Crystallographic and conformational analysis of 2-methyl-3-(2-nitro-phenyl)-4-phenyl-[1,2,4]oxadiazolidin-5-one

Molecular and crystal structure of 2-methyl-3-(2-nitro-phenyl)-4-phenyl-[1,2,4]oxadiazolidin-5-one, C₁₅H₁₃N₃O₄, have been determined by single crystal X-ray diffraction study. The title compound is monoclinic, with a = 10.0313(8) Å, b = 9.0372(5) Å, c = 15.5964(14) Å, β = 96.926(7)^∘, Z = 4, D_x = 1.42 g/cm³, μ (Mo-K_α) = 0.105 mm⁻¹, and space group is P 2₁/c. The structure was solved by direct methods and refined to a final R = 0.036 for 1894 reflections with I > 4σ (I). The crystal structure is stabilized by C–H⋅sO type inter-molecular, C–H⋅sN and C–H⋅sO type intra-molecular, π–π stacking and edge to face (C–H⋅s π-ring) interactions. To enlighten conformational flexibility of the title molecule, selected two torsion angles are varied from −180^∘ to +180^∘ in every 10^∘ separetely and then molecular energy profile is calculated and construed.     

Synthesis and crystal structure of 2-benzoyl-4-methyl phenyl benzoate

The crystal structure of the title compound, C₂₁H₁₆O₃, has been determined. The compound crystallizes in triclinic space group PĪ with cell parameters a = 9.2240(9) Å, b = 9.8050(8) Å, c = 10.1610(11) Å, α = 94.749(6)^∘, β = 112.544(4)^∘, γ = 102.145(6)^∘ and Z = 2. The structure exhibits both intra and intermolecular interactions of the type C–H ⋅s O. The intermolecular interaction between the molecules form centrosymmetric dimers.     

The triethyl ammonium salt of O,O′-bis(o-tolyl) dithiophosphate [Et3NH]+[(2-MeC6H4O)2PS2]?

The X-ray structure of the triethyl ammonium salt of O,O′-bis(o-tolyl)dithiophosphate, [Et₃NH]⁺[(2-MeC₆H₄O)₂PS₂]⁻, has been determined. Crystal data: Monoclinic, P2₁/c, a = 15.4342(6) Å, b = 10.1913(4) Å, c = 14.0729(6) Å, β = 100.855(1)^∘, V = 2174.0(2) Å⁻³, Z = 4. The immediate environment around phosphorous is distorted tetrahedral with two sulfur and two oxygen atoms in the coordination sphere, with N–H–S bonding involving only one of the sulfur atoms.     

C–H⋅<Emphasis Type="Italic">s</Emphasis>O hydrogen bond networks in <Emphasis Type="Italic">E</Emphasis>- and Z-unsaturated esters of C-glycosides

Methyl E(Z)-4,7 anhydro-5-benzamido-6,8-di-O-benzoyl-2,3,5-trideoxy-d-allo-oct-2-enoate have been synthesized like intermediates and isolated as single crystals during the synthesis of pyrazole-related C nucleosides as synthetic product with cytotoxic activity.¹ Crystal structures of E(Z) isomers were determined by X-ray analysis. E isomer crystallizes in the triclinic crystal system, space group P1, a = 5.319(1) Å, b = 10.758(2) Å, c = 12.229(2) Å, α = 72.38(2)^∘, β = 89.97(2)^∘, γ = 87.07(2)^∘, D_x = 1.320 Mgm⁻³ and Z isomer in the orthorhombic crystal system, space group P2₁2₁2₁, a = 5.1297(13) Å, b = 19.667(5) Å, c = 25.871(6) Å, D_x = 1.348 Mgm⁻³. The molecular structure was solved by direct method on the basis of 2609 and 2727 unique reflections recorded at the temperature 293 K (E-isomer) and 173 K (Z-isomer) up to the final R-factor 0.0378 and 0.0435, respectively. C–H⋅sO contact networks were analyzed and the correlation established between the existence of the weak C–H⋅sO hydrogen bonds and the melting point of the single crystals.     

Crystal structure of (Ph<Subscript>4</Subscript>P)[Hg(SPh)<Subscript>2</Subscript>Br]: Synthesis,characterization and structural analysis

The complex (Ph₄P)[Hg(SPh)₂Br] has been prepared and the crystal structure has been determined. The complex crystallized in the triclinic space group P with a = 9.607(5), b = 10.120(5), c = 17.071(8) Å, α = 96.00(3), β = 100.36(2), γ = 90.42(3)^∘, V = 1623(2) ų, D_c = 1.71 g cm⁻³, μ = 6.153 cm⁻¹, F(000) = 816 and Z = 2. The anionic complex [Hg(SPh)₂Br]⁻ is the monomer with distorted trigonal planar geometry. It contains relatively strongly bonded two thiolate ligands with a weaker bonding bromide ion. The crystal structure demonstrates a supramolecularity represented by nonconventional Br⋅sH–C(π) hydrogen bonds as well as aryl⋅saryl [C(π)–H⋅sC(π)] interactions. The Ph₄P⁺ cations are forming recognized extended supramolecular motifs of phenyl embraces.     

Crystal structures of mollugin and lucidin

Mollugin was isolated from the extract of Rubia tinctorum roots. Lucidin was obtained by semisynthesis from xanthopurpurin. Mollugin crystallises in space group P-1 (No. 2), a = 8.5857(7), b = 11.473(4), c = 15.024(1) Å, α = 77.64(2)^∘, β = 89.36(1)^∘, γ = 89.71(2)^∘, and V = 1445.5(5) ų, lucidin crystallises in space group P2₁/c (No.14), a = 16.800(6), b = 9.637(2), c = 7.073(7) Å, β = 98.01(5)^∘, and V = 1134(1) ų.     

Syntheses and crystal structures of two soybean isoflavone derivatives

Two soybean isoflavone derivatives, 7-methoxy-4′-hydroxyisoflavone (1) and 4′, 7-diethoxyl-5-hydroxyisoflavone (2) were synthesized and their crystal structures were determined by single-crystal X-ray diffraction. Two derivatives crystallize in the monoclinic crystal system, space group P2₁/c. The cell dimensions of 1 are a = 8.696(4) Å, b = 11.947(5) Å, c = 12.078(5) Å, β = 93.594(7)^∘, D_c = 1.423 Mg/m³, V = 1252.3(10) ų, Z = 4, and those of 2 are a = 37.672(12) Å, b = 11.228(4) Å, c = 7.582 (3) Å, β = 94.150(6)^∘, D_c = 1.355 Mg/m³, V = 3198.6(18) ų and Z = 8. They have the same isoflavone skeleton which is composed of a benzopyranone moiety and a phenyl moiety. Hydrogen bonding and π < eqid1 > π stacking interactions assemble 1 into supramolecule with a three-dimensional network. And in the crystal structure of 2, hydrogen bonding and C–H ⋅s π stacking interactions lead to the formation of a two-dimensional network.     

Synthesis and crystal structure of a novel 3D supramolecular complex [Na(DC18C6-B)][Ni(mnt)<Subscript>2</Subscript>]

A supramolecular complex [Na(DC18C6-B)][Ni(mnt)₂] (1) (DC18C6-B = cis-anti-cis-dicyclohexyl-18-crown-6, isomer B; mnt = maleonitriledithiolate) has been prepared and characterized by elementary analysis, FT-IR spectroscopy and X-ray single crystal diffraction. It crystallizes in triclinic, space group P1 with crystallographic data: a = 7.974(4) Å, b = 14.343(7) Å, c = 15.559(8) Å, α = 96.230(8)^∘, β = 100.361(8)^∘, γ = 93.849(9)^∘, V = 1733.2(15) ų, Z = 2, D_calcd = 1.408 g/cm³, F(000) = 766, R₁ = 0.0491, wR₂ = 0.1018. The formula unit contains one [Na(DC18C6-B)]⁺ complex cation and one [Ni(mnt)₂]⁻ complex anion, which are constructed into an infinite chain-like structure through Na–N bonds. The resulting chains crisscross on the [Ni(mnt)₂]⁻ complex anions and further assemble into an unusual 3D supramolecular framework via the weak interactions.     

Solid-state structure of a 1:1 adduct of 2-<Emphasis Type="Italic">t</Emphasis>-butylphenol and 3-<Emphasis Type="Italic">t</Emphasis>-butylsalicylaldehyde

The co-crystal structure of 2-t-butylphenol with 3-t-butylsalicylaldehyde (1) was obtained by single-crystal X-ray diffraction. 2-t-Butylphenol was co-crystallized with 1 equivalent of 3-t-butylsalicylaldehyde. The phase crystallizes in the monoclinic system with P2₁/c space group. The unit cell dimensions are a = 12.351(3) Å, b = 15.253(3) Å, c = 10.377(2) Å, β = 97.58(3)^∘, V = 1937.8(7) ų and Z = 4. The structure of the crystal layered by nonpolar group includes strong intramolecular and weak intermolecular hydrogen bonds. The aldehyde oxygen O2 accepts a three-centered bond through intramolecular O1–H1A⋅sO2 and intermolecular O3–H3A⋅sO2 interactions. In addition, the crystal consists of right-handed helical (P) and left-handed helical (M) chains linked by hydrogen bonding.     

Structure and magnetic properties of a dinuclear complex [Cu<Subscript>2</Subscript>(TPA)<Subscript>2</Subscript>(<Emphasis Type="Italic">o-</Emphasis>phth)](ClO<Subscript>4</Subscript>)<Subscript>2</Subscript>

A new dinuclear complex, [Cu₂(TPA)₂(o-phth)](ClO₄)₂ (TPA = tris(2-pyridylmethyl) amine, o-phth = terephthalato dianion), was synthesized and characterized by X-ray crystallography. The unit of dinuclear Cu(II) was bridged by terephthalato dianion. The complex crystallizes in triclinic space group P1, with a = 8.287(3) Å, b = 10.623(4) Å, c = 13.818(5) Å; α = 92.077(7)^∘, β = 94.768(7)^∘, γ = 90.352(6)^∘; V = 1211.4(8) ų; Z = 2; R₁ = 0.0604, wR₂ = 0.1707. In the temperature range 4–300 K, magnetic measurement shows that the exchange interaction of the two metal ions is weak ferromagnetic with J = 1.20 cm⁻¹, g = 1.97.     

Crystal structure and conformation of methionyl dipeptides: Structure of <Emphasis Type="SmallCaps">L</Emphasis>-methionyl-<Emphasis Type="SmallCaps">L</Emphasis>-asparagine: Preferred conformations of peptides containing methionyl and asparaginyl residues

Crystals of L-methionyl-L-asparagines (C₉N₃H₁₇O₄S) are orthorhombic, space group P2₁2₁2₁, with cell parameters at 294 K of a = 5.248(1), b = 13.251(2), c = 18.028(2) Å, V = 1251.6(4) ų, Z = 4, D_m = 1.40 Mg/m³, and D_x = 1.397 Mg/m³. The crystal structure was solved by direct methods and refinded by full-matrix least-squares method to a final R value of 0.059 for 1804 reflections. The peptide is slightly nonpalnar [ω = 172.0(5)^∘]; the other torsion angles ψ₁, ϕ₂, ψ₂¹, and ψ₂² are 155.6(5), −95.8(5), 152.5(5), and −29.4(6)^∘ respectively. The methionyl side chain is disordered with two possible position for its C^γ, S^δ, and C^ε atoms. The methionly side chain is twisted with χ¹ = −86.4(7), χ² = 177.5(9), and χ³ = 116.6(2)^∘ for the major conformer A. The asparaginyl side chain is also twisted with χ¹ = −76.3(5) and χ² = 102.3(6)^∘. The crystal structure is stabilized by an intermolecular network of hydrogen bonds involving the N-terminal amino group and the ε-terminal amino group of asn residue as donors and the carboxyl oxygens of the C-terminal and the peptide carbonyl oxygens as acceptor atoms.     

X-ray structure of 14-phenyldiquino[3,4 b;4′,3′-e][1,4]thiazine<Superscript>(1)</Superscript>

The title compound 1 (C₂₄H₁₅N₃S) crystallizes in an orthorhombic unit cell, with a = 8.2355(3), b = 19.1499(8), and c = 11.3520(5) Å, Z = 2, and space group Pnma. The pentacyclic ring system is folded mainly along the S–N(2) axis and slightly along the C(3)–C(4) and C(3′)–C(4′) axes. The butterfly folding angle between the two quinoline planes is 48.96(3)^∘ and the angle between the planes of the two halves of the thiazine ring is 43.46(7)^∘. The central thiazine ring is in a boat conformation. The phenyl substituent is unexpectedly in an axial location with respect to the thiazine ring with the C–N⋅ < eqid1 > ⋅S angle of 114.0(1)^∘ and it is perpendicular to the bisecting plane of the pentacyclic ring system.     

Reactivity of 1,2,4,5-tetracarboxylatebenzene with cobalt(II)

The complexes [Co(H₂O)₆][Co(BTCA)(H₂O)₄]⋅7.2H₂O (1) and [Na₂Co(H₂O)₄(μ-H₂O)₂ (μ-BTCA)] (2) (BTCA = 1,2,4,5-tetracarboxylatebenzene) have been synthesized and characterized by single crystal X-ray diffraction. Compound (1) crystallizes in the triclinic space group P-1 with a = 6.8591(9) Å, b = 9.9691(13) Å, c = 10.9231(11) Å, α = 93.021(2)^∘, β = 104.883(2)^∘, and γ = 103.702^∘ with Z = 1. This compound exhibits a 1-dimensional structure of two alternating layers. A chain of cobalt ions and BTCA constitute one layer. Cobalt complex ions and solvent water molecules occupy the other. Compound (2) crystallizes in the monoclinic space group C 2/m with a = 8.8647(6) Å, b = 10.5247(7) Å, c = 21.2265(14) Å, and β = 92.525(2)^∘, with Z = 2. This compound consists of a 3-dimensional network of cobalt and sodium ions linked by BTCA. The sodium complex moiety is disordered around a center of inversion.     

The crystal structure and thermal stability of [bis-picrate(pentaethylene glycol)] praseodymium(III)picrate complex

[Bis-picrate(pentaethylene glycol)]praseodymium(III) picrate, [Pr(pic)₂⋅(EO5]⁺[pic]⁻, was successfully obtained from the reaction of praseodymium nitrate hexahydrate, picric acid and pentaethylene glycol in acetonitrile–methanol as solvent. The crystal system is monoclinic with space group P2₁/c, a = 18.91419(11) Å, b = 9.0470(6) Å, c = 24.1209(14) Å and α = γ = 90^∘, β = 109.07(1)^∘, V = 3880.3(4) ų and Z = 4. The Pr atom is coordinated to the flexible and open EO5 ring via all the six oxygen atoms and two picrate ligands, one via phenoxo oxygen atom and the other one with both phenoxo and nitro oxygen atoms in a bidentate manner resulting a 9-coordinate tricapped trigonal prismatic geometry. The two picrate ligands coordinated to the Pr atom are at the opposite sides of the hexadentate EO5 ring with phenyl fragments almost perpendicular with dihedral angle of 89.7(3)^∘. Thermal analysis results show that the complex is stable up to 100^∘C when it began to slowly decompose and followed by an explosive decomposition at 290^∘C.     

Synthesis and crystal structures of two copper(I) π-complexes with 1-allyloxybenzotriazole of CuBr?C6H4N3(OC3H5) and 2CuCl?C6H4N3(OC3H5) compositions

Both compounds of CuBr⋅C₆H₄N₃(OC₃H₅) (sp. gr. P1, a = 7.633(1) Å, b = 9.987(1) Å, c = 14.898(2) Å, α = 104.75(1)^∘, β = 94.76(1)^∘, γ = 106.90(1)^∘) (I) and 2CuCl⋅C₆H₄N₃(OC₃H₅) (sp. gr. Cc, a = 11.2483(4) Å, b = 16.7076(6) Å, c = 7.2948(3) Å, β = 118.612(2)^∘) (II) composition were prepared by alternating-current electrochemical synthesis. In I due to a bridging function of organic moieties 16-membered cycles appear which are combined into ribbons {Cu₂Br₂[(C₆H₄N₃(OC₃H₅)]₂}_n. Each of two crystallographically independent copper atom possesses a trigonal-pyramidal arrangement with different degree of tetrahedral distortion. Distinctive numbers of hydrogen bonds around Br1 and Br2 atoms cause rather appreciable distinctions in copper–olefinic bond interaction effectiveness for each metal atom. In II Cu₂Cl₂ rhombs are joined to infinite chains oriented along [010] direction. Each ligand molecule is also coordinated through the C=C—bond of the allylic group to copper atom of one inorganic chain and through the nitrogen atom to a metal atom belonging to another copper-halide chain. Cu1 atoms is tetrahedrally surrounded by three chlorine atoms and nitrogen one, whereas a trigonal-planar arrangement of Cu2 atom is formed by two halogen atoms and slightly disordered olefinic group.     

A hydrogen-bonded dichloromethane-perchlorate-water channel in the crystal structure ofcis-[Ru(bpy)2{PPh-(o-tolyl)2}Cl+][ClO4 −]·CH2Cl2·H2O

The complexcis-[Ru(bpy)₂{PPh(o-tolyl)₂}Cl⁺][ClO₄ ^–] crystallized from a solution in dichloromethane as the dichloromethane-water solvate. The structure was refined toR=4.5% for those 2433 reflections with |F _o|>6(|F _o|). The octahedral Ru(II) cation is associated with metal-ligand distances as follows: Ru–Cl=2.434(3)Å, Ru-PPh(o-tol)₂=2.382(2)Å, and Ru–N=2.037(7)–2.088(7)Å. The structure is stabilized by a hydrogen-bonded CH₂Cl₂...ClO₄ ^–...H₂O channel which incorporates adventitious water of crystallization.     

Hydrogen bonding in aromatic formamides

The solid state structures of two p-substituted aromatic formamides have been determined. p-Nitro formamido benzene (1) crystallizes in the monoclinic space group C2/c with a = 10.9859(7), b = 10.0576(7), c = 13.0331(9) Å, β = 97.148(1)^∘ and Z = 8. p-formamido anisole (2) crystallizes in the orthorhombic space group Pna2₁ with a = 10.5598(7), b = 7.6553(5), c = 9.2522(6) Å and Z = 4. Both compounds show hydrogen bonding in the solid state, forming infinite chains via N–H⋅ < eqid1 > ⋅O = C bridges. For the anisole formamide (2), the molecules exhibit in a zig-zag arrangement. The nitro compound (1) exhibits a spiral-like wavy line with a fourfold repeating unit, making it the first formamide having a chiral N–H⋅ < eqid2 > ⋅O bridged chain reminiscent of those found for α-helices in proteins. While the individual spirals of 1 are orientated either clockwise or counterclockwise, their orientation towards each other is random.     

X-ray crystallographic structure of the 9,10-dihydro-11,12bis[(1,3,3-trimethylureido)methyl]-9,10ethanoanthracene dihydrate

As a part of studies on MDR reversal agents, structure of the 9,10-dihydro-11,12-bis[(1,3,3-trimethylureido)methyl]-9,10-ethanoanthracene dihydrate is reported. Crystal data: C₂₆H₃₄N₄O₂ × 2 H₂O; mol. mass 470.60; monoclinic; space group: C2/c, a = 15.7492(6) Å; b = 7.2245(3) Å; c = 24.3442(10) Å; β = 106.795(2)^∘; V = 2651.73(22) ų; z = 4; dx = 1.179 mg/m³; μ = 0.64 mm⁻¹; F(000) = 1016; final R = 0.061 for 2501 reflections [I > 4 σ (I)]. Only half of the molecule is unique. The two nonplanar rings from the independent part of 9,10-dihydro-9,10-ethanoanthracene adopt a boat conformation. Crystallographic data demonstrate the “syn-syn” conformation of urea substituents in the molecule. In the crystal, water molecules are linked to the main species by H-bonds: O3′⋅sH12w—O1—H11w⋅sO3′(1.5 − x, 0.5 − y, 1 − z).     

Synthesis,bioactivities, and X-ray structure analysis of 2-cyano-5-methylpyrazolo[1,5-a]pyrimidine

The title compound crystallizes in the monoclinic space group P2₁/c with unit cell parameters a = 3.8380(12), b = 11.994(4), and c = 16.245(5) Å, β = 90.743(5)^∘, V = 747.7(4) ų, and Z = 4. The final reliability index is 0.0409 for 1088 observed reflections. All the non-hydrogen atoms in the title compound are almost coplanar, the largest deviation from the mean plane being 0.030(2) Å for atom C5. The crystal cohesion is accentuated by C–H⋅sN hydrogen bond. The X-ray crystallography analysis indicates that the methyl group is at the 5-position of the compound 4 rather than at the 7-position of the isomer 4-1. The preliminary biological test shows that the title compound has moderate herbicidal activity.     

Synthesis and crystal structure of 3-chloro-<Emphasis Type="Italic">N</Emphasis>-(2-chloro-5-(1,3-dioxo-4,5,6,7-tetrahydro-1H-isoindol-2(3H)-yl)-4-fluorophenyl)-2,2-dimethylpropanamide

The title compound 3-chloro-N-(2-chloro-5-(1,3-dioxo-4,5,6,7-tetrahydro-1H-isoindol-2(3H)-yl)-4-fluorophenyl)-2,2-dimethylpropanamide was synthesized by the reaction of 2-(5-amino-4-chloro-2-fluorophenyl)-4,5,6,7-tetrahydro-2H-isoindole-1,3-dione with 3-chloro-2,2-dimethylpropanoyl chloride. Its structure was determined by X-ray single crystal diffraction. The crystal belongs to triclinic, space group P-1 with the following crystallographic parameters: a = 9.595(3) Å, b = 12.093(4) Å, c = 18.433(6) Å, α = 83.961(5)^∘, β = 84.819(5)^∘, γ = 67.920(5)^∘, μ = 0.361 mm⁻¹, V = 1967.9(10) ų, Z = 4, Dx = 1.395 mg/m³, F(000) = 856, T = 293(2) K, 1.11^∘ ≤ θ ≤ 25.01^∘. The X-ray results demonstrated that the reaction of 2-(5-amino-4-chloro-2-fluorophenyl)-4,5,6,7-tetrahydro-2H-isoindole-1,3-dione with 3-chloro-2,2-dimethylpropanoyl chloride in tetrahydrofuran at room temperature yielded 3-chloro-N-(2-chloro-5-(1,3-dioxo-4,5,6,7-tetrahydro-1H-isoindol-2(3H)-yl)-4-fluorophenyl)-,2-dimethylpropanamide.