Ethyl 3‐[1‐(5,5‐dimethyl‐2‐oxo‐1,3,2‐dioxaphosphorin‐2‐yl)propan‐2‐ylidene]carbazate: a combined X‐ray and density functional theory (DFT) study

In the title compound, C₁₁H₂₁N₂O₅P, one of the two carbazate N atoms is involved in the C=N double bond and the H atom of the second N atom is engaged in an intramolecular hydrogen bond with an O atom from the dimethylphosphorin‐2‐yl group, which is in an uncommon cis position with respect to the carbamate group. The cohesion of the crystal structure is also reinforced by weak intermolecular hydrogen bonds. Density functional theory (DFT) calculations at the B3LYP/6‐311++g(2d,2p) level revealed the lowest energy structure to have a Z configuration at the C=N bond, which is consistent with the configuration found in the X‐ray crystal structure, as well as a less stable E counterpart which lies 2.0 kcal mol⁻¹ higher in potential energy. Correlations between the experimental and computational studies are discussed.     

Synthesis,Crystal Structure,Photophysical and Electrochemical Properties of rac‐6,13‐Dihydro‐6,13‐methanopentacene

The title compound, rac‐6,13‐dihydro‐6,13‐methanopentacene ( 1 ), has been synthesized and characterized by elemental analysis, FT‐IR, ¹H NMR, UV‐Vis, HRMS spectra, cyclic voltammetry and single‐crystal X‐ray diffraction. The crystal belongs to orthorhombic, space group P2₁2₁2₁, with Z = 4 and cell dimensions a = 6.0185(4), b = 8.1914(6), c = 31.4080(19) Å. In the crystal structure, two types of intermolecular C–H···π hydrogen bonds are observed, and further stabilize the crystal structure. Its photophysical and electrochemical properties and complementary density functional theory (DFT) calculations are reported.     

N-(4-甲基苯甲酰氨基) N’-[5-(2-三氟甲基苯基)-2-呋喃甲酰硫脲的合成、晶体结构测定与生物活性测定

本文首次合成标题化合物N-(4-甲基苯甲酰氨基)-N’-[5-(2-三氟甲基苯基)-2-呋喃甲酰硫脲。化合物(C21H16F3N3O3S, Mr = 447.43)单晶经测定为单斜晶体,空间群为P -1。在晶体中,存在一些分子内和分子间的相互作用,分子间还有C—H···π 的相互作用,这可能导致晶体更稳定的原因。目标产物的结构经IR, H NMR和元素分析测定确证。初步生物活性测试表明,部分化合物对棉花枯萎病、黄瓜灰霉病、苹果轮纹病和棉花炭疽病有较好的选择性杀菌活性;部分目标化合物有较好的除草活性。     

The first square‐planar copper(II) 1:2 complex with differently coordinated 2‐hydroxybenzaldehyde 4‐allylthiosemicarbazone ligands

The title compound, [(Z)‐4‐allyl‐2‐(2‐hydroxybenzylidene)thiosemicarbazide‐κS][(E)‐4‐allyl‐1‐(2‐oxidobenzylidene)thiosemicarbazidato‐κ³O,N¹,S]copper(II) monohydrate, [Cu(C₁₁H₁₁N₃OS)(C₁₁H₁₃N₃OS)]·H₂O, crystallized as a rotational twin in the monoclinic crystal system (space group Cc) with two formula unit (Z′ = 2) in the asymmetric unit, one of which contains an allyl substituent disordered over two positions. The Cu^II atom exhibits a distorted square‐planar geometry involving two differently coordinated thiosemicarbazone ligands. One ligand is bonded to the Cu^II atom in a tridentate manner via the phenolate O, azomethine N and thioamide S atoms, while the other coordinates in a monodentate manner via the S atom only. The complex is stabilized by an intramolecular hydrogen bond, which creates a six‐membered pseudo‐chelate metalla‐ring. The structure analysis indicates the presence of the E isomer for the tridentate ligand and the Z isomer for the monodentate ligand. The crystal structure contains a three‐dimensional network built from intermolecular O—H...O, N—H...O, O—H...N and N—H...S hydrogen bonds.     

1,3‐Ninhydrin dihydrazone featuring an R44(12) motif with symmetry and comprising only N and H atoms

In the title compound [systematic name: (1Z,3Z)‐1,3‐dihydrazinylidene‐1H‐inden‐2(3H)‐one], C₉H₈N₄O, isolated molecules possess approximate noncrystallographic C_2v symmetry and their cis conformation and planarity are assisted by a pair of short intramolecular N—H...O hydrogen bonds. Each molecule is asymmetrically involved in an extensive three‐dimensional network of N—H...O and N—H...N hydrogen bonds, and the structure also exhibits weaker π–π and C=O...C interactions. The structure features an R₄⁴(12) motif consisting solely of N and H atoms and possessing crystallographic symmetry.     

dl‐Alaninium semi‐oxalate monohydrate

The structure of the title compound, C₃H₈NO₂⁺·C₂HO₄⁻·H₂O, is formed by two chiral counterparts (l ‐ and d ‐alaninium cations), semi‐oxalate anions and water molecules, with a 1:1:1 cation–anion–water ratio. The structure is compared with that of the previously known anhydrous dl ‐alaninium semi‐oxalate [Subha Nandhini, Krishnakumar & Natarajan (2001). Acta Cryst. E 57 , o666–o668] in order to investigate the role of water molecules in the crystal packing. The structure of the hydrate resembles that of anhydrous alaninium semi‐oxalate, with the water molecule incorporated into the general three‐dimensional network of hydrogen bonds where it forms four hydrogen bonds with neighbours disposed tetrahedrally about it. Although the main structural motifs in the hydrate and in the anhydrous form are topologically similar, the incorporation of water molecules in the network results in significant geometric distortion. There are several types of hydrogen bond in the crystal structure of the hydrate, two of which (O—H...O bonds between the semi‐oxalate anions and O—H...O hydrogen bonds between water and alaninium cations) are very short. Such hydrogen bonds between semi‐oxalate anions are also present in the anhydrous form of this compound. Short distances between semi‐oxalate anions in neighbouring chains in the hydrate alternate with longer ones, whereas in the anhydrous structure they are equidistant. Despite the similarity of these compounds, dehydration of the hydrate on storage is not of a single‐crystal to single‐crystal type, but gives a polycrystalline pseudomorph, preserving the crystal habit. This transformation proceeds through the formation of an intermediate compound, presumably a hemihydrate.     

Experimental and Theoretical Studies of 4‐(1‐benzyl‐5‐methyl‐1H‐1,2,3‐triazol‐4‐yl)‐6‐(2,4‐dichlorophenyl)pyrimidin‐2‐amine: A Potential Antibacterial Agent

The title compound ( 1 ), 4‐(1‐benzyl‐5‐methyl‐1H‐1,2,3‐triazol‐4‐yl)‐6‐(2,4‐dichlorophenyl)pyrimidin‐2‐amine (C₂₀H₁₆Cl₂N₆), was synthesized and structurally characterized by elemental analysis, ¹H NMR and ¹³C NMR and single crystal X‐ray diffraction. The compound crystallizes as a colourless needle shaped in the triclinic system, space group P‐1 with cell constants: a = 10.7557(11) Å, b = 12.7078(17) Å, c = 15.511(2) Å, α = 68.029(4)0, β = 86.637(5)0, γ = 87.869(4)0; V = 1962.4 (4) ų, Z = 4. There are two structurally similar but crystallographically independent molecules (A and B) in the asymmetric unit of the title compound, which is linked via N‐H…Cl hydrogen bond. An intramolecular C‐H…N hydrogen also occurs in each molecule. In the crystal, each of independent molecules forms a centrosymmetric dimer with an R²₂(8) ring motifs through a pair of N‐H…N hydrogen bonds. These dimers are further connected by intermolecular N‐H…Cl and C‐H…Cl hydrogen bonds, forming an infinite two dimensional supramolecular network lying parallel to the [010] plane. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6‐311G (d, p) basis set and compared with the experimental data. Mulliken population analyses on atomic charges, HOMO‐LUMO energy levels, Molecular electrostatic potential and chemical reactivity of the title compound were investigated by theoretical calculations. The thermo dynamical properties of the title compound at different temperature have been calculated and corresponding relations between the properties and temperature have also been obtained. The in vitro antibacterial activity has been screened against Gram‐positive (Bacillus cerus and Staphylococcus epidermidis) and Gram‐Negative (Escherichia coli, Acinetobacter baumannii and Proteus vulgaris). The results revealed that the compound exhibited good to moderate antibacterial activity.     

Hydrogen‐bonding and π–π inter­actions in 2‐amino‐4,6‐dimethyl­pyrimidinium salicylate

In the crystal structure of the title compound, C₆H₁₀N₃⁺·C₇H₅O₃⁻, the asymmetric unit contains four crystallographically independent 2‐amino‐4,6‐dimethyl­pyrimidinium and salicylate ions (Z = 8). In each of these, one of the pyrimidine N atoms is protonated, and the carboxyl­ate group of the salicylate ion inter­acts with the pyrimidine group through a pair of N—H⋯O hydrogen bonds, forming an R₂²(8) motif. The pyrimidine cations also form base pairs via a pair of N—H⋯N hydrogen bonds (involving the amino group and the unprotonated ring N atom), forming another R₂²(8) motif. Three such R₂²(8) motifs, fused together, constitute a closed cyclic aggregate, and the linking of these aggregates, arranged in consecutive layers, can be analysed in terms of off‐face stacking inter­actions.     

Preparation,Structure, and Second‐order Nonlinear Optical Properties of a Borate‐Carboxylic Acid Compound: NH4B[d‐(+)‐C4H4O5]2·H2O

The organic‐inorganic hybrid nonlinear optical (NLO) material NH₄B(d‐ (+)‐C₄H₄O₅)₂ · H₂O (NBC) was synthesized in a borate‐carboxylic acid system. Its structure was determined by single crystal X‐ray diffraction. It crystallizes in the orthorhombic system, space group Pna2₁ (No. 33), with cell parameters a = 11.484(6) Å, b = 5.354(3) Å, c = 21.079(12) Å, V = 1296.0(12), Z = 4. It exhibits a three‐dimensional pseudo tunnel structure consisting of fundamental building block [B(d‐ (+)‐C₄H₄O₅)₂]^– anions. The small cavities are occupied by the H₂O molecules and NH₄⁺ cations, which stabilize the whole structure by O–H ··· O and N–H ··· O hydrogen bonds. The powder X‐ray diffraction (PXRD) of the crystal was also recorded. Elemental analyses, FT‐IR and FT‐Raman spectra analyses, thermal analysis, and diffuse‐reflectance spectra for the compound are also presented, as are band structures and density of states calculation. Nonlinear optical measurements indicate that the material has second harmonic generation (SHG) properties and is phase‐matchable.     

Combined experimental and computational modeling studies on 3,5‐dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester

The title compound, 3,5‐Dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester, has been synthesized and structurally characterized by X‐ray single crystal diffraction, elemental analysis, IR spectra, and UV‐Vis spectrum. The crystal belongs to orthorhombic, space group P212121, with a = 5.3829(15), b = 11.193(3), c = 21.824(6) Å, V = 1315.0(6) ų, and Z = 4. The molecules are connected via intermolecular C–H···N hydrogen bonds into 1D infinite chains. The crystal structure is consolidated by the intramolecular C–H···S hydrogen bonds. Furthermore, Density functional theory (DFT) calculations of the structure, stabilities, orbital energies, composition characteristics of some frontier molecular orbitals and Mulliken charge distributions of the title compound were performed by means of Gaussian 03W package and taking B3LYP/6‐31G(d) basis set. The time‐dependent DFT (TD‐DFT) calculations have been employed to calculate the electronic spectrum of the title compound, and the UV‐Vis spectra has been discussed on this basis. The results show that DFT method at B3LYP/6‐31G(d) level can well reproduce the structure of the title compound. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

4‐Amino‐7‐(2‐de­oxy‐2‐fluoro‐β‐d‐arabinofuranos­yl)‐5‐fluoro‐7H‐pyrrolo[2,3‐d]pyrimidine: a bis‐fluorinated analogue of 2′‐deoxy­tubercidin

The title compound, C₁₁H₁₂F₂N₄O₃, exhibits an anti glycosylic bond conformation, with a torsion angle χ = −117.8 (2)°. The sugar pucker is N‐type (C4′‐exo, between ³T₄ and E₄, with P = 45.3° and τ_m = 41.3°). The conformation around the exocyclic C—C bond is −ap (trans), with a torsion angle γ = −177.46 (15)°. The nucleobases are stacked head‐to‐head. The crystal structure is characterized by a three‐dimensional hydrogen‐bond network involving N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds.     

Sodium 2‐oxo‐3‐semicarbazono‐2,3‐dihydro‐1H‐indole‐5‐sulfonate dihydrate

The title compound, Na⁺·C₉H₇N₄O₅S⁻·2H₂O, presents a Z configuration around the imine C=N bond and an E configuration around the C(O)NH₂ group, stabilized by two intra­molecular hydrogen bonds. The packing is governed by ionic inter­actions between the Na⁺ cation and the surrounding O atoms. The ionic unit, Na⁺ and 2‐oxo‐3‐semicarbazono‐2,3‐dihydro‐1H‐indole‐5‐sulfonate, forms layers extending in the bc plane. The layers are connected by hydrogen bonds involving the water mol­ecules.     

2‐[(E)‐(4‐Hydroxy‐3‐methoxybenzylidene)amino]‐N‐(2‐methylphenyl)‐4,5,6,7‐tetrahydro‐1‐benzothiophene‐3‐carboxamide

The title compound, C₂₄H₂₄N₂O₃S, exhibits antifungal and antibacterial properties. The compound crystallizes with two molecules in the asymmetric unit, with one molecule exhibiting `orientational disorder' in the crystal structure with respect to the cyclohexene ring. The o‐toluidine groups in both molecules are noncoplanar with the respective cyclohexene‐fused thiophene ring. In both molecules, there is an intramolecular N—H...N hydrogen bond forming a pseudo‐six‐membered ring which locks the molecular conformation and eliminates conformational flexibility. The crystal structure is stabilized by O—H...O hydrogen bonds; both molecules in the asymmetric unit form independent chains, each such chain consisting of alternating `ordered' and `disordered' molecules in the crystal lattice.     

3‐Benzyl‐2‐(4‐fluorophenyl)‐1,3‐thiazolidin‐4‐one

The title compound, C₁₆H₁₄FNOS, crystallizes with Z′ = 2 in the space group P2₁/c. In one of the two independent molecules, the heterocyclic ring is effectively planar, but in the other molecule this ring adopts an envelope conformation. The molecules are weakly linked by two C—H...O hydrogen bonds to form C₂²(14) chains. Comparisons are made with some symmetrically substituted 2‐aryl‐3‐benzyl‐1,3‐thiazolidin‐4‐ones.     

rac‐(Z)‐Ethyl 2‐bromo‐2‐[(3R,5R)‐3‐bromo‐5‐methyl­tetra­hydro­furan‐2‐yl­idene]acetate

In the title compound, C₉H₁₂Br₂O₃, a (tetra­hydro­furan‐2‐yl­idene)acetate, the double bond has the Z form. In the tetra­hydro­furan group, the relative configuration of the Br atom in the 3‐position and the methyl group in the 5‐position is anti. The compound crystallizes with two independent mol­ecules per asymmetric unit and, in the crystal structure, the individual mol­ecules are linked to their symmetry‐equivalent mol­ecules by C—H⋯O hydrogen bonds, so forming centrosymmetric hydrogen‐bonded dimers.     

Hydrogen Bonds in Rubidium Amide‐Ammonia(3/2), RbNH2·2/3NH3

Rubidium amide‐ammonia(3/2), RbNH₂·2/3NH₃, was synthesized from Rubidiumhydride, RbH, in liquid ammonia at ?78 °C. The compound crystallizes in the cubic space group I2₁3 with Z = 4, a = 10.0490(12) Å, and V = 1014.77(20) Å as isometric colorless crystals. The crystal structure was solved from single‐crystal X‐ray data. The structure contains a three‐dimensional network of amide anions and ammonia molecules, which are interconnected via hydrogen bonds.     

Wave‐like structure in 3‐(4,6‐diamino‐1,3,5‐triazin‐2‐yl)‐2‐naphthonitrile

In the title compound, C₁₄H₁₀N₆, which crystallizes with Z′ = 2 in the C2/c space group, the molecules are linked by N—H...N hydrogen bonds into chains, which are arranged in a wave‐like form stabilized by aromatic π–π stacking interactions. This work demonstrates the usefulness of aromatic triazine derivatives in crystal engineering.     

2‐tert‐Butylamino‐4‐chloro‐6‐ethylamino‐1,3,5‐triazine: a structure with Z′ = 4 containing two different molecular conformations and two independent chains of hydrogen‐bonded R22(8) rings

The title compound (trivial name terbutylazine), C₉H₁₆ClN₅, (I), crystallizes with Z′ = 4 in the space group Pca2₁, and equal numbers of molecules adopt two different conformations for the ethylamine groups. The four independent molecules form two approximately enantiomorphic pairs. Eight independent N—H...N hydrogen bonds link the molecules into two independent chains of R₂²(8) rings, in which the arrangement of the alkylamine substituents in the independent molecules precludes any further crystallographic symmetry. The significance of this study lies in its finding of two distinct molecular conformations within the structure and two distinct ways in which the molecules are organized into hydrogen‐bonded chains, and in its comparison of the hydrogen‐bonded structure of (I) with those of analogous 1,3,5‐triazines and pyrimidines.     

1‐(Thiophen‐3‐yl)ethanone

The structure of the title compound, C₆H₆OS, exhibits a flip‐type disorder of the thiophene ring [occupancy ratio = 0.848 (3):0.152 (3)], which is typical for many thiophene derivatives. The puckered thiophene ring is essentially coplanar with the plane formed by the non‐H atoms of the acetyl substituent, similar to its simple analogues, i.e. 3‐acetyl‐2‐carboxythiophene, 4‐acetyl‐3‐carboxythiophene and 3,5‐diacetyl‐2‐ethylamino‐4‐methylthiophene. In the crystal structure, molecules are connected by C—H...π hydrogen bonds, forming a sheet parallel to the (001) plane. Moreover, an inspection of the crystal lattice reveals that there are short S...O contacts connecting the molecules of adjacent sheets. Comparison of the title crystal structure with its simple 3‐methoxythiophene analogue shows a close similarity in the herringbone arrangement of molecules and in the presence of C—H...π interactions and S...O contacts.     

Methyl 3,6‐di‐O‐pivaloyl‐α‐d‐manno­pyran­oside

The X‐ray crystal structure analysis of the title compound, C₁₇H₃₀O₈, revealed a ⁴C₁ conformation of the pyran­osyl ring [Cremer–Pople puckering parameters of Q = 0.568 (2) Å, θ = 5.1 (2) and ϕ = 218 (3)°]. The structure shows no deviations from the geometric parameters of pyran­oside carbohydrates. The hydroxyl groups participate in O—H⃛O hydrogen bonds, forming a two‐dimensional pattern [O⃛O = 2.811 (3) and 2.995 (3) Å].