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Gao M, Zhao Q, Yu H, Fu M, Li Q. Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study. Molecules 2022; 27:molecules27092885. [PMID: 35566234 PMCID: PMC9101229 DOI: 10.3390/molecules27092885] [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: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023] Open
Abstract
The spodium–π bonding between MX2 (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C2H2/C2H4 acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX2⋯C2F2 complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.
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Affiliation(s)
- Meng Gao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
- Correspondence: (M.G.); (Q.L.)
| | - Qibo Zhao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Hao Yu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Min Fu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
- Correspondence: (M.G.); (Q.L.)
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2
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Shan A, Li X, Zeng Y, Meng L, Zhang X. Theoretical investigation on the nature of substituted benzene⋯AuX interactions: covalent or noncovalent? NEW J CHEM 2022. [DOI: 10.1039/d1nj05328k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of interactions between AuX (X = F, Cl, Br, CN, NO2, CH3) and aromatic moieties with different electronic properties has been investigated for possible tuning of coinage–metal bonds by varying the substituents.
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Affiliation(s)
- Aiting Shan
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Xiaoyan Li
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Yanli Zeng
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Lingpeng Meng
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Xueying Zhang
- Hebei Key Laboratory of Inorganic Nano-materials, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China
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3
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Grabowski SJ. The coordination of beryllium and magnesium centres in half-sandwich and sandwich compounds. J Organomet Chem 2021. [DOI: 10.1016/j.jorganchem.2021.121906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Classification of So-Called Non-Covalent Interactions Based on VSEPR Model. Molecules 2021; 26:molecules26164939. [PMID: 34443526 PMCID: PMC8399763 DOI: 10.3390/molecules26164939] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.
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Martins JBL, Quintino RP, Politi JRDS, Sethio D, Gargano R, Kraka E. Computational analysis of vibrational frequencies and rovibrational spectroscopic constants of hydrogen sulfide dimer using MP2 and CCSD(T). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 239:118540. [PMID: 32502813 DOI: 10.1016/j.saa.2020.118540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Previous studies have shown that the weakly bonded H2S dimer demands high level quantum chemical calculations to reproduce experimental values. We investigated the hydrogen bonding of H2S dimer using MP2 and CCSD(T) levels of theory in combination with aug-cc-pV(D,T,Q)Z basis sets. More precisely, the binding energies, potential energy curves, rovibrational spectroscopic constants, decomposition lifetime, and normal vibrational frequencies were calculated. In addition, we introduced the local mode analysis of Konkoli-Cremer to quantify the hydrogen bonding in the H2S dimer as well as providing for the first time the comprehensive decomposition of normal vibrational modes into local modes contributions, and a decomposition lifetime based on rate constant. The local mode force constant of the H2S dimer hydrogen bond is smaller than that of the water dimer, in accordance with the weaker hydrogen bonding in the H2S dimer.
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Affiliation(s)
- João B L Martins
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil.
| | - Rabeshe P Quintino
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil
| | - José R Dos S Politi
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, United States
| | - Ricardo Gargano
- Institute of Physics, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, United States
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Yu D, Wu D, Liu JY, Li SY, Li Y. On single-electron magnesium bonding formation and the effect of methyl substitution. RSC Adv 2020; 10:34413-34420. [PMID: 35514394 PMCID: PMC9056782 DOI: 10.1039/d0ra06591a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
The complexes formed between MgX2 (X = F, H) molecules and alkyl radicals Y [Y = CH3, CH2CH3, CH(CH3)2, and C(CH3)3] have been characterized by using quantum chemical methods. The binding distance in all cases is less than the sum of vdW radii of Mg and C, indicating the formation of a non-covalent interaction, namely single-electron magnesium bond. Energy decomposition analysis reveals that electrostatic and polarization contributions are the major components responsible for the stability of the studied complexes. According to interaction energy, atoms in molecules, and independent gradient model analyses, methyl substitution on electron donor Y imposes a positive effect on its complexation with MgX2. When compared with other nonbonded interactions, the single-electron magnesium bond is found to have strength comparable to those of the single-electron beryllium bond and π-magnesium bond. The complexes formed between MgX2 (X = F, H) molecules and alkyl radicals Y [Y = CH3, CH2CH3, CH(CH3)2, and C(CH3)3] have been characterized by using quantum chemical methods.![]()
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Affiliation(s)
- Dan Yu
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
| | - Di Wu
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
| | - Jing-Yao Liu
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
| | - Si-Yi Li
- Department of Transdisciplinary Science and Engineering, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro Tokyo 152-8551 Japan
| | - Ying Li
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
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Molecular Hydrogen as a Lewis Base in Hydrogen Bonds and Other Interactions. Molecules 2020; 25:molecules25143294. [PMID: 32698483 PMCID: PMC7397284 DOI: 10.3390/molecules25143294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 11/23/2022] Open
Abstract
The second-order Møller–Plesset perturbation theory calculations with the aug-cc-pVTZ basis set were performed for complexes of molecular hydrogen. These complexes are connected by various types of interactions, the hydrogen bonds and halogen bonds are most often represented in the sample of species analysed; most interactions can be classified as σ-hole and π-hole bonds. Different theoretical approaches were applied to describe these interactions: Quantum Theory of ‘Atoms in Molecules’, Natural Bond Orbital method, or the decomposition of the energy of interaction. The energetic, geometrical, and topological parameters are analysed and spectroscopic properties are discussed. The stretching frequency of the H-H bond of molecular hydrogen involved in intermolecular interactions is considered as a parameter expressing the strength of interaction.
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8
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Grabowski SJ. Triel bond and coordination of triel centres – Comparison with hydrogen bond interaction. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213171] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Villablanca D, Durán R, Lamsabhi AM, Herrera B. Reaction Mechanism of Li and Mg Carbenoid Cyclopropanations: Metal-π and σ Interactions. ACS OMEGA 2019; 4:19452-19461. [PMID: 31763569 PMCID: PMC6868892 DOI: 10.1021/acsomega.9b02905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
The mechanism of the reaction of lithium and magnesium carbenoids with ethylene to give cyclopropane has been explained in detail in all the steps at the G4 level of theory. We explored the lithium and magnesium interaction toward πC=C and σC-C bonds in the reactants and the products. We have also investigated the reaction path by means of the force profile formalism in order to highlight the electronic and the structural rearrangements along the potential energy surface of the cyclopropanation. The results indicate that all of the reactions are stepwise, exoenergetic, with low barriers. All our findings were confirmed by dynamic simulations for chlorometal carbenoids. Furthermore, from the intrinsic reaction coordinate procedure, we were able to find out the intermediates that can take place when the reaction is descending from the transition state to the products or reactants. The reaction force analysis at B3LYP/6-311G(d,p) indicates that the energy barriers are mostly due to structural rearrangements which are produced by the approach of the carbenoid to ethylene. Quantum theory of atoms in molecules and electron localization function analyses indicate that products, reactants, and intermediates form complexes stabilized by attractive forces between Li/Mg and single/double bonds.
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Affiliation(s)
- Daniel Villablanca
- Laboratorio
de Química Teórica Computacional (QTC), Facultad de
Química, Pontificia Universidad Católica
de Chile, Santiago 7820436, Región Metropolitana, Chile
| | - Rocio Durán
- Laboratorio
de Química Teórica Computacional (QTC), Facultad de
Química, Pontificia Universidad Católica
de Chile, Santiago 7820436, Región Metropolitana, Chile
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Facultad de Ciencias,
Módulo
13 and Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Barbara Herrera
- Laboratorio
de Química Teórica Computacional (QTC), Facultad de
Química, Pontificia Universidad Católica
de Chile, Santiago 7820436, Región Metropolitana, Chile
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10
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Carvalho LC, Bueno MA, de Oliveira BG. The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C 2H 2⋯HF and C 2H 4⋯HF small dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:438-455. [PMID: 30738351 DOI: 10.1016/j.saa.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C2H2⋯(HF), C2H2⋯2(HF), C2H2⋯4(HF), C2H4⋯(HF), C2H4⋯2(HF) and C2H4⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).
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11
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Comparison of halide donators based on pi···M (M = Cu, Ag, Au), pi···H and pi···halogen bonds. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2390-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Lu W, Kinjo R. Complexation of asymmetric diborenes with magnesium bromide. Chem Commun (Camb) 2018; 54:8842-8844. [PMID: 30027954 DOI: 10.1039/c8cc04775h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of neutral Mg complexes of asymmetric diborenes is reported. X-ray diffraction analysis reveals that the Mg center is unsymmetrically coordinated to the B2 units of diborenes. Theoretical calculations manifest the donation of electrons from the π-type orbitals of diborenes to an empty orbital of Mg.
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Affiliation(s)
- Wei Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Nanyang Link 21, Singapore 637371, Singapore.
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13
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Grabowski SJ. Coordination of Be and Mg Centres by HCN Ligands - Be…N and Mg…N Interactions. Chemphyschem 2018; 19:1830-1840. [PMID: 29709103 DOI: 10.1002/cphc.201800274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 11/06/2022]
Abstract
ωB97XD/aug-cc-pVTZ calculations were performed for clusters of Z2+ cations (Z=Be and Mg) and HCN molecules (up to six molecules). The clusters of Be(CH3 )2 and Mg(CH3 )2 with HCN species were also calculated to analyse the influence of the Be/Mg-C formally covalent bonds on interactions of Be or Mg centre with ligands. The beryllium and magnesium centres possess different areas of a positive electrostatic potential that depend on a number of HCN ligands in the cluster considered. Numerous correlations between geometrical, energetic and topological parameters of the clusters considered are discussed since various theoretical approaches are applied; Quantum Theory of 'Atoms in Molecules', Natural Bond Orbital method and decomposition of the energy of interaction. The Be/Mg…N interactions classified as beryllium and magnesium bonds possess numerous characteristics which are known for the hydrogen bonds. Different types of coordination of Be and Mg centres analysed here exist also in crystal structures.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia, International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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Xu HL, Li QZ, Scheiner S. Effect of Magnesium Bond on the Competition Between Hydrogen and Halogen Bonds and the Induction of Proton and Halogen Transfer. Chemphyschem 2018; 19:1456-1464. [PMID: 29544030 DOI: 10.1002/cphc.201800102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Indexed: 01/18/2023]
Abstract
HOX (X=Cl, Br, I, and At) can engage in either a H-bond (HB) or halogen bond (XB) with a base-like HCN, NH3 , and imidazole. Although the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY2 forms a Mg-bond with the O atom of HOX, which grows stronger in the order X=Cl<Br<I<At and Y=F<Cl<Br. When all three molecules are combined, both the Mg and the H/X bonds are cooperatively strengthened to a large degree. Rather than causing a reversal in the HB/XB competition, the Mg-bond acts primarily to amplify the natural preference within the dimer. The Mg-bond induces a certain degree of transfer from O to N of the bridging atom in the H/X bond. Comparison is also made with the effects of a Be-bond.
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Affiliation(s)
- Hui-Li Xu
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qing-Zhong 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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15
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Grabowski SJ. Magnesium Bonds: From Divalent Mg Centres to Trigonal and Tetrahedral Coordination. ChemistrySelect 2018. [DOI: 10.1002/slct.201703137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sławomir J. Grabowski
- Faculty of Chemistry; University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072; 20080 San Sebastian Spain
- IKERBASQUE; Basque Foundation for Science; 48011 Bilbao Spain
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16
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Grabowski SJ. Hydrogen bonds, and σ-hole and π-hole bonds – mechanisms protecting doublet and octet electron structures. Phys Chem Chem Phys 2017; 19:29742-29759. [DOI: 10.1039/c7cp06393h] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For various interactions electron charge shifts try to protect the former doublet or octet electronic structure of the Lewis acid centre.
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Affiliation(s)
- Sławomir J. Grabowski
- Faculty of Chemistry
- University of the Basque Country and Donostia International Physics Center (DIPC)
- P.K. 1072 20080 Donostia
- Spain
- IKERBASQUE
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