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).     

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‐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).     

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.     

7‐Fluorotubercidin: a halogenated derivative of a naturally occurring nucleoside antimetabolite

The title compound [systematic name: 4‐amino‐5‐fluoro‐7‐(β‐d ‐ribofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine], C₁₁H₁₃FN₄O₄, exhibits an anti glycosylic bond conformation, with a χ torsion angle of −124.7 (3)°. The furanose moiety shows a twisted C2′‐endo sugar pucker (S‐type), with P = 169.8 (3)° and τ_m = 38.7 (2)°. The orientation of the exocyclic C4′—C5′ bond is +sc (gauche, gauche), with a γ torsion angle of 59.3 (3)°. The nucleobases are stacked head‐to‐head. The extended crystal structure is a three‐dimensional hydrogen‐bond network involving O—H...O, O—H...N and N—H...O hydrogen bonds. The crystal structure of the title nucleoside demonstrates that the C—C bonds nearest the F atom of the pyrrole system are significantly shortened by the electronegative halogen atom.     

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).     

π‐Stacked hydrogen‐bonded dimers in 2‐(2‐nitro­phenyl­amino­carbonyl)­benzoic acid,and hydrogen‐bonded sheets in orthorhombic and monoclinic polymorphs of 2‐(4‐nitro­phenyl­amino­carbonyl)­benzoic acid

Molecules of 2‐(2‐nitrophenylaminocarbonyl)benzoic acid, C₁₄H₁₀N₂O₅, are linked into centrosymmetric R(8) dimers by a single O—H⋯O hydrogen bond [H⋯O = 1.78 Å, O⋯O = 2.623 (2) Å and O—H⋯O = 178°] and these dimers are linked into sheets by a single aromatic π–π stacking interaction. The isomeric compound 2‐(4‐nitrophenylaminocarbonyl)benzoic acid crystallizes in two polymorphic forms. In the orthorhombic form (space group P2₁2₁2₁ with Z′ = 1, crystallized from ethanol), the mol­ecules are linked into sheets of R(22) rings by a combination of one N—H⋯O hydrogen bond [H⋯O = 1.96 Å, N⋯O = 2.833 (3) Å and N—H⋯O = 171°] and one O—H⋯O hydrogen bond [H⋯O = 1.78 Å, O⋯O = 2.614 (3) Å and O—H⋯O = 173°]. In the monoclinic form (space group P2₁/n with Z′ = 2, crystallized from acetone), the mol­ecules are linked by a combination of two N—H⋯O hydrogen bonds [H⋯O = 2.09 and 2.16 Å, N⋯O = 2.873 (4) and 2.902 (3) Å, and N—H⋯O = 147 and 141°] and two O—H⋯O hydrogen bonds [H⋯O = 1.84 and 1.83 Å, O⋯O = 2.664 (3) and 2.666 (3) Å, and O—H⋯O = 166 and 174°] into sheets of some complexity. These sheets are linked into a three‐dimensional framework by a single C—H⋯O hydrogen bond [H⋯O = 2.45 Å, C⋯O = 3.355 (4) Å and C—­H⋯O = 160°].     

2′‐Deoxy‐5‐fluorotubercidin

In the title compound, 4‐amino‐7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐fluoro‐7H‐pyrrolo[2,3‐d]pyrimidine, C₁₁H₁₃FN₄O₃, the conformation of the glycosyl bond lies between anti and high anti [χ = −101.1 (3)°]. The furanose moiety adopts the S‐type sugar pucker (²T₃), with P = 164.7 (3)° and τ = 40.1 (2)°. The extended structure is a three‐dimensional hydrogen‐bond network involving a C—H⋯F, two N—H⋯O and two O—H⋯O hydrogen bonds.     

N‐Chloro­acetyl‐β‐alanine

The β‐alanine residue of the title compound, C₅H₈ClNO₃, has a ggt folded conformation, which is mainly stabilized through intermolecular N—H⋯O=C (amide–acid) and O—H⋯O=C (acid–amide) hydrogen bonds. In addition, a cis conformation is found for the Cl—CH₂—C(=O)—NH torsion angle, which is associated with the presence of an intramolecular hydrogen bond.     

N,N′‐Bis(2‐pyridyl)benzene‐1,2‐diamine

Hindered rotation about the partial double C—N bonds between the amine and pyridine moieties in the title mol­ecule, C₁₆H₁₄N₄, results in two different conformations of the N‐aryl‐2‐amino­pyridine units. One, assuming an E conformation, is involved in a pair of N—H⋯N hydrogen bonds that generate a centrosymmetric (8) motif. The second, adopting a Z conformation, is not engaged in any hydrogen bonding and is flattened, the dihedral angle between the benzene and pyridine rings being 12.07 (7)°. This conformation is stabilized by an intramolecular C—H⋯N interaction [C⋯N = 2.9126 (19) Å, H⋯N = 2.31 Å and C—H⋯N = 120°].     

Three N2‐benzoyl­oxybenz­amidines: sheet structures built from hard and soft hydrogen bonds and aromatic π–π stacking interactions

Molecules of the title compounds N²‐(benzoyl­oxy)­benz­ami­dine, C₁₄H₁₂N₂O₂, (I), N²‐(2‐hydroxy­benzoyl­oxy)­benz­ami­dine, C₁₄H₁₂N₂O₃, (II), and N²‐benzoyloxy‐2‐hydroxybenzamidine, C₁₄H₁₂N₂O₃, (III), all have extended chain conformations, with the aryl groups remote from one another. In (I), the mol­ecules are linked into chains by a single N—H⋯N hydrogen bond [H⋯N = 2.15 Å, N⋯N = 3.029 (2) Å and N—H⋯N = 153°] and these chains are linked into sheets by means of aromatic π–π stacking interactions. There is one intramolecular O—H⋯O hydrogen bond in (II), and a combination of one three‐centre N—H⋯(N,O) hydrogen bond [H⋯N = 2.46 Å, H⋯O = 2.31 Å, N⋯N = 3.190 (2) Å, N⋯O = 3.146 (2) Å, N—H⋯N = 138° and N—H⋯O = 154°] and one two‐centre C—H⋯O hydrogen bond [H⋯O = 2.46 Å, C⋯O = 3.405 (2) Å and C—H⋯O = 173°] links the mol­ecules into sheets. In (III), an intramolecular O—H⋯N hydrogen bond and two N—H⋯O hydrogen bonds [H⋯O = 2.26 and 2.10 Å, N⋯O = 2.975 (2) and 2.954 (2) Å, and N—H⋯O = 138 and 163°] link the molecules into sheets.     

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.     

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.     

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.     

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.     

4‐[(3‐Chloro­phenyl)­diazenyl]‐2‐{[tris(hydroxy­methyl)­methyl]amino­methyl­ene}cyclo­hexa‐3,5‐dien‐1(2H)‐one

The title compound, C₁₇H₁₈ClN₃O₄, adopts the keto–amine tautomeric form and displays an intramolecular N—H⋯O hydrogen bond [N⋯O = 2.639 (2) Å]. The configuration around the azo N=N double bond is trans, and the dihedral angle between the planes of the two aromatic rings is 20.5 (2)°. The mol­ecules are linked by O—H⋯O hydrogen bonds to form a three‐dimensional network.     

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.     

Bilayers in 4‐iodo‐N‐(2‐iodo‐4‐nitrophenyl)benzamide generated by a combination of an N—H⋯O=C hydrogen bond and two independent iodo–nitro interactions

Molecules of the title compound, C₁₃H₈I₂N₂O₃, are linked into C(4) chains by a single N—H⋯O=C hydrogen bond [H⋯O = 2.10 Å, N⋯O = 2.832 (5) Å and N—H⋯O = 140°]. Two independent two‐centre iodo–nitro interactions, both involving the same O atom but different I atoms [I⋯O = 3.205 (3) and 3.400 (3) Å, and C—I⋯O = 160.4 (2) and 155.7 (2)°], link the hydrogen‐bonded chains into bilayers.     

2‐Amino‐5‐nitro­thia­zole monoethanol solvate: triply‐interwoven hydrogen‐bonded sheets containing centrosymmetric R(8) and R(38) rings

2‐Amino‐5‐nitro­thia­zole crystallizes from solution in ethanol as a monosolvate, C₃H₃N₃O₂S·C₂H₆O, in which the thia­zole component has a strongly polarized molecular–electronic structure. The thia­zole mol­ecules are linked into centrosymmetric dimers by paired N—H⋯N hydrogen bonds [H⋯N = 2.09 Å, N⋯N = 2.960 (6) Å and N—H⋯N = 169°], and these dimers are linked by the ethanol mol­ecules, via a two‐centred N—H⋯O hydrogen bond [H⋯O = 1.98 Å, N⋯O = 2.838 (5) Å and N—H⋯O = 164°] and a planar asymmetric three‐centred O—H⋯(O)₂ hydrogen bond [H⋯O = 2.07 and 2.53 Å, O⋯O = 2.900 (5) and 3.188 (5) Å, O—H⋯O = 169 and 136°, and O⋯H⋯O = 55°], into sheets built from alternating (8) and (38) rings. These sheets are triply interwoven.