Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds IUCr Journals CHEMISTRYjCRYSTENG Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds

International audienceThe likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogenÁ Á Áhalogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, CÁ Á ÁC interactions in parallel-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-HÁ Á ÁCl and O-HÁ Á ÁO are the preferred interactions in compounds containing both O and Cl

Crystal structure, Hirshfeld surface analysis, and physicochemical studies of a new Cu(II) complex with 2-amino-4-methylpyrimidine

International audienceThe chemical preparation, crystal structure, magnetic study and spectroscopic characterization of the new Cu(II) complex with the monodentate ligand 2-amino-4-methylpyrimidine [Cu2(CH3COO)4(C5N3H7)2] are reported. The copper atoms are surrounded by one nitrogen atom from one 2-amino-4-methylpyrimidine ligand and four oxygen atoms of CH3COO − groups yielding to a penta-coordination of the metal ion. In the structural arrangement, the amino group and the pyrimidine nitrogen atom of neighboring molecules are linked together through a pair of N-H…N hydrogen bonds forming a 1-D corrugated chain running along the [111] direction wherein the complex molecules are located parallel to the (a, c) plane at z = ½. Intermolecular interactions were investigated by Hirshfeld surfaces and contact enrichment tools. Mulliken charge distribution, molecular electrostatic potential (MEP) maps and HOMO and LUMO energy gaps have been computed. The vibrational absorption bands were identified by infrared spectroscopy. Magnetic properties were also studied to characterize the complex

Crystal structure of 2-amino-5-methylsulfanyl-1,3,4-thiadiazol-3-ium chloride monohydrate

International audienceThe title salt, C3H6N3S2 (+)·Cl(-)·H2O, crystallized with two organic cations, two chloride anions and two water mol-ecules in the asymmetric unit. The methyl C atoms deviate from their respective bound ring planes by 0.081 and 0.002 Å. In the crystal, the components are connected via N-H⋯O, N-H⋯Cl and O-H⋯Cl hydrogen bonds, forming sheets lying parallel to (100). The sheets are linked into bilayers by O-H⋯Cl hydrogen bonds involving the chloride ions and water mol-ecules. Within the bilayers there are π-π inter-actions [inter-centroid distances = 3.4654 (4) and 3.4789 (4) Å] involving inversion-related cations

Bis(2-amino-4-methyl-6-oxo-3,6-dihydropyrimidin-1-ium) sulfate monohydrate

In the title hydrated molecular salt, 2C5H8N3O+·SO42−·H2O, the components are linked by N—H...Os and Ow—H...Os (s = sulphate, w = water) hydrogen bonds, generating a layer by a+b+c and 2a−b translations. The cations are arranged nearly in parallel and show displaced π–π stacking centroid–centroid distance = 4.661 (2) Å between adjacent layers

o -Phenylenediaminium chloride nitrate

International audienceIn the title mol­ecular salt, C6H10N2 2+·NO3 −·Cl−, the complete cation is generated by a crystallographic mirror plane. The complete nitrate ion is also generated by reflection, with the N atom and one O atom lying on the mirror plane; the chloride ion also lies on the reflection plane. In the crystal, the components are linked by N—H⋯Cl and N—H⋯(N,O) hydrogen bonds, forming (001) layers with the benzene rings projecting into the inter­layer regions. The layers are linked by weak C—H⋯O hydrogen bonds, generating a three-dimensional network

Poly[diaquatris(μ 6 -4,6-dioxo-1,4,5,6-tetrahydro-1,3,5-triazine-2-carboxylato)tripotassium]

International audienceThe asymmetric unit of the title compound, [K3(C4H2N3O4)3(H2O)2]n, contains two potassium cations (one in general position, one located on a twofold rotation axis), one and a half oxonate anions (the other half generated by twofold symmetry) and one water mol­ecule. As a result of the twofold symmetry, one H atom of the symmetric anion is statistically occupied. Both potassium cations are surrounded by eight oxygen atoms in the form of distorted polyhedra. Adjacent cations are inter­connected by oxygen bridges, generating layers parallel to (100). The aromatic ring system of the oxonate anions link these layers into a network structure. The crystal packing is stabilized by N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds, three of which are bifurcated. In addition, inter­molecular π–π stacking inter­actions exist between neighboring aromatic rings with a centroid–centroid distance of 3.241 (2) Å

Crystal and geometry-optimized structure, Hirshfeld surface analysis and spectroscopic studies of tetrachlorocuprate and nitrate salts of 1-(2-fluorophenyl)piperazine cations, (C10H15FN2)[CuCl4] (I) and (C10H14FN2)[NO3] (II)

Two new organic-inorganic hybrid materials, 1-(2-fluorophenyl)piperazine-1,4-diium tetrachlorocuprate, (C10H15FN2)[CuCl4] (I) and 1-(2-fluorophenyl)piperazin-4-ium nitrate, (C10H14FN2)[NO3] (II), have been synthesized by an acid/base reaction at room temperature in the presence of 1-(2-fluorophenyl)piperazine as an organic-structure directing agent and their structures were determined by single crystal X-ray diffraction. Compound (I), (C10H15FN2)[CuCl4], crystallizes in the monoclinic system and P21/c space group with a = 7.5253 (2), b = 20.6070 (7), c = 9.7281 (3) Ã\u85, β = 103.6730 (17)°, V = 1465.82 (8) Ã\u853with Z = 4. Full-matrix least-squares refinement converged at R = 0.037 and wR(F2) = 0.088. Compound (II), (C10H14FN2)[NO3], belongs to the monoclinic system, space group P21/c with the following parameters: a = 10.8034 (2), b = 7.5775 (1), c = 14.4670 (3) Ã\u85, β = 111.761 (2)°, V = 1099.91 (4) Ã\u853and Z = 4. The structure was refined to R = 0.044, wR(F2) = 0.136. In the structures of (I) and (II), the anionic and cationic entities are interconnected by means of set of hydrogen bonding contacts forming three-dimensional networks. Intermolecular interactions were investigated by Hirshfeld surfaces and the contacts of the four different chloride atoms were notably compared. The results of the optimized molecular structure are presented and compared with the experimental one. The Molecular Electrostatic Potential (MEP) maps and the HOMO and LUMO energy gap of both compounds were computed. The vibrational absorption bands were identified by infrared spectroscopy. Theory (DFT) calculations of normal mode frequencies are compared with experimental ones