Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

A novel porous supramolecular complex constructed by the co-crystallization of melamine and sulfate via hydrogen bonds and aromatic π-π interaction

Co-crystallization of melamine(MA) and sulfate results in crystalline product [(C₃H₇N₆⁺)₂(SO₄²⁻)] · 2H₂O. The novel supramolecular complex has been characterized by elemental analysis, thermal analysis (TGA and DSC), nuclear magnetic resonance (NMR), and single crystal X-ray diffraction. X-ray crystallographic studies of the complex reveal that the title complex has a 3-D microporous structure which is linked by intense intermolecular hydrogen-bonding interactions (N–H······O, N–H······N, O–H······O) and aromatic π-π interaction, which stabilize the whole crystal framework. The TGA curve shows that the complex is stable up to 500 °C, above which its structure begins to collapse.     

Syntheses and crystal structures of cobalt(II) and zinc(II) complexes with 4′-methoxy-5,6,7-trihydroxyisoflavone-3′-sulfonate

Abstract Sodium 4′-methoxy-5,6,7-trihydroxyisoflavone-3′-sulfonate (1) is synthesized by the sulfonation of 6-hydroxybiochanin A and its structure is characterized by elemental analysis, ¹H-NMR, and IR spectroscopy. It is assembled with cobalt(II) or zinc(II), hexaquacobalt(II) bis(4′-methoxy-5,6,7-trihydroxyisoflavone-3′-sulfonate) tetrahydrate (2) and hexaquazinc(II) bis(4′-methoxy-5,6,7-trihydroxyisoflavone-3′-sulfonate) tetrahydrate (3) are obtained and characterized by IR spectroscopy. Simultaneously, their three-dimensional structures are determined by single-crystal X-ray analysis. It turns out that 2 and 3 are isomorphous and crystallize in the triclinic crystal system, space group P-1. Hydrophilic regions are defined by O–H···O hydrogen bonds involving the coordinated water molecules, the included water molecules, and sulfonate groups. Aromatic π...π stacking interactions assemble the isoflavone skeletons into columns and these columns formed hydrophobic regions. The sulfonate group is an important bridge as a structural link between the hydrophilic regions and the hydrophobic regions. Hydrogen bonds, π...π stacking interactions and the electrostatic interactions assemble 2 and 3 into three-dimensional network structures. Graphical abstract Sodium 4′-methoxy-5,6,7-trihydroxyisoflavone-3′-sulfonate (1) is synthesized and assembled with cobalt(II) or zinc(II). Hexaquacobalt(II) bis(4′-methoxy-5,6,7-trihydroxyisoflavone-3′-sulfonate) tetrahydrate (2) and hexaquazinc(II) bis(4′-methoxy-5,6,7-trihydroxyisoflavone-3′-sulfonate) tetrahydrate (3) are obtained and determined by single-crystal X-ray analysis. It turns out that 2 and 3 are isomorphous and assembled into three-dimensional network structures, characterized by hydrophilic regions defined by hydrogen bonds involving the coordinated water molecules, the included water molecules, and the sulfonate groups and by hydrophobic columns, formed by the isoflavone skeletons, interacting through π...π stacking interactions.      

X-ray crystal structures of halogen containing nucleobase derivatives in unsolvated and DMSO solvated forms

A series of halogenated nucleobase derivatives 1–4 is reported to yield solvent-free (2) and DMSO solvated crystals (1, 3, 4) on the crystallization from DMSO with one of them (4) containing an additional molecule of water. The molecular and crystal structures are described and comparatively discussed with reference to previous results on related compounds. The molecule of 1 is planar, molecules of 2 and 3 show syn alignment with reference to the heterocyclic ring and common C2′-endo conformation of the ribose residue, while 4 is also syn aligned but C4′-exo in the sugar conformation. The packing structures reveal typical aggregations created via networks of hydrogen bonds. These involve conventional N–H···N, N–H···O and O–H···O interactions between nucleobase and ribose units as well as solvent molecules, additionally supported by weak C–H···O contacts but excluding the participation of halogen···halogen interactions as well as halogen···heteroatom contacts in the supramolecular structure formation.     

Synthesis, spectral and thermal properties, and crystal structure of catena-poly-μ-ethylenediamine(dipicolinato)zinc(II) trihydrate, {[Zn(dipic)(μ-en)]·3H2O}n

A novel metal–organic coordination polymer framework formulated as {[Zn(dipic)(μ-en)]·3H₂O} _n (1) (catena-poly-μ-ethylenediamine(dipicolinato)zinc(II) trihydrate) has been synthesized and characterized by spectral method (IR), elemental analysis, thermal analysis (TG, DTG, DTA) and single crystal X-ray diffraction techniques. It crystallizes in the triclinic system, space group P−1. The asymmetric unit contains three hydrogen-bonded water molecules and the Zn atom is five-coordinated by three N and two O atoms. In fact, it is a new one-dimensional zinc complex with the peculiarity of having the ethylenediamine ligand very unusually acting as bridge to form polymeric chains. In the crystal structure, intramolecular O–H···O and intermolecular O–H···O and N–H···O hydrogen bonds result in the formation of a supramolecular structure, in which they seem to be effective in the stabilization of the structure.     

Synthesis,IR spectrum,thermal property and crystal structure of cyano-bridged heteronuclear polymeric complex, [Cd(teta)Ni(μ-CN)<Subscript>2</Subscript>(CN)<Subscript>2</Subscript>] · 2H<Subscript>2</Subscript>O

The cyano-bridged heteronuclear polymeric complex, [Cd(teta)Ni(μ-CN)₂(CN)₂] · 2H₂O (1), (teta = triethylenetetraamine) was synthesized and characterized by FT-IR spectroscopy, thermal analysis and single crystal X-ray diffraction techniques. It crystallizes in the orthorhombic system, space group Pccn. The asymmetric unit also contains two uncoordinated water molecules. The coordination geometry around the Cd(II) centre is a highly distorted octahedral. In the crystal structure, intramolecular N–H···O and intermolecular N–H···O, O–H···O and O–H···N hydrogen bonds, beside the cyano-bridged chains made up of tetracyanonickelate ions coordinated to Cd(II) ions, where the Ni(II) ion is coordinated by four cyanoligands in a square-planar arrangement, link the molecules into polymeric networks parallel to (001) plane, where the hydrogen bonded water molecules occupy the cavities between the layers. The FT-IR spectrum was reported in the 4,000–400 cm⁻¹ region. Vibration assignments were given for all the observed bands and the spectral feature also supported the structure of the polymeric complex. The decomposition reaction takes place in the temperature range 20–1,000 °C in the static air atmosphere.     

Structures of an infinite helical water chain and discrete lattice water in metal–organic framework structures

Two supramolecular complexes Ni[(Py)₂C(OH)₂]₂·(CH₃COO)₂·4H₂O 1 and Co[(Py)₂C(OH)₂]₂·(CH₃COO)₂·2H₂O 2 have been synthesized under hydrothermal conditions and structurally characterized by elemental analysis, IR spectra, and X-ray single-crystal diffraction. The X-ray diffraction analysis indicates that the center metal (Ni²⁺ and Co²⁺) ions having the same coordination environments are chelated by two pyridyl N atoms and a hydroxyl O atom of the gem-diol ligand in an octahedral geometry. In 1, the lattice water molecules form infinite single helical chains, while in 2, two lattice water molecules are discrete. In their crystal structures, intermolecular O–H···O and C–H···O hydrogen bonds form an extensive three-dimensional network, which consolidates the crystal packing.     

Crystallographic and theoretical studies of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid (1/1) with intermolecular O–H···N hydrogen bonds and S···O heteroatom interactions

Abstract  The molecular and crystal structure of a 1:1 co-crystal of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid, (1), has been determined by X-ray diffraction at the monoclinic space group P2₁/c with cell parameters of a = 8.422(6), b = 7.343(4), c = 16.112(7) ?, β = 104.988(8)°, V = 962.5(10) ?³ and Z = 2. In the crystal structure, two components connect via the intermolecular O–H···N hydrogen bonds [2.804(4) ?] and S···O heteroatom interaction [2.945(3) ?] with R ₂ ²(7) couplings to form a unique and infinite one-dimensional supramolecular tape structure. The calculations of (1) at the HF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels can almost reproduce X-ray geometry. In addition, the distances of the intermolecular O–H···N and S···O interactions by MP2/6-31G(d) and B3LYP/6-31G(d) levels agree well with those in the crystal. The calculated binding energies corrected BSSE and ZPE are −4.487 (HF), −7.473 (MP2), and −5.640 (B3LYP) kcal/mol. The results suggest that the complex (1) is very stable and the dispersion interaction is significantly important for the attractive intermolecular interaction in (1). The NBO analysis has revealed that the n(N) → σ*(O–H) interaction gives the strongest stabilization to the system and the major interaction for the intermolecular S···O contact is n(O) → σ*(S–N). Index Abstract  In the crystal structure of the title compound, the molecules are linked by intermolecular O–H···N hydrogen bonds and short S···O heteroatom interactions with R ₂ ²(7) couplings to construct a unique and infinite one-dimensional supramolecular tape structure.      

The synthesis,crystal structure and thermal studies of a mixed-ligand 1,10-phenanthroline and hexamethylenetetramine complex of lanthanum nitrate. Insight into coordination sphere geometry changes of lanthanide(III) 1,10-phenanthroline complexes

The structure of tetraaqua-bis(nitrato-O,O′)-(1,10-phenanthroline-N,N′)-lanthanum(III) 1,3,5,7-tetraazatricyclo[3.3.1.1^3,7]decane nitrate dihydrate, [La(NO₃)₂ · phen · (H₂O)₄]⁺ · hmt · NO ₃ ⁻ · 2H₂O, is presented. The lanthanum ion exhibits tenfold coordination and the polyhedron can be described as tetradecahedron. The complex cations, nitrate ions, water and hexamethylenetetramine molecules are assembled via hydrogen bonds, H–π rings and π–π stacking interactions into 3D supramolecular network. The bond strength of coordination sphere was calculated by means of the bond-valence method. The influence of La:phen stoichiometry and additional ligand on the changes of lanthanum(III) coordination sphere geometry in ten-coordinated complexes with 1,10-phenanthroline was discussed. The infrared spectrum of structure optimised by means of quantum mechanical calculations was analysed and compared with measured one. The obtained compound was characterised by thermogravimetric analysis in conjunction with evolved gases in the air atmosphere.     

Molecular structure and character of bonding of mono and divalent metal cations (Li+, Na+, K+, Mg2+, Ca2+, Zn2+, and Cu+) with guanosine: AIM and NBO analysis

The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Zn²⁺, and Cu⁺ cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 2′-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn²⁺ than do with Mg²⁺, Ca²⁺, and Cu⁺ and therefore stronger interactions lead to higher MIA. In both free molecules and their complexes, the Syn orientation of the base is stabilized by an intramolecular O5′–H···N3 hydrogen bond and the anti orientation of the base is stabilized by an intramolecular C–H···O hydrogen bond formed between the (C8-H8) and the O5′ atom of the sugar moiety. It is also interesting to mention that linear correlation between calculated MIA values and the atomic numbers (Z) of the metal ions of Li⁺, Na⁺, and K⁺ were found. Furthermore, the influences of metal cationization on the strength of the N-glycosidic bond, torsion angles, angle of pseudorotation (P), and intramolecular C–H···O and O–H···O hydrogen bonds have been studied. Natural bond orbital (NBO) analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of interactions.     

The structure and thermal behaviour of sodium and potassium multinuclear compounds with hexamethylenetetramine

Sodium and potassium thiocyanate complex compounds of formulae [Na(hmta)(H₂O)₄]₂²⁺·2SCN⁻ (1) and [K₂(hmta)(SCN)₂] _n (2) have been synthesized and characterised by IR spectroscopy, thermogravimetry coupled with differential thermal analysis, elemental analysis and X-ray crystallography. Each sodium and potassium cation is six co-ordinated, the sodium by one monofunctional hmta molecule, three terminal water molecules and two bridging water molecules, and the potassium by two bridging tetrafunctional hmta molecules and four bridging tetrafunctional thiocyanate ions. The coordination polyhedra of the central atoms can be described as distorted tetragonal bipyramids. The complex cations and anions of (1) are interconnected by multiple intramolecular O(water)—H···N(hmta/NCS) and O(water)—H···S hydrogen bonds to the three dimensional net. In each complex cation the intramolecular O–H···O hydrogen bonds link two terminal water molecules bonded to two metal cations. The compound (2) forms the three dimensional hybrid network in which the classical two-dimensional coordination polymers are linked by inorganic SCN⁻ spacers to the third-dimension. Thermal analyses show that the compounds decompose gradually in three (for 1) and two (for 2) steps with formation of Na₂SO₄ and K₂S as the final products, respectively, for 1 and 2.     

Unsymmetrical 1-naphthyltellurium(IV) dihalides: the interplay of Te···Br,C–H···Br and C–H···π interactions in the crystal structure of (1-naphthyl)(4-methylphenyl)tellurium(IV) dibromide

The crystal structure of (1-naphthyl)(4-methyl- phenyl)tellurium(IV) dibromide, the first unsymmetrical naphthyl containing diorganotellurium(IV) dibromide, shows the formation of one-dimensional supramolecular arrays where Te···Br secondary bonds link two parallel rows of molecules in a gear-teethed fashion. The weaker C–H···Br and C–H···π hydrogen bonds play important role in the formation of three-dimensional crystal lattice by cross linking these supramolecular motifs.     

Synthesis,crystal structure and other properties of the complexes of Er(III), Yb(III) and Lu(III) with 4,4′-bipyridine and dichloroacetates

A novel mixed-ligand complexes of Er(III), Yb(III) and Lu(III) with title ligands were prepared and characterized by chemical and elemental analysis and IR spectroscopy, conductivity (in methanol, dimethyloformamide and dimethylsulphoxide). The thermal properties of complexes in the solid state were studied. The mode of metal–ligand coordination was discussed. The title compounds are isomorphic and isostructural in solid state. All atoms in studied compounds lie in general positions but occurrence of inversion on the midpoint of the bond linking two pyridine rings leads to existence in asymmetric unit one complex molecule and half of outer coordination sphere 4-bpy molecule. All chelating carboxylate groups are symmetrically bonded to the metal cations. The molecules of studied compounds are connected to the three dimensional network via O–H···O and O–H···N intermolecular hydrogen bonds. In the structures also exist C–H···O, C–H···Cl weak hydrogen bonds and π····π stacking interactions.     

Synthesis, Characterization and Crystal Structure of [Na2(APZC)2(μ-H2O)2(μ3-H2O)]n

The synthesis and spectroscopic properties of a Na^＋ complex with ligand 3-aminopyrazine-2-carboxylic acid were described. The resulting complex was characterized by elemental analysis, IR, UV-Vis, NMR spectroscopy and single crystal X-ray diffraction method. The title compound crystallizes in the triclinic system with space group . The crystalline structure of this compound consists of supramolecular architectures involving strong intramolecular N—H…O in pyrazine molecules and intermolecular O—H…N, O—H…O, and N—H…N hydrogen bonds between substituted pyrazine and water molecules.     

Crystal Structures of [Cu2(bpy)2(H2O)(OH)2(SO4)]·4H2O and [Cu(bpy)(H2O)2]SO4 with bpy = 2, 2′‐Bipyridine

Two sulfato Cu^II complexes [Cu₂(bpy)₂(H₂O)(OH)₂(SO₄)]· 4H₂O ( 1 ) and [Cu(bpy)(H₂O)₂]SO₄ ( 2 ) were synthesized and structurally characterized by single crystal X—ray diffraction. Complex 1 consists of the asymmetric dinuclear [Cu₂(bpy)₂(H₂O)(OH)₂(SO₄)] complex molecules and hydrogen bonded H₂O molecules. Within the dinuclear molecules, the Cu atoms are in square pyramidal geometries, where the equatorial sites are occupied by two N atoms of one bpy ligand and two O atoms of different μ₂—OH groups and the apical position by one aqua ligand or one sulfato group. Through intermolecular O—H···O and C—H···O hydrogen bonds and intermolecular π—π stacking interactions, the dinuclear complex molecules are assembled into layers, between which the hydrogen bonded H₂O molecules are located. The Cu atoms in 2 are octahedrally coordinated by two N atoms of one bpy ligand and four O atoms of two H₂O molecules and two sulfato groups with the sulfato O atoms at the trans positions and are bridged by sulfato groups into ¹[Cu(bpy)(H₂O)₂(SO₄)_2/2] chains. Through the interchain π—π stacking interactions and interchain C—H···O hydrogen bonds, the resulting chains are assembled into bi—chains, which are further interlinked into layers by O—H···O hydrogen bonds between adjacent bichains.     

A spiral-like chain from a hydrogen-bonded cyclic dichloride containing a water dimer in a quaternary diammonium dichloride trihydrate

The reaction of benzyl chloride with tetramethylethylenediamine (tmen) results in the formation of the quaternary diammonium dichloride trihydrate (dbtmen)Cl₂·3H₂O 1 (dbtmen is N,N′-dibenzyl-N,N,N′,N′-tetramethylethylenediammonium) in good yields. 1 crystallises in the monoclinic P2₁/c space group and its structure consists of N,N′-dibenzyl-N,N,N′,N′-tetramethylethylenediammonium dication, two chloride anions and three crystal water molecules all of which are located in general positions. The organic dication is H-bonded to the chloride anions and the crystal waters with the help of intra-and intermolecular C-H···Cl and C-H···O interactions, while the chloride anions are linked to the crystal waters via O-H···Cl interactions. One of the crystal waters is linked through an intermolecular O-H···O bond with another water resulting in the formation of a water dimer. The O-H···Cl and O-H···O interactions between the chloride anions and water molecules lead to the formation of a five-membered {O₃Cl₂} cyclic dichloride containing a water dimer. The five-membered rings are linked into a chain with the aid of a O-H···Cl interaction. The organic cations are organised in zigzag fashion on either side of the chain and are further linked to the anionic water chain via weak C-H···O and C-H···Cl interactions, leading to the supramolecular organisation of the rings into a spiral-like of chain. Dedicated to Prof. Sabyasachi Sarkar on the occasion of his 60^th birthday     

Coordination behaviour of 2,2′-bipyridine towards the dichloroacetates of zinc and cadmium

The coordiantion compounds [Zn(C₁₀H₈N₂)(Cl₂HCCOO)(H₂O)₃]⁻·[Zn(C₁₀H₈N₂)(Cl₂HCCOO)₃]⁺ and [Cd(C₁₀H₈N₂)₂(Cl₂CHCOO)₂] were synthesised and characterised by elemental and thermal analysis, IR and UV–VIS spectroscopy, and X-ray crystallography. The complexes are air stable and well-soluble in water. The zinc atoms are five and six coordinated and the cadmium atom is six coordinated. The coordination polyhedra of central atoms can be described as trapezoidal pyramid and octahedron in zinc compound and as rectangular bipyramid strongly distorted towards skew trapezoidal bipyramid in cadmium compound. In both compounds all dichloroacetate groups are monodentate. The bond valences considerations show that all 2,2′-bipyridine molecules are bonded almost 2 times stronger than carboxylate groups. In the structure of zinc compound exist O–H···O hydrogen bonds and in both structures can be found weak C–H···O hydrogen bonds. Additionally, both compounds are pile-stacked by π···π interactions. The IR spectra show typical vibrations for chelating 2,2′-bipyridine molecules and terminal monodentate carboxylate groups. The thermal decomposition studies show zinc compound decomposes in 4 steps and cadmium compound decomposes in 5 steps with formation of oxides as a final products. The ligands decompose gradually, first dichloroacetates and next 2,2′-bipyridine.     

Thiocyanato-copper(II) complexes derived from a tridentate amine ligand and from alanine

Two thiocyanato-Cu(II) complexes including mononuclear dithiocyanato Cu(Me₃dpt)(NCS)₂ (1) and the polymeric 1D [Cu(d,l-Ala)(μ_N,S–NCS)(H₂O)] _n (2) were synthesized and structurally characterized (Me₃dpt = bis(N-methyl-3-propyl)methylamine, Ala = alaninate anion). The IR spectrum of complex 1 confirmed the N-bonding coordination mode of the thiocyanate groups, and its visible spectrum revealed the square pyramidal geometry around the central Cu²⁺ ion. Single X-ray crystallography of 1 showed that the Cu(II) center displays square pyramidal geometry with severe distortion toward trigonal bipyramidal environment. Complex 2 forms a 1-D polymeric chain with the NCS⁻ acting as a μ_N,S-ligand. A distorted SP geometry around the Cu²⁺ centers was achieved by the O and N atoms of alaninato anion, the aqua ligand and by the N and S atoms of the bridging thiocyanate groups. Hydrogen bonds of the type N–H···O, N–H···S and O–H···O are formed in this complex leading to the extension of the 1D chain to a supramolecular network.     

Four complexes with a bulky carboxylate ligand: syntheses,crystal structures,and luminescent properties

Abstract  

Four complexes of 3,3-diphenylpropanoate (L) and 4,4′-bipyridine as auxiliary bridging ligands were synthesized and characterized, namely [Zn(L)₂(4bpy)(EtOH)₂]_∞ (1), [Co(L)₂(4bpy)(EtOH)₂]_∞ (2), [Ni(L)₂(4bpy)(EtOH)₂]_∞ (3), and [Cu(L)₂(4bpy)(H₂O)]_∞ (4) (4bpy = 4,4′-bipyridine). X-ray single-crystal diffraction analyses show that complexes 1–4 all take one-dimensional (1D) fishbone-like structures incorporating bridging 4bpy ligands. The complexes show different supramolecular frameworks interlinked via intermolecular hydrogen bonds, π···π stacking, and/or C–H···π supramolecular interactions. Complex 3 only has a simple one-dimensional fishbone-like chain, whereas complexes 1 and 2 show two-dimensional supramolecular structures by interchain C–H···O hydrogen bonds. Complex 4 is assembled into two-dimensional layers and then an overall three-dimensional framework by a combination of interchain O–H···O hydrogen bonds and C–H···π supramolecular interactions. The luminescent properties of the ligands and their complexes were investigated.     

On the relationships between molecular conformations and intermolecular contacts toward crystal self-assembly of mono-, di-, tri-, and tetra-oxygenated xanthone derivatives

Oxygenated xanthones have been extensively investigated over the years, but there are few reports concerning their crystal structure. Our chemical investigations of Brazilian plants resulted in the isolation of four natural products named 1-hydroxyxanthone (I), 1-hydroxy-7-methoxyxanthone (II), 1,5-dihydroxy-3-methoxyxanthone (III), and 1,7-dihydroxy-3,8-dimethoxyxanthone (IV). The structures of these compounds were established on the basis of single crystal X-ray diffraction. The xanthone nucleus conformation is essentially planar with the substituents adopting the orientations less sterically hindered. In addition, classical intermolecular hydrogen bonds (O–H···O) present in III and IV give rise to infinite ribbons. However, the xanthone I does not present any intermolecular hydrogen bonds, meanwhile the xanthone II presents only a non-classical one (C–H···O). The crystal packing of all xanthone structures is also stabilized by π–π interactions. The fingerprint plots, derived from the Hirshfeld surfaces, exhibited significant features of each crystal structures.