5-(thien-2-yl) uracil analogs: 5-(5-methylthien-2-yl)-2′-deoxyuridine, 5-(5-thien-2-yl)-2′-deoxyuridine,and 5-(5-bromothien-2-yl)-2′-deoxyuridine

Crystal structures of 5-(5-methylthien-2-yl)-2-deoxyuridine (I), 5-(5-thien-2-yl)-2-deoxyuridine (II) and 5-(5-bromothien-2-yl)-2-deoxyuridine (III) have been obtained from data collected on a four-circle Enraf-Nonius diffractometer (CAD-4 system). Space group, unit/cell parameters and finalR indices are:I, monoclinic,P2₁,a=9.105(2),b=20.819(2),c=7.932(2) Å, =98.79(2)°,R=5.7%;II, monoclinic,P2₁,a=8.720(4),b=20.793(4),c=7.884(4) Å, =95.06(2)°,R=5.8%;III, monoclinic,P2₁,a=9.260(2),b=41.655(7),c=7.926(2) Å, =97.996(13)°,R=9.4%. Structural properties of the title compounds are compared with those of 5-(5-chlorothien-2-yl)-2-deoxyuridine (IV) previously reported in order to explain their affinity for HSV-1 thymidine kinase and their eventual interaction with viral DNA polymerase. The main structural features observed are the coplanarity of the uracil and thienyl cycles stabilized by a S–O intramolecular interaction and the formation of dimeric intermolecular H bonds between two uracil moieties.     

X-ray crystal structure of 2-hydroxy-2′-(1,4-bisoxo-6-hexanol)-1,1′-biphenyl

The X-ray crystal structure of 2-hydroxy-2-(1,4-bisoxo-6-hexanol)-1,1-biphenyl, 3, is presented. This molecule crystallizes in the monoclinic space group P2₁/n (a = 9.440(2), b = 12.679(3), c = 11.679(3) Å = 94.60(2)° V = 1382.5(5) ų; Z = 4). One of the unique features of the X-ray structure of 3 is the intramolecular hydrogen bonding. The hydrogens of the phenolic and hydroxy groups occupies bridging positions via hydrogen bonding to an ether oxygen (O₁) and a phenolic oxygen (O₄), respectively. This hydrogen bonding does not affect the interplanar angle between phenyl rings (49.34°), which is in the range expected for ortho-disubstituted biphenyl compounds. The hydrogen bonding of this type explains why it is difficult to alkylate both phenoxy groups of 2,2-biphenol with tetrahydropyranyl protected 2-(2-chloroethoxy)ethanol.     

The X-ray Structures of (R)-2,2′-Dimethyl-1,1′-binaphthyl and (±)-2-Bromomethyl-2′-dibromomethyl-1,1′-binaphthyl

Journal of Chemical Crystallography - Molecular structures of (R)-2,2′-dimethyl-1,1′-binaphthyl [monoclinic, a?=?11.24420 (11), b?=?10.56190 (9),...     

Crystal structures of two substituted biphenyl derivatives: 5,5′-di t-butyl-2-2′-biphenyldiol and 5,5′-dimethyl-2,2′-biphenyldiol

5,5-Di t-butyl-2,2-biphenyldiol (I), C₂₀H₂₆O₂, crystallizes in the orthorhombic space group P2₁2₁2₁ with a = 18.243(2), b = 9.947(2), c = 9.685(3) Å, and Z = 4; 5,5-dimethyl-2,2-biphenyldiol (II), C₁₄H₁₄O₂, crystallizes in the monoclinic space group P2₁/c with a = 9.959(2), b = 7.932(3), c = 15.392(2) Å, = 105.43(2)°, and Z = 4. The aromatic rings are tilted by 52.7(1) and 43.8(1)° to each other in compounds (I) and (II), respectively. Strong intra- and inter-molecular H-bonds connect the molecules in the crystals.     

X-ray structure investigation of two polymorphic modifications of 1-acetyl-3-(4-nitrophenyl)-5-(2′-furyl)pyrazoline

Two polymorphic modifications of 1-acetyl-3-(4-nitrophenyl)-5-(2′-furyl)pyrazoline (I) are investigated by X-ray diffraction with the purpose of analyzing the factors responsible for the formation of crystal structures of the optical nonlinear organic compounds. Both modifications crystallize simultaneously upon slow evaporation of a solution of compound I in an isopropanol-acetonitrile (3: 1) mixture. It is found that the molecular geometry of the polymorphic modifications is characterized by the rotation of the furan substituent with respect to the plane of the pyrazoline ring. The molecular hyperpolarizabilities (β) of both conformers are calculated.     

The molecular structure of acetato[2-(pyridin-2′-yl)phenyl]mercury(II)

The crystal structure of the title compound was determined by X-ray crystallography. The compound crystallizes in the monoclinic crystal system witha=8.152(4),b=17.994(7),c=8.634(9) Å, =108.92(5)°, space group P2₁/c (N:14),V=1198.02 ų,Z=4. The mercuryl(II) atom forms two strong, almost colinear bonds (bond angle 176.1(4)°) with a carbon of the phenyl ring (Hg–C=1.99(1) Å) and one of the acetate oxygen atoms (Hg–O(1)=2.005(7) Å). These primary bonds are supplemented by secondary intramolecular interactions with the pyridine nitrogen (Hg...N=2.727(9) Å) and the other acetate oxygen (Hg...O(2)=2.925(8) Å), although the latter is very weak and the acetate anion therefore practically monodentate. Weak additional intermolecular Hg–C and Hg–O(1)interactions contribute to the lattice structure.     

Structure of 1-ethyl-2-(2′-chloro-4′-nitrostyryl)benzimidazole

The title compound C₁₇H₁₄ClN₃O₂ (et-4-nsbiz) is monoclinic, witha=12.240(2),b=12.144(4),c=10.544(4)Å,=100.09(2)°,V=1543(1)ų,Z=4,D _x =1.411 g cm^–3, (MoK)=0.71073Å,=2.57 cm^–1,F(000)=680,M _r =327.77,T=298K. The structure was solved by heavy atom and Fourier methods and refined toR=0.049 for 1503 unique observed reflections in space groupP2₁/c. Except for the ethyl group, the molecule is almost planar, with a dihedral angle of 9.5(5)° between the benzimidazole and phenyl rings. The dihedral angle between the ethyl group and the benzimidazole ring to which it is attached is 91.5(2)°.     

Crystal and Molecular Structures of 2-Amino-4-Nitrobenzoic Acid and Its Cocrystals with 2,2′-Bipyridine (2/1) and Bis(pyridin-2-yl)ketone (1/1)

Abstract  

The eight-membered {···HOC=O}₂ synthon featured in the crystal structure of 2-amino-4-nitrobenzoic acid (1) is replaced by carboxylic acid···N-pyridine hydrogen bonds in its cocrystals with 2,2′-bipyridine (2/1; 2) and bis(pyridin-2-yl)ketone (1/1; 3) indicating the robust nature of the latter synthon. Disruption of the three-dimensional architecture based on O–H···O and N–H···O(nitro) hydrogen bonds in (1) is evident in the cocrystals which form supramolecular tubes (2) and chains (3) based on O–H···N and N–H···O hydrogen bonding. Compound (1) crystallizes in the monoclinic space group P2₁/n with a = 3.6291(1) ?, b = 7.7339(3) ?, c = 26.561(1) ?, β = 91.385(2)°, and Z = 4. Compound (2) crystallizes in the monoclinic space group C2/c with a = 27.562(3) ?, b = 6.8300(6) ?, c = 12.923(1) ?, β = 110.593(5)°, and Z = 4. Compound (3) crystallizes in the monoclinic space group P2₁/c with a = 3.795(3) ?, b = 12.024(8) ?, c = 35.65(2) ?, β = 92.131(6)°, and Z = 4 (determined from synchrotron data).     

Crystal structures of 1,1′-di(2-propanone)-2,2′-biimidazole dihydrazone and 2,6-diacetylpyridine dihydrazone

The nucleophilic addition reactions between 1,1′-di(2-propanone)-2,2′-biimidazole or 2,6-diacetylpyridine and hydrazine hydrate afford 1,1′-di(2-propanone)-2,2′-biimidazole dihydrazone (1) and 2,6-diacetylpyridine dihydrazone (2), respectively. Compound1 crystallizes in the orthorhombic space groupP2₁2₁2₁, witha=9.042(2),b=9.731(3),c=15.683(4)Å, V = 1379.9(6)Å^? andZ=4. Compound2 crystallizes in the orthorhombic space groupPnma, witha=10.948(2),b=19.742(6),c=4.566(1)Å, V=986.9(4)Å^? andZ=8. A pseudo center of inversion is present at the midpoint of the C?C bond joining the imidazole rings of1, whose substituents crystallize in atrans configuration. The imidazole rings are rotated 2.5(3)° about the C?C bond. In contrast to the essentially planar structure of2, the hydrazone substituent groups of1 are at angles of 89.9(1)° and 88.4(1)° with respect to the plane of the adjacent imidazole moiety.     

Synthesis and crystal structure of 2-trifluoromethyl-1-[(2′-1H-tetrazole-5-yl-biphenyl-4-yl) methyl]benzimidazole

The crystal structure of 2-trifluoromethyl-1-[(2'-1H-tetrazle-5-yl-biphenyl-4-yl) methyl]-benzimidazole and a methylene chloride have been determined by X-ray crystallography. The compound crystallizes in the monoclinic space group, P2 ₁/n with cell dimensions a = 10.931(2) Å, b = 12.31(3) Å, c = 17.901(4) Å, = 102.45(3)°, V = 2352.9(8) ų, D _calc = 1.427 g/cm³, Z = 4, = 0.324 mm^–1, and F(000) = 1032, and its structure was refined to R ₁ = 0.0663 and wR ₂ = 0.1668 for 1910 observed reflections I > 2(I)). Intermolecular hydrogen bonds were identified between the N and H atoms of intermolecular benzimidazole group and tetrazole group.     

Structure of 2-(2′-bromo-5′-nitrostyryl)benzothiazole

The title compound C₁₅H₉BrN₂O₂S (brnsb) is monoclinic, witha=7.730(2),b=26.847(5),c=7.773(2) Å,=117.48(1)°,V=1431(1) ų,Z=4,D _x=1.677,(MoK)=29.9 cm^–1,F(000)=720,T=298K in space groupP2₁/c. The structure was solved by heavy atom and Fourier methods and refined toR=0.034 for 1776 unique observed reflections. The molecule is nearly planar, with a dihedral angle of only 3.8(1.1)° between the benzothiazole and phenyl rings. The C-S-C angle in the thiazole ring is 89.0°, while the C-N-C angle in that ring is 111.5(3)°.     

Structure of 1-(2′-tosyloxyethoxy)-8-tosyloxy-9,10-anthraquinone

The title compound crystallizes in the monoclinic space group, P2₁/c;a=12.938(1),b=11.041(1),c=19.285(2) Å, =104.314(8)°,Z=4. Refinement based on 1660 unique observed reflections converged toR=0.054. The anthraquinone moiety is distorted due to intramolecular steric hindrance from the tosylate groups.     

Molecular structure and absolute configuration of (−)-(1R, 2S, 6R, 7S, 2′S)-5-(2′-hydroxymethylpyrrolidin-1′-yl)-endo-tricyclo[5.2.1.02,6]deca-4,8-dien-3-one

The crystal and molecular structure of (–)-(1R, 2S, 6R, 7S, 2S)-5-(2-hydroxymethyl-pyrrolidin-1-yl)-endo-tricyclo[5.2.1.0^2,6]deca-4,8-dien-3-one is described. Knowing the absolute configuration of the prolinol moiety (S) the X-ray diffraction study established the absolute configuration of the title compound. The structure was refined to R ₁ = 0.0322 for 1237 reflections (with I > 2(I)). Crystal data: C₁₅H₁₉NO₂, monoclinic, space group P2₁, a = 6.0757(4), b = 11.3473(5), c = 9.5114(7)Å, = 104.686(6)°, V = 634.32(7)ų, and Z = 2.     

Distortions in nitramine substituted cubanes: The structures of N,N′-dinitro-1,4-diaminocubane,N,N′-dinitro-N,N′-(2-pyridyl)-1,4-diaminocubane,and 1,2,4,7-tetrakis(N-methoxycarbonylnitramino)cubane

The structures of three nitramine substituted cubane molecules, N,N-dinitro-1,4-diaminocubane (1), N,N-dinitro-N,N-(2-pyridyl)-1,4-diaminocubane (2), and 1,2,4,7-Tetrakis(N-methoxycarbonylnitramino)-cubane (3), have been determined.1 crystallized in the space group P2₁/a with cell dimensionsa=6.545(1),b=9.331(1),c=7.459(1) Å, =105.80(1),2 crystallized in the monoclinic space group P2₁/a with cell dimensionsa=7.545(2),b=8.697(3),c=12.406(4 Å, =96.28(3)°, while3 crystallized in the monoclinic space group P2₁/c with cell dimensionsa=10.866(3),b=6.866(2),c=16.167(6) Å, =108.79(3)°. The metrical parameters of the cubane skeleton showed no significant deviations from those found in other similarly substituted cubane molecules. For2 and3 there were considerable distortions of the nitramine moiety from planarity in contrast to1 where the nitramine moiety was almost exactly planar. The bond distances and angles for the nitramine group in1 indicates a substantial introduction of double bond character into the N–N bond in1, achieved by delocalization of the amine lone pair, compared with2 and3.     

X-ray structure of 3,3′-bis(4-methylthioquinolinyl) sulfide

The structure of the title compound has been solved by direct methods, and refined to anR value of 0.035 for 1613 reflections. Both methyl carbon atoms deviate from the plane of the pyridine ring by 1.505(3) Å in opposite directions. Both sulfur atoms S(1) and S(2) remain in short contact, at 3.247(1) Å. The two pyridine rings are inclined at 61.4(2)° to each other.Part XIV in the series of Azinyl Sulfides.     

Crystal and molecular structures of three 2,2′-thio- and 2,2′-sulfonyl-bis(1,3-diarylprop-2-en-1-ones)

The X-ray crystal structures of 2,2-thio- and 2,2-sulfonylbis(1,3-diarylprop-2-en-1-ones) are determined [1: 2,2-thiobis(3-(p-chlorophenyl)-1-phenylprop-2-en-1-one), C₃₀H₂₀Cl₂O₂S, space group C2/c, a = 14.275(3), b = 6.280(1), c = 26.533(5) Å, = 94.55(3)°, Z = 1/2; 2: 2,2-sulfonylbis(1,3-diphenylprop-2-en-1-one), C₃₀H₂₂O₄S, space group P , a = 9.652(1), b = 12.044(1), c = 12.182(1) Å, = 61.985(6), = 77.511(5), = 74.340(6)°, Z = 1; 3: 2,2-sulfonylbis(3-(p-chlorophenyl)-1-phenylprop-2-en-1-one), C₃₀H₂₀Cl₂O₄S, space group P , a = 8.294(1), b = 13.175(2), c = 13.470(1) Å, = 62.870(9), = 83.796(7), = 85.282(8)°, Z = 1]. The C=C double bonds are all clearly defined. The sulfide 1 crystallizes on a crystallographic twofold axis, leading to a symmetric molecular conformation. The sulfones 2 and 3 crystallize on general positions, with different and irregular conformations.     

Syntheses and structures of square-pyramidal acetonitrile coordinated copper(II) complexes with N-(aroyl)-N′-(5-nitrosalicylidene)hydrazines

The syntheses and structures of two square-pyramidal acetonitrile coordinated copper(II) complexes, [Cu(HbhsNO₂)(CH₃CN)₂]ClO₄ (1) and [Cu(HahsNO₂)(CH₃CN)(ClO₄)] (2), are described. The mononegative ligands are obtained by deprotonation of the phenolic-OH of N-(benzoyl)-N-(5-nitrosalicylidene)hydrazine (H₂bhsNO₂) and of N-(anisoyl)-N-(5-nitrosalicylidene)hydrazine (H₂ahsNO₂). Crystal data for 1: monoclinic, P2₁/c (#14), a = 9.7245(14), b = 20.23(4), c = 11.042(3) Å, = 91.86(2)°, V = 2171.0(7) ų, and Z = 4 and for 2: triclinic, P1¯ (#2), a = 9.7710(19), b = 9.9687(15), c = 11.062(5) Å, = 73.10(3), = 88.77(3), = 88.379(14)°, V = 1030.4(5) ų, and Z = 2. In each complex the planar ligand binds the metal ion via phenolate-O, imine-N, and amide-O. The nitrogen of an acetonitrile molecule satisfies the fourth site of the square-plane containing the metal ion. In 1 the axial coordination is provided by the nitrogen of a second acetonitrile molecule, whereas in 2 one of the oxygen atoms of the perchlorate occupies the fifth axial site. The axial acetonitrile molecule of 1 is bound to the metal center in a bent mode. The other noticeable difference between the two structures is in the geometry at the metal center. A large displacement (0.23 Å) of the metal ion from the ONON basal plane towards the axial coordinating atom is observed in 1. On the other hand, there is no displacement of the metal center from the same ONON basal plane in 2. The EPR and electronic spectral features in acetonitrile solutions are consistent with the solid state structures.     

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.     

Structural study of nitrovinylindoles: (I) 2-methyl-3-(2′-methyl-2′-nitrovinyl)indole and (II) 3-(2′-nitrovinyl)indole

Compound (I) is 2-methyl-3-(2-methyl-2-nitrovinyl)indole, C₁₂H₁₂N₂O₂,M _r=216.24, monoclinic,P2₁/n,a=16.710(1),b=7.627(1),c=17.646(1) Å,=104.8(1)°,V=2174.7(1) ų,Z=8.D _x=1.321 g cm^–3, MoK, =0.71073 Å,=0.858 cm^–1,F(OOO)=912, room temperature,R=0.061 for 1956 observed reflections. Compound (II) is 3-(2-nitrovinyl)indole, C₁₀H₈N₂O₂,M _r=188.18, monoclinic,P2₁/n,a=10.178(1),b=10.608(1),c=8.411(1) Å,=105.5(2)°,V=875.0(1) ų,Z=4,D _x=1.4284 g cm^–3, CuK, =1.5418 Å,=8.068 cm^–1,F(000)=392, room temperature,R=0.040 for 1330 observed reflections. Compounds (I) and (II) have a similar geometry, the only significant difference lying in the rotation of the nitrovinyl chain. This feature could be responsible for the difference in biological activity. In both compounds, the molecules are associated, forming charge-transfer complexes.