7‐Deaza‐2′‐deoxyinosine: a nucleoside showing ambiguous base‐pairing properties against the four canonical DNA constituents

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐3,7‐dihydro‐4H‐pyrrolo[2,3‐d]pyrimidin‐4‐one], C₁₁H₁₃N₃O₄, represents an acid‐stable derivative of 2′‐deoxyinosine. It exhibits an anti glycosylic bond conformation, with a χ torsion angle of 113.30 (15)°. The furanose moiety adopts an S‐type sugar pucker ⁴T₃, with P = 221.8 (1)° and τ_m = 40.4 (1)°. The conformation at the exocyclic C4′—C5′ bond of the furanose ring is ap (trans), with γ = 167.14 (10)°. The extended structure forms a three‐dimensional hydrogen‐bond network involving O—H...O, N—H...O and C—H...O hydrogen bonds. The title compound forms an uncommon hydrogen bond between a CH group of the pyrrole system and the ring O atom of the sugar moiety of a neighbouring molecule.     

1,7‐Dideaza‐2′‐deoxy‐6‐nitronebularine: a pyrrolo[2,3‐b]pyridine nucleoside with an intramolecular hydrogen bond stabilizing the syn conformation

The title compound [systematic name: 1‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐4‐nitro‐1H‐pyrrolo[2,3‐b]pyridine], C₁₂H₁₃N₃O₅, forms an intramolecular hydrogen bond between the pyridine N atom as acceptor and the 5′‐hydroxy group of the sugar residue as donor. Consequently, the N‐glycosylic bond exhibits a syn conformation, with a χ torsion angle of 61.6 (2)°, and the pentofuranosyl residue adopts a C2′‐endo envelope conformation (²E, S‐type), with P = 162.1 (1)° and τ_m = 36.2 (1)°. The orientation of the exocyclic C4′—C5′ bond is +sc (gauche, gauche), with a torsion angle γ = 49.1 (2)°. The title nucleoside forms an ordered and stacked three‐dimensional network. The pyrrole ring of one layer faces the pyridine ring of an adjacent layer. Additionally, intermolecular O—H...O and C—H...O hydrogen bonds stabilize the crystal structure.     

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.     

A toyocamycin analogue with the sugar moiety in a syn conformation

The title compound [systematic name: 4‐amino‐5‐cyano‐1‐(β‐d ‐ribofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine hemihydrate], C₁₂H₁₃N₅O₄·0.5H₂O, is a regioisomer of toyocamycin with the ribofuranosyl residue attached to the pyrimidine moiety of the heterocycle. This analogue exhibits a syn glycosylic bond conformation with a χ torsion angle of 57.51 (17)°. The ribofuranose moiety shows an envelope C2′‐endo (²E) sugar conformation (S‐type), with P = 161.6 (2)° and τ_m = 41.3 (1)°. The conformation at the exocyclic C4′—C5′ bond is +sc (gauche, gauche), with a γ torsion angle of 54.4 (2)°. The crystal packing is stabilized by intermolecular O—H...O, N—H...N and O—H...N hydrogen bonds; water molecules, located on crystallographic twofold axes, participate in interactions. An intramolecular O—H...N hydrogen bond stabilizes the syn conformation of the nucleoside.     

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).     

2′‐Deoxyimmunosine: a thiazolo[4,5‐d]pyrimidine nucleoside adopting the syn conformation

The title compound [systematic name: 5‐amino‐3‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)thiazolo[4,5‐d]pyrimidine‐2,7‐(3H,6H)‐dione], C₁₀H₁₂N₄O₅S, exhibits a syn glycosylic bond conformation, with a torsion angle χ of 61.0 (3)°. The furanose moiety adopts the N‐type sugar pucker (³T₄), with P = 33.0 (5)° and τ_m = 15.1 (1)°. The conformation at the exocyclic C4′—C5′ bond is +ap (trans), with the torsion angle γ = 176.71 (14)°. The extended structure is a three‐dimensional hydrogen‐bond network involving O—H...O and N—H...O hydrogen bonds.     

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‐Amino‐1‐(2‐deoxy‐β‐erythro‐pentofuranosyl)‐1H‐1,2,3‐triazolo[4,5‐d]pyrimidine: an 8‐azaadenine nucleoside with the nucleobase in a syn conformation

The title compound, C₉H₁₂N₆O₃, shows a syn‐glycosylic bond orientation [χ = 64.17 (16)°]. The 2′‐deoxyfuranosyl moiety exhibits an unusual C1′‐exo–O4′‐endo (₁T⁰; S‐type) sugar pucker, with P = 111.5 (1)° and τ_m = 40.3 (1)°. The conformation at the exocyclic C4′—C5′ bond is +sc (gauche), with γ = 64.4 (1)°. The two‐dimensional hydrogen‐bonded network is built from intermolecular N—H...O and O—H...N hydrogen bonds. An intramolecular bifurcated hydrogen bond, with an amino N—H group as hydrogen‐bond donor and the ring and hydroxymethyl O atoms of the sugar moiety as acceptors, constrains the overall conformation of the nucleoside.     

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.     

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‐5‐propynyluridine: a nucleoside with two conformations in the asymmetric unit

The title compound, 1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐(prop‐1‐ynyl)pyrimidin‐2,4(1H,3H)‐dione, C₁₂H₁₄N₂O₅, shows two conformations in the crystalline state: conformer 1 adopts a C2′‐endo (close to ²E; S‐type) sugar pucker and an anti nucleobase orientation [χ = −134.04 (19)°], while conformer 2 shows an S sugar pucker (twisted C2′‐endo–C3′‐exo), which is accompanied by a different anti base orientation [χ = −162.79 (17)°]. Both molecules show a +sc (gauche, gauche) conformation at the exocyclic C4′—C5′ bond and a coplanar orientation of the propynyl group with respect to the pyrimidine ring. The extended structure is a three‐dimensional hydrogen‐bond network involving intermolecular N—H...O and O—H...O hydrogen bonds. Only O atoms function as H‐atom acceptor sites.     

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).     

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.     

Different hydrogen‐bonding modes in two closely related oximes

Two closely related oximes, namely 1‐chloroacetyl‐3‐ethyl‐2,6‐diphenylpiperidin‐4‐one oxime, C₂₁H₂₃ClN₂O₂, (I), and 1‐chloroacetyl‐2,6‐diphenyl‐3‐(propan‐2‐yl)piperidin‐4‐one oxime, C₂₂H₂₅ClN₂O₂, (II), despite their identical sets of hydrogen‐bond donors and acceptors, display basically different hydrogen‐bonding patterns in their crystal structures. While the molecules of (I) are organized into typical centrosymmetric dimers, created by oxime–oxime O—H...N hydrogen bonds, in the structure of (II) there are infinite chains of molecules connected by O—H...O hydrogen bonds, in which the carbonyl O atom from the chloroacetyl group acts as the hydrogen‐bond acceptor. Despite the differences in the hydrogen‐bond schemes, the –OH groups are always in typical anti positions (C—N—O—H torsion angles of ca 180°). The oxime group in (I) is disordered, with the hydroxy groups occupying two distinct positions and C—C—N—O torsion angles of approximately 0 and 180° for the two alternatives. This disorder, even though the site‐occupancy factor of the less occupied position is as low as ca 0.06, is also observed at lower temperatures, which seems to favour the statistical and not the dynamic nature of this phenomenon.     

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.     

2‐Amino‐8‐(2‐deoxy‐2‐fluoro‐β‐d‐arabinofuranosyl)imidazo[1,2‐a][1,3,5]triazin‐4(8H)‐one monohydrate,a 2′‐deoxyguanosine analogue with an altered Watson–Crick recognition site

The title compound, C₁₀H₁₂FN₅O₄·H₂O, shows an anti glycosyl orientation [χ = −123.1 (2)°]. The 2‐deoxy‐2‐fluoroarabinofuranosyl moiety exhibits a major C2′‐endo sugar puckering (S‐type, C2′‐endo–C1′‐exo, ²T₁), with P = 156.9 (2)° and τ_m = 36.8 (1)°, while in solution a predominantly N conformation of the sugar moiety is observed. The conformation around the exocyclic C4′—C5′ bond is −sc (trans, gauche), with γ = −78.3 (2)°. Both nucleoside and solvent molecules participate in the formation of a three‐dimensional hydrogen‐bonding pattern via intermolecular N—H...O and O—H...O hydrogen bonds; the N atoms of the heterocyclic moiety and the F substituent do not take part in hydrogen bonding.     

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.     

2,2′‐Anhydro‐1‐(3′,5′‐di‐O‐acetyl‐β‐D‐arabinofuranosyl)uracil,a cyclouridine nucleoside with a C4′‐endo furanosyl conformation

2,2′‐Anhydro‐1‐(3′,5′‐di‐O‐acetyl‐β‐D‐arabinofuranosyl)uracil, C₁₃H₁₄N₂O₇, was obtained by refluxing 2′,3′‐O‐(methoxymethylene)uridine in acetic anhydride. The structure exhibits a nearly perfect C4′‐endo (⁴E) conformation. The best four‐atom plane of the five‐membered furanose ring is O—C—C—C, involving the C atoms of the fused five‐membered oxazolidine ring, and the torsion angle is only −0.4 (2)°. The oxazolidine ring is essentially coplanar with the six‐membered uracil ring [r.m.s. deviation = 0.012 (5) Å and dihedral angle = −3.2 (3)°]. The conformation at the exocyclic C—C bond is gauche–trans which is stabilized by various C—H...π and C—O...π interactions.     

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).     

A 2′‐deoxycytidine long‐linker click adduct forming two conformers in the asymmetric unit

The title compound {systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐[6‐(1‐benzyl‐1H‐1,2,3‐triazol‐4‐yl)hex‐1‐ynyl]pyrimidin‐2(1H)‐one}, C₂₄H₂₈N₆O₄, shows two conformations in the crystalline state, viz. (I‐1) and (I‐2). The pyrimidine groups and side chains of the two conformers are almost superimposable, while the greatest differences between them are observed for the sugar groups. The N‐glycosylic bonds of both conformers adopt similar anti conformations, with χ = −168.02 (12)° for conformer (I‐1) and χ = −159.08 (12)° for conformer (I‐2). The sugar residue of (I‐1) shows an N‐type (C3′‐endo) conformation, with P = 33.1 (2)° and τ_m = 29.5 (1)°, while the conformation of the 2′‐deoxyribofuranosyl group of (I‐2) is S‐type (C3′‐exo), with P = 204.5 (2)° and τ_m = 33.8 (1)°. Both conformers participate in hydrogen‐bond formation and exhibit identical patterns resulting in three‐dimensional networks. Intermolecular hydrogen bonds are formed with neighbouring molecules of different and identical conformations (N—H...N, N—H... O, O—H...N and O—H...O).