Crystallographic and theoretical studies of 1-(1-naphthyl)-2-thiourea with intermolecular N-H...S heteroatom interaction and N-H...π interaction

A single crystal X-ray diffraction study of 1-(1-naphthyl)-2-thiourea (1) C₁₁H₁₀N₂S indicates crystallization in the monoclinic space group C2/c, Z = 8, with unit cell parameters a = 15.3864(14) Å, b = 7.6090(7) Å, c = 17.0836(16) Å, β = 91.7420(30)°. In the crystal structure, two components of 1 are connected via intermolecular NH...S hydrogen bonds (the N...S distance of 3.371 Å). In 1 there is an NH...π interaction (with the N...π distance of 3.804 Å and a possible N-H...π distance of 3.196 Å). The calculations of 1 at the B3LYP/cc-pVTZ, RHF/cc-pVTZ, RIMP2/cc-pVDZ, and RIMP2/cc-pVTZ levels of theory can almost reproduce the X-ray geometry. In addition, the binding energies of a dimer of 1 calculated by RIMP2 using the cc-pVDZ and cc-pVTZ corrected BSSE basis sets are ?36.1 kJ/mol and ?41.7 kJ/mol. The results suggest that complex 1 is significantly important for the attractive intermolecular interaction in 1.     

DFT studies and AIM analysis of intramolecular N–H···O hydrogen bonds in 3-aminomethylene-2 methoxy-5,6-dimethyl-2-oxo-2,3-dihydro-2λ5-[1,2]oxaphosphinin-4-one and its derivatives

The intramolecular N–H···O hydrogen bonds in 3-aminomethylene-2 methoxy-5,6-dimethyl-2-oxo-2,3-dihydro-2λ⁵-[1,2]oxaphosphinin-4-one and its derivatives (F, H, Li, -BeH) were studied by DFT (density functional theory) methods. The results of calculations were obtained at B3LYP/6-311++G(d,p) level on model species, with the resonance-assisted hydrogen bonds (RAHB). Topological parameters such an electron density, its Laplacian, kinetic electron energy density, potential electron energy density, and total electron energy density at the bond critical points (BCP) of H···O/N–H contact bonds from Bader’s ‘Atoms in molecules’ (AIM) theory were analyzed in details. The energy of the N–H···O interactions studied here was found rather weak (E _HB = 2.53–12.08 kcal/mol). The results of AIM ellipticity indicated π-delocalization over all six atoms within ring.     

Co-crystal/salt crystal structure disorder of trichloroacetic acid–N-methylurea complex with double system of homo- and heteronuclear O–H···O/N–H···O hydrogen bonds: X-ray investigation, ab initio and DFT studies

The X-ray diffraction studies revealed disorder of a trichloroacetic acid?CN-methylurea complex crystal structure, connected with a proton transfer via O?CH···O hydrogen bond. The observed structure corresponds to a co-existence of ionic (salt) and neutral (co-crystal) forms of the complex in the solid state in ratio 3:1, respectively. The geometrical analysis based on ab initio and density functional theory methods combined with the experimental research indicated that two different N-methylurea molecular conformations, defined by CNCN torsion angle, correspond to the neutral and the ionic form of the complex, respectively. The conformational changes seem to be connected with stabilization of the ionic structure after a proton transfer, as according to theoretical calculations this form of the complex (the ionic one) was unstable in the gas phase. A particular attention was focused on a system of a double intermolecular hydrogen bonds, O?CH···O and N?CH···O which join molecules into the title complex. The analysis of these interactions performed in terms of their geometry, energetic and topological electron density properties let for their classification into strong and medium strength hydrogen bonds. It was also found that the antibonding hydrogen bonding donor orbital occupation corresponded to the stabilization energy resulting from charge transfer in hydrogen bonds. Hence, it is postulated as a possible indicator of interaction strength.     

A theoretical evidence for mutual influence between S···N(C) and hydrogen/lithium/halogen bonds: competition and interplay between π-hole and σ-hole interactions

Ab initio calculations were performed to investigate the cooperativity between the S···N(C) bond and the hydrogen/lithium/halogen bond interactions in O₂S···NCX···NCH and O₂S···CNX···CNH triads (X=H, Li, Cl, and Br). To understand the properties of the systems better, the corresponding dyads are also studied. It is evident that the lithium bond has a bigger influence on the chalcogen bond than vice versa. The results indicate that the enhanced interaction energies of the S···N(C) and X···N(C) interactions in the triad increase in the order NCCl < NCBr < NCH < NCLi and CNCl < CNBr < CNH < CNLi. This is the order of the increasing positive electrostatic potential V _S,max on the X atom. The nature of S···N(C) and X···N(C) interactions of the complexes is unveiled by energy decomposition analysis and natural bond orbital (NBO) theory. The cooperativity between both types of interaction is chiefly caused by the electrostatic effects.     

The first C(O)NHP(O)-based phosphoric triamide structure with an N‒H···π hydrogen bonding: A combination of X-ray crystallography and theoretical study to evaluate the strength of hydrogen bonds

The hydrogen bond pattern of N-(4-methoxybenzoyl)-N′,N″-bis(4-methylbenzyl)-phosphoric triamide, C₂₄H₂₈N₃O₃P, (I), was investigated. In the crystal structure, the molecules are aggregated through N_CP―H···O═P and N_P―H···O═C hydrogen bonds in a one-dimensional arrangement parallel to the c axis (N_CP is the nitrogen atom in the C(O)NHP(O) segment and N_P stands for the two other nitrogen atoms bonded to the P atom). There is also a novel N_P?H···π hydrogen bond in the crystal which extends the aggregation of the molecules to a two-dimensional array parallel to the bc plane. A Cambridge Structural Database (CSD, version 5.37, Feb 2016) analysis shows that the N―H···π hydrogen bond was not observed in any of 156 [RC(O)NH]P(O)[NR¹R² Allen, F. H.; Taylor, R. Chem. Soc. Rev. 2004, 33, 463-475.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]₂ (R¹ ≠ H, R² = H or ≠ H) phosphoric triamide structures reported so far. The theoretical calculations at the B3LYP/6-311G^** level of theory (DFT, AIM, and NBO) were performed to evaluate the strengths of N_CP―H···O═P, N_P―H···O═C and N_P―H···π hydrogen bonds, considering two-aggregate molecular assemblies containing these hydrogen bonds. The calculations on the title compound suggest that the intermolecular N_CP―H···O═P hydrogen bond is stronger than N_P―H···O═C and N_P―H···π interactions. The hydrogen bond strength was investigated by NBO, topological analysis, geometry calculation, Hirshfeld surface analysis and experimental spectroscopic results, which are in agreement with each other.     

Synthesis,Reactions, and Antiviral Activity of 1-(1H-Pyrazolo[3,4-b]pyridin-5-yl)ethanone and Pyrido[2′,3′:3,4]pyrazolo[5,1-c][1,2,4]triazine Derivatives

1-(3-Amino-6-methyl-4-pyridin-3-yl-1H-pyrazolo[3,4-b]pyridin-5-yl)ethanone (3) was obtained in very pure state and used as a good starting material for the present study. It diazotized to give the corresponding diazonium salt 9 and also reacted with phenyl isothiocyanate to give the corresponding thiourea derivative 4. Compound 4 was used for the preparation of thiazole derivatives 5–8 via the reaction with active halogen-containing compounds. On the other hand, compound 9 coupled with several active –CH₂- containing compounds to afford the corresponding triazine derivatives 10–17. Considering the data from IR, ¹ H NMR, mass spectra, and elemental analyses, the chemical structures of the newly synthesized heterocyclic compounds were elucidated. Cytotoxicity, anti-HSV1, and anti-HAV-MBB activity were evaluated for the newly synthesized heterocyclic compounds.     

Hydrothermal synthesis and structure characterization of a new organic–inorganic composite (4,4′-H2bipy)2(4,4′-hbipy)2(ZnW12O40)·6H2O

A new organic–inorganic composite (4,4′-H₂bipy)₂(4,4′-Hbipy)₂(ZnW₁₂O₄₀)·6H₂O has been prepared by hydrothermal reaction and characterized by elemental analysis, IR and UV spectra, thermal analysis and single-crystal X-ray structural analysis. It belongs to the monoclinic system, space group P2₁/c, with a?=?18.637(4), b?=?14.003(3), c?=?26.470(5)?Å, β?=?104.78(3)°, V?=?6680(2)?ų, Z?=?4. Structural analysis indicates that the title complex consists of a Keggin anion [ZnW₁₂O₄₀]^6?, 4,4′-bipyridine and water of crystallization, constructing a supramolecular system through hydrogen bonding interactions. Thermal analysis shows that the heteropolyanion [ZnW₁₂O₄₀]^6? starts to decompose at 587.0°C.     

Modification of supramolecular assemblies based on C4H7(CH3)Te heterocycle and cooperative participation of intermolecular I···I, Te···I, Te···O secondary bonds; C(sp3)–H···O and C(sp2)–H···O hydrogen bonds

2-Methyl-1,1-dicarboxylato-1-telluracyclopentanes C₄H₇(CH₃)Te(OCOR)₂ (R=OCO, C₆H₅, 4-NO₂C₆H₄, 3,5-(NO₂)₂C₆H₃, C₆H₅CH=CH, 4-OCH₃C₆H₄) (2–7) were synthesised from the reactions of 2-methyl-1,1-diiodo-1-telluracyclopentane (1) and corresponding silver salts and characterised by (IR &¹HNMR) spectroscopy. The structures of C₄H₇(CH₃)TeI₂ (1), C₄H₇(CH₃)Te(OCOC₆H₅)₂ (3) and C₄H₇(CH₃)Te(4-NO₂C₆H₄OCO)₂ (4) were established by single crystal X-ray diffraction studies. The structures of 1, 3 & 4 (the immediate environment about tellurium is that of distorted trigonal bipyramidal geometry with a stereochemically active electron lone pair) are described in the context of their ability to generate intermolecular I···I, Te···I, Te···O secondary bonds; C(sp³)–H···O and C(sp²)–H···O hydrogen bonds leading to the formation of polymeric, tetrameric and trimeric supramolecular assemblies. The modification of supramolecular assembly present in the precursor 1 is demonstrated and the cooperative participation of C(sp²)–H···O & C(sp³)–H···O hydrogen bonds, probably, helpful in strengthening the supramolecular assembly is discussed.

Crystal and molecular structure studies of 1′-Benzyl-8-(4-fluorobenzyl)-8-azaspiro[bicyclo-[3.2.1]octane-3,4′-imidazolidine]-2′,5′-dione

The title compound 1′-Benzyl-8-(4-fluorobenzyl)-8-azaspiro[bicyclo[3.2.1] octane-3,4′-imidazolidine]-2′,5′-dione, C₂₃H₂₃FN₃O₂ is synthesized and the structure is investigated by X-ray diffraction studies. The compound crystallizes in the triclinic crystal class in the P1 space group. The hydantoin ring adopts a planar conformation and is affected by the π conjugation. The pyrrolidine and piperidine rings in the bicyclo octane moiety adopt envelope and chair conformations respectively. The structure exhibits both inter- and intramolecular hydrogen bonds of the type N-H...O, C-H...O, and C-H...N. The oxygen atom in the hydantoin ring simultaneously accepts two hydrogen bonds to form a three-centered hydrogen bonding pattern.     

Synthesis of 3,4-Biheterylthieno[2,3-b]-thiophenes. Part I: Synthesis of 3,4-Bi(1′,3′,4′-thiadiazolyl-, s-triazolyl-,1′,3′,4′-thiadiazinyl-, 1′,3′,4′-triazinyl-, thiazolyl-, 1′,3′-thiazinyl- and primidinyl)-thieno[2,3-b]thiophenes

3,4-Diamino-2,5-dicarbethoxythieno[2,3-b]thiophene ( 1 ) was allowed to react with NaNO 2 and active methylenes to afford the corresponding azo compounds 2a-c . Hydrazonyl chloride 2a was treated with carbon disulfide, phenyl isothiocyanate, benzonitrile, benzyl cyanide, malononitrile, benzalaniline, ethyl mercaptoacetate, and ethyl glycinate to give 1,3,4-thiadiazolyl-, s-triazolyl-, 1,3,4-thiadiazinyl-, 1,3,4-triazinylthieno[2,3-b]thiophenes 3-6 respectively. The reaction of 2b,c with urea, thiourea, and guanidine afforded pyrimidinyl- and thiazinylazothieno [2,3-b]thiophenes 7-10 respectively. Bithiazolylthieno[2,3-b]thiophenes 11 and 13 were synthesized by treating compound 1 with CS 2 along with halo compounds. The addition of S,S-, N,S-, and N,O-acetals to the Schiff base 14 afforded compounds 15-17 respectively.     

[Ni(bpy)(mal)(H2O)3]·H2O and [Ni(4,4′-dmbpy)(mal)(H2O)3]·1.5H2O: syntheses,crystal structures,magnetic properties,and computational study of stacking interactions

[Ni(bpy)(mal)(H₂O)₃]·H₂O and [Ni(4,4′-dmbpy)(mal)(H₂O)₃]·1.5H₂O (mal = maleato; bpy = 2,2′-bipyridine; 4,4′-dmbpy = 4,4′-dimethyl-2,2′-bipyridine) exhibit molecular crystal structures. The Ni(II) central ions in both complexes are six-coordinate by one chelate bonded L–L ligand, three aqua ligands, and one position is occupied by a maleato oxygen donor atom. Hydrogen bonded ribbon-like supramolecular structural motifs are present in both studied complexes; these are linked by weaker C–H?O hydrogen bonds in [Ni(bpy)(mal)(H₂O)₃]·H₂O, whereas in [Ni(4,4′-dmbpy)(mal)(H₂O)₃]·1,5H₂O the hydrogen bonded ribbons are linked by O?H-O-H?O hydrogen bonds with the participation of the additional water solvate molecule positioned on the twofold axis. In both structures, π–π stacking interactions with different patterns in respective structures were found. The role of dispersion energy and many-body effects in the stabilization of bpy and 4,4′-dmbpy stacking interactions were investigated using methods of computational chemistry. Those confirm the dispersion-dominated stabilization of the 4,4′-dmbpy supramolecular chain-like structure, with only marginal impact of cooperativity effects. Thermal decompositions of both complexes start with dehydration. Magnetic susceptibility studies performed from 2 to 300 K revealed a dominant effect of the zero-field splitting of the Ni(II) ion, governing the low-temperature magnetic properties of both compounds.     

Synthesis and crystal structures of 3D supramolecular compounds: [ M (4,4′-bipy)2(H2O)4] · (4,4′-bipy)2 · (3,5-daba)2 · 8H2O ( M =Zn,Mn)

Two new supramolecular compounds [M(4,4′-bipy)₂ (H₂O)₄] ·?(4,4′-bipy)₂ ·?(3,5-daba)₂ ·?8H₂O (M=Zn(1) or Mn(2), 4,4′-bipy =?4,4′-bipyridine, 3,5-daba =?3,5-diaminobenzoic acid anion) were synthesized and characterized by elemental analysis and X-ray crystal diffraction. In [M(4,4′-bipy)₂(H₂O)₄]²⁺, the M(II) is coordinated by two nitrogen atoms from two 4,4′-bipy molecules and four oxygen atoms from four waters to form an octahedral configuration. There exist uncoordinated 4,4′-bipy molecules, 3,5-diaminobenzolate counterions and water guests in the compounds. The 3D structures of the title supramolecular compounds are constructed by rich hydrogen bonds among [M(4,4′-bipy)₂(H₂O)₄]²⁺, uncoordinated 4,4′-bipy molecules, water molecules and 3,5-daba, containing a diverting hexa-member water ring.     

Formation of [FeW12O40]5− under hydrothermal conditions: syntheses,crystal structures,and characterization of [Fe(2,2′-bipy)3]2[HFeW12O40] · 5H2O and (4,4′-H2bipy)6(Hpy)2(H3O)[FeW12O40]3 · 11H2O

Two supramolecular compounds based on tungstoferrate [FeW₁₂O₄₀]^5?, [Fe^II(2,2′-bipy)₃]₂[HFeW₁₂O₄₀] · 5H₂O (1), and [Hpy]₂[4,4′-H₂bipy]₆(H₃O)[FeW₁₂O₄₀]₃ · 11H₂O (2) (py = pyridine, bipy = bipyridine) were synthesized hydrothermally and characterized structurally. The hydrogen bonds between polyoxoanions and water and the edge-to-face π–π interaction between [Fe^II(2,2′-bipy)₃]²⁺ with a shortest C–C distance of 3.513 Å are the main forces to construct the 3-D architecture of 1. In 2, a 3-D supramolecular architecture is assembled by the tungstoferrate anions, protonated 4,4′-bipy cations, and water through hydrogen bonding. The variable-temperature magnetic susceptibilities indicate that 1 is paramagnetic with μ _eff corresponding to one Fe(III) with spin-only contribution, showing that Fe in the coordination cations has a +II oxidation number and low spin state.     

S = 1/2 Heisenberg antiferromagnetic spin chain [Cu(dmbpy)(H2O)2SO4] (dmbpy = 4,4′-dimethyl-2,2′-bipyridine): Synthesis,crystal structure and enhanced magnetocaloric effect

[Cu(dmbpy)(H₂O)₂SO₄] in the form of small blue crystals was prepared from the aqueous-ethanolic reaction mixture formed of CuSO₄ and dmbpy (dmbpy = 4,4′-dimethyl-2,2′-bipyridine). Its crystal structure consists of chains in which hexacoordinated Cu(II) atoms are linked by (μ₂-SO₄)²⁻ anions. The Cu(II) atom exhibits elongated tetragonal bipyramidal coordination with one chelate bonded dmbpy and two aqua ligands placed in the equatorial plane while the axial positions are occupied by bridging sulfato ligands. The study of electron spin resonance and specific heat enabled to identify the studied material as an S = 1/2 Heisenberg antiferromagnetic chain with weak intrachain exchange interaction, 2J/k_B = −1.12 K and a small anisotropy of g – factor, Δg/g ≈ 0.1. The analysis of the magnetic entropy revealed pronounced release of the entropy at the saturation magnetic field, which for spin chains induces quantum phase transition, namely B_sat = 1.56 T. The maximum isothermal change of the entropy ΔS_M = 2.86 J/Kmol is comparable to that released in a critical region for materials with magnetic phase transitions. The obtained results suggest that the existence of a quantum critical point significantly influences finite-temperature properties.     

Synthesis, characterisation and thermal properties of [Cu(VO)2(C2O4)3(4,4′-bpy)2·2H2O]A 2D polymer

The heterometallic complex [Cu(VO)₂(C₁₀H₈N₂)₂(C₂O₄)₃·2H₂O] has been prepared and characterised by electronic and IR spectra, molecular electrical conductivity and thermal behaviour. A polymeric structure is proposed with oxalate and 4,4′-dipyridine acting as bridging ligands and VO(IV) of C_4v symmetry and Cu(II) in octahedral surrounding the oxalate anion V_4h.     

Synthesis,characterization and 1H NMR studies of [Co(en)2(malH)2]ClO4·H2O

The trans-[Co(en)₂(malH)₂]ClO₄·H₂O complex was prepared by the reaction of sodium hydrogen malonate with [Co(en)₂(H₂O₂](ClO₄)₃ in the presence of a large concentration of perchlorate ion. It showed a three-band visible spectrum (γγ_max 357, 448 and 542.6 nm), diagnostic of a trans-MA₄B₂ system and gave characteristic IR bands as expected for a trans-bisethylenediamine cobalt(III) complex. The ¹H NMR spectrum in DMSO-d₆ revealed a broad band at 5.8 ppm assignable to the amino hydrogen and a single band at 2.68 for the ethylene group of the chelate ring. The

group of the hydrogen malonate ion appeared as a sharp singlet at 2.95 ppm and integration showed the presence of two bimalonate groups. The reactive methylene protons were found to be exchangeable. Ion association by counter ions of the complex ion in DMSO-d₆ showed no preference among amino protons. This is as expected for trans complexes with D_2h-symmetry.     

Three-component condensation of 5-aminopyrazole derivatives with isatins and Meldrum’s acid. Synthesis of 1,7-dihydrospiro[pyrazolo[3,4-b]-pyridine-4,3′-indole]-2′,6(1′H,5H)-diones

A new method for the synthesis of hitherto unknown substituted 1,7-dihydrospiro-[pyrazolo[3,4-b]pyridine-4,3′-indole]-2′,6(1′H,5H)-diones based on three-component condensation of 5-aminopyrazoles with Meldrum’s acid and isatins is developed.     

Synthesis and crystal structure characterization of supramolecular complex [Cd2(Bipy)2(L)2(H2O)2] · 9H2O (H2L = 2,2′-bipyridyl-6,6′-dicarboxylic acid)

In the complex [Cd₂(Bipy)₂(L)₂(H₂O)₂] · 9H₂O, the center atom Cd(II) presents a seven-coordinated pentagonal bipyramidal geometry with seven coordination bonds, four Cd-N bonds, and three Cd-O bonds. X-ray structural analysis shows that nineteen water molecules formed a large water cluster, the cluster and the composition connected to form 2D plane areolar framework and 3D zigzag networks structure through π-π-stacking and hydrogen bonding. This composition in the previous report is rare.     

Synthesis and Structure of an Interlock Network Frame of Cobalt(Ⅱ) Coordination Polymer {[Co(azpy)_2(NCS)_2]·1/4EtOH·1/2H_2O}_n (azpy=4,4′-Azobispyridine)

A compound {[Co(azpy)_2(NCS)_2]·1/4EtOH·1/2H_2O}_n(1), where azpy=4,4'-azobispyridine, was synthesized and characterized by means of IR, TGA-DTA, magnetic susceptibility and X-ray single crystal diffraction. It consists of two independent sets of fully interlocked two-dimensional networks with the dihedral angle 61.7°, organized in parallel stacks of the sheets which are made of edge-shared [Co(Ⅱ)]_4 squares separated by 0. 9062nm, and defined size rhombic channels. The thermal gravimetric analysis indicates that the framework is stable up to 198℃. The variable-temperature magnetic susceptibility measurements indicated that there is a weak antiferromagnetic interaction between the cobalt(Ⅰ) ions in the complex (1).     

Tricarbonylrhenium(I) bromide complexes with N,N′-bis[1-(4-chlorophenyl)ethylidene]ethane-1,2-diamine and N,N′-bis[1-(4-nitrophenyl)ethylidene]ethane-1,2-diamine–syntheses,structures, electrochemical and spectroscopic studies

Two rhenium(I) complexes, [Re(CO)₃Br(L ⁿ )] (n = 1, 2), (L¹= N,N′-bis[1-(4-chlorophenyl)ethylidene]ethane-1,2-diamine and L² = N,N′-bis[1-(4-nitrophenyl)ethylidene]ethane-1,2-diamine) have been synthesized and characterized by CHN analyses, ¹H NMR, IR, and UV-Vis spectroscopy. The molecular structure of [Re(CO)₃Br(L¹)] is a distorted octahedron around rhenium with one Br, facial arrangement of three CO's, and one diimine. The UV-Vis spectra of the complexes have metal-to-ligand charge transfer bands increasing in wavelength when the L² ligand is replaced by L¹, in agreement with the oxidation potential of the complexes.