Classical Hydrogen-bonding Inter-actions Research Articles

Crystal structures of anhydrous and hydrated N-benzyl-cinchonidinium bromide.

N-benzyl-cinchonidinium bromide, C26H29N2O+·Br-, with the systematic name (R)-[(2S,4S,5R)-1-benzyl-5-ethenyl-1-azoniabi-cyclo-[2.2.2]octan-2-yl](quinolin-4-yl)-methanol bromide, is a quaternary ammonium salt of the cinchona alkaloid cinchonidine. This salt is widely used as a chiral phase-transfer catalyst and chiral resolution agent. Both classical and non-classical hydrogen-bonding inter-actions, as well as anion effects have been shown to play key mechanistic roles in the catalysis of cinchona alkaloids. In an effort to understand the effects of water on these inter-molecular inter-actions, the structures of anhydrous N-benzyl-cinchonidinium bromide, (I), and the sesquihydrate, C26H29N2O+·Br-·1.5H2O, (II), were determined.

Cobalt(II) complexes with small variations in the heterocycle ligand, crystal structure and DFT calculations

Novel mononuclear cobalt(II) complexes, [Co(mbipy)(H2O)(η2-NO3)(η-NO3)] (1), [Co(dmbipy)(H2O)(η2-NO3)(η-NO3)] (2) and [Co(dmphen)(H2O)(η2-NO3)(η-NO3)] (3) were synthesized by the reactions of Co(NO3)2·6H2O with bipyridine and phenanthroline derivatives (mbipy = 6-methyl-2,2́-bypiridine; dmbipy = 6,6́-dimethyl-2,2́-bypiridine and dmphen = 2,9-dimethyl-1,10-phenanthroline). The complexes were identified by elemental analysis, IR, UV–Vis spectroscopy and X-ray crystallography. In the molecular structure of the three complexes, the coordination geometry around Co(II) is distorted octahedral in a [CoN2O4] system. The crystal structure was stabilized with a network of OH···O and (CH···O classical hydrogen bond interactions as well as π-π interactions between the pyridine rings in 2 and 3. Furthermore, the density functional theory (DFT) calculations have been performed. Good consistency was observed between the calculated results and the experimental structure, in gas phase and aqua phase. DFT approach was used to interpreter the optical characterization. The electronic properties of the complexes were also calculated and compared. The origin of the intermolecular OH···O hydrogen bond in 3D structure of the complexes was explored by MEP.

Structural and spectral characterization of Cu(II) complexes of N(4)-substituted thiosemicarbazones derived from 2-hydroxyacetophenone: Crystal structure of a dinuclear Cu(II) complex

Copper(II) complexes of 2-hydroxyacetophenone-N(4)-cyclohexylthiosemicarbazone (H2L1) and 2-hydroxyacetophenone-N(4)-phenylthiosemicarbazone (H2L2) have been synthesized and characterized by different physicochemical techniques like magnetic studies and electronic, infrared and EPR spectral studies. [(CuL1)2] (1) is a dinuclear complex having four coordination around copper(II) with distorted square planar geometry. The two individual dinuclear complexes are interconnected through two bifurcated classical hydrogen bond interactions producing a sheet-like structure along b axis. [(CuL2)2]·1/2H2O (2) also has a dimeric structure. The thiosemicarbazones bind to the metal as dianionic ONS donor ligand in all the complexes, except in the complexes [Cu(HL1)Cl]·2H2O (3), [Cu(HL1)Br]·4H2O (4) and [Cu(HL1)NO3]·C2H5OH(H2O) (5), where the ligand moieties are coordinated as monoanionic (HL¯) ones. Complexes [CuL1dmbipy] (6), [CuL2dmbipy]·3H2O (7), [CuL2bipy]·H2O (8) and [CuL2phen]·2C2H5OH (9) are heterocyclic base adducts. The synthesis and characterization of monomeric and dimeric Cu(II) complexes with 2-hydroxyacetophenone-N(4)-cyclohexyl/phenyl substituted ONS donor ligands is described. It also reports the crystal structure of a novel binuclear Cu(II) complex with oxygen bridging and its interesting coordination. This compound [CuL1]2 is a rare example of copper(II)-thiosemicarbazone complex with oxygen bridging structure.

Crystal structures of chlorido-[dihy-droxybis-(1-imino-eth-oxy)]arsanido-κ3 N,As,N']platinum(II) and of a polymorph of chlorido-[dihy-droxybis-(1-imino-prop-oxy)arsanido-κ3 N,As,N']platinum(II).

Each central platinum(II) atom in the crystal structures of chlorido-[dihy-droxybis-(1-imino-eth-oxy)arsanido-κ3 N,As,N']platinum(II), [Pt(C4H10AsN2O4)Cl] (1), and of chlorido-[dihy-droxybis-(1-imino-prop-oxy)arsanido-κ3 N,As,N']platinum(II), [Pt(C6H14AsN2O4)Cl] (2), is coordinated by two nitro-gen donor atoms, a chlorido ligand and to arsenic, which, in turn, is coordinated by two oxygen donor ligands, two hydroxyl ligands and the platinum(II) atom. The square-planar and trigonal-bipyramidal coordination environments around platinum and arsenic, respectively, are significantly distorted with the largest outliers being 173.90 (13) and 106.98 (14)° for platinum and arsenic in (1), and 173.20 (14)° and 94.20 (9)° for (2), respectively. One intra-molecular and four classical inter-molecular hydrogen-bonding inter-actions are observed in the crystal structure of (1), which give rise to an infinite three-dimensional network. A similar situation (one intra-molecular and four classical inter-molecular hydrogen-bonding inter-actions) is observed in the crystal structure of (2). Various π-inter-actions are present in (1) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.7225 (7) Å, and between the centroids of five-membered (Pt, As, C, N, O) rings of neighbouring mol-ecules with distances of 3.7456 (4) and 3.7960 (6) Å. Likewise, weak π-inter-actions are observed in (2) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.8213 (2) Å, as well as between the Cl atom and the centroid of a symmetry-related five-membered ring with a distance of 3.8252 (12) Å. Differences between (2) and the reported polymorph [Miodragović et al. (2013 ▸). Angew. Chem. Int. Ed. 52, 10749-10752] are discussed.

Supramolecular Architecture in a Ni(II) Complex with a Weakly Bonded N,N′-(1,4-phenylenedi- carbonyl)Diglycinate Counter-Anion: Crystal Structure Investigation and Hirshfeld Surface Analysis

In this work, we describe the structural investigation of a Ni(II) complex, [Ni(C12H8N2)2(H2O)2]2·(C12H10N2O6)·(NO3)2·10H2O, with phenanthroline ligands, a deprotonated aromatic dicarboxylic acid, N,N′-(1,4-phenylenedicarbonyl)diglycine, and a nitrate as counter-anions, as well as water molecules. Noncovalent interactions, such as π–π stacking, lone-pair···π, and C–H···π between the phenanthrolines of the cationic complex, [Ni(C12H8N2)2(H2O)2]2+, and counter-anions are observed. Moreover, the solvated and noncoordinating counter-anion, N,N′-(1,4-phenylenedicarbonyl)diglycinate, is embedded in classical and nonclassical hydrogen-bonding interactions with water molecules and phenanthrolines. The two water molecules coordinated by the NiII atom and hydrogen bonded to the carboxylate of the N,N′-(1,4-phenylenedicarbonyl)diglycinate show attractive secondary electrostatic interactions, and a DD/AA hydrogen bonding pattern is formed. The noncovalent interactions of the cationic complex and the solvated N,N′-(1,4-phenylenedicarbonyl)diglycinate counter anion were explored with a Hirshfeld surface analysis, and related contributions to crystal cohesion were determined. The results of the N,N′-(1,4-phenylenedicarbonyl)diglycinate counter anion were compared to those of a solvated N,N′-(1,4-phenylenedicarbonyl)diglycine molecule of a previously described copper(II) complex.

(Metformin-κ2N,N′)(salicylato-κ2O,O′)copper(II) trihydrate

The hydrous title complex [systematic name: (1,1-dimethylbiguanide-κ2N2,N4)(2-oxidobenzoato-κ2O,O′)copper(II) trihydrate], [Cu(C7H4O3)(C4H11N5)]·3H2O, was synthesized electrolytically from an ethanolic solution of metformin hydrochloride, acetylsalicylic acid, Pepto-Bismol and a copper sacrificial anode. Diffraction data were collected at 0.56 Å resolution, allowing the accurate determination of H-atom positions in the neutral metformin ligand. Both imine groups in metformin have very similar N=C bond lengths, 1.2978 (17) and 1.3033 (17) Å, and the salicylate dianion behaves as a chelating ligand. The coordination sphere of the copper(II) cation deviates marginally from a square-planar arrangement. In the crystal, short Cu...Cu separations of 3.5476 (3) Å are observed, along with classical hydrogen-bonding interactions.

Tuning of coordination behavior of thiosulfate ion by organic linkers in cadmium thiosulfate compounds

Three new inorganic-organic hybrid molecular cadmium thiosulfate compounds, [Cd(S2O3) (C3H10N2)2], I, [Cd2(C10H8N2)4(S2O3)2](C10H8N2)·2H2O, II and [Cd2(C10H8N2)2(H2O)2(S2O3)2](C10H8N2)·2H2O, III have been synthesized using different organic linkers as co-ligand and characterized them thoroughly. The compounds have connectivity between the Cd-centers, the thiosulfate units and the organic ligands forming molecular (zero-dimensional) structures. The ligating behaviors of thiosulfate unit have been triggered by organic linkers. The coordination number of thiosulfate ion to the metal ion can also be enhanced by varying the aromatic ligands instead of aliphatic ligand. The molecular structures are stabilized and formed three-dimensional packing structures through extensive hydrogen bonds and van der Waals interactions. The free aromatic bipyridine ligands are observed in the crystal structures II and III. The unique type of π⋯π interactions play an important role for the stabilization of these two structures. Theoretical studies also revealed that the value of π⋯π interactions are comparable with the classical hydrogen bond interactions. The present study illustrates the usefulness of the organic linkers for the structural modifications in inorganic-organic hybrid compounds.

A Combined Experimental and Theoretical Investigation on Organic Cation Dichlorocopper (II): Structural Characterization, Hirshfeld Surface Analysis, Spectroscopic Properties and DFT Calculation

The (ethylenediamine) dichlorocopper(II) complex, {[Cu(en)]Cl2}n(en:C2H8N2), was synthesized by hydrothermal technique. The X-ray structure of {[Cu(en)]Cl2}n shows that the compound crystallizes as a one dimensional chain with one chlorine that is non-bridging and the other chlorine which is triply bridging. It crystallizes at room temperature in the centrosymmetric space group P21/m. The structure of {Cu(en)Cl2}n was originally reported by Kumara et al. The surrounding copper is best described as distorted octahedral. The crystal structure was stabilized with an extensive network of N-H…Cl classical hydrogen bond interactions. The investigation on that close intermolecular interactions between the molecules via Hirshfeld surface analyses is presented to reveal subtle differences and similarities in the crystal structures. The decomposition of the fingerprint plot area provides a percentage of each intermolecular interaction, allowing for a quantified analysis of close contacts within the crystal. The optimized molecular structure and vibrational spectra were calculated by the Density Functional Theory (DFT) method using the B3LYP function with the LanL2DZ basis set. Good consistency is found between the calculated results and the experimental structure, FTIR, and FT-Raman spectra. The detailed interpretation of the vibrational modes was carried out. Optical transmission measurements performed on thin films of {[Cu(en)]Cl2}n revealed two absorption bands at 3.64 eV and 1.907 eV. The calculated HOMO-LUMO energies reveal that charge transfer occurs within the molecule.

Synthesis and characterization of two sulfonated resorcinarenes: a new example of a linear array of sodium centers and macrocycles.

Two sulfonated resorcinarenes were synthesized by reacting C-tetra(butyl)resorcinarene or C-tetra(2-(methylthio)ethyl)resorcinarene with formaldehyde in the presence of sodium sulfite. Their structures were determined via FT-IR, 1H-NMR, 13C-NMR and mass spectrometry. Thermal gravimetric analyses of the derivatives were also carried out and revealed the presence of water molecules in the solid state. The sulfonated product of C-tetra(butyl)resorcinarene was characterized by an X-ray crystal structure determination. The asymmetric unit contains eight molecules of water and two of acetone, and analysis indicated that sulfonated resorcinarene prefers a cone configuration (rccc conformation) in the solid state. In the crystal array, classical hydrogen bond interactions O-H···O and intermolecular contacts were observed. In the crystal packing, a linear array of capsules of sulfonated resorcinarenes was generated for a chain of sodium atoms and sulfonate groups.

Synthesis and Characterization of Monomeric and Polymeric Hg(II) Complexes with 5-Methyl-5-(3-pyridyl)-2,4-imidazolidenedione Showing a Wide Spectrum of Effective Antibacterial Activities

Three new mercury(II) coordination monomers, HgLX3 [X = Cl− (1) and Br− (2)], and polymer, [HgLI2]n, (3), L = 5-methyl-5-(3-pyridyl)-2,4-imidazolidenedione, have been synthesized and characterized by elemental analysis (C, H, and N %) and flame atomic absorption (Hg %), IR, and NMR spectroscopy. Complexes 1 and 2 have the same framework structure while the structure of complex 3 is an infinite 2D layers. According to X-ray diffraction analysis, complex 3 crystallizes in monoclinic system. In this polymeric complex, [Hg(C9H9N3O2)I(μ-I)2]n, HgII atom is coordinated by one L and three I− anions with a distorted tetrahedral geometry; one I− anion is in a monodentate coordination mode and the other two are bridging, linking HgII atoms into a one-dimensional chain. Classical hydrogen-bonding interactions (O···H–N) between adjacent ligands result in a zigzag type arrangement of one chain while consecutive polymeric chains are linked by non-classical ones (O···H–C) to form 2D supramolecular layers. The results indicate that the flexible ligand can form complexes with varied structures. In addition, the species of the halide were found to have great impact on the structure of the complexes. Antibacterial activity of L and the corresponding complexes investigated against six species of microorganisms. Testing was performed by disk diffusion method, and minimum inhibitory concentrations have been determined. Noteworthy antimicrobial activities for these complexes were observed.

Exploring the influence of crystal environment on the geometry of bis(pyridine-2,6-dicarboxylato) chromium (III) anionic complexes containing various cationic moieties: Synthesis, structures and Hirshfeld surface analysis

Two chromium (III) complexes with pyridine-2,6-dicarboxylate ligand have been synthesized with various cations yielding new compounds: (2a4mpy)2[Cr(pydc)2]2·9H2O (I) and (bphda)[Cr(pydc)2]2·DMF·4H2O (II) where pydc=pyridine-2,6-dicarbocylate anion, 2a4mpy=2-amino-4-methylpyrimidinium cation and bphda=1,1′-bisphenyl-4,4′-diaminium cation. These compounds have been characterized by IR spectroscopy, CHN microanalysis and X-ray structural studies along with a detailed analysis of Hirshfeld surface and 2D fingerprint plot as an assisting tool for decoding of the intermolecular interactions. In both complex fragments, Cr(III) atoms are surrounded by four oxygen atoms and two nitrogen atoms from two pydc ligands, forming a distorted octahedral environment. Crystal packing in both compounds is mostly governed by strong OH⋯O and NH⋯O classical hydrogen bond interactions and assisted by the interactions involving π-electrons, namely π⋯π off-face stacking, carbonyl⋯π or lone pair⋯π. All these interactions lead to rather complex three-dimensional structures. In this regard, the fingerprint plots enabled to explore the role of intermolecular interactions types on the distorted geometry of titled complexes and analogous structures retrieved from Cambridge Structural Database (CSD).

Synthesis, NMR Characterization and Crystal Structure of Methyl 3α,7α-Dihydroxy-12-oxo-5β-cholanate

The crystal structure and NMR characterization of methyl 3α,7α-dihydroxy-12-oxo-5β-cholanate are described. The title compound which was obtained from methyl cholanate in a 3-step synthetic sequence that does not alter the starting chirality, crystallizes in the monoclinic system with P 21 space group. While despite the substitution pattern rings A, B and C adopt chair conformations, the 5 membered D ring, that bears the side chain attached to C-17, shows a twisted conformation on C-13–C-14. In the crystal array, classical hydrogen bond interactions O–H···H and intermolecular contacts C–H···O of hydrogen bond type are observed. The crystal structure and NMR characterization of Methyl α,7α-dihydroxy-12-oxo-5β-cholanate are described.

(5E)-1-Benzyl-5-(3,3,3-tri-chloro-2-oxo-propyl-idene)pyrrolidin-2-one.

In the crystal structure of the title compound, C14H12Cl3NO2, no classical hydrogen-bonding inter­actions are observed. The methyl­ene fragments of the benzyl groups participate in non-classic hydrogen-bond inter­actions with the carbonyl O atoms of neighboring mol­ecules, generating co-operative centrosymmetric dimers with R 5 5(10) ring motifs. The overall mol­ecular arrangement in the unit cell seems to be highly influenced by secondary non-covalent weak C—Cl⋯π [Cl⋯Cg(phenyl ring) = 3.732 (2) Å] and C—O⋯π [O⋯Cg(pyrrolidine ring) = 2.985 (2) Å] contacts.

Synthesis, Crystal Structure, and Properties of a Tetranuclear Zn(II) Complex Based on 2-(1H-imidazole-1-ylmethyl)-1H-benzimidazole

A new complex with the formula {[Zn(L)3](NO3)·H2O}4 (1) has been obtained through the self-assembly of a flexible N-heterocyclic ligand 2-(1H-imidazole-1-ylmethyl)-1H-benzimidazole (L) with Zn(NO3)2·6H2O at 80 °C. In complex 1, four adjacent Zn(II) ions are joined together by four bidentate bridging ligands in trans-conformation to form a tetranuclear unit, featuring a (Zn–N–N–)4 ring on the ab plane. The Zn4L12 units are interconnected by classical hydrogen-bonding interactions (N–H···N) to lead to 1D channels in the c-direction. Additionally, the fluorescent property and thermogravimetric analysis of complex 1 also have been investigated.

Three double- or triple-stranded chains constructed from different cobalt(II) salts and a flexible bis-triazole ligand

Three coordination compounds, {[Co(btrp)2(H2O)2] · NO3 · H2O} n (1), {[Co(btrp)2(H2O)2] · H2O · 2H2btc} n (2), and {[Co(btrp)3] · 2ClO4} n (3) (btrp = 1,3-bis(1,2,4-triazol-1-yl)propane; H3btc = benzene-1,3,5-tricarboxylic acid), have been prepared via solvothermal method and characterized by single-crystal X-ray diffraction and elemental analyses. Compound 1 possesses a 1-D double-stranded chain composed of ribbons of 20-membered cycles. Binuclear water clusters link adjacent nitrate anions to form a 1-D supramolecular helix in the structure. Compound 2 has a 1-D double-stranded chain wherein free H2btc ligands constitute 1-D negative chains through classical hydrogen-bonding interactions (O–H ··· O). Compound 3 exhibits a triple-stranded 1-D chain. For 1–3, 3-D supramolecular structures are consolidated by interchain weak hydrogen-bonding interactions as well as electrostatic interactions.

Hydrogen bonded supramolecular framework in organic acid–base adducts: Crystal structures of five cocrystals/salts assembled from 2-methylquinoline with monocarboxylic acid, dicarboxylic acid, and tricarboxylic acid

► Five organic acid-base adducts assembled from 2-methylquinoline with carboxylic acid derivatives have been prepared. ► The five compounds are characterized by XRD, IR, mp, and elemental analysis. ► The classical hydrogen bond interaction modes in the compounds have been ascertained. ► The secondary propagating interactions are also analyzed. Studies concentrating on noncovalent weak interactions between the organic base of 2-methylquinoline, and carboxylic acid derivatives have led to an increased understanding of the role 2-methylquinoline has in binding with carboxylic acid derivatives. Here anhydrous and hydrous multicomponent organic acid–base adducts of 2-methylquinoline have been prepared with carboxylic acids that ranged from monocarboxylic acid to tricarboxylic acid such as 3,5-dinitrobenzoic acid, 3-hydroxy-2-naphthoic acid, oxalic acid, fumaric acid, and citric acid. The five crystalline complexes were characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. These structures adopted homo or heterosupramolecular synthons or both. Analysis of the crystal packing of 1 – 5 suggests that there are N H⋯O, O H⋯N, and O H⋯O hydrogen bonds (charge assisted or neutral) between acid and base components in the studied compounds. Except the classical hydrogen bonding interactions, the secondary propagating interactions also play an important role in structure extension. These weak interactions are responsible for the formation of 1D–3D frameworks.

Crystal structures and luminescence of two cadmium(II) polymers constructed from aromatic polycarboxylate and bis(1,2,4-triazol-1-yl)methane ligands

Two new coordination compounds, {[Cd2(btrm)(ip)2(H2O)2] · 2H2O} n (1) and {[Cd2(btrm)(hip)2(H2O)4] · 3H2O} n (2) (btrm = bis(1,2,4-triazol-1-yl)methane, H2ip = isophthalic acid, H2hip = 5-hydroxy isophthalic acid), have been synthesized and structurally characterized. Compound 1 is a 3-D network with CdSO4 topology. Compound 2 contains 1-D ladder structures, which are interconnected by classical hydrogen-bonding interactions (O–H ··· O) to lead to 3-D supramolecular architectures. Luminescence was performed on 1 and 2, both of which showed strong fluorescent emissions in the solid state at room temperature.

Catena-Poly[[diiodidocadmium]-μ-[4,4′-(2,3,5,6-tetramethyl-1,4-phenylene)bis(methylene)]bis(3,5-dimethyl-1H-pyrazole)-κ2N2:N2′

The heterocylic ligand of the polymeric title compound, [CdI2(C22H30N4)], links two adjacent CdI2 units, forming a chain running parallel to [01]. The CdII atom is located on a twofold rotation axis and shows a distorted tetra­hedral CdI2N2 coordination. The mid-point of the benzene ring of the ligand lies on a center of inversion. There are no classical hydrogen-bonding inter­actions present.

Syntheses, structures, and properties of three cadmium(II) complexes constructed from aromatic polycarboxylate and flexible triazole synthons

Three new coordination compounds {[Cd(btrp)(ip)(H 2O)]·2.5H 2O} n ( 1) {[Cd(btrp)(hip)(H 2O)]·3H 2O} n ( 2) and {[Cd(btrp) 2(H 2O) 2]·H 2O·2H 2btc} n ( 3) (btrp = 1,3-bis(1,2,4-triazol-1-yl)propane, H 2ip = isophthalic acid, H 2hip = 5-hydroxy isophthalic acid, H 3btc = benzene-1,3,5-tricarboxylic acid) have been synthesized and structurally characterized. Both 1 and 2 feature two similar 2D layer structures, and the resulting 2D structures are interconnected by hydrogen-bond and π⋯π interactions to lead to 3D supramolecular architectures. 3 possesses 1D positive double-stranded chains. In the framework of 3, the free H 2btc ligands also constitute into supremolecular 1D negative chains through classical hydrogen-bonding interactions (O H⋯O). The two kinds of 1D chains constructs into 3D supramolecular architectures through hydrogen-bonding and electrostatic interactions. Luminescence analyses were performed on all the three compounds, 1 and 2 show strong fluorescent emissions in the solid state at room temperature.

Carbonyl(N-nitroso-N-oxido-1-naphtylamine-κ2O,O′)(triphenylphosphine-κP)rhodium(I) acetone solvate

The title compound, [Rh(C10H7N2O2)(C18H15P)(CO)]·(CH3)2CO, is the second structural report of a metal complex formed with the O,O′-C10H7N2O2 (neocupferrate) ligand. In the crystal structure, the metal centre is surrounded by one carbonyl ligand, one triphenyl­phosphine ligand and the bidentate neocupferrate ligand, forming a distorted square-planar RhCO2P coordination set which is best illustrated by the small O—Rh—O bite angle of 77.74 (10)°. There are no classical hydrogen-bond inter­actions observed for this complex.