The Nature of Halogen···Halide Synthons: Theoretical and Crystallographic Studies

Competition between Binding to Various Sites of Substituted Imidazoliums

The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH₃ base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.

Keggin-Type Anions as Halogen Bond Acceptors

To study the potential of Keggin-type polyoxometalate anions to act as halogen bond acceptors, we have prepared a series of 10 halogen-bonded compounds starting from phosphomolybdic and phosphotungstic acid and halogenopyridinium cations as halogen (and hydrogen) bond donors. In all the structures, the cations and the anions were interconnected by halogen bonds, more often with terminal M=O oxygen atoms than with bridging oxygen atoms as acceptors. In four structures comprising protonated iodopyridinium cations capable of forming both hydrogen and halogen bonds with the anion, the halogen bond with the anion is apparently favored, whereas hydrogen bonds preferentially involve other acceptors present in the structure. In three obtained structures derived from phosphomolybdic acid, the corresponding oxoanion has been found in its reduced state [Mo₁₂PO₄₀]^4-, which has also led to a decrease in halogen bond lengths as compared to the fully oxidated [Mo₁₂PO₄₀]^3-. The electrostatic potential on the three types of anions involved in the study ([Mo₁₂PO₄₀]^3-, [Mo₁₂PO₄₀]^4-, and [W₁₂PO₄₀]^3-) has been calculated for optimized geometries of the anions, and it has been shown that the terminal M=O oxygen atoms are the least negative sites of the anions, indicating that they act as halogen bond acceptors primarily due to their steric availability.

Halogen Bonding and CO-Ligand Blue-Shift in Hybrid Organic—Organometallic Cocrystals [CpFe(CO)2X] (C2I4) (X = Cl, Br)

This work is focused on the complex interplay of geometry of I⋯X halogen bonds (HaB) and intermolecular interaction energy in two isomorphic cocrystals [CpFe(CO)2X] (C2I4) (X = Cl (1), Br (2)). Their IR-spectroscopic measurements in solid state and solution demonstrate the blue-shift of CO vibration bands, resulting from I⋯X HaB. The reluctance of their iodide congener [CpFe(CO)2I] to form the expected cocrystal [CpFe(CO)2I] (C2I4) is discussed in terms of different molecular electrostatic potential (MEP) of the surface of iodide ligands, as compared with chloride and bromide, which dictate a different angular geometry of HaB around the metal-I and metal-Br/Cl HaB acceptors. This study also suggests C2I4 as a reliable HaB donor coformer for metal-halide HaB acceptors in the crystal engineering of hybrid metal–organic systems.

Isostructural Halogen Exchange and Halogen Bonds: The Case of N-(4-Halogenobenzyl)-3-halogenopyridinium Halogenides

Six N-(4-halogenobenzyl)-3-halogenopyridinium cations were prepared by reacting meta-halogenopyridines (Cl, Br, and I) with (4-halogenobenzyl) bromides (Br and I) and were isolated as bromide salts, which were further used to obtain iodides and chlorides. Sixteen compounds (out of 18 possible cation/anion combinations) were obtained; two crystallized as hydrates and 14 as solvent free salts, 11 of which belonged to one isostructural series and 3 to another. All crystal structures comprise halogen-bonded chains, with the anion as an acceptor of two halogen bonds, with the pyridine and the benzyl halogen substituents of two neighboring cations. The halogen bonds with the pyridine halogen show a linear correlation between the relative halogen bond length and angle, which primarily depend on the donor halogen. The parameters of the other halogen bonds vary with all three halogens, indicating that the former halogen bond is the dominant interaction. This is also in accord with the calculated electrostatic potential in the σ-holes of the halogens and the thermal properties of the solids. The second isostructural group comprises combinations of the best halogen bond donors and acceptors, and features a more favorable halogen bond geometry of the dominant halogen bond, reaffirming its significance as the main factor in determining the structure.

Polymorphism and isomorphism in trans-bis(2,5-diiodopyridine)dihalocopper(ii) complexes: theoretical and crystallographic studies

Two conformational polymorphs of [Cu(25dIpy)2Cl2] have been prepared, the anti-polymorph crystallized from 2-propanol at room temperature (green) and the syn-polymorph crystallized from acetonitrile at 60 °C (brown).

Towards hydrogen and halogen bonded frameworks based on 3,5-bis(triazolyl)pyridinium motifs

Construction of supramolecular assemblies using hydrogen and halogen bonding between anions and the 3,5-bis(triazolyl)pyridinium motif was investigated.

Evaluation of Halogenopyridinium Cations as Halogen Bond Donors

We have performed a database survey and a structural and computational study of the potential and the limitations of halogenopyridinium cations as halogen bond donors. The database survey demonstrated that adding a positive charge on a halogenopyridine ring increases the probability that the halogen atom will participate in a halogen bond, although for chloropyridines it remains below 60%. Crystal structures of both protonated and N-methylated monohalogenated pyridinium cations revealed that the iodo- and bromopyridinium cations always form halogen-bonding contacts with the iodide anions shorter than the sum of the vdW radii, while chloropyridinium cations mostly participate in longer contacts or fail to form halogen bonds. Although a DFT study of the electrostatic potential has shown that both protonation and N-methylation of halogenopyridines leads to a considerable increase in the ESP of the halogen σ-hole, it is generally not the most positive site on the cation, allowing for alternate binding sites.

Halogen and Hydrogen Bond Motifs in Ionic Cocrystals Derived from 3-Halopyridinium Halogenides and Perfluorinated Iodobenzenes

Four halopyridinium salts, 3-chloro- and 3-bromopyridinium chlorides and bromides, have been successfully cocrystallized with two ditopic perfluorinated iodobenzenes, 1,4-diiodotetrafluorobenzene and 1,2-diiodotetrafluorobenzene. These halogen bond donor molecules were chosen because the different positionings of halogen bond donor atoms can lead to different supramolecular architectures. In this work, we present insight into the halogen bond acceptor potential of chloride and bromide ions, as well as the halogen bond donor potential of chlorine and bromine atoms substituted on the pyridinium ring when combined with the expectedly very strong hydrogen bonds between halopyridinium ions and free halogenide anions. A series of eight cocrystals were obtained in which three pairs of isostructural cocrystals were formed. Dominant interactions in the obtained cocrystals were charge-assisted hydrogen bonds between halopyridinium cations and halogenide ions as well as halogen bonds between halogen atoms on the pyridinium ring and halogenide ions.

Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts

We performed a structural study of N-alkylated halogenopyridinium cations to examine whether choice of the N-substituent has any considerable effect on the halogen bonding capability of the cations. For that purpose, we prepared a series of N-ethyl-3-halopyridinium iodides and compared them with their N-methyl-3-halopyridinium analogues. Structural analysis revealed that N-ethylated halogenopyridinium cations form slightly shorter C−X⋯I− halogen bonds with iodide anion. We have also attempted synthesis of ditopic symmetric bis-(3-iodopyridinium) dications. Although successful in only one case, the syntheses have afforded two novel ditopic asymmetric monocations with an iodine atom bonded to the pyridine ring and another on the aliphatic N-substituent. Here, the C−I⋯I− halogen bond lengths involving pyridine iodine atom were notably shorter than those involving an aliphatic iodine atom as a halogen bond donor. This trend in halogen bond lengths is in line with the charge distribution on the Hirshfeld surfaces of the cations—the positive charge is predominantly located in the pyridine ring making the pyridine iodine atom σ-hole more positive than the one on the alkyl chan.

Two new canted antiferromagnetic systems: magnetic, theoretical, and crystallographic studies on trans-bis(2-iodopyridine)dihalocopper(ii)

The two complexes Cu(2ip)X₂ were prepared (where 2ip = 2-iodopyridine and X = Cl or Br), and their crystal structures were determined. The two complexes are isomorphous and form a magnetic chain based on the two-halide exchange pathway. The powder and single crystal magnetic susceptibility data were measured down to 1.8 K. The exchange is antiferromagnetic along the chain; the exchange is stronger in the bromide complex than in the corresponding chloride complex. In the ordered state, weak moments appear along some of the axes, indicative of spin-canting. The calculated spin densities and the mapped surface of spin density on total electron density were used to rationalize qualitatively the observed magnetic behavior. Low temperature structures are compared with the room temperature data; the C-IX-Cu and Cu-XX-Cu distances are shorter at low temperatures; in contrast, the covalent bonds of the organic ligand (2-iodopyridine) are longer (negative thermal expansion of the covalent bonds). The anomalous behavior is rationalized using charge transfer from Cu-X group to the anti-bonding orbital of the organic ligand. Quantum theory of atoms in molecules was used to analyze C-IX halogen bonding interactions.

Crystal engineering strategies towards halogen-bonded metal–organic multi-component solids: salts, cocrystals and salt cocrystals

This highlight presents an overview of the current advances in the preparation of halogen bonded metal–organic multi-component solids, including salts and cocrystals comprising neutral and ionic constituents.

A Novel Halogen Bond Acceptor: 1-(4-Pyridyl)-4-Thiopyridine (PTP) Zwitterion

Sulfur is a widely used halogen bond (XB) acceptor, but only a limited number of neutral XB acceptors with bifurcated sp3-S sites have been reported. In this work a new bidentate XB acceptor, 1-(4-pyridyl)-4-thiopyridine (PTP), which combines sp3-S and sp2-N acceptor sites, is introduced. Three halogen bonded cocrystals were obtained by using 1,4-diiodobenzene (DIB), 1,4-diiodotetrafluorobenzene (DIFB), and iodopentafluorobenzene (IPFB) as XB donors and PTP as acceptor. The structures of the cocrystals showed some XB selectivity between the S and N donors in PTP. However, the limited contribution of XB to the overall molecular packing in these three cocrystals and the results from DSC measurements clearly point out the synergetic influence and interplay of all noncovalent interactions in crystal packing of these compounds.

Intermolecular Interaction in Methylene Halide (CH2F2, CH2Cl2, CH2Br2 and CH2I2) Dimers

The intermolecular interaction in difluoromethane, dichloromethane, dibromomethane, and diiodomethane dimers has been investigated using high level quantum chemical methods. The potential energy curve of intermolecular interaction along the C⋯C bond distance obtained using the coupled-cluster theory with singles, doubles, and perturbative triples excitations CCSD(T) were compared with values given by the same method, but applying the local (LCCSD(T)) and the explicitly correlated (CCSD(T)-F12) approximations. The accuracy of other theoretical methods-Hartree-Fock (HF), second order Møller-Plesset perturbation (MP2), and dispersion corrected DFT theory-were also presented. In the case of MP2 level, the canonical and the local-correlation cases combined with the density-fitting technique (DF-LMP2)theories were considered, while for the dispersion-corrected DFT, the empirically-corrected BLYP-D and the M06-2Xexchange-correlation functionals were applied. In all cases, the aug-cc-pVTZ basis set was used, and the results were corrected for the basis set superposition error (BSSE) using the counterpoise method. For each molecular system, several dimer geometries were found, and their mutual orientations were compared with the nearest neighbor orientations obtained in recent neutron scattering studies. The nature of the intermolecular interaction energy was discussed.

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.

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.

Weak hydrogen and halogen bonding in 4-[(2,2-difluoroethoxy)methyl]pyridinium iodide and 4-[(3-chloro-2,2,3,3-tetrafluoropropoxy)methyl]pyridinium iodide

To enable a comparison between a C-H...X hydrogen bond and a halogen bond, the structures of two fluorous-substituted pyridinium iodide salts have been determined. 4-[(2,2-Difluoroethoxy)methyl]pyridinium iodide, C₈H₁₀F₂NO⁺·I^-, (1), has a -CH₂OCH₂CF₂H substituent at the para position of the pyridinium ring and 4-[(3-chloro-2,2,3,3-tetrafluoropropoxy)methyl]pyridinium iodide, C₉H₉ClF₄NO⁺·I^-, (2), has a -CH₂OCH₂CF₂CF₂Cl substituent at the para position of the pyridinium ring. In salt (1), the iodide anion is involved in one N-H...I and three C-H...I hydrogen bonds, which, together with C-H...F hydrogen bonds, link the cations and anions into a three-dimensional network. For salt (2), the iodide anion is involved in one N-H...I hydrogen bond, two C-H...I hydrogen bonds and one C-Cl...I halogen bond; additional C-H...F and C-F...F interactions link the cations and anions into a three-dimensional arrangement.

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.

2-Amino-5-iodopyridinium bromide hemihydrate and 2-amino-5-iodopyridinium chloride monohydrate

The hydrobromide and hydrochloride salts of 2-amino-5-iodopyridine were prepared from aqueous solutions. The hydrobromide salt, C5H6IN2+·Br−·0.5H2O, crystallizes as a hemihydrate, and exhibits hydrogen bonding and π-stacking which stabilize the crystal structure. The hydrochloride salt, C5H6IN2+·Cl−·H2O·0.375HCl, crystallized as the hydrate and exhibits similar hydrogen bonding and π-stacking in the lattice. The most interesting feature of the hydrochloride salt is the presence of an additional fractional HCl molecule which introduces disorder in the location of the water molecule. The additional proton from the fractional HCl molecule is accounted for by the presence of a partial hydronium ion on one of the water sites.

Ab initio study of weakly bound halogen complexes: RX⋯PH3

Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).

The subtle balance of weak supramolecular interactions: The hierarchy of halogen and hydrogen bonds in haloanilinium and halopyridinium salts

THE SERIES OF HALOANILINIUM AND HALOPYRIDINIUM SALTS: 4-IPhNH₃Cl (1), 4-IPhNH₃Br (5), 4-IPhNH₃H₂PO₄ (6), 4-ClPhNH₃H₂PO₄ (8), 3-IPyBnCl (9), 3-IPyHCl (10) and 3-IPyH-5NIPA (3-iodopyridinium 5-nitroisophthalate, 13), where hydrogen or/and halogen bonding represents the most relevant non-covalent interactions, has been prepared and characterized by single crystal X-ray diffraction. This series was further complemented by extracting some relevant crystal structures: 4-BrPhNH₃Cl (2, CCDC ref. code TAWRAL), 4-ClPhNH₃Cl (3, CURGOL), 4-FPhNH₃Cl (4, ANLCLA), 4-BrPhNH₃H₂PO₄, (7, UGISEI), 3-BrPyHCl, (11, CIHBAX) and 3-ClPyHCl, (12, VOQMUJ) from Cambridge Structural Database for sake of comparison. Based on the X-ray data it was possible to highlight the balance between non-covalent forces acting in these systems, where the relative strength of the halogen bonding C-X...A⁻ (X = I, Br or Cl) and the ratio between the halogen and hydrogen bonds [C-X...A⁻ : D-H...A⁻] varied across the series.

Bis(2,6-diamino-3,5-dibromo-pyridinium) hexa-bromidostannate(IV)

The asymmetric unit of the title compound, (C₅H₆Br₂N₃)₂[SnBr₆], contains one cation and one half-anion in which the Sn atom is located on a crystallographic centre of inversion and is in a quasi-octa­hedral geometry. The crystal structure is assembled via hydrogen-bonding inter­actions of two kinds, N(pyridine/amine)—H⋯Br—Sn, along with C—Br⋯Br—Sn interactions [3.4925 (19) Å]. The cations are involved in π–π stacking, which adds an extra supra­molecularity as it presents a strong case of offset-face-to-face motifs [centroid–centroid distance = 3.577 (3) Å]. The inter­molecular hydrogen bonds, short Br⋯Br inter­actions and π–π stacking result in the formation of a three-dimensional supra­molecular architecture.

2,5-Dibromopyridine

In the title compound, C₅H₃Br₂N, C—H⋯N hydrogen-bonding inter­actions and Br⋯Br inter­actions [3.9418 (3) and 3.8986 (3) Å] connect the mol­ecules into planar sheets stacked perpendicular to the b axis. In addition, pyrid­yl–pyridyl inter­sheet π–π stacking inter­actions [centroid–centroid distance = 4.12 (1) Å] result in a three-dimensional network.

Bis(2-bromo-pyridinium) hexa-chlorido-stannate(IV)

The asymmetric unit of the title compound, (C₅H₅BrN)₂[SnCl₆], contains one cation and one half-anion. The [SnCl₆]²⁻ anion is located on an inversion center and forms a quasi-regular octa­hedral arrangement. Hydrogen-bonding inter­actions of two kinds, viz. N—H⋯Cl—Sn and C—H⋯Cl—Sn, along with Cl⋯Br inter­actions [3.4393 (15) Å], connect the ions in the crystal structure into two-dimensional supra­molecular arrays. These supra­molecular arrays are arranged in layers approximately parallel to (110) built up from anions inter­acting with six symmetry-related surrounding cations.