Br Halogen Bonds Research Articles

Networks of non-planar molecules with halogen bonds studied using scanning tunneling microscopy on Au (111)

Molecular networks connected by halogen bonds have been actively studied due to their ubiquity in biological systems and complementary role to hydrogen bonds. Although networks of planar molecules with halogen ligands have been studied using scanning tunneling microscopy (STM), those of non-planar molecules have not. Here, we report on the network structures of non-planar molecules containing Br-ligands, tetrabromo-spirobifluorene on Au (111), studied using STM. One and two-dimensional networks were observed and their intermolecular interactions were investigated. In two-dimensional networks, a molecule forms 3.5 Br⋯Br halogen bonds and 2 Br⋯H hydrogen bonds, as supported by our density functional theory calculation results. Our study demonstrates that intermolecular structures of non-planar molecules with halogen bonds can be probed on surfaces using STM.

High-Pressure Crystallizations of meta-Dichlorobenzene and Dibromobenzene and Their Solid Solutions

Similar halobenzene derivatives 1,3-dichlorobenzene (m-C6H4Br2) and 1,3-dibromobenzene (m-C6H4Cl2) form crystals remarkably similar in the unit-cell dimensions, in two symmetry-independent molecules (Z′ = 2) and in their atomic positions along plane yz. However, the atomic x-coordinates are different and the space-group symmetry of m-C6H4Cl2 is P21/c and that of m-C6H4Br2 is P212121. These symmetries are not changed by isochoric recrystallizations at least to 2.7 and 1.6 GPa, respectively. The one-dimensional structural differences originate from one additional Br···Br halogen bond in otherwise very similar halogen···halogen bonds patterns. Of the m-C6H4Br2/m-C6H4Cl2 1:1 mixture a solid solution (symmetry of space-group P21/c) is formed at 0.5 GPa. However, an addition of methanol to the mixture counteracts the formation of the solid solution, and at 0.45 GPa the pristine m-C6H4Cl2 crystals precipitate. For the 1:1:6 mixture with methanol, a pressure of 1.0 GPa is required for the formation of solid solut...

Structure-Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand.

The shock-induced serine protease HtrA1 is a potential regulator of human placenta development during pregnancy. The protein contains a functional PDZ domain that has been solved in complex with a phage display-derived heptapeptide: Asp-6 Ser-5 Arg-4 Ile-3 Trp-2 Trp-1 Val0 . In this study, a rationally designed halogen bond was introduced to the domain-peptide complex based on its NMR structure in solution. We computationally compared the stabilization energies and hindrance effects due to the presence of different halogens X (X = F, Cl, Br, or I), using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, and found that the Br atom could considerably promote the peptide binding free energy (ΔΔG = -5.2 kcal/mol). Fluorescence assays confirmed that the peptide affinity to the HtrA1 PDZ domain was improved by approximately sevenfold upon bromination. Structural analysis identified a geometrically perfect halogen bond between the Br atom of the peptide Trp-1 residue and the carbonyl O atom of the HtrA1 Ile385 residue, with a bond length and an interaction energy of d = 3.20 Å and ΔE = -3.7 kcal/mol, respectively.

Crystal and mol-ecular structure of meso-2,6-di-bromo-hepta-nedioic acid (meso-2,6-di-bromo-pimelic acid).

The mol-ecular structure of the title compound, C7H10Br2O4, confirms the meso (2R,6S) configuration. In the crystal, mol-ecules are linked by pairs of O-H⋯O=C hydrogen bonds between their terminal carboxyl groups in an R 2 (2)(8) motif, forming extended chains that propagate parallel to the c axis. Adjacent chains are linked by C=O⋯Br halogen bonds.

NXY halogen bonds. Comparison with NHY H-bonds and CXY halogen bonds.

Quantum calculations examine how the NHY H-bond compares to the equivalent NXY halogen bond, as well as to comparable CH/CX donors. Succinimide and saccharin, and their corresponding halogen-substituted derivatives, are chosen as the prototype NH/NX donors, paired with a wide range of electron donor molecules. The NHY H-bond is weakened if the bridging H is replaced by Cl, and strengthened by I; a Br halogen bond is roughly comparable to a H-bond. The lone pairs of the partner molecule are stronger electron donors than are π-systems. Whereas Coulombic forces represent the largest fraction of the attractive force in the H-bonds, induction energy is magnified in the halogen bonds, surpassing electrostatics in several cases. Mutation of NH/NX to CH/CX weakens the binding energy to roughly half its original value, while also lengthening the intermolecular distances by 0.3-0.8 Å.

Influence of methoxy-substituents on the strength of Br … Br type II halogen bonds in bromobenzoic acid

4-bromo-3,5-di(methoxy)benzoic acid (I) crystallizes in the monoclinic C2/c space group, a = 22.3405 (6) Å, b = 4.85142 (14) Å, c = 18.1583 (5) Å, β = 93.086 (2)°. The crystal structure shows head-to-head dimeric units linked via type II Br … Br interactions as well as Br … π and weak H-bonding interactions. The whole structure exhibits features similar to those of the parent 4-bromobenzoic acid (II), most notably the overall geometrical features involved in the Br … Br type II interactions. Both structures display comparable C–Br … Br angles (θ1 = 98.3 and 91.6° and θ2 = 163.0 and 163.5° for (I) and (II) respectively), but the Br … Br distance is significantly shorter in (I) (3.58 Å) than in (II) (3.81 Å). QM computations provide the magnitude of the intermolecular interactions present in both (I) and (II), and allow disclosing the individual covalent and electrostatic contributions to the Br⋯Br halogen bond in terms of interaction energies, electrostatic potentials, and a molecular orbital (MO) analysis.

Halogen-bonded adduct of 1,2-dibromo-1,1,2,2-tetrafluoroethane and 1,4-diazabicyclo[2.2.2]octane.

Halogen bonding is an intermolecular interaction capable of being used to direct extended structures. Typical halogen-bonding systems involve a noncovalent interaction between a Lewis base, such as an amine, as an acceptor and a halogen atom of a halofluorocarbon as a donor. Vapour-phase diffusion of 1,4-diazabicyclo[2.2.2]octane (DABCO) with 1,2-dibromotetrafluoroethane results in crystals of the 1:1 adduct, C2Br2F4·C6H12N2, which crystallizes as an infinite one-dimensional polymeric structure linked by intermolecular N...Br halogen bonds [2.829 (3) Å], which are 0.57 Å shorter than the sum of the van der Waals radii.

Halogen Bonding Synthon Modularity in Coordination Compounds

In this Communication, the modulation of halogen bonding synthons in the crystal structure of [HgBr2(L3,4-diCl)] from [HgBr2(L3-Cl)] and [HgBr2(L4-Cl)], as single components, where L is a N-(chlorinatedphenyl)-2-pyrazinecarboxamide ligand, has been investigated. Reviewing the crystal packing reveals that Cl···N and Cl···Br halogen bonds stood as a remembrance of the crystal structures of single components in the packing of [HgBr2(L3,4-diCl)].

Tunable Interaction Strength and Nature of the S···Br Halogen Bonds in [(Thione)Br2] Systems

The strength and nature of the S···Br and Br···Br interactions were systematically tuned by altering the electron donor properties of the thione group. Three new halogen-bonded compounds, [(N-methylbenzothiazole-2-thione)Br2]·0.5CH2Cl2 (1), [(2(3H)-benzothiazolethione)Br2] (2), and [(2-benzimidazolethione)Br]·[Br3] (3), were synthesized and studied structurally by using X-ray crystallography and computationally by using charge density analysis based on QTAIM calculations. Analysis of the interaction strength indicated a formation of surprisingly strong S···Br halogen bonds in 1 (−104 kJ mol–1, and RBrS = 0.64) and 2 (−116 kJ mol–1, and RBrS = 0.63) with a substantial covalent contribution. The strong electron donor character of the thione ligand in 3 induced a heterolytic cleavage of the dibromine molecule and a change in the S···Br interaction nature to form a covalent bond with a high interaction energy (−147 kJ mol–1, and RBrS = 0.60).

Three mixed-ligand coordination networks modulated by flexible N-donor ligands: syntheses, topological structures, and temperature-sensitive luminescence properties

Three new mixed-ligand metal–organic coordination networks based on tetrabromoterephthalic acid and different bis-imidazole or bis-triazole ligands, [Zn2(bmib)(tbtpa)2·2H2O]n (1), [Cd(ditb)(tbtpa)(H2O)2·2H2O]n (2), and [Zn(ditp)(tbtpa)]n (3) (bmib = 1,4-bis(2-methyl-1H-imidazol-1-yl)butane, ditb = 1,4-di(1H-1,2,4-triazol-1-yl)butane, ditp = 1,3-di(1H-1,2,4-triazol-1-yl)propane, H2tbtpa = tetrabromoterephthalic acid), have been synthesized under solvothermal conditions and structurally characterized by single-crystal X-ray diffraction analyses, infrared spectroscopy (IR), elemental analyses, powder X-ray diffraction (PXRD) and thermogravimetric analyses (TGA). Single-crystal X-ray diffraction analysis reveals that 1 features a 4-fold class IIIa interpenetrated dia framework strengthened by Br⋯Br halogen bonds. Complex 2 possesses an infinite 2D layer structure with a 44-sql topology, and the 2D sheets were further packed into the 3D supramolecular framework in an –ABAB– fashion which is reinforced by hydrogen bonds and Br⋯Br halogen bonds. Complex 3 is a 2D 63-hcb network incorporating [Zn2(tbtpa)2] cyclic subunits, and the 2D layers were further extended to a 3D supramolecular framework incorporating π⋯π interactions and Br⋯Br and Br⋯O halogen bonds. In 1–3, all flexible N-donor ligands and dicarboxylates are 2-connected linkers, but networks with diverse topologies are formed, which indicates the coordination preferential geometries of the central metal ion and that the coordination conformations and modes of the ligands have important influences on the resultant structures. Furthermore, there is no solid-state photoluminescence observed for 1–3 at 298 K, and only 2 and 3 are emissive when cooled to liquid nitrogen temperature. The nanosecond range of lifetimes of 2 and 3 in the solid state at 77 K reveals that their emission is fluorescent in nature.

Structure-melting relations in isomeric dibromobenzenes.

1,4-Dibromobenzene melts at a considerably higher temperature than the 1,2- and 1,3-isomers. This melting-point difference is consistent with the molecular symmetry, as described by Carnelley's rule, and with the frequency of Br...Br halogen bonds. The lowest melting point of 1,3-dibromobenzene correlates with its two symmetry-independent molecules, indicating their inability to pack closely. Single crystals of 1,2- and 1,3-dibromobenzene have been grown under isochoric conditions in a diamond-anvil cell and at isobaric conditions in a glass capillary. Their structures have been determined in situ by X-ray diffraction. At 295 K 1,2-dibromobenzene crystallizes at 0.2 GPa as orthorhombic, space group Pbca, Z' = 1, and 1,3-dibromobenzene at 0.3 GPa as orthorhombic, space group P212121, Z' = 2. The same crystal phases are formed at ambient pressure by freezing these liquids below 256.15 and 248.45 K, respectively. The third isomer, 1,4-dibromobenzene, is a solid at room temperature and crystallizes as monoclinic, space group P21/a. Striking relations between the structures and melting points of the corresponding dibromobenzene and dichlorobenzene isomers have been discussed.

Tetragonal porous networks made by rod-like molecules on Au(1 1 1) with halogen bonds

Abstract Supramolecular structures of two rod-like molecules whose both ends are terminated with Br-ligands were studied using scanning tunneling microscopy (STM). Rectangular and square porous networks were observed in 4,4″-dibromo-p-terphenyl (DBTP) and 4,4″-dibromo-p-quaterphenyl (DBQP) molecules on Au(1 1 1) with the void areas of 3.5 and 5.6 nm2, respectively. Both networks had chiral quadrupole nodes that could be explained with four Br⋯Br halogen bonds and four Br⋯H hydrogen bonds. The reversible transformations of network structures were observed in consecutive STM images, possibly mediated by a liquid phase surrounding the networks. The molecules also formed close-packing ladder-like networks with triple nodes that could be explained with four Br⋯H bonds. Our study shows that Br-ligands play key roles in forming molecular networks for both rod-like molecules.

2-{2,4,6-Tris(bromo-meth-yl)-3,5-bis-[(1,3-dioxoisoindolin-2-yl)meth-yl]benz-yl}iso-indoline-1,3-dione toluene monosolvate.

In the title compound, C36H24Br3N3O6·C7H8, the toluene solvent mol­ecule is associated with the receptor mol­ecule via C—H⋯π bonding. The planes of the phthalimido groups are inclined at 77.0 (1), 63.0 (1) and 77.8 (1)° with respect to the benzene ring. The mol­ecular conformation is stabilized by C—H⋯O and C—H⋯Br hydrogen bonds. The crystal structure features non-classical hydrogen bonds of the C—H⋯N, C—H⋯O and C—H⋯Br type, leading to a three-dimensional cross-linking of molecules. The pattern of non-covalent inter­molecular bonding is completed by O⋯Br halogen bonds [3.306 (3) Å], which link the receptor mol­ecules into infinite strands extending along the a-axis direction.

Supramolecular self-assembled network formation containing N···Br halogen bonds in physisorbed overlayers.

The formation of a halogen bonded self-assembled co-crystal physisorbed monolayer containing N···Br interactions is reported for the first time. The co-crystal monolayer is identified experimentally by synchrotron X-ray diffraction and the structure determined. Density functional theory (DFT) calculations are also employed to assess the magnitudes of the different interactions in the layer. Significantly, compared to other halogen bonds in physisorbed monolayers we have reported recently, the N···Br bond here is found to be non-linear. It is proposed that the increasing importance of the lateral hydrogen bond interactions, relative to the halogen bond strength, leads to the bending of the halogen bonds.

Zigzag Arrangement of Bromo-substituted 2,5-Di(1,3-dithiol-2-ylidene)-1,3-dithiolane-4-thione Derivatives and Their Physical Properties

Abstract Four bromine-substituted 2,5-di(1,3-dithiol-2-ylidene)-1,3-dithiolane-4-thione derivatives, 1a, 1b, 1c, and 1d, were synthesized, and their physical properties were investigated. These compounds were obtained from the reaction of a corresponding zinc complex of 2-(1,3-dithiol-2-ylidene)-1,3-dithiole-4,5-bis(thiolate) derivatives and corresponding tetrafluoroborate salts of 1,3-dithiol-2-ylium derivatives. Recrystallization of 1a from carbon disulfide and n-hexane gave single crystals suitable for X-ray structure analysis. In the crystal, 1a molecules are one-dimensionally stacked and one molecule is rotated relative to the neighboring molecules by an angle of 92° about its longer molecular axis. On the (010) plane, the molecules were arranged in a zigzag manner along the a axis. This interesting feature is accomplished by intermolecular S···Br halogen bonds.

Bis[2,4-dibromo-6-(N-{4-[(E)-1-(benzyloxyimino)ethyl]phenyl}carboximidoyl)phenolato]copper(II)

In the title complex, [Cu(C22H17Br2N2O2)2], the CuII ion is four-coordinated in a trans-CuN2O2 square-planar geometry by two phenolate O and two imino N atoms from two deprotonated N,O-bidentate ligands. In the crystal, the packing of the mol­ecules is controlled by C—H⋯π and π–π inter­actions [centroid–centroid distances = 3.568 (3), 3.678 (2), 3.717 (3) and 3.799 (2) Å] and weak Br⋯Br halogen bonds [3.508 (4) Å], linking the mol­ecules into an infinite three-dimensional supra­molecular network.

Halogen bond induced phosphorescence of capped γ-amino acid in the solid state

The Boc and N,N'-dicyclohexylurea capped γ-amino acid upon monobromination showed phosphorescence in the solid state. The compound exhibited different photoluminescence intensity and lifetimes in crystals obtained from ethyl acetate and methanol. X-ray crystallography revealed that the intermolecular C=O…Br halogen bond directs the heavy atom effect to produce the phosphorescence.

Molecular Multistate Systems Formed in Two-Dimensional Porous Networks on Ag(111)

Host–guest interactions in porous supramolecular structures have been studied on surfaces using scanning tunneling microscopy, with anticipation of biochemical and sensor applications, but limited to cases of van der Waals interactions and hydrogen bonds. Here, we studied the intermolecular structures of 4,4″-dibromo-p-terphenyl molecules self-caged in porous supramolecular structures with halogen bonds on Ag(111). The caged molecules hopped among six different configurations at higher than 50 K, showing a propeller-like pattern. At 30 K, they stayed at one of six states that were stabilized with Br···Br halogen bonds and Br···H hydrogen bonds with energy gains of 225, 197, and 163 meV, as revealed by our density functional theory calculations. The self-caged structure provides a model system to simulate multistate supramolecular memories.

A theoretical investigation of the characteristics of hydrogen/halogen bonding interactions in dibromo-nitroaniline

In this work, computations of density functional theory (DFT) were carried out to investigate the nature of interactions in solid 2,6-dibromo-4-nitroaniline (DBNA). This system was selected to mimic the hydrogen/halogen bonding found within crystal structures as well as within biological molecules. DFT (M06-2X/6-311++G**) calculations indicated that the binding energies for different of interactions lie in the range between -1.66 and -9.77 kcal mol(-1). The quantum theory of atoms in molecules (QTAIM) was applied to provide more insight into the nature of these interactions. Symmetry-adapted perturbation theory (SAPT) analysis indicated that stability of the Br···Br halogen bonds is predicted to be attributable mainly to dispersion, while electrostatic forces, which have been widely believed to be responsible for these types of interactions, play a smaller role. Our results indicate that, for those nuclei participating in hydrogen/halogen bonding interactions, nuclear quadrupole resonance parameters exhibit considerable changes on going from the isolated molecule model to crystalline DBNA.

The cosolvent-dependent assembly of a family of three blue fluorescent lead(ii)-coordination polymers with 5-amino-2,4,6-tribromoisophthalic acid

By modulating the synthetic strategy based on changing the cosolvent in the synthesis, the aqueous medium assembly of lead(II) with H2ATBIP in the presence of different cosolvents, N,N-dimethylacetamide (DMA), methanol (CH3OH) or N,N-dimethylformamide (DMF), leads to a family of three lead(II) coordination polymers: [Pb(ATBIP)(H2O)2]·2H2O (1), [Pb(ATBIP)(H2O)(CH3OH)]·H2O (2) and [Pb(ATBIP)(H2O)(DMF)]·H2O (3) [H2ATBIP = 5-amino-2,4,6-tribromoisophthalic acid]. Complex 1 exhibits an interesting double chain structure with [Pb2(OH2)2] as the secondary building unit (SBU), which further assembles into a 3D supramolecular framework through the C–Br⋯Br halogen bonds and hydrogen bonds. Furthermore, the discrete water octamer (H2O)8 is found. The cosolvents, DMF and CH3OH, which simultaneously act as the coordinated small molecules, have significant influences on the formation of different crystalline architectures. Complex 2 features a 2D network constructed by the 21 helical carboxylate-bridged Pb(II) chains [Pb2(COO)2]n (SBUs) linked by the ligand ATBIP2−. The intralayer C–Br⋯Br halogen bond is found and a 3D supramolecular framework is formed by the interlayer hydrogen bonds. Complex 3 crystallizes in the chiral space group P41212 and possesses a 2D (4,4)-homochiral layer built from the centrosymmetrical SBU [Pb2(COO)2] bridged by the ligand ATBIP2−. The interlayer hydrogen bonds further extend the chiral layers in 3 into a 3D supramolecular homochiral framework. The coordination modes of the ligand ATBIP2− are greatly dependent on the cosolvents. Complex 3 loses crystallinity in the air and forms the material [Pb(ATBIP)(DMF)] (3A). Thermal stability and solid state fluorescent properties of 1, 2 and 3A have been studied. The second harmonic generation (SHG) property of 3A is also studied.