Crystal and molecular structure of voacangine: An alkaloid fromStemmadenia Donnell-Smithii

C₂₂H₂₈N₂O₃,M _r=368.5, orthorhombic, D ₂ ⁴ -P2₁2₁2₁. Unit cell dimensions at 293 K area=8.753(3),b=9.252(2),c=24.422(7) Å,V=1978(1) ų,D _c=1.24 g cm^–3, andZ=4. The structure has been determined from single-crystal data collected with a four-circle diffractometer and refined from 1562 reflections down toR=0.050 andwR=0.055. The structural features determined from chemical and spectroscopic studies are confirmed and extended. The stereochemistry at C(4) and C(18) is 4S and 18S. The indole ring is not planar and the seven-membered nitrogen-containing ring adopts a distorted-chair conformation. The indole and seven-membered rings lie on the same plane with a dihedral angle of 0.7 (1)°, while the C(5)-N(6)-C(19)-C(2) atoms of the central axis of the iso-quinuclidine tricyclic structure is perpendicular to seven-membered ring [dihedral angle is 92.7 (1)°]. The packing in the crystal is entirely due to van der Waals forces.     

Structure analyses of menthone- and isomenthone-tosylhydrazones,C17H26N2O2S

The crystal and molecular structures of two configurational isomers of the title compound have been determined by three-dimensional, single-crystal X-ray diffractometry. Both (2S,5R)- and (2R,5R)-4-methylbenzenesulfonic acid-[5-methyl-2-(1-methylethyl)cyclohexylidene] hydrazide (hereafter referred to as menthone- and isomenthone-tosylhydrazone, orI andII, respectively) crystallize in the orthorhombic space groupP2₁2₁2₁ (No. 19, D ₂ ⁴ ) with four formula units per cell anda=5.209(1),b=17.501(1),c=20.154(1)Å anda=5.281(1),b=17.300(1),c=20.422(1)Å, respectively. The phase problems were solved by direct methods and the respective final full-matrix least-squares refinements of 1767 and 3010 unique reflections converged toR=0.046 and 0.052. In both structures, the toluenesulfonamide group occupies a positionanti to the more substituted side of the cyclohexyl ring, the C(16)-C(11)-N(2) angles are significantly wider than 120°, and each sulfonamide nitrogen (1) atom appears to exhibit a distorted trigonal pyramidal geometry. The structures differ in the positioning of the isopropyl and methyl substituents on the cyclohexane ring, with thetrans isomerI having both groups equatorial, while thecis isomerII exhibits an axial isopropyl group. The molecules in the crystal lattice are held together by van der Waals forces. X-ray powder diffraction, conoscopic, infrared, and¹H and¹³C NMR analyses have been performed.(2S,5R)- and (2R,5R)-4-Methylbenzenesulfonic acid-[5-methyl-2-(1-methylethyl)cyclohexylidene]hydrazide.     

Crystal and molecular structure of ibogamine: An alkaloid fromStemmadenia galeottiana

C₁₉H₂₄N₂ is orthorhombic,D ₂ ⁴ -P2₁2₁2₁. Unit cell dimensions at 293 K area=10.346(7),b=10.464(3),c=29.083(10)Å,V=3149(4) ų,D _c =1.18 g cm^–3, andZ=8. The structure has been determined from single-crystal data collected with a four-circle diffractometer and refined from 1968 reflections down toR=0.045 and R=0.047. The structural features determined from chemical and spectroscopic studies are confirmed and extended. There are two crystallographically independent molecules (A and B). In both A and B molecules the indole ring system is planar and attached to a seven-membered nitrogen-containing ring with a distorted-chair conformation. The indole and seven-membered rings lie close to the same plane [dihedral angles are 6.6(5) and 4.1(5)° for the A and B molecules, respectively], while the C(5)-N(6)-C(19)-C(2) atoms of the central axis of theiso-quinuclidine tricyclic structure are almost perpendicular to seven-membered ring [dihedral angles are 84.7(5) and 87.9(5)° for the A and B molecules, respectively]. The A and B molecules in the crystal are packed at normal van der Waals distances.     

Structure ofcis-2,4-bis (trichloromethyl)-1,3,5,-trioxane

cis-2,4-Bis(trichloromethyl)-1,3,5-trioxane is monoclinic,C2/c, a=19.432(4),b=5.895(1),c=20.721(6) Å,=100.66(2)°,Z=8. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least-squares to a finalR value of 0.034 using 1786 reflections. The molecule is in the chair conformation with the –CCl₃ groups located equatorially [at C(2) and C(6) in the numbering scheme used in the paper]. Endocyclic parameters quoted cyclically are O(1)-C(2) 1.418(3), C(2)-O(3) 1.387(3), O(3)-C(4) 1.419(3), C(4)-O(5) 1.416(3), O(5)-C(6) 1.391(4), C(6)-O(1) 1.415(3) Å; and angles at O(1) 108.7(2), C(2) 110.5(2), O(3) 110.1(2), C(4) 109.5(2), O(5) 109.9(2), C(6) 110.5(2)°. The average endocyclic torsion angle is 59.1(5)°.     

Crystal structure of 3‐hydroxy methyl 4,6‐dimethoxy‐9‐phenylsulfonyl‐carbazole

The crystal structure of 3‐Hydroxy methyl 4,6‐dimethoxy‐9‐phenylsulfonyl‐carbazole. (C₂₁H₁₉NO₅S) has been determined [CCDC 194425]. The compound crystallizes from methanol in the monoclinic system, space group I2/c, with unit cell parameters: a = 20.498(2), b = 9.258(2), c = 21.866(3)Å, β = 116.450(10)°, Z = 8, V = 3715.2(10)ų. The crystal structure was solved by direct methods and refined by full‐matrix least squares to a final R‐value of 0.050 with 3508 unique reflections. The planar carbazole ring fragment is inclined at an angle of 79.9(1)° to the phenylsulfonyl group. The sum of the angle about N is 351.6(2)°. The atoms linked to the central hexavalent S atom are arranged in a tetrahedral configuration with the larger deviations in the O‐SO angles [O1‐S‐O2 = 119.7(2)°] and the O1‐S‐N and O2‐S‐N angles [106.1(2) and 106.9(1)°, respectively].     

Crystal and molecular structure of isovoacangine: An alkaloid from Stemmadenia Donnell-Smithii

C₂₂H₂₈N₂O₃ is monoclinic,P2₁. Unit-cell dimensions at 293 K area=10.023(5),b=6.615(3),c=14.749(6) Å,=91.41(4)°,V=978(1) ų,D _c =1.25 g cm^–3, andZ=2. The structure has been determined from single-crystal data collected with a four-circle diffractometer and refined from 1421 reflections toR=0.057. The structural features determined from chemical and spectroscopic studies are confirmed and extended. The stereochemistry at C(4) and C(18) is 4S and 18S. The indole ring is not planar and the seven-membered nitrogen-containing ring adopts a distorted-chair conformation. The angle between the normals to the planes of the indole and sevenmembered rings is 15.2(1)°, while the C(5)-N(6)-C(19)-C(2) atoms of the central axis of the iso-quinuclidine tricyclic structure is 69.1(1)°. The molecules in the crystal are held together by a hydrogen bond, a C-HO contact, and van der Waals interactions.     

Crystal Structure of 2′,3′-Di-<Emphasis Type="Italic">O</Emphasis>-Acetyl-5′-Deoxy-5-Fluorocytidine with N–H···(O,F) Proton Donor Bifurcated and (C,N)–H···O Bifurcated Acceptor Dual Three-Center Hydrogen Bond Configurations

Abstract  The title compound, C₁₃H₁₆O₆N₃F, features a central furan ring containing four carbon atom chiral centers with a 4-amino-5-fluoro-2-oxopyrimidine group, two acetyl groups and a methyl group bonded at the 2,3,4,5 positions, each in an absolute R configuration (2R,3R,4R,5R). It crystallizes in the monoclinic space group C2 with unit cell parameters a = 14.5341(3), b = 7.26230(10), c = 16.2197(3) ?, β = 116.607(2)°, Z = 4. An extensive array of intra and intermolecular hydrogen bond interactions dominate crystal packing in the unit cell highlighted by a relatively rare three-center proton-bifurcated donor N–H···(O,F) hydrogen bond interaction in cooperation with a second, (C,N)–H···O bifurcated acceptor three-center hydrogen bond in a supportive fashion. Additional weak Cg π-ring intermolecular interactions between a fluorine atom and the 4-amino-5-fluoro-2-oxopyrimidine ring in concert with multiple donor and acceptor hydrogen bonds significantly influence the bond distances, bond angles and torsion angles of the deoxy-5-fluorocytidine group. Comparison to a MOPAC computational calculation provides support to these observations. Index Abstract  Crystal structure of (2R,3R,4R,5R)-2-(4-amino-5-fluoro-2-oxopyrimidin-1(2H)-yl)-5-methyl-tetrahydrofuran-3,4-diyl diacetate with dual N–H···(O,F) proton donor bifurcated and (C,N)–H···O bifurcated acceptor three-center hydrogen bond configurations is reported and its geometric and packing parameters described and compared to a MOPAC computational calculation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The cyanocarbonyl group: synthesis and crystal structure of an imidazole carbonyl cyanide, C12N5OH17

1-t-Butyl-5-N-(dimethylaminomethylene)aminoimidazole-4-carbonyl cyanide (BUNDAMIC) is the first acyl cyanide to be synthesized from an imidazole-4-carboxylic acid, diethylphosphorocyanidate, and triethylamine and its structure determined by x-ray crystallography. It crystallizes with four molecules in the monoclinic space group C2/m with a = 17.824(2), b = 6.784(2), c = 11.039(2) Å, and = 96.17(1)°; R = 0.036 over 1086 unique x-ray reflections. The cyanocarbonyl group is nearly linear, C-C N angle 174.4(3)°, with dimensions C N, 1.137(3); C-C 1.493(3); and C=O N 1.224(3) Å. The imidazole ring, in the mirror plane, has a lengthened C4 = C5 bond of 1.421(3) A, and there is a short ring-closing approach, H O6 =2.07 Å, between the methyleneamino hydrogen and the carbonyl oxygen.     

Crystal structure of enantiomeric 3-amino-6,7-dihydro-6-hydroxy-5H-1,2,4-triazolo [3,4-b] 1,3-thiazine

The crystals of C₅H₈N₄OS are orthorhombic, space group P2₁2₁2₁ (Z=4),a=5.601(1),b=10.224(3), andc=12.233(2) Å. 1,2,4-Triazole ring is approximately planar while 1,3-thiazine ring adopts a C(5)-sofa conformation flattened at the N–C–S end with axial hydroxy group at the opposite side of the ring. The three intermolecular hydrogen bonds, N(3)...O(8), N(3)...N(2), and O(8)...N(1) form a three-dimensional hydrogen bonds network in the crystal. The structure is the first 5H-1,2,4-triazolo [3,4-b] 1,3-thiazine reported in the literature. It shows less aromatic character and smaller delocalization of electrons of the triazole ring than those in known analogs with [5,1-b] junction.     

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.     

Crystal and molecular structure of (2-amino-4-methyl-1-pyridinio) cyanoborane

The crystal structure of the title compound, C₇H₁₀N₃B, has been determined by X-ray diffraction using CuK radiation. The crystals are monoclinic,P2₁/c witha=6.941(2),b=15.961(3),c=7.739(2) Å,=90.5(2)° andZ=4. The structure was solved by direct methods, and refined by full matrix least squares to a finalR-value of 056 with 833 observed reflections. The molecule is in the elongated form, but is not planar; the torsion angle C(2)-N(1)-B-C(8) is 82.9(4)°. The bond distances N(1)-B=1.587(5) Å; B-C(8)=1.586(6) Å; C(8)N(3)=1.134(5) Å. The B-C-N moiety is slightly [176.9(4)°] nonlinear. The molecules are linked by weak hydrogen bonds N(2)-H(1N)N(3), N(2)-N(3)=3.055(5) Å and N(2)-H(2N)N(3), N(2)-N(3)=3.165 Å.     

Crystal and Molecular Structure of (9R)‐10,11‐dihydro‐6′‐methoxy‐cinchonan‐9‐ol‐4‐chlorobenzoate hydrochloride

The crystal structure of the title compound has been determined by single crystal X‐ray diffraction methods. C₂₇H₂₉N₂O₃Cl.HCl is one of the cinchona alkaloids. It crystallizes in the space group P2₁2₁2₁ with a = 11.745(3), b = 12.353(6), c = 17.253(6) Å and Z = 4. The structure was refined to a final R value of 0.062 for 2155 observed reflections. The C—N distances are unequal in the quinoline ring system. In quinulidine ring, the bonds around N are more tetrahedral. The spatial arrangement and torsion angles show the open conformation of the molecule. The molecular packing is stabilized by hydrogen bonding.     

Crystal Packing of Potentially Mesomorphic Azobenezene Derivatives R1–C6H4–N=N–C6H4–R2 (R1, R2 = CH3COO,C2H5O; CH2=C(CH3)COO,C2H5; C6H13COO,C2H5O)

Crystallography Reports - The structure and thermal properties of azobenzene derivatives R1–C6H4–N=N–C6H4–R2, where R1/R2 = CH3COO/C2H5O (I), CH2=C(CH3)COO/C2H5 (II), or...     

Molecular structure of the 3-oxide of N-benzyl-3,6-dithiacyclohexene-1,2-dicarboximide

Crystals of the title compound (C₁₃H₁₁,NO₃S₂) are orthorhombic: space groupPbca,a=23.030(3),b=12.897(2),c=8.695(1). The structure was solved by direct methods and refined by full-matrix least-squares procedures to giveR=0.073 andR _w =0.071 for 1303 intensities above 3(I). The 3,6-dithiacyclohexene ring has a deformed half-chair conformation with the axial configuration of the S(3)=O bond. Oxidation of the S(3) atom brings about different lengths of analogous intraring bonds [S(3)-C(2)=1.756(7) and S(6)-C(1)=1.710(7) Å] and angles [C(4)-S(3)-C(2)=95.5(3)° and C(1)-S(6)-C(5)=98.7(3)°]. The structure contains a shortened SO intermolecular contact of 3.053(5) Å.     

Structure and conformation of a nickel complex: {2‐Hydroxo‐3‐piperidine‐1‐yl‐methyl‐N,N′(bis‐5‐bromobenzylpropylenediimine)nickel(II)perchlorate}

The title compound, a nickel complex [C₂₃H₂₆N₃O₂Br₂Ni.(ClO₄)] (CCDC 199520) crystallizes in triclinic space group P with the cell parameters a = 10.2560(4), b = 10.8231(4), c = 12.0888(5)Å, α = 99.404(1), β = 99.780(1), γ = 92.252(1)° and V = 1301.49(9)ų. The structure was solved by Patterson method and refined by full‐matrix least‐squares procedures to a final R = 0.0497 using 6287 observed reflections. In the complex, the piperidine ring takes chair conformation and the geometry around the Ni ion is slightly distorted square planar. The dihedral angle between the planes [N‐Ni‐N and O‐Ni‐O] is 9.4(1)°. The chelate ring containing both the nitrogen atoms adopts twisted boat conformation. The molecules in the crystal are stabilized by N‐H…O and C‐H…O types of hydrogen bonds in addition to a C‐H…π interaction. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Isomerism in some 1-oxa-3,5-dithians and the X-ray structure determination of 2,6-bis(trichloromethyl)-4-dichloromethylene-1-oxa-3,5-dithian

2,6-bis (trichloromethyl)-4-dichloromethylene-1-oxa-3,5-dithian is triclinic,P¯1,a=10.125(3),b=10.294(3),c=14.631(10) Å,=92.84(5),=96.51(5), =96.18(2)°,V=1503 ų,Z=4. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least squares to a finalR value of 0.035 using 3961 reflections. The conformation of the molecules is twist-boat, one molecule being almost symmetrically twisted about the O-C(Cl₂) direction. The range of endocyclic O-C-S angles is 111.8(3) to 115.1(3)° and data are given which support the possibility of there being a correlation between the endocyclic O-C(X)-S angle, the C-O-C(X)-C(Cl₃) torsion angle, and the C-S-C(X)-C(Cl₃) torsion angle. The -CCl₃ groups are in pseudoequatorial positions. Average bond lengths (Å) for the two molecules are C-O 1.405, C(sp ³)-S 1.822, C(sp ²)-S 1.759, C-C_eq 1.529 and average endocyclic angles (°) are O 117.3, C (sp ³) 113.5, S 97.4, C(sp ²) 119.3, the esds on the individual bond lengths and angles being in the ranges of 0.003–0.004 Å and 0.2–0.4° respectively.     

Crystal and Molecular Structure of 3,5-Diphenyl-4,5-dihydro-2-phenylcarboxamide-1H-pyrazole

Crystal structure of the title compound C₂₂H₁₉N₃O is determined by single crystal X-ray diffraction (sp. gr. P2₁/c, Z = 4). The molecule as a whole, is not planar: phenyl cycles are rotated relative to the plane of pyrazole ring. N?H···N intramolecular hydrogen bond forms five-membered ring fused to pyrazole ring. There are also intramolecular C?H···O and C?H···π interactions. Intermolecular C?H···O hydrogen bond links the molecules into a C(7) chain along the a axis. The crystal structure is stabilized also by C–H···π and π···π intermolecular hydrogen bonds.     

Studies of substituted quinoxaline-di-N-oxides. Part 1. Crystal structure and molecular conformation of 2-[N-(2-hydroxyethyl)carboxamide]-3-methylquinoxaline 1,4-dioxide

A single crystal X-ray investigation of the yellow 2-[N-(2-hydroxyethyl) carboxamide]-3-methylquinoxaline 1,4-dioxide, a commercially available growth promoter used in agricultural stock farming, shows that the molecule is planar. The dihedral angle between the benzene and heterocyclic rings is 0.5°. The N(1)-O(1) and N(2)-O(2) distances are: 1.286(1) and 1.304(1) Å. The C(1)-C(2) bond of the pyrazine ring is not lengthened by substitution at the C(1) and C(2) atoms and is 1.421(2) Å. The atoms O(1) and O(2) deviate by 0.036(2) and 0.123(2) Å from the least-squares plane through the heterocyclic ring. The deviation of the C(12) atom is –0.012(2) Å. The plane through the atoms C(1), C(9), N(3), and O(3) makes an angle of 100.5(2)° with the heterocyclic ring plane. Intermolecular hydrogen bonds O(4)-HO(4)O(3) between the hydroxyl and carbonyl groups generated alternating, antiparalled chains extending in thea direction. The crystals are triclinic,P¯1 (No. 2), witha=7.469(2),b=8.111(2),c=10.357(3) Å,=80.11(2),=88.90(2), =67.73(2)°, andV=571.3(2) ų. The structure was solved by direct phase determination guided by negative quartets and refined by full-matrix least squares to anR value of 0.041 for 2159 observed reflections.Commercially known asOlaquindox.     

Synthesis and X‐ray structure of two conformational isomers of [Zn(medpt)(SCN)2], medpt = bis (3 – aminopropyl)methylamine

Two conformational isomers of [Zn (medpt)(NCS)₂], medpt=bis(3‐aminopropyl) methylamine, (1) and (2) have been synthesised and the crystal structures are determined using single crystal X‐ray diffraction. The structures of the complexes have been solved by Patterson method and refined by full‐matrix least‐ squares techniques to R1 = 0.0524 for (1) and R1 = 0.0506 for (2), respectively. The geometry around the Zn(II) centre in both isomers is distorted trigonal bipyramidal. The two pendent thiocyanate moieties in (1), with Zn–N–C angles 167.9(4)–173.9(4)º, coordinate the mental centre almost linearly while the corresponding coordinations in (2) are significantly bent [Zn–N–C angles 150.8(3)–153.1(2)°]. Intermolecular N–H…S hydrogen bonds stabilise the crystal packing in the complexes forming infinite chains parallel to the [100] direction. The combinations of molecular chains generate three/two dimensional supramolecular framework in complexes (1) and (2). (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

α-Hydroxymethylaspartic acid: Synthesis and absolute configuration by X-ray analysis of its derivative (+)-4-benzoylamino-4-carboxy-γ-butyrolactone

(+)-4-Benzoylamino-4-carboxy--butyrolactone was synthesized, and its structure solved by direct methods and refined toR=0.033. The molecule adopts a skew conformation with a C7-N1-C8-C12 torsion angle of 59.6(2)°. The lactone ring has an envelope conformation, with the C(8) atom deflected from the ring plane. The absolute configuration of (+)-benzylami-no-4-carboxy--butyrolactone5 was assigned asR by the application of Hamilton's test to the unique diffraction data, and confirmed by the estimation of the Bijvoet coefficientB fromhkl and diffraction data. This result proves theR configuration for (+) enantiomer of the parent-hydroxymethylaspartic acid.