The Nature of Halogen⋅⋅⋅Halogen Synthons: Crystallographic and Theoretical Studies

Dihalogen and Pnictogen Bonding in Crystalline Icosahedral Phosphaboranes

Noncovalent interactions in the single crystal of 3,6-Cl2-closo-1,2-P2B10H8 and in the crystal of closo-1,7-P2B10Cl10•toluene were analyzed by means of quantum chemical computations. The crystal packing in the second crystal was dominated by numerous B-Cl···Cl-B dihalogen and strong B-P···π pnictogen bonds, the latter of which were characterized by a small length of 3.08 Å and a large interaction energy value, exceeding −10 kcal mol−1.

Melting point, molecular symmetry and aggregation of tetrachlorobenzene isomers: the role of halogen bonding

Tetrachlorobenzenes represent one of the best known, but not yet fully understood, group of isomers of the structure-melting point relationship. The differences in melting temperatures of these structurally related compounds were rationalized in terms of the hierarchy and nature of formed noncovalent interactions, and the molecular aggregation that is influenced by molecular symmetry. The highest melting point is associated with the highly symmetric 1,2,4,5-tetrachlorobenzene isomer. The structures of less symmetrical 1,2,3,4-tetrachlorobenzene and 1,2,3,5-tetrachlorobenzene, determined at 270 and 90 K, show a distinct pattern of halogen bonds, characterized by the different numbers and types of interactions. The evolution of Cl...Cl/H distances with temperature indicates the attractive character of intermolecular interactions and their importance to the structural and thermodynamic parameters of isomeric compounds. The favoured Cl...Cl halogen bonds were found to play a decisive role in differentiating the melting temperatures of tetrachlorobenzene isomers. It was also found that, besides the molecular symmetry and ability to form specific intermolecular interactions, both the type and the distribution of interactions are the important factors responsible for the melting behaviour of the studied isomers. The observed preferences, in tetrachlorobenzenes, for the formation of specific noncovalent interactions correspond to the distribution of calculated partial atomic charges and to the magnitudes of electrostatic potential on the molecular surfaces as well as correlate with the enthalpy of melting parameters.

3,4-Dibromo-2,2,5,5-tetraphenyl-2,5-dihydrofuran

The crystal structure of the title compound, C28H20Br2O, was solved in the orthorhombic space group P212121 with one molecule in the asymmetric unit. The phenyl rings are nearly planar and inclined at angles of 67.7 (1), 68.8 (1), 79.3 (1) and 62.3 (1)° to the plane of the 2,5-dihydrofuran ring. The crystal structure features C—H...π and Br...Br interactions, which connect the molecules to a three-dimensional supramolecular network.

Synthesis and crystal structures of 2-bromo-1,3-di-methyl-imidazolium iodides

Attempts at direct bromination of 1,3-di-methyl-imidazolium salts were futile. The title compounds, 2-bromo-1,3-di-methyl-imidazolium iodide chloro-form 0.33-solvate, C5H8BrN2+·I-·0.33CHCl3, 2-bromo-1,3-di-methyl-imidazolium iodide di-chloro-methane hemisolvate, C5H8BrN2+·I-·0.5CH2Cl2, and 2-bromo-1,3-di-methyl-imidazolium iodide hemi(diiodide), C5H8BrN2+·I-·0.5I2, were obtained by methyl-ation of 2-bromo-1-methyl-imidazole. They crystallized as CHCl3, CH2Cl2 or I2 solvates/adducts. The Br atom acts as a σ-hole to accept short C-Br⋯I inter-actions. C-H⋯I hydrogen bonds are observed in each structure.

From Molecules to Materials: Engineering New Ionic Liquid Crystals Through Halogen Bonding

Herein, we demonstrate that a bottom-up approach, based on halogen bonding (XB), can be successfully applied for the design of a new type of ionic liquid crystals (ILCs). Taking advantages of the high specificity of XB for haloperfluorocarbons and the ability of anions to act as XB-acceptors, we obtained supramolecular complexes based on 1-alkyl-3-methylimidazolium iodides and iodoperfluorocarbons, overcoming the well-known immiscibility between hydrocarbons (HCs) and perfluorocarbons (PFCs). The high directionality of the XB combined with the fluorophobic effect, allowed us to obtain enantiotropic liquid crystals where a rigid, non-aromatic, XB supramolecular anion acts as mesogenic core. X-ray structure analysis of the complex between 1-ethyl-3-methylimidazolium iodide and iodoperfluorooctane showed the presence of a layered structure, which is a manifestation of the well-known tendency to segregation of perfluoroalkyl chains. This is consistent with the observation of smectic mesophases. Moreover, all the reported complexes melt below 100 °C, and most are mesomorphic even at room temperature, despite that the starting materials were non-mesomorphic in nature. The supramolecular strategy reported here provides new design principles for mesogen design allowing a totally new class of functional materials.

The σ-hole revisited

A covalently-bonded atom typically has a region of lower electronic density, a "σ-hole," on the side of the atom opposite to the bond, along its extension. There is frequently a positive electrostatic potential associated with this region, through which the atom can interact attractively but noncovalently with negative sites. This positive potential reflects not only the lower electronic density of the σ-hole but also contributions from other portions of the molecule. These can significantly influence both the value and also the angular position of the positive potential, causing it to deviate from the extension of the covalent bond. We have surveyed these effects, and their consequences for the directionalities of subsequent noncovalent intermolecular interactions, for atoms of Groups IV-VII. The overall trends are that larger deviations of the positive potential result in less linear intermolecular interactions, while smaller deviations lead to more linear interactions. We find that the deviations of the positive potentials and the nonlinearities of the noncovalent interactions tend to be greatest for atoms of Groups V and VI. We also present arguments supporting the use of the 0.001 a.u. contour of the electronic density as the molecular surface on which to compute the electrostatic potential.

Halogen bonds in 2,5-dihalopyridine-copper(ii) chloride complexes

In the (2,5-dihalopyridine)₂·CuCl₂ complexes varying the C5-position halogens affects the halogen bonding properties so that the C5–X5⋯Cl–Cu halogen bonds follow the order F5 < Cl5 < Br5 < I5 when the substituent at 2-position is chlorine and Cl5 < Br5 < I5 when it is bromine.

Loose crystals engineered by mismatched halogen bonds in hexachloroethane

The shortest intermolecular contacts in the engineered loose crystal of hexachloroethane are longer than the sum of van der Waals radii, reached only at the pressure of 1.2 GPa.

May halogen bonding interactions compete with Cu⋯Cl semi-coordinate bonds? Structural, magnetic and theoretical studies of two polymorphs of trans-bis(5-bromo-2-chloro pyridine)dichlorocopper(ii) and trans-bis(2,5-dichloropyridine)dichlorocopper(ii)

Interaction of the negative potential area from one molecule with the positive areas I and II from two different molecules produces polymorphs 1 and 2.

Substituent Effects in Multivalent Halogen Bonding Complexes: A Combined Theoretical and Crystallographic Study

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.

Probing halogen-halogen interactions in solution

Halogen-halogen interactions are a particularly interesting class of halogen bonds that are known to be essential design elements in crystal engineering. In solution, it is likely that halogen-halogen interactions also play a role, but the weakness of this interaction makes it difficult to characterize or even simply detect. We have designed a supramolecular balance that allows detecting BrBr interactions between CBr₃ groups in solution and close to room temperature. The sensitivity and versatility of the chosen platform have allowed accumulating consistent data. In halogenoalkane solvents, we propose estimates for the free energy of these weak halogen bond interactions. In toluene solutions, we show that the interactions between Br atoms and the solvent aromatic groups dominate over the BrBr interactions.

Systematic Coupled Cluster Study of Noncovalent Interactions Involving Halogens, Chalcogens, and Pnicogens

The noncovalent interactions of 32 complexes involving pnicogens, chalcogens, and halogens atoms were investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Two different types of complexes could be distinguished on the basis of geometric parameters, electron difference densities, and the charge transfer mechanisms associated with each type. In the type I conformation, the monomers adopt a skewed orientation allowing charge to be transfer between both monomers, whereas in the type II conformation the monomers adopt a linear arrangement, maximizing charge transfer in only one direction. Type I complexes involving the interaction between pnicogens and chalcogens cannot be unambiguously defined as chalcogen or pnicogen bonds, they are an admixture of both. The charge transfer dependence on the conformation adopted by the complexes described in this work can serve as a novel conformationally driven design concept for materials.

The crystal structure of carbonyl-[4-(2,4-dichlorophenylamino)pent-3-en-2-onato-κ2N,O]-(triphenylphosphine-κP)rhodium(I), RhC30H25Cl2NO2P

RhC30H25Cl2NO2P, orthorhombic P212121 (no. 19), a = 7.6656(5) Å, b = 16.6097(11) Å, c = 20.9423(14) Å, V = 2666.4(3) Å3, Z = 4, Rgt(F) = 0.0649, wRref(F2) = 0.1632, T = 100 K.

N-H...X (X = Cl and Br) hydrogen bonds in three isomorphous 3,5-dichloropyridinium salts

Specific short contacts are important in crystal engineering. Hydrogen bonds have been particularly successful and together with halogen bonds can be useful for assembling small molecules or ions into crystals. The ionic constituents in the isomorphous 3,5-dichloropyridinium (3,5-diClPy) tetrahalometallates 3,5-dichloropyridinium tetrachloridozincate(II), (C₅H₄Cl₂N)₂[ZnCl₄] or (3,5-diClPy)₂ZnCl₄, 3,5-dichloropyridinium tetrabromidozincate(II), (C₅H₄Cl₂N)₂[ZnBr₄] or (3,5-diClPy)₂ZnBr₄, and 3,5-dichloropyridinium tetrabromidocobaltate(II), (C₅H₄Cl₂N)₂[CoBr₄] or (3,5-diClPy)₂CoBr₄, arrange according to favourable electrostatic interactions. Cations are preferably surrounded by anions and vice versa; rare cation-cation contacts are associated with an antiparallel dipole orientation. N-H...X (X = Cl and Br) hydrogen bonds and X...X halogen bonds compete as closest contacts between neighbouring residues. The former dominate in the title compounds; the four symmetrically independent pyridinium N-H groups in each compound act as donors in charge-assisted hydrogen bonds, with halogen ligands and the tetrahedral metallate anions as acceptors. The M-X coordinative bonds in the latter are significantly longer if the halide ligand is engaged in a classical X...H-N hydrogen bond. In all three solids, triangular halogen-bond interactions are observed. They might contribute to the stabilization of the structures, but even the shortest interhalogen contacts are only slightly shorter than the sum of the van der Waals radii.

Synthesis and crystal structures of non-symmetric 1,3-di(alkyloxy)imidazolium salts

A series of non-symmetric 1,3-di(alkyloxy)imidazolium salts were synthesized by stepwise alkylation of 1-hydroxyimidazole-3-oxide. The quaternary salts were subsequently functionalized by bromination in 2-position. A 2-azidoimidazolium salt and an imidazoline-2-thione were prepared exemplarily. Crystal structures of two 2-bromo-1-alkyloxy-3-methyloxyimidazolium tribromides and a mercury(II)-thione complex have been determined by X-ray diffraction.

σ-Hole Interactions: Perspectives and Misconceptions

After a brief discussion of the σ-hole concept and the significance of molecular electrostatic potentials in noncovalent interactions, we draw attention to some common misconceptions that are encountered in that context: (1) Since the electrostatic potential reflects the contributions of both the nuclei and the electrons, it cannot be assumed that negative potentials correspond to “electron-rich” regions and positive potentials to “electron-poor” ones; (2) The electrostatic potential in a given region is determined not only by the electrons and nuclei in that region, but also by those in other portions of the molecule, especially neighboring ones; (3) A σ-hole is a region of lower electronic density on the extension of a covalent bond, not an electrostatic potential; (4) Noncovalent interactions are between positive and negative regions, which are not necessarily associated with specific atoms, so that “close contacts” between atoms do not always indicate the actual interactions.

Halogen bonding in hypervalent iodine and bromine derivatives: halonium salts

Halogen bonds have been identified in a series of ionic compounds involving bromonium and iodonium cations and several different anions, some also containing hypervalent atoms. The hypervalent bromine and iodine atoms in the examined compounds are found to have positive σ-holes on the extensions of their covalent bonds, while the hypervalent atoms in the anions have negative σ-holes. The positive σ-holes on the halogens of the studied halonium salts determine the linearity of the short contacts between the halogen and neutral or anionic electron donors, as usual in halogen bonds.

1,3,5-Tri(iodoethynyl)-2,4,6-trifluorobenzene: halogen-bonded frameworks and NMR spectroscopic analysis

Halogen bonding is the non-covalent interaction between the region of positive electrostatic potential associated with a covalently bonded halogen atom, named the σ-hole, and a Lewis base. Single-crystal X-ray diffraction structures are reported for a series of seven halogen-bonded cocrystals featuring 1,3,5-tris(iodoethynyl)-2,4,6-trifluorobenzene (1) as the halogen-bond donor, and bromide ions (as ammonium or phosphonium salts) as the halogen-bond acceptors: (1)·MePh3PBr, (1)·EtPh3PBr, (1)·acetonyl-Ph3PBr, (1)·Ph4PBr, (1)·[bis(4-fluorophenyl)methyl]triphenylphosphonium bromide, and two new polymorphs of (1)·Et3BuNBr. The cocrystals all feature moderately strong iodine–bromide halogen bonds. The crystal structure of pure [bis(4-fluorophenyl)methyl]triphenylphosphonium bromide is also reported. The results of a crystal engineering strategy of varying the size of the counter-cation are explored, and the features of the resulting framework materials are discussed. Given the potential utility of (1) in future crystal engineering applications, detailed NMR analyses (in solution and in the solid state) of this halogen-bond donor are also presented. In solution, complex13C and19F multiplets are explained by considering the delicate interplay between variousJcouplings and subtle isotope shifts. In the solid state, the formation of (1)·Et3BuNBr is shown through significant13C chemical shift changes relative to pure solid 1,3,5-tris(iodoethynyl)-2,4,6-trifluorobenzene.

Atom interaction propensities of oxygenated chemical functions in crystal packings

The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O-H⋯O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C-H⋯O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms. The over-represented contacts in crystals of oxygenated hydrocarbons are generally of two types: electrostatic attractions (hydrogen bonds) and hydrophobic interactions. While Cl⋯O interactions are generally avoided, in a minority of chloro-oxygenated hydrocarbons, significant halogen bonding does occur. General tendencies can often be derived for many contact types, but outlier compounds are instructive as they display peculiar or rare features. The methodology also allows the detection of outliers which can be structures with errors. For instance, a significant number of hydroxylated molecules displaying over-represented non-favorable oxygen-oxygen contacts turned out to have wrongly oriented hydroxyl groups. Beyond crystal packings with a single molecule in the asymmetric unit, the behavior of water in monohydrate compounds and of crystals with Z' = 2 (dimers) are also investigated. It was found in several cases that, in the presence of several oxygenated chemical groups, cross-interactions between different chemical groups (e.g. water/alcohols; alcohols/phenols) are often favored in the crystal packings. While some trends in accordance with common chemical principles are retrieved, some unexpected results can however appear. For example, in crystals of alcohol-phenol compounds, the strong O-H⋯O hydrogen bonds between two phenol groups turn out to be extremely rare, while cross contacts between phenols and alcohols have enriched occurrences.

Theoretical Study of Intramolecular Interactions in Peri-Substituted Naphthalenes: Chalcogen and Hydrogen Bonds

A theoretical study of the peri interactions, both intramolecular hydrogen (HB) and chalcogen bonds (YB), in 1-hydroxy-8YH-naphthalene, 1,4-dihydroxy-5,8-di-YH-naphthalene, and 1,5-dihydroxy-4,8-di-YH-naphthalene, with Y = O, S, and Se was carried out. The systems with a OH:Y hydrogen bond are the most stable ones followed by those with a chalcogen O:Y interaction, those with a YH:O hydrogen bond (Y = S and Se) being the least stable ones. The electron density values at the hydrogen bond critical points indicate that they have partial covalent character. Natural Bond Orbital (NBO) analysis shows stabilization due to the charge transfer between lone pair orbitals towards empty Y–H that correlate with the interatomic distances. The electron density shift maps and non-covalent indexes in the different systems are consistent with the relative strength of the interactions. The structures found on the CSD were used to compare the experimental and calculated results.

Harnessing uranyl oxo atoms via halogen bonding interactions in molecular uranyl materials featuring 2,5-diiodobenzoic acid and N-donor capping ligands

The supramolecular assembly of molecular uranyl species via halogen-oxo interactions and spectroscopic manifestations thereof are probed in the solid state.

Conformations of benzene-based tripodal isatin-bearing compounds in the crystalline state

Studies of molecular conformations, examples of polymorphic forms, new solvates and analysis of supramolecular motifs giving interesting insights into molecular recognition phenomena are reported.

Trimethyl-, triethyl- and trimethoxybenzene-based tripodal compounds bearing pyrazole groups: conformations and halogen-/hydrogen-bond patterns in the crystalline state

X-ray analyses of a series of benzene-based tripodal molecules1–9provide interesting insights into the molecular recognition phenomena and give information about the different conformations which adopt the molecules in the solvent-free crystals and in solvates.

Superfluorinated Ionic Liquid Crystals Based on Supramolecular, Halogen-Bonded Anions

Unconventional ionic liquid crystals in which the liquid crystallinity is enabled by halogen-bonded supramolecular anions [Cn F2 n+1 -I⋅⋅⋅I⋅⋅⋅I-Cn F2 n+1 ](-) are reported. The material system is unique in many ways, demonstrating for the first time 1) ionic, halogen-bonded liquid crystals, and 2) imidazolium-based ionic liquid crystals in which the occurrence of liquid crystallinity is not driven by the alkyl chains of the cation.

Directing the Crystallization of Dehydro[24]annulenes into Supramolecular Nanotubular Scaffolds

The self-assembly of a series of dehydro[24]annulene derivatives into columnar stacks has been examined for its latent ability to form π-conjugated carbon-rich nanotubular structures through topochemical polymerizations. We have studied the parameters affecting self-assembly, including the nature of the substituent and crystallization conditions, using 10 different dehydro[24]annulene derivatives. In particular, hydrogen-bonding interactions through carbamate groups were found to be especially useful at directing the formation of nanotubular supramolecular assemblies. We have also evaluated the electronic coupling between neighboring dehydroannulene molecules within these supramolecular assemblies. Density functional calculations on the stacked supramolecular nanotube assemblies show that transfer integrals vary considerably between the three columnar assemblies, ranging from moderate to high (59-98 meV for the highest occupied molecular orbitals, 63-97 meV for the lowest unoccupied molecular orbitals), depending on the local molecular topology. In addition, the dehydro[24]annulene derivatives afforded distinct architectures in the crystal, including nanochannel arrays, sheets with solvent-filled pores, and lamellae. This work is an essential step toward a controlled formation of covalently linked carbon-rich nanostructures generated from molecular precursors with a latent diacetylene reactivity.

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

σ-Hole Bond vs π-Hole Bond: A Comparison Based on Halogen Bond

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.