2′‐Deoxy‐7‐propynyl‐7‐deaza­adenosine: a DNA duplex‐stabilizing nucleoside

In the title compound, 2′‐deoxy‐7‐propynyl‐7‐deaza­adenosine, C₁₄H₁₆N₄O₃, the torsion angle of the N‐glycosylic bond is anti [χ = −130.7 (2)°]. The sugar pucker of the 2′‐deoxy­ribo­furanosyl moiety is C2′‐endo–C3′‐exo, ²T₃ (S‐type), with P = 185.9 (2)° and τ_m = 39.1 (1)°, and the orientation of the exocyclic C4′—C5′ bond is −ap (trans). The 7‐substituted propynyl group is nearly coplanar with the heterocyclic base moiety. Mol­ecules of the nucleoside form a layered network in which the heterocyclic bases are stacked head‐to‐tail with a closest distance of 3.197 (1) Å. The crystal structure of the nucleoside is stabilized by three inter­molecular hydrogen bonds of types N—H⋯ O, O—H⋯ N and O—H⋯ O.     

2′‐De­oxy‐2‐fluoro­tubercidin

In the title compound [systematic name: 7‐(2‐de­oxy‐β‐d ‐erythro‐pentofuranos­yl)‐2‐fluoro‐7H‐pyrrolo[2,3‐d]pyrimidin‐2‐amine], C₁₁H₁₃FN₄O₃, the conformation of the N‐glycosylic bond is between anti and high‐anti [χ = −110.2 (3)°]. The 2′‐deoxy­ribofuranosyl unit adopts the N‐type sugar pucker (₄T³), with P = 40.3° and τ_m = 39.2°. The orientation of the exocyclic C4′—C5′ bond is −ap (trans), with a torsion angle γ = −168.39 (18)°. The nucleobases are arranged head‐to‐head. The crystal structure is stabilized by four inter­molecular hydrogen bonds of types N—H⋯N, N—H⋯O and O—H⋯O.     

7‐Deaza‐2,8‐diaza­adenosine

In the title compound [systematic name: 4‐amino‐7‐(β‐d ‐ribofuranos­yl)‐7H‐pyrazolo[3,4‐d][1,2,3]triazine], C₉H₁₂N₆O₄, the torsion angle of the N‐glycosylic bond is high anti [χ = −83.2 (3)°]. The ribofuran­ose moiety adopts the C2′‐endo–C1′‐exo (²T₁) sugar conformation (S‐type sugar pucker), with P = 152.4° and τ_m = 35.0°. The conformation at the C4′—C5′ bond is +sc (gauche,gauche), with the torsion angle γ = 52.0 (3)°. The compound forms a three‐dimensional network that is stabilized by several hydrogen bonds (N—H⋯O, O—H⋯N and O—H⋯O).     

1‐(2‐Deoxy‐β‐d‐erythro‐pento­furan­osyl)‐4‐nitro‐1H‐indazole

In the title compound, C₁₂H₁₃N₃O₅, the conformation of the gly­cosyl­ic bond is anti [torsion angle = −105.3 (2)°]. The 2′‐deoxy­ribo­furan­ose moiety adopts an S‐type sugar pucker and the orientation of the exocyclic C—C bond is −sc (trans).     

N8‐(2′‐O‐Methyl­ribofuranos­yl)‐8‐aza‐7‐deaza­adenine monohydrate

In the title compound, 4‐amino‐2‐(2‐O‐methyl‐β‐d ‐ribofuranos­yl)‐2H‐pyrazolo[3,4‐d]pyrimidine monohydrate, C₁₁H₁₅N₅O₄·H₂O, the conformation of the N‐glycosylic bond is syn [χ = 20.1 (2)°]. The ribofuran­ose moiety shows a C3′‐endo (³T₂) sugar puckering (N‐type sugar), and the conformation at the exocyclic C4′—C5′ bond is −ap (trans). The nucleobases are stacked head‐to‐head. The three‐dimensional packing of the crystal structure is stabilized by hydrogen bonds between the 2′‐O‐methyl­ribonucleosides and the solvent mol­ecules.     

2‐Amino‐7‐chloro‐2′‐deoxy­tubercidin

In 4‐chloro‐7‐(2‐de­oxy‐β‐d ‐erythro‐pento­furanos­yl)‐7H‐pyr­rolo­[2,3‐d]­pyrimidine‐2,4‐diamine, C₁₁H₁₄ClN₅O₃, the conformation of the N‐glycosylic bond is between anti and high‐anti [χ = −102.5 (6)°]. The 2′‐deoxy­ribofuranosyl unit adopts the C3′‐endo‐C4′‐exo (³T₄) sugar pucker (N‐type) with P = 19.6° and τ_m = 32.9° [terminology: Saenger (1989). Landolt‐Börnstein New Series, Vol. 1, Nucleic Acids, Subvol. a, edited by O. Madelung, pp. 1–21. Berlin: Springer‐Verlag]. The orientation of the exocyclic C4′—C5′ bond is +ap (trans) with a torsion angle γ = 171.5 (4)°. The compound forms a three‐dimensional network that is stabilized by four inter­molecular hydrogen bonds (N—H⋯O and O—H⋯N) and one intra­molecular hydrogen bond (N—H⋯Cl).     

6‐Aza‐2′‐deoxy‐2′‐arabino­fluoro­uridine,a 2′‐deoxy­ribonucleoside with an N‐sugar conformation in the solid state and in solution

In the title compound, 2‐(2‐deoxy‐2‐fluoro‐β‐d ‐arabino­fur­anosyl)‐1,2,4‐triazine‐3,5(2H,4H)‐dione, C₈H₁₀FN₃O₅, the torsion angle of the N‐gly­cosylic bond is anti [χ = −125.37 (13)°]. The furan­ose moiety adopts the N‐type sugar pucker (³T₂), with P = 359.2° and τ_m = 31.4°. The conformation around the C4′—C5′ bond is antiperiplanar (trans), with a torsion angle γ of 177.00 (11)°. A network is formed via hydrogen bonds from the nucleobases to the sugar residues, as well as through hydrogen bonds between the sugar moieties.     

4‐Amino‐7‐(2‐de­oxy‐2‐fluoro‐β‐d‐arabinofuranos­yl)‐5‐fluoro‐7H‐pyrrolo[2,3‐d]pyrimidine: a bis‐fluorinated analogue of 2′‐deoxy­tubercidin

The title compound, C₁₁H₁₂F₂N₄O₃, exhibits an anti glycosylic bond conformation, with a torsion angle χ = −117.8 (2)°. The sugar pucker is N‐type (C4′‐exo, between ³T₄ and E₄, with P = 45.3° and τ_m = 41.3°). The conformation around the exocyclic C—C bond is −ap (trans), with a torsion angle γ = −177.46 (15)°. The nucleobases are stacked head‐to‐head. The crystal structure is characterized by a three‐dimensional hydrogen‐bond network involving N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds.     

7‐Cyclopropyl‐2′‐deoxytubercidin: a carbocyclic side‐chain derivative of 7‐deaza‐2′‐deoxyadenosine

The title compound {systematic name: 4‐amino‐5‐cyclopropyl‐7‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine}, C₁₄H₁₈N₄O₃, exhibits an anti glycosylic bond conformation, with the torsion angle χ = −108.7 (2)°. The furanose group shows a twisted C1′‐exo sugar pucker (S‐type), with P = 120.0 (2)° and τ_m = 40.4 (1)°. The orientation of the exocyclic C4′—C5′ bond is ‐ap (trans), with the torsion angle γ = −167.1 (2)°. The cyclopropyl substituent points away from the nucleobase (anti orientation). Within the three‐dimensional extended crystal structure, the individual molecules are stacked and arranged into layers, which are highly ordered and stabilized by hydrogen bonding. The O atom of the exocyclic 5′‐hydroxy group of the sugar residue acts as an acceptor, forming a bifurcated hydrogen bond to the amino groups of two different neighbouring molecules. By this means, four neighbouring molecules form a rhomboidal arrangement of two bifurcated hydrogen bonds involving two amino groups and two O5′ atoms of the sugar residues.     

trans‐4‐Bromo‐ONN‐azoxy­benzene at 100 K

The crystal structure of the α isomer of trans‐4‐bromo­azoxy­benzene [systematic name: trans‐1‐(bromophenyl)‐2‐phenyl­diazene 2‐oxide], C₁₂H₉BrN₂O, has been determined by X‐ray dif­frac­tion. The geometries of the two mol­ecules in the asymmetric unit are slightly different and are within ∼0.02 Å for bond lengths, ∼2° for angles and ∼3° for torsion angles. The azoxy bridges in both mol­ecules have the typical geometry observed for trans‐azoxy­benzenes. The crystal network contains two types of planar mol­ecules arranged in columns. The torsion angles along the Ar—N bonds are only 7 (2)°, on either side of the azoxy group.     

8‐Aza‐7‐deaza‐7‐propynyladenosine methanol solvate

In the title compound, 4‐amino‐3‐propynyl‐1‐(β‐d ‐ribofur­anosyl)‐1H‐pyrazolo[3,4‐d]pyrimidine methanol solvate, C₁₃H₁₅N₅O₄·CH₃OH, the torsion angle of the N‐glycosylic bond is between anti and high‐anti [χ = −101.8 (5)°]. The ribofuranose moiety adopts the C3′‐endo (³T₂) sugar conformation (N‐type) and the conformation at the exocyclic C—C bond is +sc (gauche, gauche). The propynyl group is out of the plane of the nucleobase and is bent. The compound forms a three‐dimensional network which is stabilized by several hydrogen bonds (O—H·O and O—H·N). The nucleobases are stacked head‐to‐tail. The methanol solvent mol­ecule forms hydrogen bonds with both the nucleobase and the sugar moiety.     

6‐Aza‐2′‐deoxy­uridine and N3‐anisoyl‐6‐aza‐2′‐deoxy­uridine

In 2‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐1,2,4‐triazine‐3,5(2H,4H)‐dione (6‐aza‐2′‐deoxy­uridine), C₈H₁₁N₃O₅, (I), the conformation of the glycosylic bond is between anti and high‐anti [χ = −94.0 (3)°], whereas the derivative 2‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐N⁴‐(2‐methoxy­benzoyl)‐1,2,4‐triazine‐3,5(2H,4H)‐dione (N³‐anisoyl‐6‐aza‐2′‐deoxy­uridine), C₁₆H₁₇N₃O₇, (II), displays a high‐anti conformation [χ = −86.4 (3)°]. The furanosyl moiety in (I) adopts the S‐type sugar pucker (²T₃), with P = 188.1 (2)° and τ_m = 40.3 (2)°, while the sugar pucker in (II) is N (³T₄), with P = 36.1 (3)° and τ_m = 33.5 (2)°. The crystal structures of (I) and (II) are stabilized by inter­molecular N—H⋯O and O—H⋯O inter­actions.     

Ethyl 3‐(2′‐deoxyuridin‐5‐yl)‐3‐hydroxy‐2‐iodopropanoate,a ­nucleoside analogue

In the title compound, C₁₄H₁₉IN₂O₈, an almost planar heterocyclic base is oriented anti with respect to the puckered sugar moiety. The sugar pucker is C2′‐endo/C3′‐exo, the N‐glycosidic torsion angle is 166.4 (4)° and the conformation of O5′ is +sc. The mol­ecules are linked by hydrogen bonds of the types N—H?O and O—H?O.     

(E,E,E)‐1,6‐Bis(2,4‐di­chloro­phenyl)­hexa‐1,3,5‐triene

The title mol­ecule, C₁₈H₁₂Cl₄, lies about an inversion centre and the hexatriene chain is planar. The torsion angle of the single bond between the planes of the chain and the benzene ring is −8.6 (3)°. The dihedral angle between the planes defined by the chains of adjacent mol­ecules is 50.0 (2)°. The shortest intermolecular distance between the Cl atoms is 3.514 (1) Å. The mol­ecules are joined through π–π‐stacking and strong attractive Cl⃛Cl interactions.     

3,4‐Di­hydro‐6‐methyl‐3‐β‐d‐ribo­furan­osyl‐4,5′‐cyclo‐9H‐imidazo[1,2‐a]­purin‐9‐one hydrate

In the title compound, C₁₃H₁₃N₅O₄·H₂O (4,5′‐cyclo­wyosine·H₂O), the cyclization forces a syn arrangement of the aglycon with respect to the sugar moiety. The ribo­furan­ose part of the mol­ecule displays a β‐d configuration with an envelope C1′‐endo pucker. The mol­ecules are arranged in columns along the short a axis and are linked to water mol­ecules through O—H?O and O—H?N hydrogen bonds.     

The 7‐bromo derivative of 2‐amino‐2′‐deoxytubercidin fluorinated at the sugar moiety

The title compound, 2,4‐diamino‐5‐bromo‐7‐(2‐deoxy‐2‐fluoro‐β‐d ‐arabinofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine, C₁₁H₁₃BrFN₅O₃, shows two conformations of the exocyclic C4′—C5′ bond, with the torsion angle γ (O5′—C5′—C4′—C3′) being 170.1 (3)° for conformer 1 (occupancy 0.69) and 60.7 (7)° for conformer 2 (occupancy 0.31). The N‐glycosylic bond exhibits an anti conformation, with χ = −114.8 (4)°. The sugar pucker is N‐type (C3′‐endo; ³T₄), with P = 23.3 (4)° and τ_m = 36.5 (2)°. The compound forms a three‐dimensional network that is stabilized by several intermolecular hydrogen bonds (N—H...O, O—H...N and N—H...Br).     

7‐Deaza‐2′‐deoxy­guanosine

In the title compound, 2‐amino‐7‐(2‐deoxy‐β‐d ‐erythro‐pentofuran­osyl)‐3,7‐dihydro­pyrrolo[2,3‐d]pyrimidin‐4‐one, C₁₁H₁₄N₄O₄, the N‐glycosylic bond torsion angle, χ, is anti [−106.5 (3)°]. The 2′‐deoxy­ribofuran­osyl moiety adopts the ³T₄ (N‐type) conformation, with P = 39.1° and τ_m = 40.3°. The conformation around the exocyclic C—C bond is ap (trans), with a torsion angle, γ, of −173.8 (3)°. The nucleoside forms a hydrogen‐bonded network, leading to a close‐packed multiple‐layer structure with a head‐to‐head arrangement of the bases. The nucleobase interplanar O=C—C⋯NH₂ distance is 3.441 (1) Å.     

3,6‐Di­hydroxy‐2‐(11‐phenyl­undecan­oyl)­cyclo­hex‐2‐en‐1‐one from Virola venosa bark

The structure of the title compound, C₂₃H₃₂O₄, an aryl­alkanone isolated from the petroleum ether fraction of the ethanol extract of the bark of Virola venosa, has been established by NMR spectroscopy and, for the first time, by X‐ray structure analysis. Two independent mol­ecules of the same enantiomer are present in the unit cell. Both mol­ecules exhibit an intramolecular hydrogen bond, which can be correlated with a rare signal observed at 18.28 p.p.m. in the ¹H NMR spectrum. The packing, in space group P1, is determined by a pseudo‐center of symmetry leading to a short intermolecular contact, which is present in one mol­ecule but does not occur in the other. As a consequence, the O—C—C—O torsion angles [−16.9 (3) and −12.7 (3)°] through the ketone and its adjacent hydroxy group are significantly different in the two mol­ecules.     

4‐Fluoro‐2‐(phospho­no­methyl)­benzene­sulfonic acid monohydrate

The title compound, C₇H₈FO₆PS·H₂O, contains both phospho­nic and sulfonic acid functionalities. An extensive network of O—H?O hydrogen bonds is present in the crystal structure. The three acidic protons are associated with the phospho­nate group. Two protons experience typical hydrogen‐bond contacts with the sulfonate‐O atoms, while the third has a longer covalent bond of 1.05 (3) Å to the phospho­nate‐O atom and a short hydrogen‐bond contact of 1.38 (3) Å to the water O atom (all O—H?O angles are in the range 162–175°). The sulfonate group is positioned so that one S—O bond is nearly coplanar with the phenyl ring [torsion angle O—S—C—C ?8.6 (2)°]. The phospho­nate group is oriented approximately perpendicular to the ring [torsion angle P—C—C—C 99.2 (2)°] with one P—O bond anti to the benzyl C—C bond. The mol­ecules pack in layers in the b–c plane with the water mol­ecules in between adjacent pairs of inverted layers.     

The N1‐(2′‐deoxyribofuranoside) of 3‐iodo‐5‐nitroindole: a universal nucleoside forming nitro–iodo interactions

The title compound [systematic name: 1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐3‐iodo‐5‐nitro‐1H‐indole], C₁₃H₁₃IN₂O₅, exhibits an anti glycosylic bond conformation with a χ torsion angle of −114.9 (3)°. The furanose moiety shows a twisted C2′‐endo sugar pucker (S‐type), with P = 141.3° and τ_m = 40.3°. The orientation of the exocyclic C4′—C5′ bond is +ap (gauche, trans), with a γ torsion angle of 177.4 (2)°. The extended crystal structure is stabilized by hydrogen bonding and I...O contacts, as well as by stacking interactions. The O atoms of the nitro group act as acceptors, forming bifurcated hydrogen bonds within the ac plane. Additionally, the iodo substituent forms an interplanar contact with an O atom of the nitro group, and another contact with the O atom of the 5′‐hydroxy group of the sugar moiety within the ac plane is observed. These contacts can be considered as the structure‐determining factors for the molecular packing in the crystal structure.