidad de Alcalá, Campus Universitario, 28871 Madrid, Spain.
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Revision of the Crystal Structure of the Orthorhombic Polymorph of Oxyma: On the Importance of π–Hole Interactions and Their Interplay with H–Bonds. CRYSTALS 2022. [DOI: 10.3390/cryst12060823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this work the crystal structure of the previously described orthorhombic polymorph of the coupling reagent Oxyma has been revised, corrected now as centrosymmetric and analyzed by means of DFT calculations. In the solid state the structure forms a network of H-bonds and self–assembled dimers that are held together by the formation of N···C π–hole interactions involving the C-atom of the imino group. The H-bonding and π–hole interactions observed in the solid state were rationalized using molecular electrostatic potential (MEP) surfaces, focusing on the H-bond donor-acceptor groups and the π-hole observed above and below the molecular plane. The interactions and their interplay have been characterized by using two methodologies based on the topology of the electron density, which are the quantum theory of “atom-in-molecules” (QTAIM) and the noncovalent interaction plot (NCIplot).
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5
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Wang X, Li B, Wang H, Song Q, Ni Y, Wang H. Strong σ-hole triel-bond between C5H5Tr (Tr B, Al, Ga) and N‐base (N‐base NCH, NH3, NC−): Cooperativity and solvation effects. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Weinhold F. Anti-Electrostatic Pi-Hole Bonding: How Covalency Conquers Coulombics. Molecules 2022; 27:377. [PMID: 35056689 PMCID: PMC8780338 DOI: 10.3390/molecules27020377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/30/2021] [Accepted: 12/30/2021] [Indexed: 12/20/2022] Open
Abstract
Intermolecular bonding attraction at π-bonded centers is often described as "electrostatically driven" and given quasi-classical rationalization in terms of a "pi hole" depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO-, CN-) with simple atomic anions (H-, F-) or with one another. Such "anti-electrostatic" anion-anion attractions are shown to lead to robust metastable binding wells (ranging up to 20-30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi-Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that "deletion" of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi-Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency ("charge transfer") rather than envisioned Coulombic properties of unperturbed monomers.
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Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
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7
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Michalczyk M, Zierkiewicz W, Wysokiński R, Scheiner S. Triel bonds within anion ···anion complexes. Phys Chem Chem Phys 2021; 23:25097-25106. [PMID: 34751289 DOI: 10.1039/d1cp04296c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ability of two anions to interact with one another is tested in the context of pairs of TrX4- homodimers, where Tr represents any of the triel atoms B, Al, Ga, In, or Tl, and X refers to a halogen substituent F, Cl, or Br. None of these pairs engage in a stable complex in the gas phase, but the situation reverses in water where the two monomers are held together by Tr⋯X triel bonds, complemented by stabilizing interactions between X atoms. Some of these bonds are quite strong, notably those involving TrF4-, with interaction energies surpassing 30 kcal mol-1. Others are very much weaker, with scarcely exothermic binding energies. The highly repulsive electrostatic interactions are counteracted by large polarization energies.
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Affiliation(s)
- 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.
| | - Rafał Wysokiński
- 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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Jing X, Zeng Y, Zhang X, Meng L, Li X. Competition and conversion between pnicogen bonds and hydrogen bonds involving prototype organophosphorus compounds. Phys Chem Chem Phys 2021; 23:18794-18805. [PMID: 34612418 DOI: 10.1039/d1cp00474c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio calculations have been performed to investigate the competition and conversion between the pnicogen bonds and hydrogen bonds in complexes containing prototype organophosphorus compounds RPO2 (R = CH3 and CH3O). The competition between the pnicogen bonds and hydrogen bonds is controlled by the magnitude of Vs,min and Vs,max in the prototype organophosphorus compounds. Monomeric methyl metaphosphate (CH3OPO2), with more positive π-holes, is more likely to form pnicogen bonds with different electron donors, such as NH3, H2O, HNC and HCCH. Methoxyphosphinidene oxide (trans- and cis-CH3OPO) is inclined to form hydrogen bonds with H2O, HNC and HCCH. Most of the pnicogen bonds have covalent or partially covalent character, while most of the hydrogen bonds exhibit the noncovalent characteristics of weak interactions. The mechanisms of three typical conversions between the pnicogen bond and the hydrogen bond have been investigated and the breakage and formation of the bonds along the reaction pathways have been analyzed using topological analysis of electron density. For the three studied conversion processes, the transformation between the hydrogen-bonded complex and pnicogen-bonded complex is achieved readily through several T-shape structure transition states.
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Affiliation(s)
- Xinyue Jing
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China.
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9
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Scheiner S. Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage. J Phys Chem A 2021; 125:6514-6528. [PMID: 34310147 DOI: 10.1021/acs.jpca.1c05431] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.
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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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10
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π-hole interactions of group III–VI elements with π-systems and Lewis bases: a comparative study. Struct Chem 2021. [DOI: 10.1007/s11224-021-01817-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Zhao C, Lin H, Shan A, Guo S, Li X, Zhang X. Theoretical study on the noncovalent interactions involving triplet diphenylcarbene. J Mol Model 2021; 27:224. [PMID: 34244865 DOI: 10.1007/s00894-021-04838-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/23/2021] [Indexed: 11/27/2022]
Abstract
The properties of some types of noncovalent interactions formed by triplet diphenylcarbene (DPC3) have been investigated by means of density functional theory (DFT) calculations and quantum theory of atoms in molecule (QTAIM) studies. The DPC3···LA (LA = AlF3, SiF4, PF5, SF2, ClF) complexes have been analyzed from their equilibrium geometries, binding energies, and properties of electron density. The triel bond in the DPC3···AlF3 complex exhibits a partially covalent nature, with the binding energy - 65.7 kJ/mol. The tetrel bond, pnicogen bond, chalcogen bond, and halogen bond in the DPC3···LA (LA = SiF4, PF5, SF2, ClF) complexes show the character of a weak closed-shell noncovalent interaction. Polarization plays an important role in the formation of the studied complexes. The strength of intermolecular interaction decreases in the order LA = AlF3 > ClF > SF2 > SiF4 > PF5. The electron spin density transfers from the radical DPC3 to ClF and SF2 in the formation of halogen bond and chalcogen bond, but for the DPC3···AlF3/SiF4/PF5 complexes, the transfer of electron spin density is minimal.
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Affiliation(s)
- Chunhong Zhao
- Huihua College of Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Hui Lin
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Aiting Shan
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Shaofu Guo
- Huihua College of Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Xiaoyan Li
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China.
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12
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Wang X, Li Y, Wang H, Ni Y, Wang H. Which triel bond is stronger? TrHX⋯H2Y versus TrH2X⋯H2Y (Tr = Ga, In; X = F, Cl, Br, I; Y = O, S). Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02790-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Shen S, Jing X, Zhang X, Li X, Zeng Y. The competition and cooperativity of hydrogen/halogen bond and π-hole bond involving the heteronuclear ethylene analogues. J Comput Chem 2021; 42:908-916. [PMID: 33729600 DOI: 10.1002/jcc.26513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/07/2021] [Accepted: 03/01/2021] [Indexed: 11/08/2022]
Abstract
The noncovalent interactions involving heteronuclear ethylene analogues H2 CEH2 (E = Si, Ge and Sn) have been studied by the Møller-Plesset perturbation theory to investigate the competition and cooperativity between the hydrogen/halogen bond and π-hole bond. H2 CEH2 has a dual role of being a Lewis base and acid with the region of π-electron accumulation above the carbon atom and the region of π-electron depletion (π-hole) above the E atom to participate in the NCX···CE (X = H and Cl) hydrogen/halogen bond and CE···NCY (Y = H, Cl, Li and Na) π-hole bond, respectively. When HCN/ClCN interacts with H2 CEH2 by two sites, the strength of hydrogen bond/halogen bond is stronger than that of π-hole bond. The π-hole bond becomes obviously stronger when the metal substituent of YCN (Y = Li and Na) interacting with H2 CEH2 , showing the character of partial covalent, its strength is much greater than that of hydrogen/halogen bond. In the ternary complexes, both hydrogen/halogen bond and π-hole bond are simultaneously strengthened compared to those in the binary complexes, especially in the systems containing alkali metal.
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Affiliation(s)
- Shaojie Shen
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Xinyue Jing
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Xiaoyan Li
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Yanli Zeng
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, China
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14
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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; 26:1740. [PMID: 33804617 PMCID: PMC8003638 DOI: 10.3390/molecules26061740] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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
| | - 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, Logan, UT 84322-0300, USA;
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15
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Yang Q, Zhou B, Li Q, Scheiner S. Weak σ‐Hole Triel Bond between C
5
H
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Tr (Tr=B, Al, Ga) and Haloethyne: Substituent and Cooperativity Effects. Chemphyschem 2021; 22:481-487. [DOI: 10.1002/cphc.202000955] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/13/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Qingqing Yang
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering Yantai University 264005 Yantai China
| | - Bohua Zhou
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering Yantai University 264005 Yantai China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering Yantai University 264005 Yantai China
| | - Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University 84322-0300 Logan UT USA
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16
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Li Y, Meng L, Zeng Y. Comparison of Anion‐Anion Halogen Bonds with Neutral‐Anion Halogen Bonds in the Gas Phase and Polar Solvents. Chempluschem 2021; 86:232-240. [DOI: 10.1002/cplu.202000734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/25/2021] [Indexed: 01/23/2023]
Affiliation(s)
- Ying Li
- College of Chemistry and Materials Science Hebei Normal University Shijiazhuang 050024 P. R. China
| | - Lingpeng Meng
- College of Chemistry and Materials Science Hebei Normal University Shijiazhuang 050024 P. R. China
| | - Yanli Zeng
- College of Chemistry and Materials Science Hebei Normal University Shijiazhuang 050024 P. R. China
- National Experimental Chemistry Teaching Center Hebei Normal University) Shijiazhuang 050024 P. R. China
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17
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Zhang Y, Wang W. The σ-hole⋯σ-hole stacking interaction: An unrecognized type of noncovalent interaction. J Chem Phys 2020; 153:214302. [PMID: 33291911 DOI: 10.1063/5.0033470] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The σ-hole⋯σ-hole stacking interaction, an unrecognized type of noncovalent interaction, has been found to be present in large quantities in the Cambridge Structural Database. In the σ-hole⋯σ-hole stacking interaction, each of the two interacting σ-holes has the dual electron donor/electron acceptor character; when one σ-hole acts as an electron donor, the other σ-hole acts as an electron acceptor, and vice versa. The σ-hole⋯σ-hole stacking interaction is clearly different from the σ-hole bond in which the charge transfer occurs mainly from the electron donor to the σ-hole. Energy component analysis shows that the σ-hole⋯σ-hole stacking interaction is dominated by the dispersion energy, which is similar to the nature of the aromatic stacking interaction between unsaturated molecules or the σ⋯σ stacking interaction between saturated molecules.
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Affiliation(s)
- Yu Zhang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China
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18
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Lü L, Liu J, Wang H, Jin WJ. π–ring–hole bond around difluoroethyne: stabilization of hydrogen bonding cyclohexamer and dicyclohexamer of ammonia molecules. J Mol Model 2020; 26:259. [DOI: 10.1007/s00894-020-04515-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
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Yang Q, Yao X, Yang X. Influence of N-Base and O-Base Hybridization on Triel Bonds. ACS OMEGA 2020; 5:21300-21308. [PMID: 32875266 PMCID: PMC7450710 DOI: 10.1021/acsomega.0c03394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
Abstract
The complexes of TrR3 (Tr = B and Al; R = H, F, Cl, and Br) with three N-bases (NH3, CH2NH, and HCN) and three O-bases (CH3OH, H2CO, and CO) are utilized to explore the hybridization effect of N and O atoms on the strength, properties, and nature of the triel bond. The sp-hybridized O and N atoms form the weakest triel bond, followed by the sp2-hybridized O atom or the sp3-hybridized N atom, and the sp3-hybridized O atom or the sp2-hybridized N atom engages in the strongest triel bond. The hybridization effect is also related to the substituent of TrR3. Most complexes are dominated by electrostatic, with increasing polarization contribution from sp to sp2 to sp3. Although the CO oxygen engages in a weaker triel bond, its carbon atom is a better electron donor and the interaction energy even amounts to -37 kcal/mol in the BH3 complex.
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20
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Local Vibrational Mode Analysis of π–Hole Interactions between Aryl Donors and Small Molecule Acceptors. CRYSTALS 2020. [DOI: 10.3390/cryst10070556] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds.
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21
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Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
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22
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Zierkiewicz W, Michalczyk M, Scheiner S. Competition between Intra and Intermolecular Triel Bonds. Complexes between Naphthalene Derivatives and Neutral or Anionic Lewis Bases. Molecules 2020; 25:E635. [PMID: 32024163 PMCID: PMC7037318 DOI: 10.3390/molecules25030635] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
: A TrF2 group (Tr = B, Al, Ga, In, Tl) is placed on one of the α positions of naphthalene, and its ability to engage in a triel bond (TrB) with a weak (NCH) and strong (NC-) nucleophile is assessed by ab initio calculations. As a competitor, an NH2 group is placed on the neighboring Cα, from which point it forms an intramolecular TrB with the TrF2 group. The latter internal TrB reduces the intensity of the π-hole on the Tr atom, decreasing its ability to engage in a second external TrB. The intermolecular TrB is weakened by a factor of about two for the smaller Tr atoms but is less severe for the larger Tl. The external TrB can be quite strong nonetheless; it varies from a minimum of 8 kcal/mol for the weak NCH base, up to as much as 70 kcal/mol for CN-. Likewise, the appearance of an external TrB to a strong base like CN- lessens the ability of the Tr to engage in an internal TrB, to the point where such an intramolecular TrB becomes questionable.
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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;
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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23
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Regulating PdC3/PtC3···thiophene interaction by small molecule doping (AgOTf, CuBr, CuI, CuBr2, PdCl2). Struct Chem 2019. [DOI: 10.1007/s11224-019-01362-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Xu Z, Li Y. Triel bonds in RZH 2···NH 3: hybridization, solvation, and substitution. J Mol Model 2019; 25:219. [PMID: 31300929 DOI: 10.1007/s00894-019-4089-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022]
Abstract
The influence of hybridization, substitution, and solvation on the triel bond has been investigated in the complexes of RZH2···NH3 (Z = B and Al). The magnitude of the π-hole on the triel atom is related to the nature of the Z atom and the hybridization of R. CH3BH2 has the largest π-hole among RBH2, while for RAlH2 the largest π-hole is found in CH≡CAlH2. The interaction energy is partly inconsistent with the magnitude of the π-hole on the triel atom and the orbital interaction from the N lone pair of NH3 into the empty p orbital of the triel atom. The strongest B···N triel bond is found in CH≡CBH2···NH3, while the weakest Al···N triel bond is in CH3AlH2···NH3. The strength of the triel bond is increased in solvents, and its enhancement is prominent with the increase of solvent polarity. Solvents also change the nature of the Al···N triel bond from an electrostatic interaction to a partially covalent one. The F substituent in the triel donor strengthens the triel bond, depending on the substitution position and number. Graphical Abstract The π-hole triel bonded complexes between RZH2 (Z =B and Al) and NH3 have been investigated. We focused on the effects of hybridization, solvent, and substitution on the strength and nature of π-hole triel bond.
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Affiliation(s)
- Zhefeng Xu
- Department of Chemical Engineering, Inner Mongolia Vocational College of Chemical Engineering, Hohhot, 010070, People's Republic of China
| | - Yan Li
- Department of Chemical Engineering, Inner Mongolia Vocational College of Chemical Engineering, Hohhot, 010070, People's Republic of China.
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25
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On the ability of pnicogen atoms to engage in both σ and π-hole complexes. Heterodimers of ZF 2C 6H 5 (Z = P, As, Sb, Bi) and NH 3. J Mol Model 2019; 25:152. [PMID: 31069527 DOI: 10.1007/s00894-019-4031-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/07/2019] [Indexed: 01/11/2023]
Abstract
When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH3 base lies opposite one F atom. In addition to this σ-hole complex, the ZF2C6H5 molecule can distort in such a way that the NH3 approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4-13 kcal/mol. On the other hand, this large interaction energy is countered by the considerable deformation energy required for the Lewis acid to adopt the geometry necessary to form the π-hole complex. The overall energetics of the complexation reaction are thus more exothermic for the σ-hole dimers than for the π-hole dimers.
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26
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Enhancing effects of π-hole tetrel bonds on the σ-hole interactions in complexes involving F2TO (T = Si, Ge, Sn). Struct Chem 2019. [DOI: 10.1007/s11224-018-1274-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Michalczyk M, Zierkiewicz W, Scheiner S. Triel-Bonded Complexes between TrR3
(Tr=B, Al, Ga; R=H, F, Cl, Br, CH3
) and Pyrazine. Chemphyschem 2018; 19:3122-3133. [DOI: 10.1002/cphc.201800774] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 01/20/2023]
Affiliation(s)
- 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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28
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Li Y, Xu Z. Competition between tetrel bond and pnicogen bond in complexes of TX 3-ZX 2 and NH 3. J Mol Model 2018; 24:247. [PMID: 30128640 DOI: 10.1007/s00894-018-3732-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/22/2018] [Indexed: 11/29/2022]
Abstract
The complexes formed between TX3-ZX2 (T = C, Si, Ge; Z = P, As, Sb; X = F, Cl) and NH3 were studied at the MP2/aug-cc-pVTZ(PP) level. For each TX3-ZX2, two types of complex were obtained. For CX3-ZX2, NH3 is inclined to approach the σ-hole on the Z atom, forming a pnicogen bond. For TX3-ZX2 (T = Si and Ge), however, the base favors engaging in a tetrel bond with the σ-hole on the T atom although the corresponding pnicogen-bonded complex is also stable. When NH3 approaches the CX3 terminal of CX3-ZX2, weak interactions are observed that may be classified as van der Waals interactions. The relative stability of both types of complexes is not affected by the substituent X. The tetrel bond is very strong and the largest interaction energy is up to -144 kJ mol-1. Dispersion is dominant in the weak van der Waals complexes, while tetrel- and pnicogen-bonded complexes are dominated by electrostatic interactions, with comparable contributions from polarization.
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Affiliation(s)
- Yan Li
- Department of Chemical Engineering, Inner Mongolia Vocational College of Chemical Engineering, Hohhot, 010070, People's Republic of China.
| | - Zhefeng Xu
- Department of Chemical Engineering, Inner Mongolia Vocational College of Chemical Engineering, Hohhot, 010070, People's Republic of China
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29
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Dong W, Wang Y, Cheng J, Yang X, Li Q. Competition between σ-hole pnicogen bond and π-hole tetrel bond in complexes of CF2=CFZH2 (Z = P, As, and Sb). Mol Phys 2018. [DOI: 10.1080/00268976.2018.1508782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | | | | | - 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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30
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Dong W, Wang Y, Yang X, Cheng J, Li Q. Dual function of the boron center of BH(CO) 2/BH(N 2) 2 in halogen- and triel-bonded complexes with hypervalent halogens. J Mol Graph Model 2018; 84:118-124. [PMID: 29960254 DOI: 10.1016/j.jmgm.2018.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022]
Abstract
The complexes between BH(CO)2/BH(N2)2 and XF3/XF5 are stabilized by a halogen bond and a triel bond. The MEP analyses of BH(CO)2/BH(N2)2 indicate that there are both a region with negative MEPs on the B atom in the vertical direction of the molecular plane and a σ-hole at the B-H bond end. Therefore, the boron atom in BH(CO)2/BH(N2)2 plays a dual role of a Lewis base and an acid in the halogen bond and triel bond, respectively. The halogen and triel bonds are stronger in order of IF3< BrF3< ClF3, IF5< BrF5< ClF5, and BH(CO)2< BH(N2)2 in most complexes. These complexes have large stability since the interaction energy varies from -5 to -115 kcal/mol. The halogen bond belongs to a covalent interaction or a partially covalent interaction in most complexes. The subsystems in these complexes have prominent deformation, accompanied with big charge transfer and large polarization.
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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, People's Republic of China
| | - Yanqing Wang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, People's Republic of China
| | - Xin Yang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, People's Republic of China.
| | - Jianbo Cheng
- 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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31
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Abstract
With molecular orbital theory it is possible to distinguish and design σ, π and the elusive δ electrostatic holes.
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Affiliation(s)
- V. Angarov
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 841051
- Israel
| | - S. Kozuch
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 841051
- Israel
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32
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Echeverría J. Frustrated Lewis Trios and Long-Range Hole Interactions: A Combined Structural and Theoretical Study of LB−AX3
⋅⋅⋅LB and LB⋅⋅⋅AX3
⋅⋅⋅LB (A=B, Al, Ga, In) Systems. Chemphyschem 2017; 18:2864-2872. [DOI: 10.1002/cphc.201700856] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Jorge Echeverría
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional IQTC-UB; Universitat de Barcelona; Martí i Franquès 1-11 08028 Barcelona Spain
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Pang W, Lv J, Du S, Wang J, Wang J, Zeng Y. Preparation of Curcumin-Piperazine Coamorphous Phase and Fluorescence Spectroscopic and Density Functional Theory Simulation Studies on the Interaction with Bovine Serum Albumin. Mol Pharm 2017; 14:3013-3024. [PMID: 28703594 DOI: 10.1021/acs.molpharmaceut.7b00217] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the present study, a new coamorphous phase (CAP) of bioactive herbal ingredient curcumin (CUR) with high solubilitythe was screened with pharmaceutically acceptable coformers. Besides, to provide basic information for the best practice of physiological and pharmaceutical preparations of CUR-based CAP, the interaction between CUR-based CAP and bovine serum albumin (BSA) was studied at the molecular level in this paper. CAP of CUR and piperazine with molar ratio of 1:2 was prepared by EtOH-assisted grinding. The as-prepared CAP was characterized by powder X-ray diffraction, modulated temperature differential scanning calorimetry, thermogravimetric analysis, Fourier-transform infrared, and solid-state 13C nuclear magnetic resonance. The 1:2 CAP stoichioimetry was sustained by C═O···H hydrogen bonds between the N-H group of the piperazine and the C═O group of CUR; piperazine stabilized the diketo structure of CUR in CAP. The dissolution rate of CUR-piperazine CAP in 30% ethanol-water was faster than that of CUR; the t50 values were 243.1 min for CUR and 4.378 min for CAP. Furthermore, interactions of CUR and CUR-piperazine CAP with BSA were investigated by fluorescence spectroscopy and density functional theory (DFT) calculation. The binding constants (Kb) of CUR and CUR-piperazine CAP with BSA were 10.0 and 9.1 × 103 L mol-1 at 298 K, respectively. Moreover, DFT simulation indicated that the interaction energy values of hydrogen-bonded interaction in the tryptophan-CUR and tryptophan-CUR-piperazine complex were -26.1 and -17.9 kJ mol-1, respectively. In a conclusion, after formation of CUR-piperazine CAP, the interaction forces between CUR and BSA became weaker.
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Affiliation(s)
- Wenzhe Pang
- College of Pharmaceutical Sciences, Hebei Medical University , Shijiazhuang, 050017, China
| | - Jie Lv
- College of Pharmaceutical Sciences, Hebei Medical University , Shijiazhuang, 050017, China
| | - Shuang Du
- College of Pharmaceutical Sciences, Hebei Medical University , Shijiazhuang, 050017, China
| | - Jiaojiao Wang
- College of Chemistry and Material Science, Hebei Normal University , Shijiazhuang 050024, China
| | - Jing Wang
- College of Pharmaceutical Sciences, Hebei Medical University , Shijiazhuang, 050017, China
| | - Yanli Zeng
- College of Chemistry and Material Science, Hebei Normal University , Shijiazhuang 050024, China
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34
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Wang Y, Li X, Zeng Y, Meng L, Zhang X. Theoretical insights into the π-hole interactions in the complexes containing triphosphorus hydride (P 3H 3) and its derivatives. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:195-202. [PMID: 28362282 DOI: 10.1107/s2052520616019223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/02/2016] [Indexed: 06/07/2023]
Abstract
The π-hole of triphosphorus hydride (P3H3) and its derivatives Z3X3 (Z = P, As; X = H, F, Cl, Br) was discovered and analyzed. MP2/aug-cc-pVDZ calculations were performed on the π-hole interactions in the HCN...Z3X3 complexes and the mutual influence between π-hole interactions and the hydrogen bond in the HCN...HCN...Z3X3 and HCN...Z3X3...HCN complexes studied. The π-hole interaction belongs to the typical closed-shell noncovalent interaction. The linear relationship was found between the most positive electrostatic potential of the π-hole (VS,max) and the interaction energy. Moreover, the VS,max of the π-hole was also found to be linearly correlated to the electrostatic energy term, indicating the important contribution of the electrostatic energy term to the π-hole interaction. There is positive cooperativity between the π-hole interaction and the hydrogen bond in the termolecular complexes. The π-hole interaction has a greater influence on the hydrogen bond than vice versa. The mutual enhancing effect between the π-hole interaction and the hydrogen bond in the HCN...HCN...Z3X3 complexes is greater than that in the HCN...Z3X3...HCN complexes.
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Affiliation(s)
- Yuehong Wang
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Xiaoyan Li
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Yanli Zeng
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Lingpeng Meng
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Xueying Zhang
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
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35
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Abstract
A combined structural and computational analysis has demonstrated that alkyl groups can act as Lewis bases in π-hole bonding.
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Affiliation(s)
- Jorge Echeverría
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTC-UB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
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36
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Wang J, Mo L, Li X, Geng Z, Zeng Y. The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactions. J Mol Model 2016; 22:299. [PMID: 27900582 DOI: 10.1007/s00894-016-3169-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/15/2016] [Indexed: 01/15/2023]
Abstract
The σ-hole and π-hole of the protonated 2-halogenated imidazolium cation (XC3H4N2+; X = F, Cl, Br, I) were investigated and analyzed. The monomers of (CH3)3SiY(Y=F, Cl, Br, I), considered as the Lewis base, were combined with the σ-hole and π-hole of XC3H4N2+ to form the σ-hole and π-hole interactions in the bimolecular complexes (CH3)3SiY · · · XC3H4N2+ and (CH3)3SiY · · · C3(X)H4N2+(X/Y=F, Cl, Br, I), respectively. For both the σ-hole and π-hole interactions, the equilibrium geometries of complexes show regular changes according to the sequence of heavy sequence of the noncovalent interaction acceptors and donors. The electrostatic energy is the main contribution in the formation of both kinds of interactions, it has linear relations with the V S,max values of σ-hole and the V' S,max values of π-hole. Both the σ-hole and π-hole interactions belong to the closed-shell and noncovalent interactions. The π-hole interactions are stronger than the σ-hole interactions. For the π-hole interactions, the contribution percents of the dispersion energies are somewhat greater than those of the σ-hole interactions, while it is contrary for the polarization energy. Graphical Abstract The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactionsᅟ.
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Affiliation(s)
- Jingjing Wang
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Lixin Mo
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Xiaoyan Li
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Zongke Geng
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China.
| | - Yanli Zeng
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China.
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37
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Pandiyan BV, Deepa P, Kolandaivel P. Studies on the σ–hole bonds (halogen, chalcogen, pnicogen and carbon bonds) based on the orientation of crystal structure. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1255796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - P. Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - P. Kolandaivel
- Department of Physics, Bharathiar University, Coimbatore, India
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38
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Kirshenboim O, Kozuch S. How to Twist, Split and Warp a σ-Hole with Hypervalent Halogens. J Phys Chem A 2016; 120:9431-9445. [PMID: 27783513 DOI: 10.1021/acs.jpca.6b07894] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Halogen bonds (XB) are no longer newcomers in the chemistry family. However, XB in hypervalent halogens has not been thoroughly studied. We provide a molecular orbital explanation of the shape and strength of XBs in hypervalent halogens and other species, focusing on the charge transfer and electrostatic aspects of these bonds. Our results show that σ-holes (and subsequently the XBs associated with them) can be easily divided and bent by the influence of equatorial substituents. The inductive effect of both the equatorial and axial groups can affect these distortions, but also the angle between the equatorial ligands has a large influence on the shape of the σ-holes and the molecular orbitals acting as electron acceptor. Although the observation of these warped XB can be hindered by other noncovalent interactions, they may be ubiquitous in crystal structures of hypervalent species, where multiple XB can appear as secondary interactions on each halogen. We propose what can be considered the archetypal hypervalent halogen donor (a pincer type iodosodilactone) and a Lewis dot structure that includes the σ-holes.
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Affiliation(s)
- Omer Kirshenboim
- 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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Affiliation(s)
- Bo Lu
- College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 P. R. China
| | - Xueying Zhang
- College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 P. R. China
| | - Lingpeng Meng
- College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 P. R. China
| | - Yanli Zeng
- College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 P. R. China
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Caballero-García G, Romero-Ortega M, Barroso-Flores J. Reactivity of electrophilic chlorine atoms due to σ-holes: a mechanistic assessment of the chemical reduction of a trichloromethyl group by sulfur nucleophiles. Phys Chem Chem Phys 2016; 18:27300-27307. [PMID: 27722305 DOI: 10.1039/c6cp04321f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
σ-Holes are shown to promote the electrophilic behavior of chlorine atoms in a trichloromethyl group when bound to an electron-withdrawing moiety. A halogen bond-type non-covalent interaction between a chlorine atom and a negatively charged sulfur atom takes place, causing the abstraction of such a chlorine atom while leaving a carbanion, subsequently driving the chemical reduction of the trichloromethyl group to a sulfide in a stepwise process. The mechanism for the model reaction of trichloromethyl pyrimidine 1 with thiophenolate and thiophenol to yield phenylsulfide 4 was followed through 1H-NMR and studied using DFT transition state calculations, and the energy profile for this transformation is fully discussed. MP2 calculations of the electrostatic potential were performed for a series of trichloromethyl compounds in order to assess the presence of σ-holes and quantify them by means of the maximum surface electrostatic potential. Such calculations showed that the chlorine atoms behave as electrophilic leaving groups toward a nucleophilic attack, opening a new possibility in the synthetic chemistry of the trichloromethyl group.
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Affiliation(s)
- Guillermo Caballero-García
- Centro Conjunto de Investigación en Química Sustentable UAEM - UNAM, Carretera Toluca-Atlacomulco km 14.5, Unidad San Cayetano, Personal de la UNAM, Toluca 50200, Estado de México, Mexico. and Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan, s/n, Toluca 50000, Estado de México, Mexico
| | - Moisés Romero-Ortega
- Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan, s/n, Toluca 50000, Estado de México, Mexico
| | - Joaquín Barroso-Flores
- Centro Conjunto de Investigación en Química Sustentable UAEM - UNAM, Carretera Toluca-Atlacomulco km 14.5, Unidad San Cayetano, Personal de la UNAM, Toluca 50200, Estado de México, Mexico.
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Li W, Zeng Y, Li X, Sun Z, Meng L. Insight into the pseudo π-hole interactions in the M3H6(NCF)n (M = C, Si, Ge, Sn, Pb; n = 1, 2, 3) complexes. Phys Chem Chem Phys 2016; 18:24672-80. [PMID: 27545836 DOI: 10.1039/c6cp03713e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
For cyclopropane and its derivatives M3H6 (M = C, Si, Ge, Sn, Pb), "pseudo π-hole" regions above and below the M-M-M three-membered ring have been discovered, and pseudo π-hole interactions between M3H6 and F-CN have been designed and investigated by MP2/aug-cc-pVTZ and MP2/aug-cc-pVTZ-pp calculations. To investigate the enhancing effects of FN halogen bonds on the pseudo π-hole interactions, the termolecular and tetramolecular complexes M3H6(NCF)n (n = 2, 3) were constructed. Energy decomposition analysis shows that the dispersion term contributes the most among the three attractive components in the C3H6(NCF)n (n = 1, 2, 3) complexes while in the Si3H6(NCF)n and Ge3H6(NCF)n complexes, the electrostatic term has the largest contribution. The electrostatic and polarization energies have more effect than the dispersion energy for the enhancement of the FN halogen bond on the pseudo π-hole interactions. With the increase in the number of NCF units from 1 to 3, the VS,min values outside the nitrogen atom of NCF become increasingly negative, the electric field of the lone pair of nitrogen becomes greater and causes a further increase of electron density outside the nitrogen atom and a further decrease of electron density outside the pseudo π-hole region, resulting in a stronger pseudo π-hole interaction.
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Affiliation(s)
- Wei Li
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050024, P. R. China.
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42
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Kozuch S. Should “anion–π interactions” be called “anion–σ interactions”? A revision of the origin of some hole-bonds and their nomenclature. Phys Chem Chem Phys 2016; 18:30366-30369. [DOI: 10.1039/c6cp06416g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The so-called anion–π interactions are dissected to test if indeed the π system of the aromatic ring is the reason for the bond.
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Affiliation(s)
- S. Kozuch
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 841051
- Israel
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