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Dukhnovsky EA, Novikov AS, Kubasov AS, Borisov AV, Sikaona ND, Kirichuk AA, Khrustalev VN, Kritchenkov AS, Tskhovrebov AG. Halogen Bond-Assisted Supramolecular Dimerization of Pyridinium-Fused 1,2,4-Selenadiazoles via Four-Center Se 2N 2 Chalcogen Bonding. Int J Mol Sci 2024; 25:3972. [PMID: 38612782 PMCID: PMC11011651 DOI: 10.3390/ijms25073972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
The synthesis and structural characterization of α-haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles with various counterions is reported herein, demonstrating a strategy for directed supramolecular dimerization in the solid state. The compounds were obtained through a recently discovered 1,3-dipolar cycloaddition reaction between nitriles and bifunctional 2-pyridylselenyl reagents, and their structures were confirmed by the X-ray crystallography. α-Haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles exclusively formed supramolecular dimers via four-center Se···N chalcogen bonding, supported by additional halogen bonding involving α-haloalkyl substituents. The introduction of halogens at the α-position of the substituent R in the selenadiazole core proved effective in promoting supramolecular dimerization, which was unaffected by variation of counterions. Additionally, the impact of cocrystallization with a classical halogen bond donor C6F3I3 on the supramolecular assembly was investigated. Non-covalent interactions were studied using density functional theory calculations and topological analysis of the electron density distribution, which indicated that all ChB, XB and HB interactions are purely non-covalent and attractive in nature. This study underscores the potential of halogen and chalcogen bonding in directing the self-assembly of functional supramolecular materials employing 1,2,4-selenadiazoles derived from recently discovered cycloaddition between nitriles and bifunctional 2-pyridylselenyl reagents.
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Affiliation(s)
- Evgeny A. Dukhnovsky
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Alexander S. Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russia
| | - Alexey S. Kubasov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 31, Moscow 119334, Russia
| | - Alexander V. Borisov
- Department of Chemistry, R.E. Alekseev Nizhny Novgorod State Technical University, Minin St., 24, Nizhny Novgorod 603155, Russia
| | - Nkumbu Donovan Sikaona
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Anatoly A. Kirichuk
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Victor N. Khrustalev
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 47, Moscow 119334, Russia
| | - Andreii S. Kritchenkov
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Alexander G. Tskhovrebov
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
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Sapronov AA, Artemjev AA, Burkin GM, Khrustalev VN, Kubasov AS, Nenajdenko VG, Gomila RM, Frontera A, Kritchenkov AS, Tskhovrebov AG. Robust Supramolecular Dimers Derived from Benzylic-Substituted 1,2,4-Selenodiazolium Salts Featuring Selenium⋯π Chalcogen Bonding. Int J Mol Sci 2022; 23:ijms232314973. [PMID: 36499302 PMCID: PMC9740427 DOI: 10.3390/ijms232314973] [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: 11/18/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
The series of benzylic-substituted 1,2,4-selenodiazolium salts were prepared via cyclization reaction between 2-pyridylselenyl chlorides and nitriles and fully characterized. Substitution of the Cl anion by weakly binding anions promoted the formation supramolecular dimers featuring four center Se2N2 chalcogen bonding and two antiparallel selenium⋯π interactions. Chalcogen bonding interactions were studied using density functional theory calculations, molecular electrostatic potential (MEP) surfaces, the quantum theory of atoms-in-molecules (QTAIM), and the noncovalent interaction (NCI) plot. The investigations revealed fundamental role of the selenium⋯π contacts that are stronger than the Se⋯N interactions in supramolecular dimers. Importantly, described herein, the benzylic substitution approach can be utilized for reliable supramolecular dimerization of selenodiazolium cations in the solid state, which can be employed in supramolecular engineering.
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Affiliation(s)
- Alexander A. Sapronov
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
| | - Alexey A. Artemjev
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
| | - Gleb M. Burkin
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
| | - Victor N. Khrustalev
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp., 119334 Moscow, Russia
| | - Alexey S. Kubasov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119071 Moscow, Russia
| | - Valentine G. Nenajdenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, 1, Leninskie Gory, 119991 Moscow, Russia
| | - Rosa M. Gomila
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Andreii S. Kritchenkov
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- Institute of Technical Acoustics NAS of Belarus, Ludnikova Prosp. 13, 210009 Vitebsk, Belarus
| | - Alexander G. Tskhovrebov
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- Correspondence:
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Structural Organization of Dibromodiazadienes in the Crystal and Identification of Br···O Halogen Bonding Involving the Nitro Group. Molecules 2022; 27:molecules27165110. [PMID: 36014350 PMCID: PMC9414975 DOI: 10.3390/molecules27165110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Nitro functionalized dibromodiazadiene dyes were prepared and fully characterized including X-ray single crystal analysis. Electron deficient dibromodiazadienes were found to be able to act as donors of halogen bonding (XB), while the nitro group acted as an acceptor of the XB. Depending on the substituents, the Br···O XB competed with other weak interactions, and for some of the dyes, they even outcompeted the XB involving the nitro group. However, the nitro functionalized dibromoalkenes 6a and 10a, which had only the nitro moiety as the most plausible acceptor of the XB, reliably formed 1D chains via Br⋯O XB. Experimental work was supported by the DFT calculations and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method).
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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Majumdar D, Frontera A, Gomila RM, Das S, Bankura K. Synthesis, spectroscopic findings and crystal engineering of Pb(ii)-Salen coordination polymers, and supramolecular architectures engineered by σ-hole/spodium/tetrel bonds: a combined experimental and theoretical investigation. RSC Adv 2022; 12:6352-6363. [PMID: 35424552 PMCID: PMC8982041 DOI: 10.1039/d1ra09346k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
Spontaneous self-assembly is one of the available synthetic routes to achieve structurally versatile and unique crystal complexes with selected metal-ligand combinations in the spirit of pseudohalides. In this endeavour, we designed a novel 1D coordination polymer (CP), [(Cd)(Pb)(L)(η1-NCS)(η1-SCN)] n (1), using a compartmental Salen ligand (H3L) in the presence of NaSCN. The characterization of the CP was accomplished using several spectroscopic techniques: MALDI-TOF, PXRD, SEM, EDX mapping, and single-crystal X-ray crystallography. The CP crystallizes in the monoclinic space group P21/c with Z = 4. SCXRD reveals Cd(ii) and Pb(ii) metal ions fulfilled distorted square pyramidal and hemi-directed coordination spheres. Cd(ii) is placed in the inner N2O2 and heavier Pb(ii) in the outer O4 compartments of the de-protonated form of the ligand [L]2-. Supramolecular interactions in the intricate crystal structure produced attractive molecular architectures of the compound. The flexible aliphatic -OH pendent group coordinates with the Pb(ii) ions. This unique binding further elevates the supramolecular crystal topographies. The supramolecular interactions were authenticated by Hirshfeld surface analysis (HSA). The observation of the recurring unconventional tetrel bonds was rationalized by DFT calculations and surface plots of molecular electrostatic potential (MEP). In the 1D polymeric chain in the complex, the O-atom of the -OH groups shows a tetrel bonding interaction with the Pb atom. We have found that the combination of QTAIM/NCI and QTAIM/ELF plots helps reveal the nature of these contacts. Moreover, the QTAIM/ELF plot determines the donor-acceptor interaction between the O-atom and the Pb atom, establishing the σ-hole. Agreeably, the σ-hole interaction also helps Pb(ii) serve as a Lewis acid in the complex. Finally, spodium and tetrel bonds are formed, possible thanks to a hemi-directional coordination sphere of the Pb atoms in the polymer described.
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Affiliation(s)
- Dhrubajyoti Majumdar
- Department of Chemistry, Tamralipta Mahavidyalaya Tamluk 721636 West Bengal India .,Department of Chemistry, Indian Institute of Technology (Indian School of Mines) Dhanbad Jharkhand 826004 India
| | - A Frontera
- Department de Quimica, Universitat de les Illes Balears Cra. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Rosa M Gomila
- Department de Quimica, Universitat de les Illes Balears Cra. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Sourav Das
- Department of Basic Sciences, Chemistry Discipline, Institute of Infrastructure Technology Research and Management Near Khokhara Circle, Maninagar East Ahmedabad-380026 Gujarat India
| | - Kalipada Bankura
- Department of Chemistry, Tamralipta Mahavidyalaya Tamluk 721636 West Bengal India
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On the Importance of Halogen Bonding Interactions in Two X-ray Structures Containing All Four (F, Cl, Br, I) Halogen Atoms. CRYSTALS 2021. [DOI: 10.3390/cryst11111406] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This manuscript reports the synthesis and X-ray characterization of two octahydro-1H-4,6-epoxycyclopenta[c]pyridin-1-one derivatives that contain the four most abundant halogen atoms (Ha) in the structure with the aim of studying the formation of Ha···Ha halogen bonding interactions. The anisotropy of electron density at the heavier halogen atoms provokes the formation of multiple Ha···Ha contacts in the solid state. That is, the heavier Ha-atoms exhibit a region of positive electrostatic potential (σ-hole) along the C–Ha bond and a belt of negative electrostatic potential (σ-lumps) around the atoms. The halogen bonding assemblies in both compounds were analyzed using density functional theory (DFT) calculations, molecular electrostatic potential (MEP) surfaces, the quantum theory of “atom-in-molecules” (QTAIM), the noncovalent interaction plot (NCIplot), and the electron localization function (ELF).
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Wang R, Lu Y, Xu Z, Liu H. Triangular Interchalcogen Interactions: A Joint Crystallographic Data Analysis and Theoretical Study. J Phys Chem A 2021; 125:4173-4183. [PMID: 33957751 DOI: 10.1021/acs.jpca.1c03244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent chalcogen-chalcogen interactions are being actively investigated from both crystallographic and theoretical viewpoints in recent years. According to our search of the Cambridge Structural Database (CSD), a huge number of crystal structures containing triangular Ch3 synthons were extracted. On the basis of the results of the CSD survey, a series of trimeric complexes of organic divalent chalcogen molecules were selected to model such interaction motifs. Similar to that in conventional chalcogen bonds, triangular interchalcogen interactions become gradually stronger along the sequence of Ch = S, Se, Te. Particularly, hydrogen bonds between the chalcogen centers and the H atoms in the substituents occur, which play a significant role in stabilizing the Ch3 motifs in the trimers. Through multibody energy calculations, the complexes under study exhibit no or only weak cooperativity. Finally, the differences between the Ch3 interaction motifs and the well-studied windmill X3 bonding (X means halogen and this is halogen bond) patterns were elucidated.
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Affiliation(s)
- Ranran Wang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yunxiang Lu
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhijian Xu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglai Liu
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
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Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4'-Bipyridine Derivatives. Molecules 2020; 25:molecules25194409. [PMID: 32992941 PMCID: PMC7582854 DOI: 10.3390/molecules25194409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/08/2023] Open
Abstract
Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader-Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4'-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C-Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.
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Abstract
The CH3Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base (such as O=CH2). The induced positive potential then has the ability to attract the negative site of the Lewis base, thus explaining the importance of polarization leading to the formation of the H3C–Cl···O=CH2 complex. By examining the nature of the chlorine’s surface in CH3Cl using the molecular electrostatic surface potential (MESP) approach, with MP2/aug-cc-pVTZ, we show that this view is not correct. The results of our calculations demonstrate that the local potential associated with the axial surface of the Cl atom is inherently positive. Therefore, it should be able to inherently act as a halogen bond donor. This is shown to be the case by examining several halogen-bonded complexes of CH3Cl with a series of negative sites. In addition, it is also shown that the lateral portions of Cl in CH3Cl features a belt of negative electrostatic potential that can participate in forming halogen-, chalcogen-, and hydrogen-bonded interactions. The results of the theoretical models used, viz. the quantum theory of atoms in molecules; the reduced density gradient noncovalent index; the natural bond orbital analysis; and the symmetry adapted perturbation theory show that Cl-centered intermolecular bonding interactions revealed in a series of 18 binary complexes do not involve a polarization-induced potential on the Cl atom.
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10
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Relativistic Effects on NMR Parameters of Halogen-Bonded Complexes. Molecules 2019; 24:molecules24234399. [PMID: 31810199 PMCID: PMC6930553 DOI: 10.3390/molecules24234399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 11/25/2022] Open
Abstract
Relativistic effects are found to be important for the estimation of NMR parameters in halogen-bonded complexes, mainly when they involve the heavier elements, iodine and astatine. A detailed study of 60 binary complexes formed between dihalogen molecules (XY with X, Y = F, Cl, Br, I and At) and four Lewis bases (NH3, H2O, PH3 and SH2) was carried out at the MP2/aug-cc-pVTZ/aug-cc-pVTZ-PP computational level to show the extent of these effects. The NMR parameters (shielding and nuclear quadrupolar coupling constants) were computed using the relativistic Hamiltonian ZORA and compared to the values obtained with a non-relativistic Hamiltonian. The results show a mixture of the importance of the relativistic corrections as both the size of the halogen atom and the proximity of this atom to the basic site of the Lewis base increase.
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11
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Varadwaj A, Marques HM, Varadwaj PR. Nature of halogen-centered intermolecular interactions in crystal growth and design: Fluorine-centered interactions in dimers in crystalline hexafluoropropylene as a prototype. J Comput Chem 2019; 40:1836-1860. [PMID: 31017721 DOI: 10.1002/jcc.25836] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/10/2019] [Accepted: 03/22/2019] [Indexed: 12/14/2022]
Abstract
The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C3 F6 ), upon its interaction with another same molecule to form (C3 F6 )2 dimers. The existence of σ- and π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C3 F6 itself and the (C3 F6 )2 dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C3 F6 )2 dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C3 F6 )2 dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt, Angew. Chem. Int. Ed. 2017, 56, 368). © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki Prefecture, 305-8560, Japan
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki Prefecture, 305-8560, Japan
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12
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Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
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Niyas MA, Ramakrishnan R, Vijay V, Sebastian E, Hariharan M. Anomalous Halogen–Halogen Interaction Assists Radial Chromophoric Assembly. J Am Chem Soc 2019; 141:4536-4540. [DOI: 10.1021/jacs.8b13754] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- M. A. Niyas
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
| | - Remya Ramakrishnan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
| | - Vishnu Vijay
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
| | - Ebin Sebastian
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
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14
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Varadwaj A, Marques HM, Varadwaj PR. Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions? Molecules 2019; 24:E379. [PMID: 30678158 PMCID: PMC6384640 DOI: 10.3390/molecules24030379] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/23/2022] Open
Abstract
Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
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15
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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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16
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Topić F, Puttreddy R, Rautiainen JM, Tuononen HM, Rissanen K. Tridentate C–I⋯O−–N+ halogen bonds. CrystEngComm 2017. [DOI: 10.1039/c7ce01381g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Oxides can act as tridentate halogen bond acceptors, or as tetradentate ligands in a pseudo-μ4 mode with silver(i).
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Affiliation(s)
- Filip Topić
- Department of Chemistry
- University of Jyvaskyla
- Finland
| | | | | | | | - Kari Rissanen
- Department of Chemistry
- University of Jyvaskyla
- Finland
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