C‒H‒O Hydrogen Bonding in Crystals

Photochemical studies on bis-sulfide and -sulfone tethered polyenic derivatives

This study focusses on the [2 + 2]-photocycloaddition of a symmetric polyenic system tethered by an aryl bis-sulfide or sulfone platform.

Synthesis and crystal structure of bis(1-{[(quinolin-8-yl)imino]methyl}pyrene-κ2N,N')silver(I) tri-fluoro-methane-sulfonate

The title compound, [Ag(qPyr)2]CF3SO3 where qPyr = 1-(quinoline-2-yl-methyl-ene)amino-pyrene, C26H16N2, was synthesized from a reaction of silver tri-fluoro-methane-sulfonate and qPyr in di-chloro-methane-methanol mixed media. In this design, the qPyr ligand was chosen for its characteristic excitation and emission profiles, which could enable the tracking of the silver complex within biological targets. The AgI atom resides in a distorted tetra-hedral N4 coordination sphere. Analysis of the packing pattern revealed significant intra- and inter-molecular π-π stacking inter-actions between the [Ag(qPyr)2]+ cations. In addition, a weak C-H⋯O hydrogen bond consolidates the packing between cations and anions.

Proton transfer aiding phase transitions in oxalic acid dihydrate under pressure

Oxalic acid dihydrate, an important molecular solid in crystal chemistry, ecology and physiology, has been studied for nearly 100 years now. The most debated issues regarding its proton dynamics have arisen due to an unusually short hydrogen bond between the acid and water molecules. Using combined in situ spectroscopic studies and first-principles simulations at high pressures, we show that the structural modification associated with this hydrogen bond is much more significant than ever assumed. Initially, under pressure, proton migration takes place along this strong hydrogen bond at a very low pressure of 2 GPa. This results in the protonation of water with systematic formation of dianionic oxalate and hydronium ion motifs, thus reversing the hydrogen bond hierarchy in the high pressure phase II. The resulting hydrogen bond between a hydronium ion and a carboxylic group shows remarkable strengthening under pressure, even in the pure ionic phase III. The loss of cooperativity of hydrogen bonds leads to another phase transition at ∼ 9 GPa through reorientation of other hydrogen bonds. The high pressure phase IV is stabilized by a strong hydrogen bond between the dominant CO2 and H2O groups of oxalate and hydronium ions, respectively. These findings suggest that oxalate systems may provide useful insights into proton transfer reactions and assembly of simple molecules under extreme conditions.

Indenopyrans - synthesis and photoluminescence properties

New indeno[1,2-c]pyran-3-ones bearing different substituents at the pyran moiety were synthesized and their photophysical properties were investigated. In solution all compounds were found to be blue emitters and the trans isomers exhibited significantly higher fluorescence quantum yields (relative to 9,10-diphenylanthracene) as compared to the corresponding cis isomers. The solid-state fluorescence spectra revealed an important red shift of λ_max due to intermolecular interactions in the lattice, along with an emission-band broadening, as compared to the solution fluorescence spectra.

Investigations into the construction of the pentasubstituted ringCof Neosurugatoxin – a crystallographic study

The mol­ecular conformations of three highly substituted cyclo­penta­[c]furans appear to correlate strongly with different intra­molecular O—H⋯O and C—H⋯O inter­actions.

The crystal structures of three cyclo­penta­[c]furans with various substituents at the 4-, 5- and 6-positions of the ring system are reported, namely, (±)-(3aR,4S,5S,6aS)-4-methyl-5-phenyl­hexa­hydro-1H-cyclo­penta­[c]furan-4,5-diol, C₁₄H₁₈O₃, (I), (±)-(3aR,4S,5S,6aS)-4-benz­yloxy-4-methyl-5-phenyl­hexa­hydro-1H-cyclo­penta­[c]furan-5-ol, C₂₁H₂₄O₃, (II), and (±)-(1aR,1bS,4aR,5S,5aR)-5-benz­yloxy-5-methyl-5a-phenyl­hexa­hydro-2H-oxireno[2′,3′:3,4]cyclopenta­[1,2-c]furan, C₂₁H₂₂O₃, (III). The dominant inter­action in (I) and (II) is an O—H⋯O hydrogen bond across the bicyclic 5,5-ring system between the non-functionalized hy­droxy group and the tetra­hydro­furan O atom, which appears to influence the envelope conformations of the fused five-membered rings, whereas in (III), the rings have different conformations. A weak intra­molecular C—H⋯O inter­action appears to influence the degree of tilt of the phenyl ring attached to the 5-position and is different in (I) compared to (II) and (III).

Two new heterodinuclear Schiff base complexes: synthesis, crystal structure and thermal studies

Two new heterodinuclear Schiff base complexes, [Hg(L)NiCl2(DMF)2] 1, and [Zn(L)NiCl2(DMF)2] 2, where H2L = N,N'-bis(salicylidene)-1,3-diaminopropane and DMF = dimethylformamide have been synthesized and characterized using elemental analysis, IR spectroscopy, thermal analysis and X-ray diffraction. Structural studies on 1 and 2 reveal the presence of a heterodinuclear [Ni(II)Hg(II)] unit and [Zn(II)Ni(II)] in which the central metal ions are connected to each other by two phenolate oxygen bridges. For complex 1 the Ni(II) ion adopts an elongated octahedral geometry (NiN2O4) while the Hg(II) ion assumes a distorted tetrahedral arrangement (HgO2Cl2) whereas for complex 2 the Zn(II) ion adopts an elongated octahedral geometry (ZnN2O4) while the Ni(II) ion assumes a distorted tetrahedral arrangement (NiO2Cl2). There are intermolecular C-H···Cl-M interactions among the dinuclear complexes which are interconnected for 1 and 2. These intermolecular interactions result in the formation of a three dimensional structure for 1 and one dimensional zig-zag chains for 2.

Bis[bis-(2,2'-bi-pyridine-κ(2) N,N')(carbon-ato-κ(2) O,O')cobalt(III)] 2-{4-[(carboxyl-atometh-yl)carbamo-yl]benz-amido}-acetate hexa-hydrate

The complex cation of the title compound, [Co(CO3)(C10H8N2)2]2(C12H10N2O6)·6H2O, contains a Co(III) atom with a distorted octa-hedral coordination environment formed by four N atoms from two bidentate 2,2'-bi-pyridine ligands and one bidentate carbonate anion. The asymmetric unit is completed by one-half of the 2-({4-[(carboxyl-atometh-yl)carbamo-yl]phen-yl}formamido)-acetate dianion, which is located on a centre of inversion, and by three water mol-ecules. Two [Co(CO3)(C10H8N2)2](+) cations are connected through C-H⋯O contacts by the uncoordinating anions. The aromatic rings of the 2,2'-bi-pyridine ligands and di-acetate anions are involved in π-π stacking and C-H⋯π inter-actions. The centroid-centroid distances are in the range 3.4898 (4)-3.6384 (5) Å. The crystal structure is stabilized by further O-H⋯O and N-H⋯O hydrogen bonds, which give rise to a three-dimensional supra-molecular network.

Synthesis, crystal structure, spectra and quantum chemical study on 1-phenyl-3-(4-nitrophenyl)-5-(2-thienyl)-2-pyrazoline

1-Phenyl-3-(4-nitrophenyl)-5-(2-thienyl)-2-pyrazoline was synthesized and characterized by elemental analysis, IR and X-ray single crystal diffraction. UV-Vis spectra and fluorescence spectra were measured. Density functional theory calculations on the structure of the title compound were performed at the B3LYP/6-311G** level of theory. NPA atomic charge distributions indicate that, although the S atom in the thienyl ring loses coordination capacity, the title compound still may be used as a potential multi-dentate ligand to coordinate with metallic ions. The calculation of the second order optical nonlinearity was carried out. Natural bond orbital analyses indicate that the electronic absorption bands are mainly derived from the contribution of n→π* and π→π* transitions. Fluorescence spectra determination shows that the title compound is a potential orange-light emitting material.

A series of ditopic receptors for succinic acid binding

Three ditopic-abiotic receptors (R1, R2 and R3) have been designed and synthesised. The receptors have been applied for the recognition of dicarboxylic acids viz. malonic, succinic, glutaric and adipic acids. Among them, succinic acid shows the highest binding efficiency to all receptors. Recognition of succinic acid is very important due to its various adverse effects on human health upon prolonged exposure.

Highly fluorinated naphthalenes and bifurcated C–H⋯F–C hydrogen bonding

Bifurcated C–H⋯(F–C)₂ hydrogen bonds are most commonly close to being symmetric and are clearly evident in structures of two new fluoronaphthalenes.

Which intermolecular interactions have a significant influence on crystal packing?

The tendency for an interaction to occur in crystal structures is not a simple function of its calculated energyin vacuo.

Rotational spectroscopy of antipyretics: conformation, structure, and internal dynamics of phenazone

The conformational and structural preferences of phenazone (antipyrine), the prototype of non-opioid pyrazolone antipyretics, have been probed in a supersonic jet expansion using rotational spectroscopy. The conformational landscape of the two-ring assembly was first explored computationally, but only a single conformer was predicted, with the N-phenyl and N-methyl groups on opposite sides of the pyrazolone ring. Consistently, the microwave spectrum evidenced a rotational signature arising from a single molecular structure. The spectrum exhibited very complicated fine and hyperfine patterns (not resolvable with any other spectroscopic technique) originated by the simultaneous coupling of the methyl group internal rotation and the spins of the two (14)N nuclei with the overall rotation. The internal rotation tunnelling was ascribed to the C-CH3 group and the barrier height established experimentally (7.13(10) kJ mol(-1)). The internal rotation of the N-CH3 group has a lower limit of 9.4 kJ mol(-1). The structure of the molecule was determined from the rotational parameters, with the phenyl group elevated ca. 25° with respect to the average plane of the pyrazolic moiety and a phenyl torsion of ca. 52°. The origin of the conformational preferences is discussed in terms of the competition between intramolecular C-H···N and C-H···O weak hydrogen bonds.

N-[2-(Phenylsulfonyl)ethyl]benzylamine

The title compound, C₁₅H₁₇NO₂S, exhibits intra­molecular hydrogen bonding between the amine H atom and a sulfonyl O atom. The conformation of the mol­ecule is described by the four PhCH₂—NH—CH₂—CH₂—SO₂Ph torsion angles of 79.6 (2), −166.21 (14), −70.29 (17) and −58.93 (13)°.

2-Hy-droxy-3-meth-oxy-benzaldehyde (o-vanillin) revisited

The structure of ortho-vanillin, C₈H₈O₃, has been revisited with modern methods and at low temperature (100 K). The previous structure [Iwasaki et al. (1976 ▶). Acta Cryst. B32, 1264–1266] is confirmed, but geometric precision is improved by an order of magnitude. The C atom of the meth­oxy group lies close to the benzene ring plane, which is the most common geometry for –OMe groups lying ortho to –OH groups on an aromatic ring. The crystal structure displays one intra­molecular O—H⋯O and three weak inter­molecular C—H⋯O hydrogen bonds.

Synthesis and supramolecular networks of 5,6-dioxo-1,10-phenanthroline-2,9-dicarboxylic acid dihydrate and its first coordination compound cis-diaquachlorido(5,6-dioxo-1,10-phenanthroline-2,9-dicarboxylic acid-κ4O2,N,N',O9)manganese(II) chloride dihydrate

5,6-Dioxo-1,10-phenanthroline-2,9-dicarboxylic acid dihydrate (H(2)pdda·2H(2)O), C(14)H(6)N(2)O(6)·2H(2)O, was obtained by carbonylation of 1,10-phenanthroline-2,9-dicarboxylic acid. Its first coordination compound, [MnCl(C(14)H(6)N(2)O(6))(H(2)O)(2)]Cl·2H(2)O, in which the H(2)pdda ligand remains protonated, was synthesized in aqueous acetic acid. H(2)pdda chelates one water molecule via hydrogen bonds in H(2)pdda·2H(2)O, whereas in the coordination compound it chelates one heptacoordinate Mn(II) atom via coordination bonds. The N atoms in H(2)pdda·2H(2)O and the Cl atoms in the coordination compound are also involved in hydrogen bonds. Extensive hydrogen bonding results in supramolecular networks in both compounds.

The axial coordination in subphthalocyanines: Geometrical and electronic aspects

Theoretical calculations were performed for studying the electronic molecular structure of axial subphthalocyanine (SubPc) derivatives. The intermolecular SubPc interactions were also investigated at theoretical level using adequate models. These models represent the interaction of one Cl (OR)-SubPc with the surrounding molecules through the Cl atom as well as the interaction of the Cl -SubPc with an incoming diiminoisoindole group in the first steps of the open ring reaction. The SubPc complexes with more electronegative atoms than Cl heteroatoms in apical positions are more pyramidal than Cl -SubPc. The B–X and B–Np are the most sensitive macrocycle positions with respect to the axial substitutions in SubPcs. The B–X bond has an elevated polarity and seems to correlate with the chemical reactivity of these compounds. The theoretical calculations of the near-frontier orbitals reveal an outstanding energetic and structural homogeneity along the studied series which is in correspondence with the fact that the axial ligand has only a small influence on the position of the maximum bands in UV-vis spectra as well as in the first half-wave potentials for oxidative processes. The study of the intermolecular interactions give information about their influence on the molecular structure of the axial complexes of the SubPcs. The characterization of the interaction of one Cl -SubPc with a pyrrol containing group may be useful in the understanding of the mechanism of the ring expansion reactions. In general, the present results indicate that the apical position may be a critical reactive center both for redox and axial substitution processes.

Dichlorido{N-[2-(diphenyl-phosphan-yl)benzyl-idene]-2-(thio-phen-2-yl)ethan-amine-κP,N}platinum(II) dichloro-methane hemisolvate

The crystal structure of the title compound, [PtCl₂(C₂₅H₂₂NPS)]·0.5CH₂Cl₂, was determined to establish the coordination properties of the (phosphan­yl)benzyl­idene–methanamine ligand to platinum. In the unit cell two mol­ecules of cis-[PtCl₂(C₂₅H₂₂NPS)] are accompanied by a dichloro­methane solvent mol­ecule. The square-planar Pt²⁺ coordination sphere is slightly distorted with the bidentate ligand coordinated via the P and the amine N atoms, and the Cl atoms located cis at the two remaining coordination sites. Parts of the thiophene ring and the solvate molecule were modeled as disordered with occupancy ratios of 0.55 (2):0.45 (2) and 0.302 (10):0.198 (10), respectively. Weak C—H⋯Cl inter­actions stabilize the crystal packing.

Preparation and spectroscopic properties of the (cyanato-N) and (oxalato) iron(III) “picket fence” porphyrins: Structure of the (cyanato-N)(α,α,α,α-tetrakis(o-pivalamidophenyl)porphinato)iron(III) complex

The reaction of the iron(III) aqua triflato picket fence porphyrin starting material with NaOCN and K 2 C 2 O 4 salts, solubilized by the crown ether 18- C -6 in organic solvents, yields respectively the iron(III) porphyrin species [ Fe III( TpivPP )( NCO )] and [ Fe III( TpivPP )( ox )]−. These compounds have been characterized by UV-vis, IR, and 1 H NMR spectroscopies. Proton NMR data for the isolated products are in accordance with high-spin ( S = 5/2) ferric porphyrin derivatives. The X-ray molecular structure of the (cyanato-N)(α,α,α,α-tertakis(o-pivalamidophenyl)porphinato)iron(III), has been determined. This structure, which is the first one reported of an iron-cyanato species, confirms the spin-state of the cyanato derivative. The iron atom is pentacoordinated by the four nitrogen atoms of the pyrrole rings and the nitrogen atom of the NCO − group. It lies at 0.540(1) Å out of the porphinato plane and 0.486(1) Å out of the four nitrogen plane of the porphyrin ring. The Fe – N ( NCO ) bond length is 1.970(2) Å and the Fe - N - C ( NCO ) bond angle is 169.9(3)°.

1-(3,4-Dimeth-oxy-phen-yl)propan-1-one

The title compound, C(11)H(14)O(3), was isolated from the stems of Trigonostemon xyphophylloides, which belongs to Trigonostemon genus of Euphorbiaceae. The plants in this genus were used in folk medicine, such as for the treatment of diseases caused by viruses and fungi. The limited investigation of the chemistry of this plant prompted an examination of constituents of its twigs, from which the title compound was isolated. The mol-ecule is approximately planar with an r.m.s. deviation of 0.1237Å. In the crystal, inter-molecular C-H⋯O hydrogen bonds connect the mol-ecules into a two-dimensional network structure with an R(2) (2)(12) graph-set motif.

Synthesis, characterization, crystal structure and DFT studies on 3-(1H-benzo[d][1,2,3]triazol-1-yl)-1-oxo-1-m-tolylpropan-2-yl-nicotinate

3-(1H-Benzo[d][1,2,3]triazol-1-yl)-1-oxo-1-m-tolylpropan-2-yl-nicotinate (BOTN) has been synthesized and characterized by elemental analysis, IR, UV-vis and fluorescence spectroscopy. Its crystal structure has also been determined by X-ray single crystal diffraction. For BOTN, density functional theory (DFT) calculations of the structure and vibrational frequencies have been performed at B3LYP/6-311G** level. The comparisons between the experimental vibrational frequencies and the predicted data show that B3LYP/6-311G** method can simulate the IR of BOTN on the whole. Based on the vibration analysis, thermodynamic properties of BOTN have been calculated. The correlative equations between the thermodynamic properties and the temperatures have also been listed. The experimental UV-vis spectra present two peaks and theoretical UV-vis spectra obtained by TD-DFT method exhibit three peaks. The comparison between them suggests that the B3LYP/6-311G** method can only approximately simulate the UV-vis spectra of BOTN. The fluorescence determination reveals two emission bands at 423 and 489 nm, respectively.