Crystal structure and absolute configuration of the indole alkaloid arborescidine C

The structure and absolute configuration (3R, 17R) of the indole alkaloid arborescidine C were determined by x-ray diffraction. The six-membered ring assumes a half-chair conformation and the seven-membered ring has a twist-like conformation. The crystal packing is characterized by intermolecular hydrogen-bonding between the hydroxyl group and nitrogen atom N4 which leads to the formation of infinite chains of molecules along the a-axis of the crystal. The absolute configurations of two related indole alkaloids, arborescidine B and arborescidine D are inferred from the experimentally determined configuration of arborescidin C molecule. A comparison of the present structure with that of a related indole alkaloid akagerine showed significant conformational and configurational differences. Crystal data: C₁₆H₁₉N₂OBr, orthorhombic, P2₁2₁2, a = 10.3376(8), b = 15.461(4), c = 9.2094(9)Å, V = 1471.9(6)ų, Z = 4, D _calc = 1.510 g cm^–3, = 1.54178Å.     

An X-ray Crystallographic Study of the Related Triazenes, 1,4-Di[(<Emphasis Type="Italic">E</Emphasis>)-2-(2-nitrophenyl)-1-diazenyl]piperazine and Methyl 4-{(E)-2-(4-methylpiperazino)-1-diazenyl}benzoate

Abstract The crystal structures of methyl 4-{(E)-2-(4-methylpiperazino)-1-diazenyl}benzoate (2a) and 1,4-di[(E)-2-(2-nitrophenyl)-1-diazenyl]piperazine (3a) have been determined by single crystal X-ray diffraction analysis. The bis-triazene (3a) adopts an unusual pseudo-boat conformation in the piperazine ring, with a dihedral angle of 52.20(0.06)° between the two planes defined within the piperazine ring. The crystal structures of 2a and 3a are compared with the structure of the triazene (4) and the closely related bis-triazene (5). The piperazine ring of 2a adopts a typical chair conformation, whereas the piperazine ring of 3a adopts an unusual boat conformation. Crystal data: 2a C₁₃H₁₈N₄O₂, monoclinic, space group P2₁ /n, a = 13.849(3) ?, b = 6.577(1) ?, c = 14.904(3) ?, α = 90°, β = 96.098(3)°, γ = 90° and V = 1,349.8(4) ?³, for Z = 4. 3a C₁₆H₁₆N₈O₄, triclinic, space group P-1, a = 7.6066(6) ?, b = 8.3741(7) ?, c = 14.507(1) ?, α = 78.673(1)°, β = 81.877(1)°, γ = 73.445(1)° and V = 865.0(1) ?³, for Z = 2. Index abstract The crystal structures of methyl 4-{(E)-2-(4-methylpiperazino)-1-diazenyl}benzoate (2a) and 1,4-di[(E)-2-(2-nitrophenyl)-1-diazenyl]piperazine (3a) have been determined by single crystal X-ray diffraction analysis.     

Crystallographic analysis of Royline monohydrate [C25H41NO7 · H2O]

The crystal and molecular structures of the alkaloid Royline {(1α,6β,14α, 16β)-20-ethyl-4-hydroxymethyl)-1,6,14,16-tetramethoxyaconitane-7,8-diol} with a water molecule has been determined by X-ray diffraction analysis. The compound crystallizes in the space group P2₁ with the unit cell parameters a = 10.985(1) Å, b = 7.898(1) Å, c = 14.956(1) Å, β = 102.96(1)°, V = 1264.52 ų, Z = 2, λMoK _α = 0.71073 Å, and R = 0.033 for 2067 observed reflections. Rings A, B, and C adopt a chair conformation, ring D is a half-boat, ring E is a half-chair, and ring F is in an envelope conformation with C(14) at the flap. Molecules are linked together in the crystal by hydrogen bonds.     

Synthesis and crystal structure of 4-(p-methoxyphenyl)-3, 5-bis(4-pyridyl)-1,2,4-triazole

The 4-(p-methoxyphenyl)-3,5-bis(4-pyridyl)-1,2,4-triazole has been synthesized and its crystal structure has been determined by X-ray diffraction methods. It crystallizes in the monoclinic space group P2₁/n, with a = 12.5832(6) Å, b = 7.0512(5) Å, c = 18.4669(12) Å, = 96.826(1)°, and D_calc = 1.345 g cm^–1 for Z = 4. In the structure, two pyridyl rings, phenyl ring, and triazole ring do not share a common plane. The most favored orientation of the pyridyl rings in the crystal is that their planes are inclined toward opposite directions with respect to the triazole ring.     

Crystal structure of 2,3-dihydronaphto[2,3-b) [1,5] dioxepin

The X-ray single crystal structure of C₁₃H₁₂O₂ compound was determined. It crystallizes in the orthorombic space group P2₁2₁2₁ with a = 7.8847(7), b = 9.639(1), c = 13.432(2) Å, Z = 4 and V = 1020.8(3) ų. The final R converged to 0.037 for 1763 independent reflexions. The title compound forms layers parallel to (1 0 0) planes and the three dimensional cohesion of the crystal is assumed by Van der Waals interactions. The molecule consists of two six-membered rings (A and B) and a seven-membered ring (C). A and B rings are planar, whereas the C ring has a chair conformation     

X-ray structure analysis of 3β-hydroxy-4-(1,4-oxazin-4-yl)-androstane (C31H54NO2)

The crystal structure of 3β-hydroxy-4-(1,4-oxazin-4-yl)-androstane (C₃₁H₅₄NO₂) has been determined by X-ray crystallographic techniques. The compound crystallizes in the orthorhombic space group P2₁2₁2 with the following unit-cell parameters: a = 7.124(1) Å, b = 10.127(1) Å, c = 40.660(1) Å, V = 2933.4(1) ų, and Z = 4. The structure has been solved by direct methods and refined to an R factor of 0.067. Three six-membered rings, A, C, and E, exist in the chair conformation, while the ring B adopts a distorted half-chair conformation. The five-membered ring, D, has a distorted envelope conformation. The crystal structure is stabilized by strong intermolecular O-H...O hydrogen bonds.     

Synthesis and crystal structure of 1-acetyl-3-bromo-3-phenylazetidine and 1-phenyl-2-(N-acetyl-N-formyl)-aminoethanone

1-Acetyl-3-bromo-3-phenylazetidine (1), C₁₁H₁₂BrNO, has been synthesized and characterized by spectroscopic methods and single crystal X-ray analysis. It crystallizes in the space group P2 ₁/c with a = 8.633(1), b = 7.461(1), c = 17.204(1) Å, = 98.403(7)°, V = 1096.2(2) ų, Z = 4, D _calc = 1.540 g cm^–3. The azetidine ring is nearly planar since the four atoms are within ±0.039(5) Å of the mean square plane calculated for the heterocycle. The attempt to obtain a highly strained 2-azetine derivative from the above compound gave, surprisingly, 1-phenyl-2-(N-acetyl-N-formyl)-aminoethanone (2), C₁₁H₁₁NO₃. This compound has been also characterized by spectroscopic methods and single crystal X-ray analysis. It crystallizes in the space group P2₁2₁2₁, with a = 5.4719(3), b = 8.3205(6), c = 23.298(3) Å, V = 1060.7(2) ų, Z = 4, D _calc = 1.286 g cm^–3. The aminoethanone residue is in a near planar conformation where the torsion angles are 7(2)° for N–C–C–=O and –173(2)° for N–C–C–C(Ph).     

Crystal and molecular structure of triacanthine, 6-amino-3-dimethylallylpurine,a naturally occurring N(3)-substituted purine

The crystal and molecular structures of the naturally occurring, N(3)-substituted purine triacanthine (6-amino-3-dimethylallylpurine) are presented. Triacanthine crystallizes, from a saturated DMSO solution, in the monoclinic system, space groupP2₁/c. Crystallographic data are as follows:a = 12.451(4),b = 8.508(4),c = 11.365(3) Å, = 122.74(2) °,V _c = 1012.66 ų,Z = 4,D _m = 1.335(1),D _x = 1.333 g cm^–3. The structural solution was obtained by direct methods and has been refined, based on full-matrix least squares with 2124 observedF _o data, to a finalR value of 0.075. The principal molecular features are (1) the occurrence of the substituted purine as the amino tautomer, (2) a nearly planar purine ring system, and (3) a highly planar dimethylallyl group oriented approximately orthogonally to the purine ring system. The crystal packing is dominated by intermolecular hydrogen bonds involving the exocyclic amino group and the acceptor sites N(1) and N(9). Sheets of such hydrogen-bonded molecules are stacked along [10¯1]. Two distinct types of molecular overlaps are observed within these stacks.     

Preparation and crystal structure of spiro(5,7-dimethoxy-1(1H)oxo-2-benzopyran-3(4H),1′-cyclohexane)

Spiro(5,7-dimethoxy-1(1H)oxo-2-benzopyran-3(4H),1-cyclohexane) (C₁₆H₂₀O₄) was prepared by alkylation of o-lithio 3,5-dimethoxy-N-methyl benzamide with methylene cyclohexane oxide followed by alkaline hydrolysis and its crystal structure was determined by X-ray crystallographic techniques. The compound crystallizes into monoclinic space group P2₁/c with unit cell parameters: a = 11.914(3) Å, b = 9.861(3) Å, c = 12.508(7) Å, = 91.34(3), Z = 4. The structure has been solved by direct methods and refined to R = 0.039 for 1870 observed reflections. The heterocyclic ring adopts distorted sofa conformation while cyclohexane ring assumes a highly symmetric chair conformation. The dihedral angle between the mean planes of isocoumarin nucleus and cyclohexane ring is 105.51(5). Molecules are held together in the crystal by C=H ... O hydrogen bonds.     

Crystal Structure Investigation of 2-Pheny limidazo [f]1,10-phenanthroline

The crystal structure of the title compound (PIP) has been determined by single crystal X-ray diffraction methods. C₁₉H₁₂N₄. C₂H₅OH crystallizes in the monoclinic space group P2₁/n with a = 11.4414(8), b = 12.6052(9), c = 12.4627(8) Å, β = 100.345(2)°, Z = 4, V = 1768.17 ų, D_cal = 1.286 Mg. m⁻³, μ (MoKα) = 0.80 cm^-1, F(000) = 720. The structure was solved by the direct methods and refined by full-matrix least-squares method to a final R = 0.0337 and R_w = 0.0332 for 2306 reflections with F₀ > 4σ(F₀). The phenl ring and the imidazo[f]1,10-phenanthroline moiety are coplanar in the crystal. The packing of the molecules involves hydrogen bonded association of the hydroxyl group of ethanol both with the N H of the imidazole moiety of one PIP and one nitrogen atom of the phenanthroline moiety of another PIP.     

Crystal structure of a dehydroabietate derivative

The crystal structure of methyl-16, nor-5-hydroxy-6,7,15-trioxo dehydroabietate has been determined from three-dimensional X-ray diffraction data. The compound crystallizes in the orthorhombic space group P2₁2₁2 with unit cell parameters a = 19.226(3) Å, b = 11.075(3) Å, c = 8.375(2) Å, Z = 4, V = 1783.3(7) ų, d₀ = 1.36 gcm⁻³. The gross structure was determined by direct methods which on refinement yielded a final value of R index as 0.038. Ring A is a chair, ring B an envelope whereas the ring C adopts a strictly planar conformation. The rings A and B are trans fused. The ester group at C4 is cis fused to methyl carbon C15 whereas another methyl carbon C18 and oxo O(15) of the isopropyl group at C13 are rotated to positions 0.107(3) Å and 0.179(2) Å out of the plane of ring C.     

Crystal and molecular structure of 10,20-epoxy-grayanotoxin-II

The photooxidation with HgO in benzene and the hydrolysis with 2%-KOH in methanol of the grayanotoxin (GTX) derivative (4) gave a 10,20-epoxy-grayanotoxin-II(5). The crystal structure of (5) has been determined by X-ray diffraction at room temperature. The crystal is monoclinic, space group P2₁, with a = 14.248(10) Å, b = 6.670(10) Å, c = 9.990(10) Å, = 105.507(8)°, V = 914.9(2) ų, Z = 2. The structure was solved by direct methods and refined by full-matrix least squares methods to a final R1 = 0.046 (wR2 = 0.0833) for 1161 independent reflections. The molecule has a pentacyclic structure consisting of two five-membered, one six-membered, one seven-membered, and one three-membered rings. The three-membered ring is connected with the seven-membered ring by spiro-type bond.     

Synthesis and crystal structure of 3,4-trans-4, 5-trans-2-amino-3-cyano-1,3-dimethyloxycarbonyl-4, 5-di(3,4-methyl-enedioxylphenyl) cyclopentene

The 3,4-trans-4,5-trans-2-amino-3-cyano-1,3-dimethyloxycarbonyl-4,5-di-(3,4-methyl-enedioxylphenyl) cyclopentene has been synthesized and characterized by IR, ¹H NMR, Elemental analysis, and X-ray crystallography. It crystallizes in the monoclinic space group P2₁/n, with a = 10.936(3) Å, b = 10.142(3) Å, c = 20.001(4) Å, = 93.81(2)°, and D _calc = 1.390 g cm^–3 for Z = 4. X-ray analysis reveals that the phenyl groups and the alkoxyl carbonyl group are in the equatorial positions. The dihedral angles between the phenyl groups and the central five-membered ring are 73.08° and 62.15°. In addition, there are intermolecular hydrogen bonds in the crystal lattices.     

Crystal structure of 1-chloroanthraquinone

The X-ray crystal structure of 1-chloroanthraquinone is determined. The compound C₁₄H₇O₂Cl, is monoclinic in P2₁(#4) with a = 7.763(1), b = 3.973(2), c = 16.947(1) Å, = 95.13(1)°, V = 520.6(3) ų, D _calc = 1.548 g/cm³, and Z = 2. In the molecular structure, the Cl atom is obviously repelled by O(1). The major force of crystal formation comes from aromatic ring stacking and C–H-aromatic interaction.     

The preparation and crystal structures of some tricarbonylmanganese(I) octahedral complexes containing the 1,1-dimethylamino-2,2-diphenylphosphinoethane ligand

Four new complexes of (pn) the titled ligand have been prepared and characterized: (CO)₃Mn(pn)Br, 1; (CO)₃Mn(pn)N₃, 2; the triazalato (tz) complex, (CO)₃Mn(pn)(tz), 3 and [(CO)₄Mn(pn)]BF₄, 4. Crystal structures for the first three of these were determined. Crystal data for 1, monoclinic crystal system, space group = C2, a = 17.8587(6) Å, b = 7.9611(3) Å, c = 14.2349(4) Å, = 90.281(1)°, V = 2023.82(12) ų, Z = 4; for 2, monoclinic crystal system, space group = P2₁/c, a = 8.8933(14) Å, b = 13.844(2) Å, c = 16.361(3) Å, = 95.712(3)°, V = 2004.4(6) ų, Z = 4; for 3, orthorhombic crystal system, space group = Pbca, a = 17.9097(4) Å, b = 13.1308(4) Å, c = 21.2838(6) Å, V = 5005.3(2) ų, Z = 8.     

Crystal structure of 2-{(R)-1-hydroxy-1-[(2S)-1-tritylaziridin-2-yl] methyl}acrylate and spectroscopic properties of the (R,S) and (S,S) stereoisomers

The crystal and molecular structure of 2-{(R)-1-Hydroxy-1-[(2S)-1-tritylaziridin-2-y1] methy1}acrylate is described. Crystal data: C₂₆H₂₅NO₃, orthorhombic, space group P2₁2₁2₁, a = 9.6954(5), b = 13.1458(5), c = 16.7885(7) Å, V = 2139.8(2) ų, Z = 4. The (R,S) diastereomer shows an intramolecular hydrogen bonding N···H—O under formation of a five-membered ring with N···O distance of 2.664 Å. IR, ¹H NMR and ¹³C NMR data are discussed. The ¹H NMR of the (R,S) diastereomer shows a singlet- whereas the (S,S) diastereomer exhibits a doublet-pattern for the hydroxyl proton.     

The Crystal and Molecular Structure of 1,8-Dioxo-9- (o-nitrophenyl)-1,2,3,4,5,6,7,8-octahydroxanthene

The crystal structure of the title compound is described. The compound crystallizes in monoclinic space group P21/a with Z=4. The unit cell dimensions are a = 10.809(2), b = 9.998(2) and c = 14.855(3) Å, V = 1592(1) ų, D_cal = 1.399 g/cm³. The central ring of the octahydroxanthene moiety is slightly folded and the two outer rings are in sofa conformations. Due to the p-conjugation there is an electron delocalized stretch. The phenyl ring of the 2-nitrophenyl substituent is perpendicular to the octahydroxanthene ring system.     

Crystal and molecular structure of trans‐(±)‐3‐acetoxy‐2‐(4‐methoxyphenyl)‐4‐oxo‐2,3,4,5‐tetrahydro‐1,5‐benzothiazepine‐1‐oxide

The title compound is a structurally related isomer of diltiazem, a well known drug. This compound (C₁₈H₁₇NO₅S) crystallizes in the space group P2₁/n with a = 13.803(4), b = 7.704(3), c = 16.093(3) Å, β = 105.37(2)º, Z = 4, V = 1650.1(9) ų. The least‐squares refinement gave residual index R = 0.067 for 2831 observed reflections. The distorted seven‐membered ring in the molecule shows twist‐boat conformation. Hydrogen bonds in which the amide group at one molecule and a carbonyl group in the adjacent molecule are involved to form centrosymmetric dimers in the crystal. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Structure of 6,13-bis(<Emphasis Type="Italic">N</Emphasis>, <Emphasis Type="Italic">N</Emphasis>-dimethylcarbamoyl) thioquinanthrene

The crystal structure of 6,13-bis-(N,N-dimethylcarbamoyl)thioquinanthrene 3 has been determined as monoclinic, with space group P2(1)/c with lattice parameters a = 10.044(2) Å, b = 21.385(4) Å, c = 10.889(3) Å, = 102.92(3)°, Z = 4 and D_calc = 1.342 Mg/m³. The middle 1,4-dithiin ring in the title compound 3, C₂₄H₂₀N₄O₂S₂ is in a boat conformation with the dihedral angle between the planes of the aromatic rings 132.45(8)°.     

Crystal structure of 3β-acetoxy-pregna-5,16-dien-20-one (16 DPA)

The title compound, 3β-acetoxy-pregna-5,16-dien-20-one, C₂₃H₃₂O₃, has been synthesized by acetylation followed by oxidation of diosgenin and its crystal structure has been solved from single crystal X-ray diffraction data. The compound crystallizes into orthorhombic space group P2₁2₁2₁ with unit cell parameters: a = 6.031(4) ?, b = 12.481(2) ?, c = 27.162(5) ?, Z = 4. The crystal structure has been refined to R = 0.0597 for 1291 observed reflections. Rings A and C of the compound are in chair conformation whereas ring B is in half-chair conformation. Ring D is in envelop conformation. The A/B ring junction is quasi-trans, while ring systems B/C and C/D are trans fused about the C8–C9 and C13–C14 bonds, respectively. The steroid nucleus has a small twist, as shown by the C19–C10⋅C13–C18 pseudo-torsion angle of 9.5°. The crystal packing is determined by a pair of weak C–H⋅O hydrogen bonds in addition to van der Waals interactions.