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.     

Methyl {1‐[2,3‐O‐iso­propyl­idene‐5‐O‐(4‐nitro­benzoyl)‐α‐d‐ribo­furan­osyl]‐4‐methoxy­carbonyl‐1H‐1,2,3‐triazol‐5‐yl}acetate

In the title compound, C₂₂H₂₄N₄O₁₁, the N‐glycosidic torsion angles O′—C′—N—C and O′—C′—N—N are ?34.1 (6) and 148.8 (3)°, respectively. The mol­ecule displays an α‐d configuration with the ribo­furan­ose moiety in an O′‐exo–C′‐endo pucker. There are only weak C—H?O and C—H?N intra‐ and intermolecular interactions.     

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‐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.     

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.     

Three different fluoro‐ or chloro‐substituted 1′‐deoxy‐1′‐phenyl‐β‐D‐ribofuranoses

Crystal structures are reported for three fluoro‐ or chloro‐substituted 1′‐deoxy‐1′‐phenyl‐β‐D‐ribofuranoses, namely 1′‐deoxy‐1′‐(2,4,5‐trifluorophenyl)‐β‐D‐ribofuranose, C₁₁H₁₁F₃O₄, (I), 1′‐deoxy‐1′‐(2,4,6‐trifluorophenyl)‐β‐D‐ribofuranose, C₁₁H₁₁F₃O₄, (II), and 1′‐(4‐chlorophenyl)‐1′‐deoxy‐β‐D‐ribofuranose, C₁₁H₁₃ClO₄, (III). The five‐membered furanose ring of the three compounds has a conformation between a C2′‐endo,C3′‐exo twist and a C2′‐endo envelope. The ribofuranose groups of (I) and (III) are connected by intermolecular O—H...O hydrogen bonds to six symmetry‐related molecules to form double layers, while the ribofuranose group of (II) is connected by O—H...O hydrogen bonds to four symmetry‐related molecules to form single layers. The O...O contact distance of the O—H...O hydrogen bonds ranges from 2.7172 (15) to 2.8895 (19) Å. Neighbouring double layers of (I) are connected by a very weak intermolecular C—F...π contact. The layers of (II) are connected by one C—H...O and two C—H...F contacts, while the double layers of (III) are connected by a C—H...Cl contact. The conformations of the molecules are compared with those of seven related molecules. The orientation of the benzene ring is coplanar with the H—C1′ bond or bisecting the H—C1′—C2′ angle, or intermediate between these positions. The orientation of the benzene ring is independent of the substitution pattern of the ring and depends mainly on crystal‐packing effects.     

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.     

7‐De­aza‐2′‐deoxy‐7‐propynyl­guanosine

The title compound, C₁₄H₁₆N₄O₄, adopts the anti conformation at the gly­cosylic bond [χ−117.1 (5)°]. The sugar pucker of the 2′‐deoxy­ribo­furan­osyl moiety is C2′‐endo–C3′‐exo, ²T₃ (S‐type). The orientation of the exocyclic C4′—C5′ bond is +sc (gauche). The propynyl group is linear and coplanar with the nucleobase moiety. The structure of the compound is stabilized by several hydrogen bonds (N—H⋯O and O—H⋯O), leading to the formation of a multi‐layered network. The nucleobases, as well as the propynyl groups, are stacked. This stacking might cause the extraordinary stability of DNA duplexes containing this compound.     

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.     

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.     

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.     

8‐Aza‐7‐deaza‐2′‐de­oxy‐2‐(methyl­sulfan­yl)adenosine

In the title compound, 4‐amino‐1‐(2‐de­oxy‐β‐d ‐erythro‐pentofuranos­yl)‐6‐methyl­sulfanyl‐1H‐pyrazolo[3,4‐d]pyrimidine, C₁₁H₁₆N₅O₃S, the conformation of the glycosidic bond is between anti and high anti. The 2′‐deoxy­ribofuranosyl moiety adopts the C3′‐exo–C4′‐endo conformation (₃T⁴, S‐type sugar pucker), and the conformation at the exocyclic C—C bond is +sc (+gauche). The exocyclic 6‐amine group and the 2‐methyl­sulfanyl group lie on different sides of the heterocyclic ring system. The mol­ecules form a three‐dimensional hydrogen‐bonded network that is stabilized by O—H⋯N, N—H⋯O and C—H⋯O hydrogen bonds.     

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).     

Intermolecular interactions in the chiral and racemic forms of 3‐­hydroxy‐2‐(1‐oxoisoindolin‐2‐yl)­butanoic acid derived from threonine

The title compounds, C₁₂H₁₃NO₄, are derived from l ‐threonine and dl ‐threonine, respectively. Hydro­gen bonding in the chiral derivative, (2S/3R)‐3‐hydroxy‐2‐(1‐oxoisoindolin‐2‐yl)­butanoic acid, consists of O—H_acid?O_alkyl—H?O=C_indole chains [O?O 2.659 (3) and 2.718 (3) Å], Csp³—H?O and three C—H?π_arene interactions. In the (2R,3S/2S,3R) racemate, conventional carboxylic acid hydrogen bonding as cyclical (O—H?O=C)₂ [graph set R₂²(8)] is present, with O_alkyl—H?O=C_indole, Csp³—H?O and C—H?π_arene interactions. The COOH group geometry differs between the two forms, with C—O, C=O, C—C—O and C—C=O bond lengths and angles of 1.322 (3) and 1.193 (3) Å, and 109.7 (2) and 125.4 (3)°, respectively, in the chiral structure, and 1.2961 (17) and 1.2210 (18) Å, and 113.29 (12) and 122.63 (13)°, respectively, in the racemate structure. The O—C=O angles of 124.9 (3) and 124.05 (14)° are similar. The differences arise from the contrasting COOH hydrogen‐bonding environments in the two structures.     

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).     

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.     

2‐Iodo‐N‐(3‐nitrobenzyl)aniline and 3‐iodo‐N‐(3‐nitrobenzyl)aniline exhibit entirely different patterns of supramolecular aggregation

In 2‐iodo‐N‐(3‐nitro­benzyl)­aniline, C₁₃H₁₁IN₂O₂, the mol­ecules are linked into a three‐dimensional structure by a combination of C—H?O hydrogen bonds, iodo–nitro interactions and aromatic π–π‐stacking interactions, but N—H?O and C—H?π(arene) hydrogen bonds are absent. In the isomeric 3‐iodo‐N‐(3‐nitro­benzyl)­aniline, a two‐dimensional array is generated by a combination of N—H?O, C—H?O and C—H?π(arene) hydrogen bonds, but iodo–nitro interactions and aromatic π–π‐stacking interactions are both absent.     

5‐Ethyl‐2′‐deoxy‐4′‐thiouridine (R)‐S‐oxide monohydrate

The pyrimidine ring of the title compound, C₁₁H₁₆N₂O₅S·H₂O, is planar to within 0.026 (1) Å and makes an angle of 77.73 (8)° with the mean plane of the thiosugar ring. In terms of standard nucleoside nomenclature, this ring has a C1′‐exo,C2′‐endo conformation. The O5′—C5′—C4′—C3′ torsion angle is ?167.4 (2)° and the glycosidic S4′—C1′—N1—C2 torsion angle is ?101.8 (2)° (anti).     

Hydro­gen‐bonded adducts of ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol): a finite cyclic 1:1 adduct with 2,2′‐dipyridyl­amine

In ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–2,2′‐dipyridyl­amine (1/1), [Fe(C₁₈H₁₅O)₂]·C₁₀H₉N₃, (I), there is an intramolecular O—H?O hydrogen bond [H?O 2.03 Å, O?O 2.775 (2) Å and O—H?O 147°] in the ferrocenediol component, and the two neutral molecular components are linked by one O—H?N hydrogen bond [H?N 1.96 Å, O?N 2.755 (2) Å and O—H?N, 157°] and one N—H?O hydrogen bond [H?O 2.26 Å, N?O 3.112 (2) Å and N—H?O 164°] forming a cyclic R(8) motif. One of the pyridyl N atoms plays no part in the intermolecular hydrogen bonding, but participates in a short intramolecular C—H?N contact [H?N 2.31 Å, C?N 2.922 (2) Å and C—H?N 122°].     

The α‐d anomer of 5‐aza‐7‐deaza‐2′‐deoxyguanosine

In the monohydrate of 2‐amino‐8‐(2‐deoxy‐α‐d ‐erythro‐pento­furan­osyl)‐8H‐imidazo­[1,2‐a]­[1,3,5]­triazin‐4‐one, C₁₀H₁₃N₅O₄·H₂O, denoted (I) or αZ_d, the conformation of the N‐gly­cosyl­ic bond is in the high‐anti range [χ = 87.5 (3)°]. The 2′‐deoxy­ribo­furan­ose moiety adopts a C2′‐endo,C3′‐exo(^2′T_3′) sugar puckering (S‐type sugar) and the conformation at the C4′—C5′ bond is ?sc (trans).