Halogen Bond Donor Research Articles

Halogen Bonding Assembles Anion···Anion Architectures in Non-centrosymmetric Iodate and Bromate Crystals.

Single crystal X-ray diffraction of iodate and bromate salts shows that the I and Br atoms in IO3- and BrO3- anions form short and linear O-I/Br···O contacts with the O atoms of nearby anions. Noncentrosymmetric systems are formed wherein anions are orderly aligned into supramolecular 1D and 2D networks. Theoretical evidences, namely the outcome of QTAIM and NCIplot studies, prove the attractive nature of these contacts and the ability of iodate and bromate anions to act as robust HaB donors. The HaB is proposed as a general and effective assisting tool to control the architecture of acentric iodate salts.

Mesomorphic and computational evaluation of C[tbnd]N‧‧‧I halogen bonded complexes of 4-alkoxy-4′-cyanobiphenyls systems with 1,6- diiodoperfluorohexane

Thermotropic halogen bonded (XB) liquid crystalline complex (A-n XB) of 4-alkoxy-4′- cyano biphenyls (A-n) systems containing nitrile (-CN) group with variable alkoxy chain length (-CnH2n+1, where n = 3 to 10) acting as halogen bond acceptor with 1,6-diiodoperfluorohexane, (I-atom) acting as halogen bond donor were prepared by the liquid-assisted grinding method. The A-n XB complex formations, through CN‧‧‧I XB interactions, were established by the FTIR, Raman, PXRD, polarizing optical microscope (POM) with hot stage, DSC and TGA techniques. Further, POM study of these homologous XB complex series showed liquid crystalline phases with a alteration of (1–10 °C) compared to their respective parent mesogenic molecules. The computational study was carried out using Frontier Molecular Orbitals (FMOs), Molecular Electrostatic Potential (MEP), Non-covalent interactions (NCI) and Quantum theory of atoms in molecule (QTAIM) analysis to evaluate the reactivity parameters and strength of XB in the complexes.

Synthesis of Amino Acids Bearing Halodifluoromethyl Moieties and Their Application to p53-Derived Peptides Binding to Mdm2/Mdm4.

Therapeutic peptides are a significant class of drugs in the treatment of a wide range of diseases. To enhance their properties, such as stability or binding affinity, they are usually chemically modified. This includes, among other techniques, cyclization of the peptide chain by bridging, modifications to the backbone, and incorporation of unnatural amino acids. One approach previously established, is the use of halogenated aromatic amino acids. In principle, they are thereby enabled to form halogen bonds (XB). In this study, we focus on the -R-CF2X moiety (R = O, NHCO; X = Cl, Br) as an uncommon halogen bond donor. These groups enable more spatial variability in protein-protein interactions. The chosen approach via Fmoc-protected building blocks allows for the incorporation of these modified amino acids in peptides using solid-phase peptide synthesis. Using a competitive fluorescence polarization assay to monitor binding to Mdm4, we demonstrate that a p53-derived peptide with Lys24Nle(εNHCOCF2X) exhibits an improved inhibition constant Ki compared to the unmodified peptide. Decreasing Ki values observed with the increasing XB capacity of the halogen atoms (F ≪ Cl < Br) indicates the formation of a halogen bond. By reducing the side chain length of Nle(εNHCOCF2X) to Abu(γNHCOCF2X) as control experiments and through quantum mechanical calculations, we suggest that the observed affinity enhancement is related to halogen bond-induced intramolecular stabilization of the α-helical binding mode of the peptide or a direct interaction with His54 in human Mdm4.

Halogen Bond‐Catalyzed Oxidative Annulation of N‐Alkyl Pyridinium Salts and Alkenes with Air as a Sole Oxidant: Metal‐free Synthesis of Indolizines

AbstractThe utilization of ambient air as a sole oxidant is highly desired for the sustainability of chemical industry. Herein, we reported a mild and metal‐free synthesis of indolizines using pyridinium salts and alkenes with ambient air as a sole oxidant. In this reaction, a halogen bond donor (perfluoro‐1‐iodooctane, 10 mol%) was successfully applied to catalyze this desired oxidative [3+2] annulation. The C−I bond of halogen bond donor is crucial for this transformation, while the corresponding C−Br bond and C−F bonds gave much lower yields. Moreover, the phenolic hydroxyl increases the amount of side‐product, probably due to the strong interaction of phenolate anion and the halogen bond donor. Finally, with the rapid development of halogen bond catalysis, this halogen bond‐catalyzed strategy could continuously promote the synthesis of indolizines in a sustainable manner.

Direct π-Activation vs. O-Activation in Halogen-Bonding Catalysis.

Halogen bond donors had an increasing impact on catalysis in recent years, and their development is highly active. In particular, numerous iodine-based halogen bond donors have been developed and used to promote various reactions through coordinating carbonyl groups, a ubiquitous mode of activation in catalysis. We now report computational data which strongly suggests that an alternative activation mode, through direct π-complexation, is operative for unsaturated carbonyl substrates. Calculations also suggest that solvent polarity could have a clear impact on the preference of the mode of activation, raising the possibility of a mechanistic manifold switch through solvent variation. These findings could profoundly impact the development of the next generation of halogen-bond donor catalysts.

Direct π‐Activation vs. O‐Activation in Halogen‐Bonding Catalysis

AbstractHalogen bond donors had an increasing impact on catalysis in recent years, and their development is highly active. In particular, numerous iodine‐based halogen bond donors have been developed and used to promote various reactions through coordinating carbonyl groups, a ubiquitous mode of activation in catalysis. We now report computational data which strongly suggests that an alternative activation mode, through direct π‐complexation, is operative for unsaturated carbonyl substrates. Calculations also suggest that solvent polarity could have a clear impact on the preference of the mode of activation, raising the possibility of a mechanistic manifold switch through solvent variation. These findings could profoundly impact the development of the next generation of halogen‐bond donor catalysts.

Halogen Bond-Involving Supramolecular Assembly Utilizing Carbon as a Nucleophilic Partner of I⋅⋅⋅C Non-covalent Interaction.

Co-crystallization of 180°-orienting σ-hole-accepting tectons, namely, 1,4-diisocyanobenzene (1) and 1,4-diisocyanotetramethylbenzene (2), with such homoditopic halogen bond donors as 1,4-diiodotetrafluorobenzene (1,4-FIB) and 4,4'-diiodoperfluorobiphenyl (4,4'-FIBP) afforded co-crystals 1 ⋅ 1,4-FIB, 1 ⋅ 4,4'-FIBP, and 2 ⋅ 1,4-FIB. Their solid-state structures exhibit 1D-supramolecular arrangements, which are based on poorly explored I⋅⋅⋅C halogen bonding; this study is the first in which the supramolecular assembly utilizing halogen bonding with a terminal C atom was performed. The use of the potentially tetrafunctional σ-hole accepting tetraiodoethylene (TIE) leads to supramolecular architecture of a higher dimension, 3D-framework, observed in the structure of 1 ⋅ TIE. DFT calculations, used to characterize the halogen bonding situation, revealed that the I⋅⋅⋅C non-covalent interactions are moderately strong, ranging from -4.07 in 1 ⋅ TIE to -5.45 kcal/mol in 2 ⋅ 1,4-FIB. The NBO analysis disclosed that LP(C)→σ* charge transfer effects are relevant in all co-crystals.

Halogen-bonded co-crystal containing 1,3-di-iodo-perchloro-benzene and the photoproduct rtct-tetra-kis-(pyridin-4-yl)cyclo-butane resulting in a zigzag topology.

The formation and crystal structure of a zigzag network held together by I⋯N halogen bonds is reported. In particular, the halogen-bond donor is 1,3-di-iodo-perchloro-benzene (C6I2Cl4 ) while the acceptor is the photoproduct rtct-tetra-kis-(pyridin-4-yl)cyclo-butane (TPCB). Curiously, within the resulting co-crystal (C6I2Cl4 )·(TPCB), the photoproduct accepts only two halogen bonds between neighbouring 4-pyridyl rings and as a result behaves as a bent two-connected node rather than the expected four-connected centre. In addition, the photoproduct, TPCB, is also found to engage in C-H⋯N hydrogen bonds, forming an extended zigzag chain.

Anticooperativity and Competition in Some Cocrystals Featuring Iodine-Nitrogen Halogen Bonds.

Phenomena such as anticooperativity and competition among non-covalent bond donors and acceptors are key considerations when exploring the polymorphic and stoichiomorphic landscapes of binary and higher-order cocrystalline architectures. We describe the preparation of four cocrystals of 1,3,5-trifluoro-2,4,6-triiodobenzene with N-heterocyclic compounds, namely acridine, 3-aminopyridine, 4-methylaminopyridine, and 1,2-di(4-pyridyl)ethane. The cocrystals, which are characterized by single-crystal and powder X-ray diffraction experiments, all show moderately strong and directional iodine⋅⋅⋅nitrogen halogen bonds with reduced distance parameters ranging from 0.79 to 0.92 and carbon-iodine⋅⋅⋅nitrogen bond angles ranging from 165.4(3) to 175.31(7)°. The cocrystal comprising 1,3,5-trifluoro-2,4,6-triiodobenzene and acridine provides a relatively rare example where all three halogen bond donor sites form halogen bonds with three acceptor molecules, overcoming an anticooperative effect. This effect manifests itself through the lengthening of non-halogen-bonded C-I bonds, weakening their potential to form halogen bonds. The effect is only observed once two halogen bonds have been formed to 1,3,5-trifluoro-2,4,6-triiodobenzene; one such bond does not appear to be adequate. Among the four cocrystals studied, competition between the pyridyl nitrogen atoms and the amine nitrogen atoms suggests that the former are the preferred halogen bond acceptors. Analysis by Hirshfeld fingerprint plots and 13 C and 19 F magic-angle spinning solid-state nuclear magnetic resonance (NMR) spectroscopy provides additional insights into the prevalence of various short contacts in the crystal structures and into the spectral response to halogen-bond-induced cocrystallization.

Reduced Nucleophilicities ИB of Lewis Bases B: Is ИB Independent of Whether B is Involved in a Hydrogen Bond or a Halogen Bond?

Reduced nucleophilicities ИB of axially symmetric molecules B were determined from , where De is the equilibrium dissociation energy of the complexes B⋅⋅⋅XY, NB is the nucleophilicity of B, EXY is the electrophilicity of the halogen-bond donor XY and is the minimum electrostatic surface potential of B. The series B⋅⋅⋅ClY, B⋅⋅⋅BrY, B⋅⋅⋅IY (Y=F, Cl, Br, I, CN, and CCH) as well as (B⋅⋅⋅XY, XY=F2 , Cl2 , Br2 ,and BrCl) of complexes were investigated. Molecules B were grouped so that the terminal atom involved in the halogen bond was fixed within the group. Groups having N as the terminal atom were RCN (R=CH3 , H, and F) or RN (R=N and P), those with C as the terminal atom were RNC (R=H and F) and RC (R=O, S and Se), and those with a terminal O atom were R=C=O (R=O or S). Graphs of versus EXY for each group were straight lines through the origin, with generally different gradients, hence implying different NB . By contrast, when was the ordinate the lines conflated to give a single straight line, which then defines a common (reduced) nucleophilicity ИB for that group of B. Hence it was concluded that ИB is an intrinsic property of the terminal atom, independent of the remainder of B, and only weakly dependent on the type (C, N or O) of the terminal atom. Moreover, ИB for each B was the same as determined previously from the hydrogen-bonded series B⋅⋅⋅HX, (X=F, Cl, Br, I, CN, CCH, and CP).

Shedding Light on the Vibrational Signatures in Halogen-Bonded Graphitic Carbon Nitride Building Blocks.

The relative contributions of halogen and hydrogen bonding to the interaction between graphitic carbon nitride monomers and halogen bond (XB) donors containing C-X and C≡C bonds were evaluated using computational vibrational spectroscopy. Conventional probes into select vibrational stretching frequencies can often lead to disconnected results. To elucidate this behavior, local mode analyses were performed on the XB donors and complexes identified previously at the M06-2X/aVDZ-PP level of theory. Due to coupling between low and high energy C-X vibrations, the C≡C stretch is deemed a better candidate when analyzing XB complex properties or detecting XB formation. The local force constants support this conclusion, as the C≡C values correlate much better with the σ-hole magnitude than their C-X counterparts. The intermolecular local stretching force constants were also assessed, and it was found that attractive forces other than halogen bonding play a supporting role in complex formation.

Iodine-Catalyzed Claisen-Rearrangements of Allyl Aryl Ethers and Subsequent Iodocyclizations.

Iodine can be considered as the simplest halogen-bond donor. Previous investigations have revealed its remarkable catalytic effect in various reactions. The catalytic activity of iodine can often even compete with that of traditional Lewis acids. So far, iodine was typically used to activate carbonyl derivatives like Michael acceptors. We now demonstrate that iodine can also be used to activate allyl aryl ethers in Claisen rearrangements. The formed ortho-allylic phenols rapidly undergo iodocyclizations to afford dihydrobenzofurans, which are important building blocks for medicinal applications. A comparison with different catalysts further highlights the potential of iodine catalysis for this reaction. Computational and mechanistic investigations provide deeper insights into the underlying non-covalent interactions and their role for the catalysis.

Halogen bonding with carbon: directional assembly of non-derivatised aromatic carbon systems into robust supramolecular ladder architectures.

Carbon, although the central element in organic chemistry, has been traditionally neglected as a target for directional supramolecular interactions. The design of supramolecular structures involving carbon-rich molecules, such as arene hydrocarbons, has been limited almost exclusively to non-directional π-stacking, or derivatisation with heteroatoms to introduce molecular assembly recognition sites. As a result, the predictable assembly of non-derivatised, carbon-only π-systems using directional non-covalent interactions remains an unsolved fundamental challenge of solid-state supramolecular chemistry. Here, we propose and validate a different paradigm for the reliable assembly of carbon-only aromatic systems into predictable supramolecular architectures: not through non-directional π-stacking, but via specific and directional halogen bonding. We present a systematic experimental, theoretical and database study of halogen bonds to carbon-only π-systems (C-I⋯πC bonds), focusing on the synthesis and structural analysis of cocrystals with diversely-sized and -shaped non-derivatised arenes, from one-ring (benzene) to 15-ring (dicoronylene) polycyclic atomatic hydrocarbons (PAHs), and fullerene C60, along with theoretical calculations and a systematic analysis of the Cambridge Structural Database. This study establishes C-I⋯πC bonds as directional interactions to arrange planar and curved carbon-only aromatic systems into predictable supramolecular motifs. In >90% of herein presented structures, the C-I⋯πC bonds to PAHs lead to a general ladder motif, in which the arenes act as the rungs and halogen bond donors as the rails, establishing a unique example of a supramolecular synthon based on carbon-only molecules. Besides fundamental importance in the solid-state and supramolecular chemistry of arenes, this synthon enables access to materials with exciting properties based on simple, non-derivatised aromatic systems, as seen from large red and blue shifts in solid-state luminescence and room-temperature phosphorescence upon cocrystallisation.

Activation of metal-involved halogen bonds and classical halogen bonds in gold(I) catalysis.

In gold(I) catalysis, the activation of Au(I) chloride catalysts via chloride abstraction and noncovalent interactions has become a research focus in organometallic catalysis. In this work, taking halogen bond donors (C4H2INO2, C6F5I, C8H9O2I) as activators for a Au(I) chloride catalyst (Ph3PAuCl), the mechanism of the cyclization reaction of propargylic amide was investigated. It was found that there are two activation modes as design principles to obtain the catalytically active species Ph3PAu+: the halogen bond donors activate the Cl atoms of Ph3PAuCl to form X-I⋯Cl (X = C, N) classical halogen bonds and activate the Au atoms of Ph3PAuCl to form X-I⋯Au (X = C, N) metal-involved halogen bonds. For the two activation modes, the mechanism of the cyclization reaction of propargylic amide has pathways: the chloride abstraction process of the first step and the 5-exo/6-endo cyclization process of the second step. Both activation modes show good activity for the cyclization reaction with the activation ability of classical halogen bonds being slightly stronger than that of the metal-involved halogen bonds, which is consistent with the strength of the X-I⋯Cl halogen bonds being slightly stronger than that of the X-I⋯Au halogen bonds. Therefore, both metal-involved halogen bonds and classical halogen bonds have important development prospects for the activation of catalysts in gold(I) catalysis.

Just at the limit: binding studies with neutral brominated terphenyl-derived halogen bond donors

A systematic comparison of brominated neutral halogen bond donors against their iodinated analogues in the gas phase, solid state, and in solution.

Solution and solid-state studies of hydrogen and halogen bonding with N-heterocyclic carbene supported nickel(II) fluoride complexes.

Nickel fluoride complexes of the type [Ni(F)(L)2(ArF)] (L = phosphine, ArF = fluorinated arene) are well-known to form strong halogen and hydrogen bonds in solution and in the solid state. A comprehensive study of such non-covalent interactions using bis(carbene) complexes as acceptors and suitable halogen and hydrogen bond donors is presented. In solution, the complex [Ni(F)(iPr2Im)2(C6F5)] forms halogen and hydrogen bonds with iodopentafluorobenzene and indole, respectively, which have formation constants (K300) an order of magnitude greater than those of structurally related phosphine supported nickel fluorides. Co-crystallisation of this complex and its backbone-methylated analogue [Ni(F)(iPr2Me2Im)2(C6F5)] with 1,4-diiodotetrafluorobenzene produces halogen bonding adducts which were characterised by X-ray analysis and 19F MAS solid state NMR analysis. Differences in the chemical shifts between the nickel fluoride and its halogen bonding adduct are well in line with data that were obtained from titration studies in solution.

X/Y platinum(II) complexes: some features of supramolecular assembly via halogen bonding.

Four series of new luminescent cyclometalated complexes [Pt(C^N)(IPy)Y] (HC^N = 2-phenylpyridine (Hppy), 2-(1-benzofuran-3-yl)pyridine (Hbfpy), methyl-2-phenylquinoline-4-carboxylate (Hmpqc), 2-(1-benzothiophen-3-yl)pyridine (Hbtpy), IPy = 4-iodopyridine, and Y = Cl, Br, I) have been investigated as X/Y 'building blocks' for the construction of a supramolecular network utilizing the I atom in IPy as a halogen bond (XB) donor (the X atom). The σ-hole of the X atom was found to provide non-covalent X⋯Y, X⋯Pt and X⋯π (π system of the metalated chelate ring) interactions for the complexes in the crystal state. NBO analysis confirms donation of the platinum electron density to iodine upon the X⋯Pt interaction. The nature of the X counterpart in XB depends on the nature of the Y atom and the cyclometalating ligand of the Pt(II) complex. DFT calculations show that the HOMO of [Pt(C^N)(IPy)Y] in the S0 state is delocalized over Pt, Y and a C-coordinating fragment of C^N, while the LUMO in most complexes is formed by the Py orbitals of IPy. However, the α-HOMO in the lowest triplet state of [Pt(C^N)(IPy)Y] contains no contribution of the IPy wavefunctions. All Pt(II) complexes exhibited triplet luminescence in solution and in the solid state (Φ up to 0.129), which is determined by the nature of the C^N ligand. The emission profile is independent of the nature of the ligand Y, while the quantum yield decreases from Cl to I. Accordingly, on the basis of DFT calculation, this emission is interpreted as a C^N intraligand charge transfer predominantly. The XB formation did not show an effect on the luminescence of the complexes in the solid phase, however grinding of crystals results in an increase of brightness.

Iodine(I)-based and iodine(III)-based halogen bond catalysis on the Friedel-Crafts reaction: a theoretical study.

Halogen bond catalysis, especially iodine derivatives catalysis, has attracted increasing attention in recent years owing to the advantages of relatively cheap, stable, green, easy to handle, and favorable catalytic activity. To obtain insights into the catalytic mechanism and activity of halogen bond donor catalysts, iodine(I)-based and iodine(III)-based halogen bond catalysis on the Friedel-Crafts reaction were investigated in this study. The entire reaction contains several key steps: carbon-carbon bond coupling, proton transfer, hydroxyl departure, indole addition, and deprotonation process. According to the energetic span model, iodine(III)-based donor catalysts exhibit higher catalytic activity than iodine(I)-based catalysts and double cationic catalysts are more potent than single cationic ones. For halogen bond catalysis, the Gibbs energy barriers have linear relation to the electron density at the halogen bond critical points. Furthermore, the Gibbs energy barriers are also linearly related to the integral charge values of the increased region of electron density outside the oxygen atom of reactants. Therefore, the stronger halogen bond results in lower Gibbs energy barrier, and the stronger polarization further benefits the halogen bond catalysis.

Anion recognition using enhanced halogen bonding through intramolecular hydrogen bonds – a computational insight

Anions have relevant roles in nature and in the chemistry industry. Here, structures containing halogen bond donors enhanced by hydrogen bonds have been tuned aiming to improve the anionic recognition.

Halogen bonding between metal-bound I3− and unbound I2: the trapped I2⋯I3− intermediate in the controlled assembly of copper(i)-based polyiodides

The identification of halogen bonded-intermediates is key to understanding the precise mechanism for the generation of I5− (and I82−) ligands from I2 and metal-coordinated I3−.