Hydrogen bonding in 4‐nitrobenzene‐1,2‐diamine and two hydrohalide salts

The structures of 4‐nitrobenzene‐1,2‐diamine [C₆H₇N₃O₂, (I)], 2‐amino‐5‐nitroanilinium chloride [C₆H₈N₃O₂⁺·Cl⁻, (II)] and 2‐amino‐5‐nitroanilinium bromide monohydrate [C₆H₈N₃O₂⁺·Br⁻·H₂O, (III)] are reported and their hydrogen‐bonded structures described. The amine group para to the nitro group in (I) adopts an approximately planar geometry, whereas the meta amine group is decidedly pyramidal. In the hydrogen halide salts (II) and (III), the amine group meta to the nitro group is protonated. Compound (I) displays a pleated‐sheet hydrogen‐bonded two‐dimensional structure with R₂²(14) and R₄⁴(20) rings. The sheets are joined by additional hydrogen bonds, resulting in a three‐dimensional extended structure. Hydrohalide salt (II) has two formula units in the asymmetric unit that are related by a pseudo‐inversion center. The dominant hydrogen‐bonding interactions involve the chloride ion and result in R₄²(8) rings linked to form a ladder‐chain structure. The chains are joined by N—H...Cl and N—H...O hydrogen bonds to form sheets parallel to (010). In hydrated hydrohalide salt (III), bromide ions are hydrogen bonded to amine and ammonium groups to form R₄²(8) rings. The water behaves as a double donor/single acceptor and, along with the bromide anions, forms hydrogen bonds involving the nitro, amine, and ammonium groups. The result is sheets parallel to (001) composed of alternating R₅⁵(15) and R₆⁴(24) rings. Ammonium N—H...Br interactions join the sheets to form a three‐dimensional extended structure. Energy‐minimized structures obtained using DFT and MP2 calculations are consistent with the solid‐state structures. Consistent with (II) and (III), calculations show that protonation of the amine group meta to the nitro group results in a structure that is about 1.5 kJ mol⁻¹ more stable than that obtained by protonation of the para‐amine group. DFT calculations on single molecules and hydrogen‐bonded pairs of molecules based on structural results obtained for (I) and for 3‐nitrobenzene‐1,2‐diamine, (IV) [Betz & Gerber (2011). Acta Cryst. E 67 , o1359] were used to estimate the strength of the N—H...O(nitro) interactions for three observed motifs. The hydrogen‐bonding interaction between the pairs of molecules examined was found to correspond to 20–30 kJ mol⁻¹.     

Hydrogen bonding and π–π interactions in the cocrystal salt [Fe(bpe)2(H2O)4](TCEP)2·2(bpe) [bpe is trans‐1,2‐bis(pyridin‐4‐yl)ethene and TCEP is 1,1,3,3‐tetracyano‐2‐ethoxypropenide]

The cocrystal salt tetraaquabis[trans‐1,2‐bis(pyridin‐4‐yl)ethene‐κN]iron(II) bis(1,1,3,3‐tetracyano‐2‐ethoxypropenide)–trans‐1,2‐bis(pyridin‐4‐yl)ethene (1/2), [Fe(C₁₂H₁₀N₂)₂(H₂O)₄](C₉H₅N₄O)₂·2C₁₂H₁₀N₂, is a rare example of a mononuclear Fe^II compound with trans‐1,2‐bis(pyridin‐4‐yl)ethane (bpe) ligands. The complex cation resides on a crystallographically imposed inversion center and exhibits a tetragonally distorted octahedral coordination geometry. Both the symmetry‐independent bpe ligand and the cocrystallized bpe molecule are essentially planar. The 1,1,3,3‐tetracyano‐2‐ethoxypropenide counter‐ion is nonplanar and the bond lengths are consistant with significant electron delocalization. The extended structure exhibits an extensive O—H…N hydrogen‐bonding network with layers of complex cations joined by the cocrystallized bpe. Both the coordinated and the cocrystallized bpe are involved in π–π interactions. Hirshfeld and fingerprint plots reveal the important intermolecular interactions. Density functional theory was used to estimate the strengths of the hydrogen‐bonding and π–π interactions, and suggest that the O—H…N hydrogen bonds enhance the strength of the π‐interactions by increasing the polarization of the pyridine rings.     

Theoretical study of molecular and electronic structure of 2‐Se‐(2‐methyl‐2‐propenyl)‐1‐benzoic acid

A theoretical study of 2‐Se‐(2‐methyl‐2‐propenyl)‐1‐benzoic acid was carried out to investigate the molecular and electronic structure of this molecule, using the B3LYP density functional theory (DFT) method with the 6‐311+G** basis set. The optimized geometry of the molecule was obtained for the ortho, meta, and para isomers of the complex. In addition, the theoretical vibrational spectrum is presented, and thermal corrections in the limit of 100–1,000 K are discussed using the Shomate thermodynamic equations. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Three cocrystals and a cocrystal salt of pyrimidin‐2‐amine and glutaric acid

Four new cocrystals of pyrimidin‐2‐amine and propane‐1,3‐dicarboxylic (glutaric) acid were crystallized from three different solvents (acetonitrile, methanol and a 50:50 wt% mixture of methanol and chloroform) and their crystal structures determined. Two of the cocrystals, namely pyrimidin‐2‐amine–glutaric acid (1/1), C₄H₅N₃·C₆H₈O₄, (I) and (II), are polymorphs. The glutaric acid molecule in (I) has a linear conformation, whereas it is twisted in (II). The pyrimidin‐2‐amine–glutaric acid (2/1) cocrystal, 2C₄H₅N₃·C₆H₈O₄, (III), contains glutaric acid in its linear form. Cocrystal–salt bis(2‐aminopyrimidinium) glutarate–glutaric acid (1/2), 2C₄H₆N₃⁺·C₆H₆O₄²⁻·2C₆H₈O₄, (IV), was crystallized from the same solvent as cocrystal (II), supporting the idea of a cocrystal–salt continuum when both the neutral and ionic forms are present in appreciable concentrations in solution. The diversity of the packing motifs in (I)–(IV) is mainly caused by the conformational flexibility of glutaric acid, while the hydrogen‐bond patterns show certain similarities in all four structures.     

Energetic propane‐1,3‐diaminium and butane‐1,4‐diaminium salts of N,N′‐dinitroethylenediazanide: syntheses,crystal structures and thermal properties

The acidity of the amine H atoms and the consequent salt formation ability of ethylenedinitramine (EDNA) were analyzed in an attempt to improve the thermal stability of EDNA. Two short‐chain alkanediamine bases, namely propane‐1,3‐diamine and butane‐1,4‐diamine, were chosen for this purpose. The resulting salts, namely propane‐1,3‐diaminium N,N′‐dinitroethylenediazanide, C₃H₁₂N₂²⁺·C₂H₄N₄O₄^2?, and butane‐1,4‐diaminium N,N′‐dinitroethylenediazanide, C₄H₁₄N₂²⁺·C₂H₄N₄O₄^2?, crystallize in the orthorhombic space group Pbca and the monoclinic space group P2₁/n, respectively. The resulting salts display extensive hydrogen‐bonding networks because of the presence of ammonium and diazenide ions in the crystal lattice. This results in an enhanced thermal stability and raises the thermal decomposition temperatures to 202 and 221 °C compared to 180 °C for EDNA. The extensive hydrogen bonding present also plays a crucial role in lowering the sensitivity to impact of these energetic salts.     

Structural characterization,gelation ability,and energy‐framework analysis of two bis(long‐chain ester)‐substituted 4,4′‐biphenyl compounds

There are few examples of single‐crystal structure determinations of gelators, as gel formation requires that the dissolved gelator self‐assemble into a three‐dimensional network structure incorporating solvent via noncovalent interactions rather than self‐assembly followed by crystallization. In the solid‐state structures of the isostructural compounds 4,4′‐bis[5‐(methoxycarbonyl)pentyloxy]biphenyl (BBO6‐Me), C₂₆H₃₄O₆, and 4,4′‐bis[5‐(ethoxycarbonyl)pentyloxy]biphenyl (BBO6‐Et), C₂₈H₃₈O₆, the molecules sit on a crystallographically imposed center of symmetry, resulting in strictly coplanar phenyl rings. BBO6‐Me behaves as an organogelator in various alcohol solvents, whereas BBO6‐Et does not. The extended structure reveals bundles of molecules that form a columnar superstructure. Framework‐energy calculations reveal much stronger interaction energies within the columns (−52 to −78 kJ mol⁻¹) than between columns (−2 to −16 kJ mol⁻¹). The intracolumnar interactions are dominated by a dispersion component, whereas the intercolumnar interactions have a substantial electrostatic component.     

Structures of N—（2,3,4,6—Tetra—O—acetyl—β—D—glycosyl） thiocarbamic Benzoyl Hydrazine

The crystal structure of N-(2,3,4,6-tetra-O-acetyl-β-D-gly-cosyl)-thiocarbamic benzoyl hydrazine(C22H27N3O9S) was determined by X-ray diffracton method.The hexopyranosyl ring adopts a chair conformation.All the ring substituents are in the equatorial positions.The acetoxyl-methyl group is in synclinal conformation.The S atom is in synperiplanar conformation while the benzoyl hydrazine moiety is anti-periplanar.The thiocarbamic moiety is almost companar with the benzoyl hydrazine group.There are two intramolecular hydrogen bonds and one intermolecular hydrogen bond for each molecule in the crystal structure.The molecules form a network structure through intermolecular hydrogen bonds.     

Charge‐assisted hydrogen bonding in salts of 2‐amino‐1H‐benzimidazole with 3‐phenylpropynoic acid and oct‐2‐ynoic acid

The 100 K structures of two salts, namely 2‐amino‐1H‐benzimidazolium 3‐phenylpropynoate, C₇H₈N₃⁺·C₉H₅O₂⁻, (I), and 2‐amino‐1H‐benzimidazolium oct‐2‐ynoate, C₇H₈N₃⁺·C₈H₁₁O₂⁻, (II), both have monoclinic symmetry (space group P2₁/c) and display N—H...O hydrogen bonding. Both structures show packing with corrugated sheets of hydrogen‐bonded molecules lying parallel to the [001] direction. Two hydrogen‐bonded ring motifs can be identified and described with graph sets R²₂(8) and R⁴₄(16), respectively, in both (I) and (II). Computational chemistry calculations performed on both compounds show that the hydrogen‐bonded ion pairs are more energetically favourable in the crystal structure than their hydrogen–bonded neutral molecule counterparts.     

Theoretical Studies on the Hydrogen‐bonding and π‐Stacking Interactions in the m‐Nisoldipine Polymorphism Dimers

The intermolecular interactions in the dimers of m‐nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a‐dimer, O···H? N), dimer II (b‐dimer, O···H? N), dimer III (b‐dimer, π‐stacking‐c), and dimer IV (b‐dimer, π‐stacking‐p). The interaction energies of the four dimers are along the sequence of II>I>III>IV. The intermolecular distance of the interactions follows the order: I (O···H? N)II>III>IV, and the electrostatic character decreases along the sequence: I>II>III>IV.     

Supramolecular interactions in carboxylate and sulfonate salts of 2,6‐diamino‐4‐chloropyrimidinium

Two new salts, namely 2,6‐diamino‐4‐chloropyrimidinium 2‐carboxy‐3‐nitrobenzoate, C₄H₆ClN₄⁺·C₈H₄NO₆⁻, (I), and 2,6‐diamino‐4‐chloropyrimidinium p‐toluenesulfonate monohydrate, C₄H₆ClN₄⁺·C₇H₇O₃S⁻·H₂O, (II), have been synthesized and characterized by single‐crystal X‐ray diffraction. In both crystal structures, the N atom in the 1‐position of the pyrimidine ring is protonated. In salt (I), the protonated N atom and the amino group of the pyrimidinium cation interact with the carboxylate group of the anion through N—H…O hydrogen bonds to form a heterosynthon with an R ₂²(8) ring motif. In hydrated salt (II), the presence of the water molecule prevents the formation of the familiar R ₂²(8) ring motif. Instead, an expanded ring [i.e. R ₃²(8)] is formed involving the sulfonate group, the pyrimidinium cation and the water molecule. Both salts form a supramolecular homosynthon [R ₂²(8) ring motif] through N—H…N hydrogen bonds. The molecular structures are further stabilized by π–π stacking, and C=O…π, C—H…O and C—H…Cl interactions.     

Combined experimental and computational modeling studies on 4‐[(2‐hydroxy‐3‐methylbenzylidene) amino]‐1,5‐dimethyl‐2‐phenyl‐1,2‐dihydro‐3H‐pyrazol‐3‐one

The Schiff base compound, 4‐[(2‐hydroxy‐3‐methylbenzylidene)amino]‐1,5‐dimethyl‐2‐phenyl‐1,2‐dihydro‐3H‐pyrazol‐3‐one, has been synthesized and characterized by IR, UV–vis, and X‐ray single‐crystal determination. Molecular geometry from X‐ray experiment of the title compound in the ground state have been compared using the density functional method (B3LYP) with 6‐31G(d,p) basis set. Calculated results show that density functional theory (DFT) can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6‐31G(d,p) basis set by applying the Onsager and the polarizable continuum model (PCM). The results obtained with these methods reveal that the PCM method provided more stable structure than Onsager's method. By using TD‐DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD‐DFT method and the experimental one is determined. The predicted nonlinear optical properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential and NBO analysis were performed at B3LYP/6‐31G(d,p) level of theory. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Crystal structures,packing features,Hirshfeld surface analyses and DFT calculations of hydrogen‐bond energy of two homologous 8a‐aryl‐2,3,4,7,8,8a‐hexahydropyrrolo[1,2‐a]pyrimidin‐6(1H)‐ones

The crystal structures and packing features of two homologous Meyer's bicyclic lactams with fused pyrrolidone and medium‐sized perhydropyrimidine rings, namely, 8a‐phenyl‐2,3,4,7,8,8a‐hexahydropyrrolo[1,2‐a]pyrimidin‐6(1H)‐one, C₁₃H₁₆N₂O ( 1 ), and 8a‐(4‐methylphenyl)‐2,3,4,7,8,8a‐hexahydropyrrolo[1,2‐a]pyrimidin‐6(1H)‐one, C₁₄H₁₈N₂O ( 2 ), were elucidated, and Hirshfeld surface plots were calculated and drawn for visualization and a deeper analysis of the intermolecular noncovalent interactions. Molecules of 1 and 2 are weakly linked by intermolecular C=O…H—N hydrogen bonds into chains, which are in turn weakly linked by other C=O…H—C_ar interactions. The steric volume of the substituent significantly affects the crystal packing pattern.     

(Hexafluorosilicato‐κ2F,F′)bis(1,10‐phenanthroline‐κ2N,N′)zinc(II) methanol monosolvate

The title compound, [Zn(SiF₆)(C₁₂H₈N₂)₂]·CH₃OH, contains a neutral heteroleptic tris‐chelate Zn^II complex, viz. [Zn(SiF₆)(phen)₂] (phen is 1,10‐phenanthroline), exhibiting approximate molecular C₂ point‐group symmetry. The Zn^II cation adopts a severely distorted octahedral coordination. As far as can be ascertained, the title complex represents the first structurally characterized example of a Zn^II complex bearing a bidentate‐bound hexafluorosilicate ligand. A density functional theory study of the isolated [Zn(SiF₆)(phen)₂] complex was undertaken to reveal the influence of crystal packing on the molecular structure of the complex. In the crystal structure, the methanol solvent molecule forms a hydrogen bond to one F atom of the hexafluorosilicate ligand. The hydrogen‐bonded assemblies so formed are tightly packed in the crystal, as indicated by a high packing coefficient (74.1%).     

Weak hydrogen bonding and fluorous interactions in the chloride and bromide salts of 4‐[(2,2,3,3‐tetrafluoropropoxy)methyl]pyridinium

Neutralization of 4‐[(2,2,3,3‐tetrafluoropropoxy)methyl]pyridine with hydrohalo acids HX (X = Cl and Br) yielded the pyridinium salts 4‐[(2,2,3,3‐tetrafluoropropoxy)methyl]pyridinium chloride, C₉H₁₀F₄NO⁺·Cl⁻, (1), and 4‐[(2,2,3,3‐tetrafluoropropoxy)methyl]pyridinium bromide, C₉H₁₀F₄NO⁺·Br⁻, (2), both carrying a fluorous side chain at the para position of the pyridinium ring. Single‐crystal X‐ray diffraction techniques revealed that (1) and (2) are isomorphous. The halide anions accept four hydrogen bonds from N—H, ortho‐C—H and CF₂—H groups. Two cations and two anions form a centrosymmetric dimeric building block, utilizing complimentary N—H…X …H—Csp ³ connections. These dimers are further crosslinked, utilizing another complimentary Csp ²—H…X …H—Csp ² connection. The pyridinium rings are π‐stacked, forming columns running parallel to the a axis that make angles of ca 44–45° with the normal to the pyridinium plane. There are also supramolecular C—H…F—C interactions, namely bifurcated C—H…F and bifurcated C—F…H interactions; additionally, one type II C—F…F—C halogen bond has been observed.     

syn and anti conformations in 2‐hydroxy‐5‐[(E)‐(4‐nitrophenyl)diazenyl]benzoic acid and two related salts

The crystal structures of 2‐hydroxy‐5‐[(E)‐(4‐nitrophenyl)diazenyl]benzoic acid, C₁₃H₉N₃O₅, (I), ammonium 2‐hydroxy‐5‐[(E)‐phenyldiazenyl]benzoate, NH₄⁺·C₁₃H₉N₂O₃⁻, (II), and sodium 2‐hydroxy‐5‐[(E)‐(4‐nitrophenyl)diazenyl]benzoate trihydrate, Na⁺·C₁₃H₈N₃O₅⁻·3H₂O, (III), have been determined using single‐crystal X‐ray diffraction. In (I) and (III), the phenyldiazenyl and carboxylic acid/carboxylate groups are in an anti orientation with respect to each other, which is in accord with the results of density functional theory (DFT) calculations, whereas in (II), the anion adopts a syn conformation. In (I), molecules form slanted stacks along the [100] direction. In (II), anions form bilayers parallel to (010), the inner part of the bilayers being formed by the benzene rings, with the –OH and –COO⁻ substituents on the bilayer surface. The NH₄⁺ cations in (II) are located between the bilayers and are engaged in numerous N—H...O hydrogen bonds. In (III), anions form layers parallel to (001). Both Na⁺ cations have a distorted octahedral environment, with four octahedra edge‐shared by bridging water O atoms, forming [Na₄(H₂O)₁₂]⁴⁺ units.     

3,4‐Lutidinium salts with the diiodidoaurate(I) anion: structure of [(3,4‐lut)2H]+·[AuI2]− and of two polymorphs of [(3,4‐lut)2H+]2·[AuI2]−·I−

Reactions between potassium tetraiodidoaurate(III) and pyridine (py, C₅H₅N) or 3,4‐lutidine (3,4‐dimethylpyridine, 3,4‐lut, C₇H₉N) were tested as possible sources of azaaromatic complexes of gold(III) iodide, but all identifiable products contained gold(I). The previously known structure dipyridinegold(I) diiodidoaurate(I), [Au(py)₂]⁺·[AuI₂]⁻, ( 3 ) [Adams et al. (1982). Z. Anorg. Allg. Chem. 485 , 81–91], was redetermined at 100 K. The reactions with 3,4‐lutidine gave three different types of crystal in small quantities. 3,4‐Dimethylpyridine–3,4‐dimethylpyridinium diiodidoaurate(I), [(3,4‐lut)₂H]⁺·[AuI₂]⁻, ( 1 ), consists of an [AuI₂]⁻ anion on a general position and two [(3,4‐lut)₂H]⁺ cations across twofold axes. Bis(3,4‐dimethylpyridine–3,4‐dimethylpyridinium) diiodidoaurate(I) iodide, [(3,4‐lut)₂H⁺]₂·[AuI₂]⁻·I⁻, ( 2 ), crystallizes as two polymorphs, each forming pseudosymmetric inversion twins, in the space groups P2₁ and Pc (but resembling P2₁/m and P2/c), respectively. These are essentially identical layer structures differing only in their stacking patterns and thus might be regarded as polytypes.     

Hydrogen-hydrogen bonding: a stabilizing interaction in molecules and crystals

Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho-hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1-C4 carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane and indacene molecules corseted with tertiary-tetra-butyl groups. It is shown that each such H-H interaction, rather than denoting the presence of "nonbonded steric repulsions", makes a stabilizing contribution of up to 10 kcal mol(-1) to the energy of the molecule in which it occurs. The quantum theory of atoms in molecules-the physics of an open system-demonstrates that while the approach of two bonded hydrogen atoms to a separation less than the sum of their van der Waals radii does result in an increase in the repulsive contributions to their energies, these changes are dominated by an increase in the magnitude of the attractive interaction of the protons with the electron density distribution, and the net result is a stabilizing change in the energy. The surface virial that determines the contribution to the total energy decrease resulting from the formation of the H-H interatomic surface is shown to account for the resulting stability. It is pointed out that H-H interactions must be ubiquitous, their stabilization energies contributing to the sublimation energies of hydrocarbon molecular crystals, as well as solid hydrogen. H-H bonding is shown to be distinct from "dihydrogen bonding", a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.     

Crystal structures of the anhydrous and two solvated forms of methyl 4‐(4‐fluorophenyl)‐6‐methyl‐2‐oxo‐1,2,3,4‐tetrahydropyrimidine‐5‐carboxylate

Methyl 4‐(4‐fluorophenyl)‐6‐methyl‐2‐oxo‐1,2,3,4‐tetrahydropyrimidine‐5‐carboxylate, ( I ), was found to exhibit solvatomorphism. The compound was prepared using a classic Biginelli reaction under mild conditions, without using catalysts and in a solvent‐free environment. Single crystals of two solvatomorphs and one anhydrous form of ( I ) were obtained through various crystallization methods. The anhydrous form, C₁₃H₁₃FN₂O₃, was found to crystallize in the monoclinic space group C2/c. It showed one molecule in the asymmetric unit. The solvatomorph with included carbon tetrachloride, C₁₃H₁₃FN₂O₃·0.25CCl₄, was found to crystallize in the monoclinic space group P2/n. The asymmetric unit revealed two molecules of ( I ) and one disordered carbon tetrachloride solvent molecule that lies on a twofold axis. A solvatomorph including ethyl acetate, C₁₃H₁₃FN₂O₃·0.5C₄H₈O₂, was found to crystallize in the triclinic space group P with one molecule of ( I ) and one solvent molecule on an inversion centre in the asymmetric unit. The solvent molecules in the solvatomorphs were found to be disordered, with a unique case of crystallographically induced disorder in ( I ) crystallized with ethyl acetate. Hydrogen‐bonding interactions, for example, N—H…O=C, C—H…O=C, C—H…F and C—H…π, contribute to the crystal packing with the formation of a characteristic dimer through N—H…O=C interactions in all three forms. The solvatomorphs display additional interactions, such as C—F…N and C—Cl…π, which are responsible for their molecular arrangement. The thermal properties of the forms were analysed through differential scanning calorimetry (DSC), hot stage microscopy (HSM) and thermogravimetric analysis (TGA) experiments.