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Amonov A, Scheiner S. Halogen Bonding to the π-Systems of Polycyclic Aromatics. Chemphyschem 2024:e202400482. [PMID: 38923736 DOI: 10.1002/cphc.202400482] [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: 04/27/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
The propensity of the π-electron system lying above a polycyclic aromatic system to engage in a halogen bond is examined by DFT calculations. Prototype Lewis acid CF3I is placed above the planes of benzene, naphthalene, anthracene, phenanthrene, naphthacene, chrysene, triphenyl, pyrene, and coronene. The I atom positions itself some 3.3-3.4 Å above the polycyclic plane, and the associated interaction energy is about 4 kcal/mol. This quantity is a little smaller for benzene, but is roughly equal for the larger polycyclics. The energy only oscillates a little as the Lewis acid slides across the face of the polycyclic, preferring regions of higher π-electron density over minima of the electrostatic potential. The binding is dominated by dispersion which contributes half of the total interaction energy.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Institute of Engineering Physics Samarkand State University, University blv. 15, 140104, Samarkand, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA
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2
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Novikov AP, Volkov MA. New O- and N-N-Bridging Complexes of Tc(V), the Role of the Nitrogen Atom Position in Aromatic Rings: Reaction Mechanism, Spectroscopy, DTA, XRD and Hirshfeld Surface Analysis. Int J Mol Sci 2022; 23:ijms232214034. [PMID: 36430512 PMCID: PMC9696901 DOI: 10.3390/ijms232214034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, O- and N-N-bridging complexes of technetium (V), previously known only for rhenium, were obtained for the first time. Tc(V) complexes with pyridazine (pyd), 1,2,4-triazole (trz), 3,5-dimethylpyrazole (dmpz) and pyrimidine (pyr) were obtained. In three complexes [{TcOCl2}2(μ-O)(μ-pyd)2], [{TcOCl2}2(μ-O)(μ-trz)2]·Htrz·Cl and [{TcO(dmpz)4}(μ-O)(TcOCl4)] two technetium atoms are linked by a Tc-O-Tc bond, and in the first two, Tc atoms are additionally linked by a Tc-N-N-Tc bond through the nitrogen atoms of the aromatic rings. We determined the role of nitrogen atom position in the aromatic ring and the presence of substituents on the formation of such complexes. For the first time, a reaction mechanism for the formation of such complexes was proposed. This article details the crystal structures of four new compounds. The work describes in detail the coordination of Tc atoms in the obtained structures and the regularities of the formation of crystal packings. The spectroscopic properties of the obtained compounds and their mother solutions were studied. The decomposition temperatures of the described complexes were determined. An assumption was made about the oligomerization of three-bridged complexes based on the results of mass spectrometry. Through the analysis of non-valent interactions in the structures, π-stacking, halogen-π and CH-π interactions were found. An analysis of the Hirshfeld surface for [{TcOCl2}2(μ-O)(μ-pyd)2], [{TcOCl2}2(μ-O)(μ-trz)2] and their rhenium analogues showed that the main contribution to the crystalline packing is made by interactions of the type Hal···H/H···Hal (45.4-48.9%), H···H (10.2-15.8%), and O···H/H···O (9.4-16.5%).
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3
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Novikov AP, Bezdomnikov AA, Grigoriev MS, German KE. Synthesis, crystal structure and Hirshfeld surface analysis of 2-(perfluoro-phen-yl)acetamide in comparison with some related compounds. Acta Crystallogr E Crystallogr Commun 2022; 78:80-83. [PMID: 35079430 PMCID: PMC8739205 DOI: 10.1107/s2056989021013359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 04/06/2024]
Abstract
The mol-ecular and crystal structures of the title compound, C8H4F5NO, were examined by single-crystal X-ray diffraction and Hirshfeld surface analysis. The title compound was synthesized by a new method at the interface of aqueous solutions of LiOH and penta-fluoro-phenyl-aceto-nitrile. In the crystal, hydrogen bonds and π-halogen inter-actions connect the mol-ecules into double layers. Analysis of the Hirshfeld surface showed that the most important contributions to the crystal packing are made by F⋯F (30.4%), C⋯F/F⋯C (22.9%), O⋯H/H⋯O (14.9%), H⋯F/F⋯H (14.0%) and H⋯H (10.2%) contacts. The Hirshfeld surfaces of analogues of the title compound were compared and the effect of perfluorination on the crystal packing was shown.
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Affiliation(s)
- Anton P. Novikov
- Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya, St, 117198, Moscow, Russian Federation
- Frumkin Institute of Physical Chemistry and Electrochemistry Russian, Academy of Sciences, 31 Leninsky Prospekt bldg 4, 119071 Moscow, Russian Federation
| | - Alexey A. Bezdomnikov
- Frumkin Institute of Physical Chemistry and Electrochemistry Russian, Academy of Sciences, 31 Leninsky Prospekt bldg 4, 119071 Moscow, Russian Federation
| | - Mikhail S. Grigoriev
- Frumkin Institute of Physical Chemistry and Electrochemistry Russian, Academy of Sciences, 31 Leninsky Prospekt bldg 4, 119071 Moscow, Russian Federation
| | - Konstantin E. German
- Frumkin Institute of Physical Chemistry and Electrochemistry Russian, Academy of Sciences, 31 Leninsky Prospekt bldg 4, 119071 Moscow, Russian Federation
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4
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Muya JT, Isamura BK, Patouossa I, Nguyen MT. Interplay between σ Holes, Anion···H-C, and Cation-π Interactions in Dibromo[2,2]paracyclophane Complexes. J Phys Chem A 2020; 124:4379-4389. [PMID: 32364383 DOI: 10.1021/acs.jpca.9b09879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Theoretical calculations were performed to investigate the interplay between σ-hole, anion-HC and cation-π interactions in the complexes of dibromo[2,2]paracyclophane (DBr[2,2]PCP) with alkali (Li+, Na+, K+), alkaline earth metal cations (Be2+, Mg2+, and Ca2+), and halogen anions (F-, Cl-, and Br-) using the wave function (MP2) and density functional theory (M06-2X and B3LYP) methods with the 6-311++G(d,p) basis set. The study reveals that DBr[2,2]PCP behaves as amphoteric molecule with a predominance of basic character. It prefers to interact with hard cations and hard anions such as Be2+ and F- through cation-π and anion···HC interactions, respectively. Substitution of Br by F and Cl atoms in DBr[2,2]PCP decreases slightly the interaction energies of DX[2,2]PCP-halogen complexes (X = F, Cl, and Br) by 2.0 and 0.3 kcal/mol (M06-2X), respectively. The anion-HC interactions in DBr[2,2]PCP complexes are ∼10 kcal/mol stronger (B3LYP; ∼15 kcal/mol at M06-2X and 7 kcal/mol at MP2) than the σ-hole interactions.
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Affiliation(s)
- Jules Tshishimbi Muya
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, DR Congo.,Department of Chemistry, Faculty of Science, University of Kinshasa, P.O. Box 190 Kinshasa XI, DR Congo.,Department of Chemistry and Research Institute for Natural Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Bienfait Kabuyaya Isamura
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, DR Congo.,Department of Chemistry, Faculty of Science, University of Kinshasa, P.O. Box 190 Kinshasa XI, DR Congo
| | - Issofa Patouossa
- Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, DR Congo.,Laboratory of Physical and Theoretical Chemistry, Faculty of Sciences, University of Yaoundé, P.O. Box 812, Yaoundé I, Cameroon
| | - Minh Tho Nguyen
- Computational Chemistry Research Group and Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
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5
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Mirosław B, Mahmoudi G, Ferenc W, Cristóvão B, Osypiuk D, Sarzyński J, Głuchowska H, Franconetti A, Frontera A. Halogen interactions in dinuclear copper(II) 2,4-dibromophenoxyacetate – crystal structure and quantum chemical calculations. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Chongboriboon N, Samakun K, Inprasit T, Kielar F, Dungkaew W, Wong LWY, Sung HHY, Ninković DB, Zarić SD, Chainok K. Two-dimensional halogen-bonded organic frameworks based on the tetrabromobenzene-1,4-dicarboxylic acid building molecule. CrystEngComm 2020. [DOI: 10.1039/c9ce01140d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
2D halogen-bonded organic frameworks were readily engineered by strong and directional effects of the primary Br⋯O and the secondary Br⋯π halogen bonding interactions from the tetrabromobenzene-1,4-dicarboxylic acid building molecule involving 100% supramolecular yields.
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Affiliation(s)
- Nucharee Chongboriboon
- Materials and Textile Technology
- Faculty of Science and Technology
- Thammasat University
- Pathum Thani 12121
- Thailand
| | - Kodchakorn Samakun
- Materials and Textile Technology
- Faculty of Science and Technology
- Thammasat University
- Pathum Thani 12121
- Thailand
| | - Thitirat Inprasit
- Materials and Textile Technology
- Faculty of Science and Technology
- Thammasat University
- Pathum Thani 12121
- Thailand
| | - Filip Kielar
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000
- Thailand
| | - Winya Dungkaew
- Department of Chemistry
- Faculty of Science
- Mahasarakham University
- Maha Sarakham 44150
- Thailand
| | - Lawrence W.-Y. Wong
- Department of Chemistry
- The Hong Kong University of Science and Technology
- Kowloon
- Hong Kong
| | - Herman H.-Y. Sung
- Department of Chemistry
- The Hong Kong University of Science and Technology
- Kowloon
- Hong Kong
| | | | - Snežana D. Zarić
- Faculty of Chemistry
- University of Belgrade
- Belgrade
- Serbia
- Science Program
| | - Kittipong Chainok
- Materials and Textile Technology
- Faculty of Science and Technology
- Thammasat University
- Pathum Thani 12121
- Thailand
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7
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Synergistic and antagonistic interplay between tetrel bond and pnicogen bond in complexes involving ring compounds. J Mol Model 2019; 25:351. [DOI: 10.1007/s00894-019-4206-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/11/2019] [Indexed: 10/25/2022]
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8
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Zhang L, Li D. A theoretical investigation on the complexes of B 3O 3H 3 with acetylene and its substituted derivatives. J Mol Model 2019; 25:332. [PMID: 31701364 DOI: 10.1007/s00894-019-4223-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/30/2019] [Indexed: 11/29/2022]
Abstract
The complexes of B3O3H3 with acetylene and its substituted derivatives C2HX (X=H, F, Cl, Br, CH3, NH2) are explored by theoretical calculations using MP2 and M06-2X methods with aug-cc-pVDZ as the basis set. The different molecular electrostatic potential features of B3O3H3 with benzene (C6H6) and borazine (B3N3H6) result in different stable structures of the complexes with C2HX. The geometric analysis indicates that the global minimum is the parallel stacked (PS) structure with the linear C-C triple bond lies on the top of B3O3H3, and this is much different from that of the B3N3H6...C2HX complex, in which the C-H bond directs towards the B3N3H6 ring (T-shaped). The H-bonded structure where the C-H interacts with the O atom of B3O3H3 is found to be a local minimum. Besides, there is an additional X…O halogen-bonded structures for the B3O3H3…C2HX (X=Cl, Br) complexes. As for the PS geometry, when one H atom in C2H2 is replaced by different X groups, the binding energies of the complexes increases in the order of F<H<Cl<Br<CH3<NH2, which is mainly determined by the strength of the π-hole bond. The nature of interaction in these complexes is further studied by the atoms-in-molecules (AIM) and noncovalent interaction (NCI) analysis. The natural bond orbital (NBO) analysis indicates that the main orbital interaction arises from LPX→BD*B‑O for B3O3H3…C2HX (X=Cl, Br, NH2), and BDC‑C→BD*B‑O for B3O3H3…C2HX (X=H, CH3) complexes. Complexes of B3O3H3 with acetylene and its substituted derivatives.
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Affiliation(s)
- Lijuan Zhang
- College of Chemical Engineering and Safety Engineering, Binzhou University, Binzhou, 256600, Shandong, People's Republic of China.
| | - Dazhi Li
- College of Chemical Engineering and Safety Engineering, Binzhou University, Binzhou, 256600, Shandong, People's Republic of China
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9
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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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10
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Enhanced dispersion of carbon nanotubes in water by plasma induced graft poly(N,N-dimethylacrylamide) and its application in humic acid capture. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Khavasi HR, Rahimi N. Lone pair⋯π interaction versus σ-hole appearance in metal-bonded halogens. CrystEngComm 2019. [DOI: 10.1039/c8ce01795f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Three complexes of N-(2,5-diluorophenyl)-2-pyrazine carboxamide and ZnX2 have been synthesized. The crystal structures reveal that in all three coordination compounds, metal-bound halides have interacted with π systems through a negative electrostatic region.
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Affiliation(s)
- Hamid Reza Khavasi
- Department of Inorganic Chemistry and Catalysis
- Shahid Beheshti University
- Tehran 1983963113
- Iran
| | - Narjes Rahimi
- Department of Inorganic Chemistry and Catalysis
- Shahid Beheshti University
- Tehran 1983963113
- Iran
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12
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Shukla R, Claiser N, Souhassou M, Lecomte C, Balkrishna SJ, Kumar S, Chopra D. Exploring the simultaneous σ-hole/π-hole bonding characteristics of a Br⋯π interaction in an ebselen derivative via experimental and theoretical electron-density analysis. IUCRJ 2018; 5:647-653. [PMID: 30224967 PMCID: PMC6126650 DOI: 10.1107/s2052252518011041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
In this study, the nature and characteristics of a short Br⋯π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br⋯π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br⋯π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).
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Affiliation(s)
- Rahul Shukla
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Nicolas Claiser
- Cristallographie, Résonance Magnétique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, CNRS and Université de Lorraine, BP 239, Vandoeuvre-les-Nancy CEDEX F54506, France
| | - Mohamed Souhassou
- Cristallographie, Résonance Magnétique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, CNRS and Université de Lorraine, BP 239, Vandoeuvre-les-Nancy CEDEX F54506, France
| | - Claude Lecomte
- Cristallographie, Résonance Magnétique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, CNRS and Université de Lorraine, BP 239, Vandoeuvre-les-Nancy CEDEX F54506, France
| | - Shah Jaimin Balkrishna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Sangit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal, Madhya Pradesh 462066, India
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13
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Grabowski SJ. Tetrel Bonds with π-Electrons Acting as Lewis Bases-Theoretical Results and Experimental Evidences. Molecules 2018; 23:molecules23051183. [PMID: 29762534 PMCID: PMC6100247 DOI: 10.3390/molecules23051183] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022] Open
Abstract
MP2/aug-cc-pVTZ calculations were carried out for the ZFH₃-B complexes (Z = C, Si, Ge, Sn and Pb; B = C₂H₂, C₂H₄, C₆H₆ and C₅H₅⁻; relativistic effects were taken into account for Ge, Sn and Pb elements). These calculations are supported by other approaches; the decomposition of the energy of interaction, Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) method. The results show that tetrel bonds with π-electrons as Lewis bases are classified as Z···C links between single centers (C is an atom of the π-electron system) or as Z···π interactions where F‒Z bond is directed to the mid-point (or nearly so) of the CC bond of the Lewis base. The analogous systems with Z···C/π interactions were found in the Cambridge Structural Database (CSD). It was found that the strength of interaction increases with the increase of the atomic number of the tetrel element and that for heavier tetrel elements the ZFH₃ tetrahedral structure is more deformed towards the structure with the planar ZH₃ fragment. The results of calculations show that the tetrel bond is sometimes accompanied by the Z-H···C hydrogen bond or even sometimes the ZFH₃-B complexes are linked only by the hydrogen bond interaction.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Spain.
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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14
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Synthesis, X-ray structure, spectroscopic, DFT study and catalytic activity of cis-[RuCl2(L)(EPh3)] complexes (E = P, As, Sb; L = NN′N″ tridentate azoimine-quinoline ligands). Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Valadbeigi Y. Organometallic acids with azaborine, oxaborine, azaborole and oxaborole scaffolds. NEW J CHEM 2018. [DOI: 10.1039/c8nj05151h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Organoboron compounds were used in the design of organometallic acids exhibiting a wide acidity range from weak acids to superacids.
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Affiliation(s)
- Younes Valadbeigi
- Department of Chemistry
- Faculty of Science
- Imam Khomeini International University
- Qazvin
- Iran
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16
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New Type of Halogen Bond: Multivalent Halogen Interacting with π- and σ-Electrons. Molecules 2017; 22:molecules22122150. [PMID: 29206144 PMCID: PMC6149982 DOI: 10.3390/molecules22122150] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 12/05/2022] Open
Abstract
MP2/aug-cc-pVTZ calculations were performed for complexes of BrF3 and BrF5 acting as Lewis acids through the bromine centre, with species playing a role of Lewis base: dihydrogen, acetylene, ethylene, and benzene. The molecular hydrogen donates electrons by its σ-bond, while in remaining moieties—in complexes of hydrocarbons; such an electron transfer follows from π-electrons. The complexes are linked by a kind of the halogen bond that is analyzed for the first time in this study, i.e., it is the link between the multivalent halogen and π or σ-electrons. The nature of such a halogen bond is discussed, as well as various dependencies and correlations are presented. Different approaches are applied here, the Quantum Theory of Atoms in Molecules, Natural Bond Orbital method, the decomposition of the energy of interaction, the analysis of electrostatic potentials, etc.
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17
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Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L. Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs. Nucleic Acids Res 2017; 45:11019-11032. [PMID: 28977572 PMCID: PMC5737201 DOI: 10.1093/nar/gkx757] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 08/17/2017] [Indexed: 12/13/2022] Open
Abstract
The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Qingyun Zhang
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy.,King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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18
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Abstract
The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future.
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Affiliation(s)
- Hui Wang
- College of Chemistry, Beijing Normal University , Beijing 100875, People's Republic of China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University , Luoyang 471022, People's Republic of China
| | - Wei Jun Jin
- College of Chemistry, Beijing Normal University , Beijing 100875, People's Republic of China
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19
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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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20
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Caracelli I, Zukerman-Schpector J, Haiduc I, Tiekink ERT. Main group metal lone-pair⋯π(arene) interactions: a new bonding mode for supramolecular associations. CrystEngComm 2016. [DOI: 10.1039/c6ce01460g] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Khanh PN, Ngan VT, Hong Man NT, Ai Nhung NT, Chandra AK, Trung NT. An insight into Csp–H⋯π hydrogen bonds and stability of complexes formed by acetylene and its substituted derivatives with benzene and borazine. RSC Adv 2016. [DOI: 10.1039/c6ra21557b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Theoretical calculations at the MP2/aug-cc-pVDZ level are used to investigate the Csp–H⋯π interactions of C2HX (X = H, F, Cl, Br, CH3, NH2) with C6H6 and B3N3H6 molecules.
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Affiliation(s)
- Pham Ngoc Khanh
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
| | - Vu Thi Ngan
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
| | - Nguyen Thi Hong Man
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
| | - Nguyen Thi Ai Nhung
- Department of Chemistry
- Hue University of Sciences – Hue University
- Hue City
- Vietnam
| | - Asit K. Chandra
- Department of Chemistry
- North-Eastern Hill University
- Shillong
- India
| | - Nguyen Tien Trung
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
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22
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Varadwaj PR, Varadwaj A, Jin BY. Hexahalogenated and their mixed benzene derivatives as prototypes for the understanding of halogen···halogen intramolecular interactions: New insights from combined DFT, QTAIM-, and RDG-based NCI analyses. J Comput Chem 2015; 36:2328-43. [DOI: 10.1002/jcc.24211] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 01/21/2023]
Affiliation(s)
| | - Arpita Varadwaj
- Department of Chemistry; National Taiwan University; Taipei 10617 Taiwan
| | - Bih-Yaw Jin
- Department of Chemistry; National Taiwan University; Taipei 10617 Taiwan
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23
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Badri Z, Foroutan-Nejad C, Kozelka J, Marek R. On the non-classical contribution in lone-pair–π interaction: IQA perspective. Phys Chem Chem Phys 2015; 17:26183-90. [DOI: 10.1039/c5cp04489h] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most and least electrostatic repulsive parts of a complex presented by red and blue isosurface repulsive potential energy density.
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Affiliation(s)
- Zahra Badri
- CEITEC – Central European Institute of Technology
- Masaryk University
- Brno
- Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC – Central European Institute of Technology
- Masaryk University
- Brno
- Czech Republic
| | - Jiri Kozelka
- Université Paris Descartes
- UMR 8601 CNRS
- 75270 Paris
- France
- Department of Condensed Matter Physics
| | - Radek Marek
- CEITEC – Central European Institute of Technology
- Masaryk University
- Brno
- Czech Republic
- Department of Chemistry
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24
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Montoro T, Tardajos G, Guerrero A, Torres MDR, Salgado C, Fernández I, Osío Barcina J. σ-Hole⋯π and lone pair⋯π interactions in benzylic halides. Org Biomol Chem 2015; 13:6194-202. [DOI: 10.1039/c5ob00366k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Depending on the relative orientation of the halogen atom and the phenyl ring, the benzylic halides studied show “classical” halogen⋯π bonds as well as intramolecular interactions without σ-hole participation based on n → π* (LP⋯π) interactions.
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Affiliation(s)
| | - Gloria Tardajos
- Departamento de Química Física
- Facultad de Ciencias Químicas
- Universidad Complutense de Madrid
- 28040 Madrid
- Spain
| | - Andrés Guerrero
- Departamento de Química Física
- Facultad de Ciencias Químicas
- Universidad Complutense de Madrid
- 28040 Madrid
- Spain
| | - María del Rosario Torres
- Laboratorio de difracción de Rayos X
- Facultad de Ciencias Químicas
- Universidad Complutense de Madrid
- 28040 Madrid
- Spain
| | - Cástor Salgado
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas. Universidad Complutense de Madrid
- 28040 Madrid
- Spain
| | - Israel Fernández
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas. Universidad Complutense de Madrid
- 28040 Madrid
- Spain
| | - José Osío Barcina
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas. Universidad Complutense de Madrid
- 28040 Madrid
- Spain
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25
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Xu Z, Yang Z, Liu Y, Lu Y, Chen K, Zhu W. Halogen Bond: Its Role beyond Drug–Target Binding Affinity for Drug Discovery and Development. J Chem Inf Model 2014; 54:69-78. [DOI: 10.1021/ci400539q] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhijian Xu
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhuo Yang
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yingtao Liu
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yunxiang Lu
- Department
of Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Kaixian Chen
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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