Structure of de-oxy corticosterone (4-pregnen-21-ol-3,20-dione)

Synthetic steroid de-oxy corticosterone (4-pregnen-21-ol-3,20-dione) crystallizes in the monoclinic space group P2₁, with a = 11.706(2); b = 11.171(3), c = 13.966(3) Å, and = 100.94(2)°, Z = 4. Ring A tends to acquire the conformation of a half-boat, rings B and C are in the chair configuration, and ring D is a 13, 14-half-chair. The ring junctions B/C and C/D are both trans, whereas the ring junction A/B is quasi-trans. The molecule as a whole is slightly convex toward the -side, with an angle of 16.01(0.36)° between the C10--C19 and C13--C18 vectors. Molecular packing and stacking interactions play the major role in structural association. Cohesion of the crystal is due to van der Waals interactions.     

Structure of 6α-methyl-17α-hydroxyprogesterone butanoate,C26H38O4

The title compound crystallizes in space groupP2₁2₁2₁ with lattice constantsa=16.253(3),b=17.107(3), andc=8.486(2) Å. The A ring has 1,2-half-chair conformation. The calculated steric energy of a 6-methyl-17-ester progesterone molecule is lower by about 4 kJ/mol for the normal A-ring conformation. The progesterone side chain has typical conformation for 17-ester steroids; the C(16)-C(17)-C(20)-O(20) torsion angle is –24.9(4)°.     

Crystal structure of an intermediate in the synthesis of artemisinin

C₁₄H₂₂O₃,M _r =238.33, P2₁2₁2₁,Z=4,a=6.892(2),b=11.453(1),c=17.159(5) Å. [1R–[1(R^*), 4, 4a, 8a]]–,4-Dimethyl-decahydro-7-oxo-1-naphtaleneacetic acid. The cyclohexane ring adopts a chair conformation and thecis-fused cyclohexanone ring is in a slightly distorted chair conformation. The molecular packing involves an hydrogen bond and C–H...O contacts.     

Crystal and molecular structure of 1,6-dimethyl-3,6-dimethoxy-3-[(N-methylindol-3-yl)methyl] piperazine-2,5-dione,C18H23N3O4

The structure of the title compound, C₁₈H₂₃N₃O₄, was determined by X-rays.M _r =344.40, triclinic, space groupP¯1,a=8.163(4),b=9.230(2),c=13.297(2) Å,=102.70(2),=103.58(3)°,=102.50(3)°,V=911.3 ų,Z=2,D _c =1.26 Mg m^–3. CuK radiation (graphite crystal monochromator,=1.54178 Å),(CuK)=7.50 cm^–1,T=290 K. Final conventionalR-factor=0.068,R _w =0.079 for 1912 unique reflections and 295 variables. The structure was solved usingMultan andDirdif. The title compound is the first example of a 3,6-tetrasubstituted dioxopiperazine adopting a folded conformation, owing to a direct interaction between the dioxopiperazine ring and the aromatic side chain.     

Crystal structure of a nucleoside analog, 2′,3′-dideoxy-3′-azido-5-chlorocytidine

The title compound, l-(2,3-dideoxy-3-azido--D-erythro pentofuranos-1-yl)-5-chlorocytosine, crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=5.840(1),b=13.780(1),c=15.396(2)Å,Z=4. The structure was solved by direct methods and refined by full-matrix least-squares calculations to a finalR value of 0.033 for 1688 unique observed reflections. The N-glycosidic torsion angle has a value of –160.8(1)°, in the and range. The sugar pucker is ₂ ³ T withP=180(1)° and=34(1)°. The C4–C5 conformation is +sc with =50.8(2)°. The azido group is nonlinear and oriented trans to the C3–C4 bond. The molecular packing in the crystalline space is stabilized by N-HN, N-HO, O-HO hydrogen bonds and C-HO close contacts.     

Crystal and molecular structure of 1,2-difluoroethane and 1,2-diiodoethane

A single crystal of phase 1 of 1,2-difluoroethane was grown from the melt directly on an X-ray diffractometer close to the melting point of 169 K. It crystallizes in the monoclinic space group C2/c with lattice parameters a = 7.775(4), b = 4.4973(7), c = 9.024(3) Å, = 101.73(1)°, V = 308.9(2) ų, d _calc = 1.420 g cm^–3 for Z = 4. A second phase of 1,2-difluoroethane was obtained under similar conditions which crystallizes in the orthorhombic space group P2₁2₁2₁ with the unit cell parameters a = 8.0467(16), b = 4.5086(9), c = 8.279(2) Å,V = 300.36(11) ų, d _calc = 1.461 g cm^–3 for Z = 4. In both phases the 1,2-difluoroethane molecules adopt the gauche conformation with F–C–C–F torsion angles close to 68°. Crystals of 1,2-diiodoethane C₂H₄I₂ were grown from pentane at –30°C. A platelet single crystal of the size 0.35 × 0.25 × 0.03 mm was measured with Mo K-radiation at 153 K. 1,2-Diiodoethane crystallizes in the monoclinic space group P2₁/n with a unit cell of a = 4.6051(7), b = 12.939(2), c = 4.7318(7) Å, = 104.636(3)°, V = 272.79(7) ų, Z = 2, d _calc = 3.431 g cm^–3, (MoK) = 11.353 mm^–1. In the molecule the two neighboring iodine atoms are positioned anti. The shortest intermolecular contacts occur via iodine–iodine interactions resulting in layers of molecules in the crystal.     

X-ray diffraction and total 1H and 13C NMR assignment of (RS)-5,6-dihydro-7,8-dimethoxy-5-methyl-6-(2-oxopropyl)-(2,3-methylenedioxyphenyl)-[c]-phenanthridine ((RS)-6-acetonyldihydrochelerythrine)

The X-ray diffraction structure of (RS)-5,6-dihydro-7,8-dimethoxy-5-methyl-6-(2-oxopropyl)-(2,3-methylenedioxyphenyl)-[c]-phenanthridine ((RS)-6-acetonyldihydrochelerythrine), isolated as an artifact from Bocconia Arborea, is reported. This compound crystallizes as orthorhombic system, space group Pna2₁, with a = 13.216(2) Å, b = 7.6547(10) Å, c = 20.096(3) Å. The phenanthridine central ring presents a distorted boat conformation, which gives rise to two planes with 21.30° between them. The acetonyl group at the six position forms weak C — H O and C — H -ring interactions. The title compound was completely characterized in solution by ¹H and ¹³C and 2D NMR experiments.     

Synthesis and crystal structure of 3,5-di(2-propenyl)-6-phenyl-1,3,5-triazine-2,4-dione and 2-dimethylamino-4-ethoxycarbonylmethoxy-6-phenyl-1,3,5-triazine

The title compound 3,5-di(2-propenyl)-6-phenyl-1,3,5-triazine-2,4-dione has been synthesized by the reaction of 6-phenyl-1,3,5-triazine-2,4-dione with allyl bromide. Its structure was determined by X-ray single crystal diffraction. The crystal belongs to orthorhombic, space group Pbca with the following crystallographic parameters: a = 16.282(4) Å, b = 8.888(2) Å, c = 19.281(5) Å, = 90°, = 90°, = 90°, = 0.088 mm^–1, V = 2790.1(13) ų, z = 8, Dx = 1.282 mg/m³, F(000) = 1136, T = 293(2) K, 2.11° 25.02°, the final R factor: R ₁ = 0.0430, wR₂ = 0.0981. The X-ray results demonstrate that the reaction of 6-phenyl-1,3,5-triazine-2,4-dione with allyl bromide in the presence of N,N-dimethylformamide and potassium carbonate yields the N-alkylated product. The title compound 2-dimethylamino-4-ethoxycarbonylmethoxy-6-phenyl-1,3,5-triazine has been synthesized by a new reaction, in which the solvent N,N-dimethylformamide involves. 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 = 7.977(2) Å, b = 10.394(3) Å, c = 10.837(3) Å, = 111.774(5)°, = 104.050(5)°, = 99.446(5)°, = 0.093 mm^–1, V = 776.6(4) ų, z = 2, Dx = 1.293 mg/m³, F(000) = 320, T = 293(2) K, 2.14° 25.03°, the final R factor: R ₁ = 0.0582, wR ₂ = 0.1399. The distance of N(4) C(2) (1.339 Å) is much shorter than the length of normal C N (1.47 Å) and very close to that of C-N (1.33 Å), which is indicative of the significant double bond character.     

Structure of 3α,12β-dihydroxy-2β-morpholino-5α-pregnan-20-one,C25H41O4N

The crystal and molecular structure of 3,12-dihydroxy-2-morpholino-5-pregnan-20-one, C₂₅H₄₁O₄N, has been determined:M _r =419.6,P2₁,a=13.5778(8),b=14.4340(8),c=5.8943(5) Å,=94.32(1)°,V _c =1151.9(3) ų,Z=2,D _x =1.21 g cm^–3, (CuK) = 1.5418 Å, =5.6 cm^–1,F(000)=460,R=0.039,R _w =0.040 for 2421 unique observed reflections. All six-membered rings have chair conformations, and theD ring has a 13-envelope conformation. The progesterone side chain has an unusual conformation, and the C16-C17-C20-O20 torsion angle, which defines the conformation, is –152.6(3)°. The unusual conformation seems to be forced by the intramolecular hydrogen bond between the hydroxyl group at C12 and the O20 atom from the side-chain.     

Molecular structure of 9α-fluoro-11β-hydroxy-16β-propionyloxy-17-(2-ethyl-2-ethoxy-1,3-dioxan-5-one-6-yl)-pregna-1,4-dien-3-one

The title compound is orthorhombic, space groupP2₁2₁2₁,a=15.992(9),b=15.693(9),c=11.205(6) Å,Z=4. The structure was solved from diffractometer data by direct methods, and refined toR 0.085 for 1216 observed (of a total of 2421) reflections. Strain in the almost planar ringA is indicated by the endocyclic torsion angles, ringsB andC, which aretrans fused and chair-shaped, while ringD is intermediate between a 13-envelope and a 13, 14-half-chair conformation. RingE, a 2,5,6-trisubstituted 1,3-dioxane-like unit, adopts a highly distorted boat conformation. The bending of the skeleton is toward its side. TheA-ring carbonyl substituent accepts one hydrogen bond involving a symmetry-related 11-ol function [O(1)-O(2) 2.81, O(2)-H 1.0, H---O(1) 1.8 Å/ O(2)-H---O(1) 165°].We thank the Schering-Plough Research Division, Bloomfield, New Jersey, for the gift of the sample and the Istituto di Chimica e Tecnologia dei Radioelementi C.N.R., Padova, for equipment and computing facilities.     

Crystal structure of a (25R)-2α,3α-epoxy-5α-spirostan-6, 23-dione hemi-ethyl acetate solvate

The compound (25R)-2,3-epoxy-5-spirostan-6,23-dione, crystallizes as a hemi-ethyl acetate solvate, having two host molecules of similar conformation per molecule of ethyl acetate, in the asymmetric unit. The O atom of the epoxy group is -oriented. The presence of the epoxy group disturbs the chair conformation in the ring A of the steroidal nucleus. Ring A has a C5,C10 half-chair conformation. The six-membered rings B, C, and F have chair conformation as expected. The D ring adopts a C14-envelope conformation and the E ring is midway between a C22,O3 half-chair and a C22-envelope conformations. The A/B, B/C, and C/D ring junctions are trans. Crystal data: C₂₇H₃₈O₅·1/2C₄H₈O₂, Monoclinic, space group P2₁, a = 7.7363(18) b = 28.769(12) c = 12.038(6) Å, = 90.88(5), V = 2679.0(10) ų, Z = 4. The packing of the molecules is assumed to be dictated by van der Waals interactions and by intermolecular C—H ··· O hydrogen bonds.     

Crystal structure of tylophorine methiodide monohydrate,C25H30NO 4 + I−·H2O

The crystal structure of tylophorine (Chemical name 2,3,6,7 tetramethoxy phenanthro [9,10:6, 7] indolizidine. Contribution No. 0871.) methiodide monohydrate has been determined. C₂₅H₃₀NO ₄ ⁺ I^–·H₂0, triclinic, P,a=8.831(1)Å, b=10.842(2),c=13.902(2), =105.0(1)^o, =104.7(1), =97.3(1),V=1210.22ų, Z=2,D _x =1.428 g./cm^–3, (CuK)=1.54184Å, (CUK)=107.2 cm^–1, F(000)=544,T=295^oK,R=0.038,Rw=0.046, for 2331 observed reflections withI2(I). Apart from van der Waals forces, the structure is stabilized by two hydrogen bonds of the type Ow(H) ... O and Ow(H) ... I^– involving the water molecule as the donor and atom O4 of the methoxy group and I^– as acceptors.     

Structure of 6β-acetoxyprogesterone,C23H32O4

The X-ray crystal structure of 6-acetoxyprogesterone, C₂₃H₃₂O₄, has been determined. This compound crystallizes in space groupP2₁2₁2₁ witha=13.195(3),b=15.035(4),c=10.705(3) Å,V=2139.8(9) ų,M _r=372.5,Z=4,D _x=1.156g cm^–3; MoK radiation (=0.7107 Å),=0.72 cm^–1,F(000)=808;R=0.069, andR _w=0.052 for 1292 reflections. RingA adopts a normal 1,2-half-chair conformation. The side chain is typical for a 20-ketosteroid conformation.     

Crystal structure of methyl-3, 4-O-ethylidene-β-L- arabinopyranoside

The acid-catalyzed ethylidenation of several methyl pentopyranosides has been studied and syntheses of many cyclic alkyl orthoacetates from pentopyranosides have been reported. In a study of the scope and limitation of the reduction of sugar epoxides with diborane/sodium borohydride, methyl-4-O-acetyl-2,3-anhydro--L-lyxopyranoside was reduced, yielding two products: methyl-2,3-anhydro--L-lyxopyranoside and methyl-3,4-O-ethylidene--L-arabinopyranoside. The latter product was characterized by X-ray diffraction and its structure indicates that the epoxide was not reduced as expected; rather, the epoxide was opened by the hydroxyl group of the reduced acetyl. Crystals of the title compound are monoclinic, space group P2₁ with the following cell dimensions: a = 5.818(l) Å, b = 10.842(2) Å, c =7.251(1) Å, = 91.47(1)°, Z = 2. Complete three-dimensional data (2_max = 150° for Cu K) were collected on a CAD-4 diffractometer by the –2 scan method. The structure was solved by the application of direct methods and refined by full-matrix least-square methods to a final reliability index of 0.04 for the observed 1031 reflections (I 3). The ethylidene ring has a twist conformation with a torsion angle of –42.8° about the C4–O bond. The pyranose ring is in a flattened chair conformation with the C2–C3–C4–C5 torsion angle of 33.5°. Of the acetal bond lengths, the C5–O5 length, (1.423 Å) is shorter than the values found in other methyl pyranosides. O2–H is involved in a bifurcated hydrogen bond intramolecularly to O1 and intermolecularly to O4.     

The structure and conformation of the tryptophanyl diketopiperazines cyclo(Trp–Trp)·C2H6SO and cyclo(Trp–Pro)

The structure and conformation of the cyclic dipeptides [cyclo(L-Trp–L-Trp)·C₂H₆SO] and cyclo(L-Trp–L-Pro) have been investigated with X-ray crystallographic and spectroscopic methods. Cyclo(L-tryptophanyl-L-tryptophanyl)·DMSO solvate crystallized in the space group P2 ₁2₁2₁ with cell dimensions a = 6.193(2), b = 11.545(3), c = 31.117(4) Å. The crystal structure is stabilized by four hydrogen bonds (three intermolecular hydrogen bonds and one intramolecular bond). The first intermolecular bond is between the oxygen of DMSO and the nitrogen of indole ring 2, in contrast to the second intramolecular hydrogen bond between the nitrogen of indole ring 1 and the oxygen of DMSO. The two remaining intermolecular hydrogen bonds are between the nitrogens of the DKP ring and the carbonyl oxygens of the DKP ring. The values of ^1A ₁ (–45.764) and ^1A ₂ (67.437) indicate an extended side chain conformation for Trp residue 1 (E_N) and a folded conformation for Trp residue 2. The DKP ring is more planar than in other cyclic dipeptide compounds (₁ = 11.414, ₁ = –7.516, ₂ = 12.471, and ₂ = –8.256). In cyclo(L-Trp–L-Trp) the C resonance of L-tryptophan (29.88 ppm) is shifted upfield 0.82 ppm when compared with the same resonance in cyclo(L-Trp–L-Gly) (30.7 ppm) and cyclo(L-Leu–L-Trp) (30.7 ppm). Two conformations of cyclo(Trp–Pro) crystallized in the space group P1 with cell dimensions a = 5.422(1), b = 9.902(1), c = 13.443(2) Å, = 80.42(1), = 78.61(1), and = 89.13(1)°. The conformation of the backbone and the orientation of the aromatic side chains for these conformers are very similar. The DKP rings for both conformers adopt a typical boat conformation in contrast to the flattened chair conformation observed for cyclo(Tyr–Pro) and cyclo(Phe–F-Pro). The tryptophan side chains of these conformers are folded towards the diketopiperazine (DKP) ring. The pyrrolidine ring for conformer 1 can be described as an envelope (Cs–C-endo) conformation in contrast to the pyrrolidine ring symmetry for conformer 2 which is an intermediate between C_s and C₂ rather than pure C_s for the proline ring with C-endo and C-exo with respect to C. The two prolyl rings are puckered at the -carbon atoms which deviate from the best planes defined by the four remaining atoms. The crystal structures are stabilized by four intermolecular hydrogens bonds. An intermolecular bond between the nitrogen of the indole ring (conformer 1) and the carbonyl oxygen of the DKP ring (conformer 2) was observed. The second hydrogen bond is between the nitrogen of the indole ring (conformer 2) and the carbonyl oxygen of the DKP ring (conformer 1). The last two hydrogens involve the carbonyl oxygens of the DKP rings and the nitrogens of the DKP rings [carbonyl oxygen of DKP ring (conformer 1)––––nitrogen of DKP ring (conformer 2); nitrogen of DKP ring (conformer 1)––––––carbonyl oxygen of DKP ring (conformer 2)].     

Crystal and molecular structures of quinazolines: A ring conformational study

The solid state structures of two dihydropyrimidines (DHPM) viz, 2-[(4-dimethylamino)phenyl]-1-phenethyl-2,3-dihydro-1H-quinazolin-4-one (compound 1) and 1-phenethyl-2p-tolyl-2,3-dihydro-1H-quinazolin-4-one (compound 2) are reported here. The compound 1 belongs to triclinic (P-1) space group with cell parameters a = 7.4314(12) Å, b = 9.9747(16) Å, c = 14.658(2) Å, = 104.142(3), = 102.584(3), = 98.188(3). The compound 2 also belongs to triclinic (P-1) space group with cell parameters a = 9.8707(11) Å, b = 9.9225(11) Å, c = 10.7425(13) Å, = 79.227(2), = 80.568(2), = 63.649(2). The structures show that the substituent at 2-position will play a key role in defining the pyrimidine ring conformation. The central dihydropyrimidine ring in both the structures are affected by conjugation. The sum of the valence angles around all the nitrogens is very close to 360, indicating that the state of hybridization of these atoms is sp². The DHP ring is puckered in such a manner that the atoms N1, C3, C4, C5, and N2 are coplanar and the sixth atom C2 is displaced 0.605 Å (0.18 Å for compound 2) above the least squares plane. The conformation of dihydropyrimidine ring can be described as a sofa with asymmetric parameters C_s[C2] = 6.09 (compound 1) and 4.73 (compound 2), respectively. The phenethyl group has a fully extended conformation with respect to the central pyrimidine ring (N2–C16–C17–C18 174.8(2) and 179.1(6) for compounds 1 and 2, respectively). The substituents on the DHPM ring, dimethylamino-phenyl/p-tolyl groups of compound 1/2 occupy equatorial/axial positions at C2. In the crystal packing, six membered rings form through dimerization using N–HO hydrogen bonding.     

Synthesis and crystal structure of 7,7-dimethyl-2,4-diphenyl-5-oxo-1,4,5,6,7,8-hexahydroquinolin

The 7,7-dimethyl-2,4-diphenyl-5-oxo-1,4,5,6,7,8-hexahydroquinolin was synthesized and the compound was identified by IR, ¹H NMR, elemental analysis and X-ray crystallography. It crystallized in the triclinic space group , with a = 7.129(2) Å, b = 10.514(3) Å, c = 13.040(3) Å, =76.58(2)°, =88.97(2)°, =79.24(2)°, and D _calc = 1.172 g cm^–3 for Z = 2. X-ray analysis revealed that the atoms C(2), C(3), C(4), C(10), C(9), and N form a six-membered ring that adopts a boat conformation, and another six-membered ring (C(10)–C(9)–C(8)–C(7)–C(6)–C(5)) adopts a half-chair conformation. In addition, there is an intermolecular hydrogen bond (N–H0O) in the product molecule.     

Synthesis and structure of 5,5′,6,6′,7,7′,8,8′-octahydro-1,1′-di(methylthio)-3,3′-biisoquinoline

Title compound, C₂₀H₂₄N₂S₂, crystallizes in the orthorhombic system, space group Pbca, with cell constants a = 5.1968(5) Å, b = 15.6692(11) Å, c = 22.3881(11) Å , Z = 4, T = 293 K, D_cal = 1.299 g cm^–3. The structure was solved by direct methods and refined to R value of 0.0465 for 1566 reflections. Two methylthio-octahydroisoquinoline parts of molecule are related by the center of symmetry and possess the trans conformation. This conformation is more energetically stable than cis but the molecule can rotate about the C(6)–C(6) central bond at room temperature (molecular mechanics calculations). There is a short intramolecular contact C(5)–H(51) N(1) in the molecule. The molecules in the crystal form molecular layers parallel to (001) crystallographic plane and the molecular packing is determined by the van der Waals forces only.     

Crystal structure of a nucleoside analog: 2′,3′-dideoxy-3′-fluoro-5-bromocytidine

The title compound crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=5.084(1),b=14.322(3),c=16.065(2)Å,Z=4. The structure was solved by the heavy atom method and refined by full-matrix least-squares calculations to a finalR value of 0.033 for 1106 unique observed reflections. The N-glycosidic torsion anglex has a value of –153.7(4)°, in the anti-range. The sugar pucker is²T₃ withP=175(1)° and=30(1)°. The C4-C5 conformation is + sc with =46.7(7)°. The structure is stabilized by N-HN, N-HO and O-HO hydrogen bonds and C-HO close contacts.     

Structure of a styrylbenzoselenazole platinum(II) complex: [NEt4][Pt(nsbse)Br3]

Tetraethylammonium tribromo[2-(2-chloro-5-nitrostyryl)benzoselenazole] platinate (II), [(C₂H₅)₄N][PtBr₃(C₁₅H₉ClN₂O₂Se)], is monoclinic, in space groupP2₁/c, witha=9.496(2),b=20.321(7),c=15.166(3)Å,=100.18(1)°,V=2880(2)ų,M _r =928.72,Z=4,D _x =2.141 g cm^–3, (MoK)=0.71073 Å,=104.1 cm^–1,F(000)=1752,T=298 K. The structure was solved by direct methods and refined toR=0.032 for 2626 unique observed reflections withI>3(I). The [Pt(nsbse)Br₃)] unit has square-planar geometry about the Pt atom, with the nsbse coordinated to the Pt through the N of the selenazole ring. The ligand molecule is non-planar, with a dihedral angle of 61.6(2)° between the benzoselenazole and phenyl rings. The dihedral angles between the PtBr₃ plane and the benzoselenazole and phenyl planes are 105.2(1) and 80.7(1)°, respectively.