Br Hydrogen Bonds Research Articles

Synthesis, crystallographic analysis and Hirshfeld surface analysis of 4-bromo-2-{[2-(5-bromo-2-nitro-phen-yl)hydrazin-1-yl-idene]meth-yl}-5-fluoro-phenol.

The title compound, C13H8Br2FN3O3, is nearly planar with a dihedral angle of 10.6 (4)° between the two benzene rings. Intra-molecular N-H⋯O and O-H⋯N hydrogen bonds occur. In the crystal, the mol-ecules are linked by weak C-H⋯O and C-H⋯Br hydrogen bonds. The roles of the inter-molecular inter-actions in the crystal packing were clarified using Hirshfeld surface analysis.

Supramolecular Organoplatinum(IV) Chemistry: Dimers and Polymers Formed by Intermolecular Hydrogen Bonding.

The reaction of [PtMe2(6-dppd)], 1, where 6-dppd is a 1,4-bis(2-pyridyl)pyridazine derivative, with bromoalkanes BrCH2R, having a hydrogen-bond donor group R, gave the corresponding chiral products of trans oxidative addition [PtBrMe2(CH2R)(6-dppd)], 2a, R = CO2H; 3, R = 4-C6H4CO2H; 4, R = 4-C6H4CH2CO2H; 7, R = 2-C6H4CH2OH; 8, R = 4-C6H4B(OH)2; 9, R = 3-C6H4B(OH)2; and 10, R = 2-C6H4B(OH)2. Complex 2a was formed in equilibrium with two isomers formed by cis oxidative addition, while the reaction of 1 with BrCH2CH2CO2H gave mostly [PtBrMe(6-dppd)], 6. The supramolecular chemistry was studied by structure determination of six of the platinum(IV) complexes, with emphasis on the preference of the hydrogen bond acceptor (O, pyridyl N, or Br atom), formation of monomer, dimer, or polymer, and self-recognition or self-discrimination in self-assembly. Complex 7 formed a monomer with the OH···N hydrogen bond, and complexes 2a and 10 formed racemic dimers by complementary hydrogen bonding with self-discrimination between CO2H or B(OH)2 groups, respectively. Complexes 3, 4, and 9 formed polymers by intermolecular hydrogen bonding with self-recognition, with 4 containing OH···N and 3 and 9 containing OH···Br hydrogen bonds. It is concluded that there is no clear preference for the hydrogen bond acceptor group, and that the observed product depends also on the orientation of the hydrogen bond donor group.

Controllable Density of Atomic Bromine in a Two-Dimensional Hydrogen Bond Network

Using atomic bromine (Br) and pentacene molecules, we successfully constructed and characterized a large-scale Br atom-mediated two-dimensional (2D) organic network on a Ag(111) surface by combining molecular beam epitaxy with scanning tunneling microscopy. The Br atoms form −C–H···Br hydrogen bonds with pentacene molecules in the network, and the number of Br atoms among pentacene molecules can be tuned from one to five by increasing the pressure or exposure time of hydrogen bromide (HBr) gas. In addition, all of the Br atoms of five 2D organic networks fill themselves in the position of maximum number of hydrogen bonds.

Cis-Bromidobis(ethylene-1,2-diamine)(2-methylpropan-1-amine)cobalt(III) dibromide

In the title compound, [CoBr(C2H8N2)2(C4H11N)]Br2, the cobalt(III) ion has a distorted octahedral coordination environment and is ligated by three N atoms and a bromine ion in the equatorial plane, and by two N atoms occupying the axial positions. In the crystal, the complex cation and the two Br− counter-anions are linked by N—H...Br hydrogen bonds, forming a supramolecular framework.

Unraveling the structural and molecular properties of 34-residue levans with various branching degrees by replica exchange molecular dynamics simulations.

Levan has various potential applications in the pharmaceutical and food industries, such as cholesterol-lowering agents and prebiotics, due to its beneficial properties, which depend on its length and branching degree. A previous study also found that the branching degree of levan affected anti-tumor activities against SNU-1 and HepG2 tumor cell lines. Despite its promising potential, the properties of levans with different branching degrees are not well understood at the molecular level. In two models of the generalized Born implicit solvent (GBHCT and GBOBC1), we employed replica-exchange molecular dynamics simulations to explore conformational spaces of 34-residue levans (L34) with branching degrees of zero (LFO34B0), one (LFO34B1), three (LFO34B3) and five (LFO34B5), as well as to elucidate their structural and molecular properties. To ensure a fair comparison of the effects of branching degree on these properties, we focused on analyzing the properties of the central 21-residue of the main chains of all systems. Our results show that all major representative conformations tend to form helix-like structures with kinks, where two-kink helix-like structures have the highest population. As branching degree increases, the population of helix-like structures with zero or one kink tends to increase slightly. As the number of kinks in the structures with the same branching degree increases, the average values of the lengths and angles among centers of masses of three consecutive turns of residue i, i+3, and i+6 tended to decrease. Due to its highest occurring frequencies, the O6 (i)—H3O (i+1) hydrogen bond could be important for helix-like structure formation. Moreover, hydrogen bonds forming among the branching residue (br), branching position (bp) and other residues of L34B1, L34B3 and L34B5 were identified. The O1(bp)—H3O(br), O1(br)—H3O(br) and O5(br)—H1O(br) hydrogen bonds were found in the first-, second- and third-highest occurrence frequencies, respectively. Our study provides novel and important insights into conformational spaces and the structural and molecular properties of 34-residue levans with various branching degrees, which tend to form helix-like structures with kinks.

Five benzoic acid derivatives: Crystallographic study using X-ray powder diffraction, electronic structure and molecular electrostatic potential calculation

Crystal structures of five ortho-, meta-, and para-substituted benzoic acid derivatives, 2-fluoro-4-hydroxymethyl benzoic acid (1), 4-chloro-3 nitrobenzoic acid (2), 5-bromo-2-methyl benzoic acid (3), 4-bromo-2 nitrobenzoic acid (4) and 4-chloro-2-iodobenzoic acid (5) have been determined using X-ray powder diffraction. DFT optimized molecular geometries of 1–5 agree closely with those obtained from the crystallographic study. The nature of intermolecular interactions in 1–5 has been analyzed through Hirshfeld surfaces and 2D fingerprint plots, and compared with that of unsubstituted benzoic acid compound. The crystal packing of 1–5 exhibits an interplay of intermolecular OH⋯O, CH⋯O and CH … X (X = F, Cl, Br) hydrogen bonds, and C-X (X = Cl, Br, I)⋯O halogen bonds, which assemble molecules into a supramolecular framework. Hydrogen- and halogen-bond based interactions in 1–5 have been complemented by the molecular electrostatic potential (MEP) surface calculation. The electronic structure of compounds (1–5) reveals that the estimated band gap in 4, with the nitro and bromo groups at the ortho and para positions with respect to the COOH group, is the lowest (2.72 eV) among the molecules; the corresponding value in the unsubstituted benzoic is 3.95 eV.

Crystal structure and Hirshfeld surface analysis of (E)-3-[(2,3-di-chloro-benzyl-idene)amino]-5-phenyl-thia-zolidin-2-iminium bromide.

In the cation of the title salt, C16H14Cl2N3S+·Br-, the central thia-zolidine ring adopts an envelope conformation. The phenyl ring is disordered over two sites with a refined occupancy ratio of 0.541 (9):0.459 (9). In the crystal, C-H⋯Br and N-H⋯Br hydrogen bonds link the components into a three-dimensional network with the cations and anions stacked along the b-axis direction. Weak C-H⋯π inter-actions, which only involve the minor disorder component of the ring, also contribute to the mol-ecular packing. In addition, there are also inversion-related Cl⋯Cl halogen bonds and C-Cl⋯π (ring) contacts. A Hirshfeld surface analysis was conducted to verify the contributions of the different inter-molecular inter-actions.

Cis-Bromido(n-butylamine-κN)bis(ethene-1,2-diamine-κ2 N,N′)cobalt(III) dibromide

In the title compound, [CoBr(C2H8N2)2(C4H11N)]Br2, the cobalt(III) ion has a distorted octahedral coordination environment and is surrounded by four N atoms in the equatorial plane made up of three N atoms from the two ethylenediamine ligands and the remaining N from the n-butyl substituent, with the other N atom from the ethylenediamine ligand and the Br atom occupying the axial positions. In the crystal, the complex cation and the two counter-anions are linked via N—H...Br and C—H...Br hydrogen bonds, forming a three-dimensional network. The crystal studied was refined as a two-component inversion twin.

Crystal structure and Hirshfeld surface analysis of a pyridiniminium bromide salt: 1-[2-(adamantan-1-yl)-2-oxoeth-yl]pyridin-4-iminium bromide.

In the cation of the title salt, C17H23N2O+·Br-, the adamantyl moiety and the pyridiniminium ring are inclined to the ketone bridge by torsion angles of -78.1 (2) (C-C-C=O) and 58.3 (2)° (C-C-N-C), respectively, and the ketone bridge has a C-C-C-N torsion angle of 174.80 (15)°. In the crystal, the cations are connected into chains parallel to the c axis by C-H⋯O hydrogen bonds. The chains are further linked into layers parallel to the bc plane by N-H⋯Br and C-H⋯Br hydrogen bonds, C-H⋯π inter-actions and π-π stacking inter-actions [centroid-to-centroid distance = 3.5657 (11) Å]. A Hirshfeld surface analysis, which comprises the dnorm surface, electrostatic potential map and two-dimensional fingerprint plots, was carried out to verify the contribution of the various inter-molecular inter-actions.

Cis-Bromidobis(1,2-diaminoethane-κ2 N,N′)(ethylamine-κN)cobalt(III) dibromide

In the title complex, [CoBr(C2H7N)(C2H8N2)2]Br2, the CoIII centre has a distorted octahedral coordination environment, and is surrounded by four N atoms in the equatorial plane, with an additional N atom and the Br atom occupying the axial positions. The complex is isostructural with the Cl compound for which the X-ray structure has also been reported [Anbalagan, Mahalakshmi & Ganeshraja (2011). J. Mol. Struct. 1005, 45–52]. In the crystal, the complex cation and the two counter-anions are linked via N—H...Br hydrogen bonds, forming a three-dimensional network.

Cis-Bromidobis(ethylene-1,2-diamine)(methylamine)cobalt(III) dibromide

In the title compound, [CoBr(CH5N)(C2H8N2)2]Br2, the cobalt(III) ion has a distorted octahedral coordination environment and is ligated by four N atoms in the equatorial plane, with an additional N atom and a Br− ion occupying the axial positions. In the crystal, the complex cation and the two counter-anions are linked via N—H...Br and C—H...Br hydrogen bonds, forming a supramolecular framework.

Bis(4-methoxybenzylammonium) tetrabromidocadmate(II)

The asymmetric unit of the organic–inorganic hybrid salt, (C8H12NO)2[CdBr4], consists of two 4-methoxybenzylammonium cations and one [CdBr4]2− anion. The cations and anions are connected by a complex series of N—H...Br and C—H...Br hydrogen bonds. No π–π stacking interactions occur between the benzene rings but two C—H...π interactions are observed.

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5-fluorocytosine.

Three new metal(II)-cytosine (Cy)/5-fluorocytosine (5FC) complexes, namely bis(4-amino-1,2-dihydropyrimidin-2-one-κN3)diiodidocadmium(II) or bis(cytosine)diiodidocadmium(II), [CdI2(C4H5N3O)2], (I), bis(4-amino-1,2-dihydropyrimidin-2-one-κN3)bis(nitrato-κ2O,O')cadmium(II) or bis(cytosine)bis(nitrato)cadmium(II), [Cd(NO3)2(C4H5N3O)2], (II), and (6-amino-5-fluoro-1,2-dihydropyrimidin-2-one-κN3)aquadibromidozinc(II)-6-amino-5-fluoro-1,2-dihydropyrimidin-2-one (1/1) or (6-amino-5-fluorocytosine)aquadibromidozinc(II)-4-amino-5-fluorocytosine (1/1), [ZnBr2(C4H5FN3O)(H2O)]·C4H5FN3O, (III), have been synthesized and characterized by single-crystal X-ray diffraction. In complex (I), the CdII ion is coordinated to two iodide ions and the endocyclic N atoms of the two cytosine molecules, leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr2(C4H5N3O)2] [Muthiah et al. (2001). Acta Cryst. E57, m558-m560]. In compound (II), each of the two cytosine molecules coordinates to the CdII ion in a bidentate chelating mode via the endocyclic N atom and the O atom. Each of the two nitrate ions also coordinates in a bidentate chelating mode, forming a bicapped distorted octahedral geometry around cadmium. The typical interligand N-H...O hydrogen bond involving two cytosine molecules is also present. In compound (III), one zinc-coordinated 5FC ligand is cocrystallized with another uncoordinated 5FC molecule. The ZnII atom coordinates to the N(1) atom (systematic numbering) of 5FC, displacing the proton to the N(3) position. This N(3)-H tautomer of 5FC mimics N(3)-protonated cytosine in forming a base pair (via three hydrogen bonds) with 5FC in the lattice, generating two fused R22(8) motifs. The distorted tetrahedral geometry around zinc is completed by two bromide ions and a water molecule. The coordinated and nonccordinated 5FCs are stacked over one another along the a-axis direction, forming the rungs of a ladder motif, whereas Zn-Br bonds and N-H...Br hydrogen bonds form the rails of the ladder. The coordinated water molecules bridge the two types of 5FC molecules via O-H...O hydrogen bonds. The cytosine molecules are coordinated directly to the metal ion in each of the complexes and are hydrogen bonded to the bromide, iodide or nitrate ions. In compound (III), the uncoordinated 5FC molecule pairs with the coordinated 5FC ligand through three hydrogen bonds. The crystal structures are further stabilized by N-H...O, N-H...N, O-H...O, N-H...I and N-H...Br hydrogen bonds, and stacking interactions.

Hydrogen bonding and fluorous weak interactions in the non-isomorphous {4,4'-bis[(2,2,3,3-tetrafluoropropoxy)methyl]-2,2'-bipyridine-κ2N,N'}dibromidopalladium and -platinum complexes.

The polyfluorinated title compounds, [MBr2(C18H16F8N2O2)] or [4,4'-(HCF2CF2CH2OCH2)2-2,2'-bpy]MBr2, (1) (M = Pd and bpy is bipyridine) and (2) (M = Pt), have -CH(α)2OCH(β)2CF2CF2H side chains with methylene H-atom donors at the α and β sites, and methine H-atom donors at the terminal sites, in addition to aromatic H-atom donors. In contrast to the original expectation of isomorphous structures, (1) crystallizes in the space group C2/c and (2) in P21/n, with similar unit-cell volumes and Z = 4. The asymmetric unit of (1) is one half of the molecule, which resides on a crystallographic twofold axis. Both (1) and (2) display stacking of the molecules, indicating a planar (bpy)MBr2 skeleton in each case. The structure of (1) exhibits columns with C-H(β)...Br hydrogen bonds between consecutive layers which conforms to a static (β,β) linkage between layers. In the molecular plane, (1) shows double C-H(α)...Br hydrogen bonds self-repeating along the b axis, the planar molecules being connected into infinite belts. Compound (2) has no crystallographic symmetry and forms π-dimer pairs as supermolecules, which then stack parallel to the a axis. The π-dimer-pair supermolecules exhibit (Pt-)Br...Br(-Pt) contacts [3.6937 (7) Å] to neighbouring π-dimer pairs crosslinking the columns. The structure of (2) reveals many C-H...F(-C) interactions between F atoms and aromatic C-H groups, in addition to those between F atoms and methylene C-H groups.

Catena-Poly[bis(4-methylbenzylammonium) [[dibromidocadmate(II)]-di-μ-bromido

The asymmetric unit of the centrosymmetric organic–inorganic hybrid salt, {(C8H12N)2[CdBr4]} n , comprises of one 4-methylbenzylammonium cation and one half of a disordered [CdBr4]2− anion that is completed by application of mirror symmetry. The resulting CdBr6 octahedra share edges to form 2 ∞[CdBr4/2Br2/2]2− layers parallel to the ac plane. Cations and anions are connected by N—H...Br and C—H...Br hydrogen bonds. No π–π stacking interactions are observed between the benzene rings, but C—H...π interactions towards them are found.

The Role of Host Molecules in the Crystalline Inclusion Compounds: Hexamethylenebis(trimethylammonium) dications as guest species

Two new inclusion compounds, namely (CH3)3N+(CH2)6N+(CH3)3·2Br–·2(NH2)2CS (1), and (CH3)3N+(CH2)6N+(CH3)3·2(p-HOC6H4COO–)·2(NH2)2CS (2), have been prepared and characterized by X-ray crystallography. In the crystal structure of 1, tetramers comprising pairs of thiourea molecules and bromide anions by N—H⋅⋅⋅S and N—H⋅⋅⋅Br hydrogen bonds are joined with the methyl groups of hexamethylenebis(trimethylammonium) dications to generate a layered 3D structure. Compound 2 exhibits a channel-type host lattice with channels of rectangular cross-section running parallel to the a axis, which are generated by N—H⋅⋅⋅O and N—H⋅⋅⋅S hydrogen bonds between p-hydroxybenzoic anions and thiourea molecules, and the hexamethylenebis(trimethylammonium) dications are arranged separately in each channel. By comparing these two inclusion compounds, the structural difference of the two inclusion compounds is due to the addition of p-hydroxybenzoic acid as the host molecule in the 2. The weak hydrogen bonds have an important role in lattice construction.

Crystal packing, high-temperature phase transition, second-order nonlinear optical and biological activities in a hybrid material: [(S)[sbnd]C7H16N2][CuBr4

The directed synthesis of non-centrosymmetric copper (II) bromo-complex has been achieved through the use of homochiral organic molecule. Reaction containing (S)-(−)-3-aminoquinuclidine, CuBr2, HBr and H2O were subjected to mild hydrothermal conditions, resulting in the growth of single crystals of [(S)C7H16N2][CuBr4]. The compound crystallizes in the non polar space group P212121(No. 19), which exhibits the enantiomorphic crystal class 222 (D2). In the crystal structure, the tetrabromocuprate(II) anion is connected to three organic cations through NH…Br hydrogen bonds to form cation-anion-cation molecular units, which are held together by means of offset face-to-face interactions to give one-dimensional chains. DSC measurements indicated that the compound [(S)C7H16N2][CuBr4] underwent a reversible phase transition at 80 °C. [(S)C7H16N2][CuBr4] is more than 1.2 times as efficient as KDP in second harmonic generation; making it a potentially attractive material for non-linear optical applications. The synthesized product was also screened for in vitro antioxidant and antimicrobial activities, while showing favorable antioxidant activities against DPPH as well as the discoloration of β-carotene.

Bis(4-methylbenzylammonium) tetrabromidozincate

The structure of the non-centrosymmetric organic–inorganic hybrid material, (C8H12N)2[ZnBr4], consists of two 4-methylbenzylammonium cations and one [ZnBr4]2− anion connected by N—H...Br and C—H...Br hydrogen bonds. The ZnII cation has a slightly distorted tetrahedral coordination environment. No π–π stacking interactions between the phenylene rings but C—H...π interactions towards them are observed. The structure was refined as a two-component inversion twin.

Crystal structure and Hirshfeld surface analysis of a pyridiniminium bromide salt: 1-[2-([1,1'-biphen-yl]-4-yl)-2-oxoeth-yl]-3-methyl-1,4-di-hydro-pyridin-4-iminium bromide.

In the cation of the title salt, C20H19N2O+·Br-, the phenyl rings are inclined to one another by 38.38 (8)°, whereas the central phenyl ring and the pyridiniminium ring are almost perpendicular with a dihedral angle of 87.37 (9)°. The N+=C cationic double bond was verified by the shortened bond length of 1.337 (2) Å. In the crystal, the Br- anion is linked to the cation by an N-H⋯Br hydrogen bond. C-H⋯O hydrogen bonds link adjacent pyridiniminium cations into inversion dimers with an R22(18) graph-set motif. These dimers are stacked in a phen-yl-phenyl T-shaped geometry through C-H⋯π inter-actions. A Hirshfeld surface analysis was conducted to verify the contributions of the different inter-molecular inter-actions.

Crystal structures of a manganese(I) and a rhenium(I) complex of a bi-pyridine ligand with a non-coordinating benzoic acid moiety.

The structures of two facially coordinated Group VII metal complexes are reported, namely: fac-bromido-[2-(2,2'-bipyridin-6-yl)benzoic acid-κ2N,N']tricarbonyl-manganese(I) tetra-hydro-furan monosolvate, [MnBr(C17H12N2O2)(CO)3]·C4H8O, I, and fac-[2-(2,2'-bipyridin-6-yl)benzoic acid-κ2N,N']tricarbonyl-chlorido-rhenium(I) tetra-hydro-furan monosolvate, [ReCl(C17H12N2O2)(CO)3]·C4H8O, II. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ion, and a 2-(2,2'-bipyridin-6-yl)benzoic acid ligand, in a distorted octa-hedral geometry. In manganese complex I, the tetra-hydro-furan (THF) solvent mol-ecule could not be refined due to disorder. The benzoic acid fragment is also disordered over two positions, such that the carb-oxy-lic acid group is either positioned near to the bromide ligand or to the axial carbonyl ligand. In the crystal of I, the complex mol-ecules are linked by a pair of C-H⋯Br hydrogen bonds, forming inversion dimers that stack up the a-axis direction. In the rhenium complex II, there is hydrogen bonding between the benzoic acid moiety and a disordered co-crystallized THF mol-ecule. In the crystal, the mol-ecules are linked by C-H⋯Cl hydrogen bonds, forming layers parallel to (100) separated by layers of THF solvent mol-ecules.