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 structure of a nucleoside analogue, 2′,3′-dideoxy-3′-fluoro-5-chlorocytidine

The title compound, 1-(2,3-dideoxy-3-fluoro--d-erythro pentofuranos-1-yl)-5-chlorocytosine, crystallises in the orthorhombic space groupP2₁2₁2₁ witha=5.142(1),b=14.177(2),c=15.721(2) Å,Z=4. The crystal structure was solved by the heavy atom method and refined by full-matrix least-squares method to a finalR value of 0.031 for 1629 unique observed reflections. The N-glycosidic torsion angle is –156.1(2)° and the sugar moiety is anti to the cytosine base. The sugar pucker is ₂ ³ T withP=178.2(1)° and=31(1)°. The atom 05 is in a +sc conformation with respect to the furanose ring. The molecular packing in the crystal is stabilized by N-HN, N-HO, O-HO hydrogen bonds and C-HO close contacts.     

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.     

Crystal and molecular structure of 2′,4′-dimethoxyflavone

C₁₇H₁₄O₄,M _r =282.3, triclinic,P-1,a=8.469(3),b=8.516(2),c=20.425(8)Å,=84.95(3),=81.98(3), =70.47(2)°,V=1373(13)ų,Z=4,D _x =1.365 g cm^–3, (MoK )=0.71069 Å,=0.91 cm^–1,F(000)=592,T=294K,R=0.038 for 3577 observed reflections (F>3 (F)). The asymmetric unit is composed of two molecules. These two molecules, which are in planar conformations, differ in 4-methoxyl group orientation. Short intramolecular contacts are found between the -benzopyran portion and the dimethoxyphenyl ring.     

X-ray structure of 3′,4-dimethylthio-3,4′-diquinolinyl sulfide

The title compound (C₂₀H₁₆N₂S₃) is monoclinic, witha=31.550(9),b=8.504(3),c=14.745(3) Å,=114.14(3)°,Z=8 and space groupC2/c. The structure was solved by direct methods and refined toR=0.038 for 3012 reflections. The molecule exists in an uncommon conformation. Two quinoline moieties are nearly perpendicular to each other (80.9(3)°). Both methylthio groups have different orientation (the 4-SCH₃ group is nearly perpendicular and the 3-SCH₃ is nearly coplanar to the quinoline moieties). Two pairs of sulfur atoms in ortho-positions remain in very close contact. The conformation of the molecule explains an unusual¹H NMR spectrum.Part XVI in the series of Azinyl Sulfides.     

The crystal structure of the molecular complex of 2′,6′-dimethoxyflavone with picric acid: Alternating π-stacking and hydrogen-bonding interactions

The title complex is monoclinic with a = 15.100(5), b = 7.624(3), c = 39.997(15) Å, = 99.49(4)°, Z = 8, and space group P2₁/c. There are two geometrically independent, hydrogen-bonded pairs of molecules in the asymmetric part of the structure. Picric acid and 2,6-dimethoxyflavone are held together by hydrogen bonding between the hydrogen of the phenol group and the oxygen of the carbonyl. Additionnally, this hydrogen forms an intramolecular hydrogen bond with the O atom of an ortho-nitro group. Moreover, a stacking interaction is observed between the -benzopyrone portion of the flavone and picric acid.     

Crystal structure of 2,5-cyclohexadien-4-one-spiro-3′-(2′-methylthio-5′,5′-dimethyl-1′-pyrroline)

The crystal structure of the pyrrole derivative 2,5-cyclohexadien-4-one-spiro-3′-(2′-methylthio-5′,5′-dimethyl-1′-pyrroline) is determined by X-ray diffraction. Two independent molecules have similar structures and close geometric parameters but differ in configuration of the pyrrole ring and orientation of the thiomethyl group with respect to the pyrrole ring.     

The structure of Wallach's compound. Single-crystal X-ray structure determination oftrans-2,5-bis(trichloromethyl)-N-(1′-hydroxy-2′,2′,2′-trichloroethyl)-4-imino-1,3-dioxolane

The structure of Wallach's compound, C₇H₄O₃NCl₉, prepared in 1874 from concentrated aqueous solutions of potassium cyanide and chloral hydrate, has long been undecided. By single crystal X-ray crystallography it has now been established astrans-2,5-bis(trichloromethyl)-N-(1-hydroxy-2,2,2-trichloroethyl)-4-imino-1,3-dioxolane, confirming the tentative assignment by¹H and¹³C NMR spectrography. The title compound is monoclinic,P2₁/c;a=8.445 (1),b=10.948(1),c=17.923(4) Å;=94.36(1)°;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 0.041 using 2101 reflections.     

Crystal structure of 1,4-dihydro-1-methyl-3′-methylsulfinyl-4-oxo-6-nitro-3,4′-diquinolinyl sulfide complex with DMF

The title compound crystallized as a complex with N,N-dimethylformamide (DMF) in a monoclinic space group P2 ₁ /c with a = 9.469(2), b = 25.168(5), c = 9.860(3) Å, and = 97.48(3)°. The two quinoline moieties are nearly perpendicular. The sulfoxide oxygen is pointed toward the H-2 proton. The S-methyl group is perpendicular to the parent pyridine ring plane.     

Three-dimensional structure of <Emphasis Type="Italic">E. Coli</Emphasis> purine nucleoside phosphorylase at 0.99 Å resolution

Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment of the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB_ID: 4RJ2).     

Crystal structure of tris-(2,2′,2″)-triaminoethylamino-salicylidene iron(III) complex

Tris-(2,2,2)-triaminoethylamino-salicylidene iron(III) crystallizes in the monoclinic crystal system witha=7.766(2),b=25.423(5),c=13.318(5) Å, =118.04(3)°, space group P2₁/c,V=2320.8(6) ų,Z=4, andD _x=1.464 g cm^–3. The center of the axially distorted octahedron is occupied by the Fe atom which is coordinated by six donor nitrogen and oxygen atoms infac positions. The planes of coordinated atoms (N and O) with the Fe(III) atom are almost planar and the maximum elevated atom from these planes is O(1) (–0.1065 Å).     

Crystal and molecular structure of chloramphenicol analog: 2-amino-4-methoxy-2′,2′-dichloroacetophenone

The crystal and molecular structure of the title compound has been determined from diffractometric data usingMo K radiation. The crystals are orthorhombic, space groupP2₁2₁2₁, witha=12.052(3),b=11.901(2),c=6.976(1) Å andZ=4. The structure was solved by the heavy-atom method and refined by full-matrix least-squares to a finalR value of 0.039 with 1096 observed reflections. The molecule is is almost planar. The acetyl group and the phenyl ring are strongly conjugated, the corresponding dihedral angle being 3.3(2)°. The structure is stabilized by an intramolecular N(1)-H(N)1O(l) hydrogen bond.     

Crystal structure ofβ-C.I. Solvent Yellow 18, 4(2′,4′-dimethylphenyl hydrazono)-5-methyl-2-phenyl-3H-pyrazol-3-one

The crystal structure of-C.I. Solvent Yellow 18, C₁₈H₁₈N₄O, has been determined by single crystal X-ray diffraction techniques. It crystallizes in the monoclinic system witha=30.948(18)Å,b=4.918(4)Å,c=20.861(9)Å,=91.68(4)°, space groupC2/c,Z=8. The structure has been solved by direct methods and least-squares refinement has been completed on three dimensional data (1237 reflections MoK radiation). The hydrogen atoms have been found but only their positional parameters refined. Final residual 0.092 (all intensity data). The molecule exists as the hydrazone tautomer and intramolecular hydrogen bonding keeps the molecule approximately planar. The molecules are packed in columns parallel to theb axis, while the molecule lies approximately parallel to the (51¯3) plane. The molecules are linked by van der Waals' force.     

Synthesis and crystal structure of 1-(1′,3′-dimethyl-5′-chloropyrazol-4′-carbonyl′-3-(2′-chlorophenyl)-5-amino-4-cyanopyrazole

The title compound 1-(1,3-dimethyl-5-chloropyrazol-4-carbonyl)-3-(2-chlorophenyl)-5-amino-4-cyanopyrazole (C₁₆H₁₂Cl₂N₆O) has been synthesized and characterized by X-ray diffraction: Triclinic, space group P1, with a = 8.6712(8) Å, b = 9.5091(10) Å, c = 11.2170(11) Å = 71.531(2)°, = 84.683(2)°, = 74.099(2)° Z = 2; V = 843.7(14) ų. C(10), O(1), C(11), and N(2) atoms are coplanar with the average deviation of 0.0071 Å, which form 11.03° and 43.93° dihedral angles with pyrazole planes (I) and (II), respectively.     

Crystal structure of the addition compound of N,N′-bi(2-pyridylmethyl)-oxamide and complex of manganese with 1,10-phenanthroline

The structure of the addition compound, Mn(phen)₃(PMoxdH₂)(ClO₄)₂ was established by X-ray crystallography, where PMoxdH₂ is N,N-bi(2-pyridylmethyl)-oxamide. Six nitrogen atoms of the three 1,10-phenanthroline bind to the manganese ion and the oxygen atom of PMoxdH₂ is uncoordinated. The addition compound crystallizes in the monoclinic space group C2/c, with lattice parameters a = 23.780(6), b = 11.948(5), c = 18.466(6) Å, = 117.38(3)°, V = 4659(3) ų, and Z = 4.     

Crystal structure of 4-phenyl-3,5-dioxacyclohexyl-1, 1′-cyclopentane-2′,3″-(1,5,8,11-tetraoxacyclotridecane)

The structure of the title compound is determined by X-ray diffraction (DAR-UMB diffractometer, θ-θ/2θ scan mode, MoK _α radiation, direct method). The crystal is monoclinic, a = 24.582(6) Å, b = 22.812(8) Å, c = 8.647(3) Å, γ = 60.64(2)°, ρ _calcd = 1.232 g/cm³ space group A2/a, and Z = 8 for C₂₂H₃₂O₆. The molecule consists of four fragments: 13-crown-4 (A), 1,3-dioxane (B), a five-membered ring (C) acting as a bridge between fragments A and B, and a phenyl ring (D). Introduction of the bulky ring C as a bridge into the molecule results in significant deviations (up to ±0.014 Å) of the ether O atoms from planarity. The conformation of the macrocyclic fragment is [3433] according to the Dale notation. The C—H?O 1,4-interactions, which are energetically favorable occur in the propylene part of 13-crown-4: the C(2)?O(5) and C(4)?O(1) distances are 2.82 Å. The molecules in the structure form planar networks parallel to the xy plane. The intermolecular contacts correspond to the van der Waals interactions.     

Mercury(II) complex with terpyridine: structure of the 2∶1 solvate of [Hg(terpy)2](CF3SO3)2 with acetone

[Hg(terpy)₂](CF₃SO₃)₂·0.5(CH₃)₂CO crystallizes in the triclinic space group witha=14.631(6),b=15.258(4),c=18.785(7) Å, =69.66(2), =70.72(1), =88.55(1)°. The crystal structure consists of two independent [Hg(terpy)₂]²⁺ cations, four trifluoromethanesulfonate anions and an acetone molecule in the asymmetric unit. Each mercury atom is coordinated by two tridentate terpyridine ligands forming an irregular six-coordination polyhedron. The Hg–N bond lengths range from 2.27(2) to 2.53(2) Å.     

X-ray crystal and molecular structure of 2,3-dideoxy-4-thio-d-arabino-heptonic acid 1,4-lactone: a key intermediate for syntheses of 2′, 3′-dideoxy-4′-thio-l-nucleosides

The structure of 2,3-dideoxy-4-thio-d-arabino-heptonic acid 1,4-lactone has been determined by X-ray diffraction. Crystals of the compound are orthorhombic, space groupP2₁2₁2₁, with cell dimensionsa=11.555(5),b=10.451(5),c=9.604(5) Å, andZ=4. The diffraction experiment has allowed to assign the absolute configuration (4R, 5R, 6R) to the chiral centers of the molecule.