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Special Issue "Halogen Bonds and Beyond"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: closed (15 November 2017)

Special Issue Editor

Guest Editor
Prof. Dr. Ibon Alkorta

Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
Website | E-Mail
Interests: hydrogen bond; weak interactions; computational chemistry

Special Issue Information

Dear Colleagues,

The field of weak interactions has witnesses a great deal of progress in recent years. New types of interactions have been described and their natures have been rationalized. Even though the most important non-covalent interaction is the hydrogen bond, the halogen bond has been recognized as the second most important interaction. Its relevance as a tool in molecular recognition has been used in different areas, such as catalysis, material science and medicinal chemistry. This Special Issue aims to show the different facets of halogen bonds. It welcomes original research papers and reviews dealing with experimental, computational studies and statistical surveys were halogen bonds are involved.

Prof. Dr. Ibon Alkorta
Guest Editor

Manuscript Submission Information

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Keywords

  • computational studies
  • databases analysis
  • crystal engineering
  • molecular recognition

Published Papers (10 papers)

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Research

Jump to: Review

Open AccessFeature PaperArticle Structural Examination of Halogen-Bonded Co-Crystals of Tritopic Acceptors
Molecules 2018, 23(1), 163; https://doi.org/10.3390/molecules23010163
Received: 16 December 2017 / Revised: 9 January 2018 / Accepted: 10 January 2018 / Published: 13 January 2018
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Abstract
A series of tritopic N-heterocyclic compounds containing electrostatically and geometrically equivalent binding sites were synthesized and subjected to systematic co-crystallizations with selected perfluoroiodoarenes in order to map out their structural landscapes. More than 70% of the attempted reactions produced a co-crystal as
[...] Read more.
A series of tritopic N-heterocyclic compounds containing electrostatically and geometrically equivalent binding sites were synthesized and subjected to systematic co-crystallizations with selected perfluoroiodoarenes in order to map out their structural landscapes. More than 70% of the attempted reactions produced a co-crystal as indicated by IR spectroscopy. Four new crystal structures are reported and in all of them, at least one potential binding site on the acceptor is left vacant. The absence of halogen bonds to all sites can be ascribed primarily due to deactivation of the σ-hole on the iodo-arene donors and partially due to steric hindrance. The tritopic acceptors containing 5,6-dimethylbenzimidazole derivatives yield discrete tetrameric aggregates in the solid state, whereas the pyrazole and imidazole analogues assemble into halogen-bonded 1-D chains. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessFeature PaperArticle Substituent Effects in Multivalent Halogen Bonding Complexes: A Combined Theoretical and Crystallographic Study
Received: 13 November 2017 / Revised: 18 December 2017 / Accepted: 20 December 2017 / Published: 22 December 2017
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Abstract
In this manuscript, we combined ab initio calculations (RI-MP2/def2-TZVPD level of theory) and a search in the CSD (Cambridge Structural Database) to analyze the influence of aromatic substitution in charge-assisted multivalent halogen bonding complexes. We used a series of benzene substituted iodine derivatives
[...] Read more.
In this manuscript, we combined ab initio calculations (RI-MP2/def2-TZVPD level of theory) and a search in the CSD (Cambridge Structural Database) to analyze the influence of aromatic substitution in charge-assisted multivalent halogen bonding complexes. We used a series of benzene substituted iodine derivatives C6H4(IF4)Y (Y = H, NH2, OCH3, F, CN, and CF3) as Lewis acids and used Cl as electron rich interacting atoms. We have represented the Hammett’s plot and observed a good regression coefficient (interaction energies vs. Hammett’s σ parameter). Additionally, we demonstrated the direct correlation between the Hammett’s σ parameter and the value of molecular electrostatic potential measured at the I atom on the extension of the C–I bond. Furthermore, we have carried out AIM (atoms in molecules) and NBO (natural bonding orbital) analyses to further describe and characterize the interactions described herein. Finally, we have carried out a search in the CSD (Cambridge Structural Database) and found several X-ray structures where these interactions are present, thus giving reliability to the results derived from the calculations. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessArticle Modulation of the Selectivity in Anions Recognition Processes by Combining Hydrogen- and Halogen-Bonding Interactions
Molecules 2017, 22(12), 2273; https://doi.org/10.3390/molecules22122273
Received: 17 November 2017 / Revised: 11 December 2017 / Accepted: 18 December 2017 / Published: 20 December 2017
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Abstract
Most of the halogen bonding receptors for anions described use halogen bonding binding sites solely in the anion recognition process; only a few examples report the study of anion receptors in which the halogen bonding interaction has been used in combination with any
[...] Read more.
Most of the halogen bonding receptors for anions described use halogen bonding binding sites solely in the anion recognition process; only a few examples report the study of anion receptors in which the halogen bonding interaction has been used in combination with any other non-covalent interaction. With the aims to extend the knowledge in the behaviour of this kind of mixed receptors, we report here the synthesis and the anion recognition and sensing properties of a new halogen- and hydrogen- bonding receptor which binds anions by the cooperation of both non-covalent interactions. Fluorescence studies showed that the behaviour observed in the anion recognition sensing is similar to the one previously described for the halogen analogue and is quite different to the hydrogen one. On the other hand, the association constants obtained by 1H-NMR data demonstrate that the mixed halogen- and hydrogen-bonding receptor is more selective for SO42− anion than the halogen or hydrogen analogues. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessFeature PaperArticle New Type of Halogen Bond: Multivalent Halogen Interacting with π- and σ-Electrons
Molecules 2017, 22(12), 2150; https://doi.org/10.3390/molecules22122150
Received: 9 November 2017 / Revised: 29 November 2017 / Accepted: 1 December 2017 / Published: 5 December 2017
Cited by 1 | PDF Full-text (1593 KB) | HTML Full-text | XML Full-text | Supplementary Files
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
[...] Read more.
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. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessFeature PaperCommunication Connectivity and Topology Invariance in Self-Assembled and Halogen-Bonded Anionic (6,3)-Networks
Molecules 2017, 22(12), 2060; https://doi.org/10.3390/molecules22122060
Received: 24 October 2017 / Revised: 14 November 2017 / Accepted: 21 November 2017 / Published: 24 November 2017
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Abstract
We report here that the halogen bond driven self-assembly of 1,3,5-trifluorotriiodobenzene with tetraethylammonium and -phosphonium bromides affords 1:1 co-crystals, wherein the mutual induced fit of the triiodobenzene derivative and the bromide anions (halogen bond donor and acceptors, respectively) elicits the potential of these
[...] Read more.
We report here that the halogen bond driven self-assembly of 1,3,5-trifluorotriiodobenzene with tetraethylammonium and -phosphonium bromides affords 1:1 co-crystals, wherein the mutual induced fit of the triiodobenzene derivative and the bromide anions (halogen bond donor and acceptors, respectively) elicits the potential of these two tectons to function as tritopic modules (6,3). Supramolecular anionic networks are present in the two co-crystals wherein the donor and the acceptor alternate at the vertexes of the hexagonal frames and cations are accommodated in the potential empty space encircled by the frames. The change of one component in a self-assembled multi-component co-crystal often results in a change in its supramolecular connectivity and topology. Our systems have the same supramolecular features of corresponding iodide analogues as the metric aspects seem to prevail over other aspects in controlling the self-assembly process. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessArticle Multicenter (FX)n/NH3 Halogen Bonds (X = Cl, Br and n = 1–5). QTAIM Descriptors of the Strength of the X∙∙∙N Interaction
Molecules 2017, 22(11), 2034; https://doi.org/10.3390/molecules22112034
Received: 10 October 2017 / Revised: 14 November 2017 / Accepted: 14 November 2017 / Published: 22 November 2017
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Abstract
In the present work an in depth deep electronic study of multicenter XBs (FX)n/NH3 (X = Cl, Br and n = 1–5) is conducted. The ways in which X∙∙∙X lateral contacts affect the electrostatic or covalent nature of the X∙∙∙N
[...] Read more.
In the present work an in depth deep electronic study of multicenter XBs (FX)n/NH3 (X = Cl, Br and n = 1–5) is conducted. The ways in which X∙∙∙X lateral contacts affect the electrostatic or covalent nature of the X∙∙∙N interactions are explored at the CCSD(T)/aug-cc-pVTZ level and in the framework of the quantum theory of atoms in molecules (QTAIM). Calculations show that relatively strong XBs have been found with interaction energies lying between −41 and −90 kJ mol−1 for chlorine complexes, and between −56 and −113 kJ mol−1 for bromine complexes. QTAIM parameters reveal that in these complexes: (i) local (kinetics and potential) energy densities measure the ability that the system has to concentrate electron charge density at the intermolecular X∙∙∙N region; (ii) the delocalization indices [δ(A,B)] and the exchange contribution [VEX(X,N)] of the interacting quantum atoms (IQA) scheme, could constitute a quantitative measure of the covalence of these molecular interactions; (iii) both classical electrostatic and quantum exchange show high values, indicating that strong ionic and covalent contributions are not mutually exclusive. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessArticle Halogen Bonding Involving CO and CS with Carbon as the Electron Donor
Molecules 2017, 22(11), 1955; https://doi.org/10.3390/molecules22111955
Received: 17 October 2017 / Revised: 7 November 2017 / Accepted: 9 November 2017 / Published: 12 November 2017
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Abstract
MP2/aug’-cc-pVTZ calculations have been carried out to investigate the halogen-bonded complexes formed when CO and CS act as electron-pair donors through C to ClF, ClNC, ClCl, ClOH, ClCN, ClCCH, and ClNH2. CO forms only complexes stabilized by traditional halogen bonds, and
[...] Read more.
MP2/aug’-cc-pVTZ calculations have been carried out to investigate the halogen-bonded complexes formed when CO and CS act as electron-pair donors through C to ClF, ClNC, ClCl, ClOH, ClCN, ClCCH, and ClNH2. CO forms only complexes stabilized by traditional halogen bonds, and all ClY molecules form traditional halogen-bonded complexes with SC, except ClF which forms only an ion-pair complex. Ion-pair complexes are also found on the SC:ClNC and SC:ClCl surfaces. SC:ClY complexes stabilized by traditional halogen bonds have greater binding energies than the corresponding OC:ClY complexes. The largest binding energies are found for the ion-pair SC–Cl+:Y complexes. The transition structures which connect the complex and the ion pair on SC:ClNC and SC:ClCl potential surfaces provide the barriers for inter-converting these structures. Charge-transfer from the lone pair on C to the σ-hole on Cl is the primary charge-transfer interaction stabilizing OC:ClY and SC:ClY complexes with traditional halogen bonds. A secondary charge-transfer occurs from the lone pairs on Cl to the in-plane and out-of-plane π antibonding orbitals of ClY. This secondary interaction assumes increased importance in the SC:ClNH2 complex, and is a factor leading to its unusual structure. C–O and C–S stretching frequencies and 13C chemical shieldings increase upon complex formation with ClY molecules. These two spectroscopic properties clearly differentiate between SC:ClY complexes and SC–Cl+:Y ion pairs. Spin–spin coupling constants 1xJ(C–Cl) for OC:ClY complexes increase with decreasing distance. As a function of the C–Cl distance, 1xJ(C–Cl) and 1J(C–Cl) provide a fingerprint of the evolution of the halogen bond from a traditional halogen bond in the complexes, to a chlorine-shared halogen bond in the transition structures, to a covalent bond in the ion pairs. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessArticle Nucleophilicities of Lewis Bases B and Electrophilicities of Lewis Acids A Determined from the Dissociation Energies of Complexes B⋯A Involving Hydrogen Bonds, Tetrel Bonds, Pnictogen Bonds, Chalcogen Bonds and Halogen Bonds
Molecules 2017, 22(10), 1786; https://doi.org/10.3390/molecules22101786
Received: 3 October 2017 / Revised: 17 October 2017 / Accepted: 19 October 2017 / Published: 23 October 2017
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Abstract
It is shown that the dissociation energy De for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N2, CO, HC≡CH, CH2=CH2, C3H6, PH
[...] Read more.
It is shown that the dissociation energy D e for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N2, CO, HC≡CH, CH2=CH2, C3H6, PH3, H2S, HCN, H2O, H2CO and NH3) and 23 Lewis acids (HF, HCl, HBr, HC≡CH, HCN, H2O, F2, Cl2, Br2, ClF, BrCl, H3SiF, H3GeF, F2CO, CO2, N2O, NO2F, PH2F, AsH2F, SO2, SeO2, SF2, and SeF2) can be represented to good approximation by means of the equation D e = c N B E A , in which N B is a numerical nucleophilicity assigned to B, E A is a numerical electrophilicity assigned to A, and c is a constant, conveniently chosen to have the value 1.00 kJ mol−1 here. The 250 complexes were chosen to cover a wide range of non-covalent interaction types, namely: (1) the hydrogen bond; (2) the halogen bond; (3) the tetrel bond; (4) the pnictogen bond; and (5) the chalcogen bond. Since there is no evidence that one group of non-covalent interaction was fitted any better than the others, it appears the equation is equally valid for all the interactions considered and that the values of N B and E A so determined define properties of the individual molecules. The values of N B and E A can be used to predict the dissociation energies of a wide range of binary complexes B⋯A with reasonable accuracy. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Open AccessFeature PaperArticle Halogen Bonds Formed between Substituted Imidazoliums and N Bases of Varying N-Hybridization
Molecules 2017, 22(10), 1634; https://doi.org/10.3390/molecules22101634
Received: 28 August 2017 / Revised: 26 September 2017 / Accepted: 27 September 2017 / Published: 29 September 2017
Cited by 4 | PDF Full-text (789 KB) | HTML Full-text | XML Full-text
Abstract
Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp3, sp2 and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with
[...] Read more.
Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp3, sp2 and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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Review

Jump to: Research

Open AccessFeature PaperReview Looking Back, Looking Forward at Halogen Bonding in Drug Discovery
Molecules 2017, 22(9), 1397; https://doi.org/10.3390/molecules22091397
Received: 7 July 2017 / Accepted: 18 August 2017 / Published: 24 August 2017
Cited by 2 | PDF Full-text (2629 KB) | HTML Full-text | XML Full-text
Abstract
Halogen bonding has emerged at the forefront of advances in improving ligand: receptor interactions. In particular the newfound ability of this extant non-covalent-bonding phenomena has revolutionized computational approaches to drug discovery while simultaneously reenergizing synthetic approaches to the field. Here we survey, via
[...] Read more.
Halogen bonding has emerged at the forefront of advances in improving ligand: receptor interactions. In particular the newfound ability of this extant non-covalent-bonding phenomena has revolutionized computational approaches to drug discovery while simultaneously reenergizing synthetic approaches to the field. Here we survey, via examples of classical applications involving halogen atoms in pharmaceutical compounds and their biological hosts, the unique advantages that halogen atoms offer as both Lewis acids and Lewis bases. Full article
(This article belongs to the Special Issue Halogen Bonds and Beyond)
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