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Zhang L, Pei L, Li D, Bian H. Theoretical Insights into Regulation of Red/Blue-Shifting Hydrogen Bonds Through Cooperativity with Regium Bonds. J Phys Chem A 2024; 128:6898-6907. [PMID: 39138147 DOI: 10.1021/acs.jpca.4c03370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
To deeply understand the characteristics and regulation of red/blue-shifting hydrogen bonds (HBs), a theoretical investigation was conducted to explore the cooperativity between regium bonds and HBs in the complexes of Y···MCN···HCX3 (M = Cu, Ag, Au; Y = H2O, HCN, NH3; X = F, Cl). When MCN formed a hydrogen bonding dimer with CHF3 or CHCl3, the blue shift of C-H vibration frequency v(C-H) decreases as the following sequence Au > Cu > Ag, and the red shift decreases following the order Ag > Cu > Au. Upon the formation of ternary complexes, the presence of regium bonding interactions exerts a positive synergistic effect, resulting in the strengthening of the HBs. This, in turn, leads to noticeable changes in the red and blue shifts of v(C-H). In CHF3 complexes, v(C-H) undergoes a decrease in the blue shift, whereas that in CHCl3 exhibits an increase in the red shift. Especially, a transition from blue to red shift is observed within the AuCN···HCCl3 complex. As the strength of the regium bond increases, the trend of shifting from blue to red becomes more pronounced. For a given MCN, the changes occur in the order of NH3 > HCN > H2O. The interplay between two interactions was revealed by the molecular electrostatic potentials (MEP), the atoms in the molecule (AIM), and natural bond orbitals (NBO) analysis. It is revealed that Δv(C-H) is linearly correlated with a series of configuration and energy parameters. We explain the red- and blue-shifting HBs and their changes from the perspective of hyperconjugation and rehybridization. The presence of the positive synergistic effect enhances the hyperconjugation effect, thereby leading to a reduction in the blue shift and an increase in the red shift of v(C-H) within the complexes. This study enriches previous mechanisms regarding red- and blue-shifting HBs and introduces a novel idea to manipulate the characteristics of HBs, with the potential to impact the functioning of intricate systems.
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Affiliation(s)
- Lijuan Zhang
- College of Chemical Engineering and Safety Engineering, Shandong University of Aeronautics, Binzhou, Shandong 256600, China
| | - Ling Pei
- College of Chemical Engineering and Safety Engineering, Shandong University of Aeronautics, Binzhou, Shandong 256600, China
| | - Dazhi Li
- College of Chemical Engineering and Safety Engineering, Shandong University of Aeronautics, Binzhou, Shandong 256600, China
| | - He Bian
- College of Chemical Engineering and Safety Engineering, Shandong University of Aeronautics, Binzhou, Shandong 256600, China
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2
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Pacholak P, Durka K, Woźniak K, Krajewska J, Laudy AE, Luliński S. Ethynyl-substituted benzosiloxaboroles: the role of C(π)⋯B interactions in their crystal packing and use in Cu(i)-catalyzed 1,3-dipolar cycloaddition. RSC Adv 2024; 14:16069-16082. [PMID: 38765480 PMCID: PMC11099988 DOI: 10.1039/d4ra02137a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
The synthesis and characterization of two novel 6-ethynyl-7-halogen substituted benzosiloxaboroles (Hal = F, Cl) is reported. The crystal structures of these compounds show a unique type of supramolecular assembly dictated by distinctive C(π)⋯B interactions resulting in the formation of columnar networks involving alternating ethynyl groups and boron atoms. The QTAIM, NBO and NCI analyses were performed in order to obtain a deeper quantitative insight into the nature of these interactions including energy and charge density distribution. The fluoro derivative 1c was used as a starting material in Cu-catalyzed 1,3-dipolar cycloaddition reactions with substituted benzenesulfonyl azides giving rise to benzosiloxaboroles with pendant 1-(arylsulfonyl)-1,2,3-triazole-4-yl functionalities or analogous ionic species, i.e., 1,2,3-triazolium arylsulfonates. Screening of antimicrobial activity of obtained derivatives against a wide selection of Gram-positive and Gram-negative bacteria as well as fungi strains was performed and the obtained results were compared with the data obtained previously for related benzosiloxaborole derivatives.
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Affiliation(s)
- P Pacholak
- Faculty of Chemistry, Warsaw University of Technology Noakowskiego 3 00-664 Warsaw Poland
- University of Warsaw, Faculty of Chemistry Pasteura 1 02-093 Warsaw Poland
| | - K Durka
- Faculty of Chemistry, Warsaw University of Technology Noakowskiego 3 00-664 Warsaw Poland
| | - K Woźniak
- University of Warsaw, Faculty of Chemistry Pasteura 1 02-093 Warsaw Poland
| | - J Krajewska
- Department of Pharmaceutical Microbiology and Bioanalysis, Medical University of Warsaw Banacha 1b 02-097 Warsaw Poland
| | - A E Laudy
- Department of Pharmaceutical Microbiology and Bioanalysis, Medical University of Warsaw Banacha 1b 02-097 Warsaw Poland
| | - S Luliński
- Faculty of Chemistry, Warsaw University of Technology Noakowskiego 3 00-664 Warsaw Poland
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3
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Grabowski SJ. Ga···C Triel Bonds-Why They Are Not Strong Enough to Change Trigonal Configuration into Tetrahedral One: DFT Calculations on Dimers That Occur in Crystal Structures. Int J Mol Sci 2023; 24:12212. [PMID: 37569593 PMCID: PMC10418643 DOI: 10.3390/ijms241512212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Structures characterized by the trigonal coordination of the gallium center that interacts with electron rich carbon sites are described. These interactions may be classified as Ga···C triel bonds. Their properties are analyzed in this study since these interactions may be important in numerous chemical processes including catalytical activities; additionally, geometrical parameters of corresponding species are described. The Ga···C triel bonds discussed here, categorized also as the π-hole bonds, do not change the trigonal configuration of the gallium center into the tetrahedral one despite total interactions in dimers being strong; however, the main contribution to the stabilization of corresponding structures comes from the electrostatic forces. The systems analyzed theoretically here come from crystal structures since the Cambridge Structural Database, CSD, search was performed to find structures where the gallium center linked to CC bonds of Lewis base units occurs. The majority structures found in CSD are characterized by parallel, stacking-like arrangements of species containing the Ga-centers. The theoretical results show that interactions within dimers are not classified as the three-centers links as in a case of typical hydrogen bonds and numerous other interactions. The total interactions in dimers analyzed here consist of several local intermolecular atom-atom interactions; these are mainly the Ga···C links. The DFT results are supported in this study by calculations with the use of the quantum theory of atoms in molecules, QTAIM, the natural bond orbital, NBO, and the energy decomposition analysis, EDA, approaches.
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Affiliation(s)
- Sławomir J. Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Spain;
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
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4
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Aragoni MC, Arca M, Lippolis V, Pintus A, Torubaev Y, Podda E. A Structural Approach to the Strength Evaluation of Linear Chalcogen Bonds. Molecules 2023; 28:molecules28073133. [PMID: 37049895 PMCID: PMC10096081 DOI: 10.3390/molecules28073133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
The experimental structural features of chalcogen bonding (ChB) interactions in over 34,000 linear fragments R–Ch⋯A (Ch = S, Se, Te; R = C, N, O, S, Se, Te; A = N, O, S, Se, Te, F, Cl, Br, I) were analyzed. The bond distances dR–Ch and the interaction distances dCh⋯A were investigated, and the functions δR–Ch and δCh⋯A were introduced to compare the structural data of R–Ch⋯A fragments involving different Ch atoms. The functions δR−Ch and δCh⋯A were calculated by normalizing the differences between the relevant bond dR–Ch and ChB interaction dCh⋯A distances with respect to the sum of the relevant covalent (rcovR + rcovCh) and the van der Waals (vdW) radii (rvdWCh + rvdWA), respectively. A systematic comparison is presented, highlighting the role of the chalcogen involved, the role of the R atoms covalently bonded to the Ch, and the role of the A species playing the role of chalcogen bond acceptor. Based on the results obtained, an innovative approach is proposed for the evaluation and categorization of the ChB strength based on structural data.
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5
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The structure, stability, thermochemistry, and bonding in SO3-(H2O)n (n = 1–7) clusters: a computational analysis. Struct Chem 2022. [DOI: 10.1007/s11224-022-02085-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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6
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Ranjbar M, Nowroozi A, Nakhaei E. The first principle study of chalcogen bonds, pnicogen bond and their mutual effects in a set of complexes between the triazine with SHF and PH2F ligands. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Pal R, Jelsch C, Momma K, Grabowsky S. π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:231-246. [PMID: 35411861 PMCID: PMC9004022 DOI: 10.1107/s2052520622001457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.
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Affiliation(s)
- Rumpa Pal
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | | | - Koichi Momma
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, Japan
| | - Simon Grabowsky
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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8
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Effect of water molecule in the structure, stability, and electronic properties of sulfur trioxide clusters: a computational analysis. MONATSHEFTE FUR CHEMIE 2022. [DOI: 10.1007/s00706-022-02909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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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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10
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Mahapatra N, Chandra S, Ramanathan N, Sundararajan K. Experimental proof for σ and π-hole driven dual pnicogen bonding in phosphoryl chloride-nitromethane heterodimers: A combined matrix isolation infrared and ab initio computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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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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12
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Liu N, Xie X, Li Q. Chalcogen Bond Involving Zinc(II)/Cadmium(II) Carbonate and Its Enhancement by Spodium Bond. Molecules 2021; 26:6443. [PMID: 34770852 PMCID: PMC8588527 DOI: 10.3390/molecules26216443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Carbonate MCO3 (M = Zn, Cd) can act as both Lewis acid and base to engage in a spodium bond with nitrogen-containing bases (HCN, NHCH2, and NH3) and a chalcogen bond with SeHX (X = F, Cl, OH, OCH3, NH2, and NHCH3), respectively. There is also a weak hydrogen bond in the chalcogen-bonded dyads. Both chalcogen and hydrogen bonds become stronger in the order of F > Cl > OH > OCH3 > NH2 > NHCH3. The chalcogen-bonded dyads are stabilized by a combination of electrostatic and charge transfer interactions. The interaction energy of chalcogen-bonded dyad is less than -10 kcal/mol at most cases. Furthermore, the chalcogen bond can be strengthened through coexistence with a spodium bond in N-base-MCO3-SeHX. The enhancement of chalcogen bond is primarily attributed to the charge transfer interaction. Additionally, the spodium bond is also enhanced by the chalcogen bond although the corresponding enhancing effect is small.
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Affiliation(s)
| | - Xiaoying Xie
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
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13
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- 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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14
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Venkataramanan NS. Electronic structure, stability, and cooperativity of chalcogen bonding in sulfur dioxide and hydrated sulfur dioxide clusters: a DFT study and wave functional analysis. Struct Chem 2021. [DOI: 10.1007/s11224-021-01827-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Bhattarai S, Sutradhar D, Huyskens TZ, Chandra AK. Nature and Strength of the π‐Hole Chalcogen Bonded Complexes between Substituted Pyridines and SO
3
Molecule. ChemistrySelect 2021. [DOI: 10.1002/slct.202101981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sumitra Bhattarai
- Department of Chemistry North-Eastern Hill University Shillong 793022 India
| | | | | | - Asit K. Chandra
- Department of Chemistry North-Eastern Hill University Shillong 793022 India
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16
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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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17
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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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18
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Li Y, Wang X, Wang H, Ni Y, Wang H. Influence of halogen atom substitution and neutral HCN/anion CN - Lewis base on the triel-bonding interactions. J Mol Model 2021; 27:93. [PMID: 33624196 DOI: 10.1007/s00894-021-04713-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/11/2021] [Indexed: 11/24/2022]
Abstract
Triel-bonding interactions composed of Lewis acid TrOHH2/TrOH2X/TrOHX2 (Tr = B, Al, Ga; X = F, Cl, Br) molecule and Lewis base neutral HCN or anionic CN- molecule are of research significance in bond properties, which has been investigated at MP2/aug-cc-pVTZ theory level. It is also feasible to study the halogen atom substituent effect and influence of different Lewis bases on the formation of triel bond. AIM analyses reveal that Tr (Tr = B, Al, Ga)···N bond critical point (BCP) exists in all studied triel bond. In the formation of triel bonding, compared with Lewis base HCN molecule, Lewis base anionic CN- can participate in a stronger triel bond. Specifically, the structural change, deformation energy, and charge transfer of CN- complexes are all larger than that of HCN complexes. In addition, halogen atom substitution effect is also discussed. MEP value and binding energy of HCN and CN- complexes all increase after replacing one or two hydrogen atoms by halogen atoms (F, Cl, Br) in Lewis acid. Especially, replacing two hydrogen atoms by halogen atoms in Lewis acid has more remarkable enhancement in MEP value and binding energy than that of replacing only one hydrogen atom. After replacement, binding energy can be increased by 21.77 kcal/mol. The neutral and anionic triel-bonded complexes composed by Lewis acid TrOHH2/TrOH2X/TrOHX2 (Tr = B, Al, Ga; X = F, Cl, Br) with Lewis base HCN and CN- are systematically investigated at MP2/aug-cc-pVTZ level. The neutral (HCN) triel bonding is weaker than the anionic (CN-) triel bonding due to the smaller MEP value of the neutral HCN molecule. The replacement of hydrogens (-H) in Lewis acid by electron-withdrawing groups (-F, -Cl, -Br) has a prominent enhancement effect on the MEP value of π-hole and triel-bonding strength.
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Affiliation(s)
- Yuchun Li
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu, 611756, People's Republic of China
| | - Xiaoting Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu, 611756, People's Republic of China
| | - Hui Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu, 611756, People's Republic of China.
| | - Yuxiang Ni
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu, 611756, People's Republic of China
| | - Hongyan Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu, 611756, People's Republic of China
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19
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Yang Q, Zhou B, Li Q, Scheiner S. Weak σ‐Hole Triel Bond between C
5
H
5
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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Wysokiński R, Michalczyk M, Zierkiewicz W, Scheiner S. Anion-anion and anion-neutral triel bonds. Phys Chem Chem Phys 2021; 23:4818-4828. [PMID: 33605957 DOI: 10.1039/d0cp06547a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability of a TrCl4- anion (Tr = Al, Ga, In, Tl) to engage in a triel bond with both a neutral NH3 and CN- anion is assessed by ab initio quantum calculations in both the gas phase and in aqueous medium. Despite the absence of a positive σ or π-hole on the Lewis acid, strong triel bonds can be formed with either base. The complexation involves an internal restructuring of the tetrahedral TrCl4- monomer into a trigonal bipyramid shape, where the base can occupy either an axial or equatorial position. Although this rearrangement requires a substantial investment of energy, it aids the complexation by imparting a much more positive MEP to the site that is to be occupied by the base. Complexation with the neutral base is exothermic in the gas phase and even more so in water where interaction energies can exceed 30 kcal mol-1. Despite the long-range coulombic repulsion between any pair of anions, CN- can also engage in a strong triel bond with TrCl4-. In the gas phase, complexation is endothermic, but dissociation of the metastable dimer is obstructed by an energy barrier. The situation is entirely different in solution, with large negative interaction energies of as much as -50 kcal mol-1. The complexation remains an exothermic process even after the large monomer deformation energy is factored in.
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Affiliation(s)
- Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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Chandra S, Suryaprasad B, Ramanathan N, Sundararajan K. Dominance of unique Pπ phosphorus bonding with π donors: evidence using matrix isolation infrared spectroscopy and computational methodology. Phys Chem Chem Phys 2020; 22:20771-20791. [PMID: 32909555 DOI: 10.1039/d0cp02880k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albeit the first account of hypervalentπ interactions has been reported with halogenπ interactions, the feasibility of their extension to other hypervalent atoms as possible Lewis acids is still open. In this work, the role of phosphorus as an acceptor from the π electron cloud (Pπ pnicogen or phosphorus bonding) in PCl3-C2H2 and PCl3-C2H4 heterodimers is explored, by combining matrix isolation infrared spectroscopy with ab initio and DFT computational methodologies. The respective potential energy surfaces of the PCl3-C2H2 and PCl3-C2H4 heterodimers reveal unique minima stabilized by a concert of reasonably strong to weak interactions, of which Pπ phosphorus bonding was energetically dominant. Heterodimers, trimers and tetramers bound primarily by this unique phosphorus bond were generated at low temperatures. The dominance of phosphorus bonding in the PCl3-C2H2 and PCl3-C2H4 heterodimers over other interactions (such as Hπ, HCl, HP, Clπ and lone pair-π interactions) was confirmed and substantiated using extended quantum theory of atoms in molecules, natural bond orbital, electrostatic potential mapping and energy decomposition analyses. The following inferences in correlation with results from non-covalent-interaction analysis offer a complete understanding of the nature of the Pπ phosphorus bonding interactions. The significance of electrostatic forces kinetically favoring the formation of phosphorus bonded heterodimers, in addition to thermodynamic stabilization, is demonstrated experimentally.
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Affiliation(s)
- Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - B Suryaprasad
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
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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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23
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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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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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Varadwaj PR, Varadwaj A, Marques HM, MacDougall PJ. The chalcogen bond: can it be formed by oxygen? Phys Chem Chem Phys 2019; 21:19969-19986. [DOI: 10.1039/c9cp03783g] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study theoretically investigates the possibility of oxygen-centered chalcogen bonding in several complexes. Shown in the graph is such a bonding scenario formed between the electrophile on O in OF2 and the nucleophile on O in H2CO.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering
- School of Engineering
- The University of Tokyo 7-3-1
- Tokyo 113-8656
- Japan
| | - Arpita Varadwaj
- Department of Chemical System Engineering
- School of Engineering
- The University of Tokyo 7-3-1
- Tokyo 113-8656
- Japan
| | - Helder M. Marques
- Molecular Sciences Institute
- School of Chemistry
- University of the Witwatersrand
- Johannesburg 2050
- South Africa
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