The first structurally analysed nucleic acid building block containing the Reese protecting group: 2′‐O‐[1‐(2‐fluorophenyl)‐4‐methoxypiperidin‐4‐yl]‐β‐D‐(1′R,2′R,3′R,4′R)‐uridine

The title compound, C₂₁H₂₆FN₃O₇, is assembled by N—H...O and O—H...O hydrogen bonds into well‐separated two‐dimensional layers of about 15 Å thickness. The crescent conformation of the molecules is stabilized by weak intramolecular C—H...O and C—H...F hydrogen bonds. The uridine moiety adopts an anti conformation. The ribofuranose ring exists in an envelope conformation. All the endocyclic uracil bonds are shorter than normal single C—N and C—C bonds, and five of them have comparable lengths, which implies a considerable degree of delocalization of the electron density within this ring.     

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.     

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.     

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′‐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.     

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.     

2,2′‐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.     

1,N6‐Etheno‐2′‐deoxytubercidin hemihydrate

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐7H‐imidazo[1,2‐c]pyrrolo[2,3‐d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N‐glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I‐1) and −107.0 (2)° for conformer (I‐2). The sugar moiety adopts an unusual N‐type (C3′‐endo) sugar pucker for 2′‐deoxyribonucleosides, with P = 36.8 (2)° and τ_m = 40.6 (1)° for conformer (I‐1), and P = 34.5 (2)° and τ_m = 41.4 (1)° for conformer (I‐2). Both conformers and the solvent molecule participate in the formation of a three‐dimensional pattern with a `chain'‐like arrangement of the conformers. The structure is stabilized by intermolecular O—H...O and O—H...N hydrogen bonds, together with weak C—H...O contacts.     

1:1 Adducts of 2,2′‐[isopropylidenebis(p‐phenyleneoxy)]diacetic acid with dimethylammonium and 4,4′‐bipyridine

The title compounds, dimethylammonium 2‐{4‐[1‐(4‐carboxymethoxyphenyl)‐1‐methylethyl]phenoxy}acetate, C₂H₈N⁺·C₁₉H₁₉O₆⁻, (I), and 2,2′‐[isopropylidenebis(p‐phenyleneoxy)]diacetic acid–4,4′‐bipyridine (1/1), C₁₉H₂₀O₆·C₁₀H₈N₂, (II), are 1:1 adducts of 2,2′‐[isopropylidenebis(p‐phenyleneoxy)]diacetic acid (H₂L) with dimethylammonium or 4,4′‐bipyridine. The component ions in (I) are linked by N—H...O, O—H...O and C—H...O hydrogen bonds into continuous two‐dimensional layers parallel to the (001) plane. Adjacent layers are stacked via C—H...O hydrogen bonds into a three‐dimensional network with an –ABAB– alternation of the two‐dimensional layers. In (II), two H₂L molecules, one bipy molecule and two half bipy molecules are linked by O—H...N hydrogen bonds into one‐dimensional chains and rectanglar‐shaped rings. They are assembled viaπ–π stacking interactions and C—H...O hydrogen bonds into an intriguing zero‐dimensional plus one‐dimensional poly(pseudo)rotaxane motif.     

Monomolecular sheets of propeller‐shaped triethyl 4,4′,4′′‐[benzene‐1,3,5‐triyltris(ethyne‐2,1‐diyl)]tribenzoate deuterochloroform monosolvate

The title compound, C₃₉H₃₀O₆·CDCl₃, has a chemical threefold axis and an approximately planar structure, with an ethoxycarbonyl substituent on each of the terminal benzenes oriented in the same direction, thus forming a propeller‐shaped molecule. This molecule is of particular interest in the field of metal–organic frameworks (MOFs), where its hydrolyzed analogue forms MOF structures with high surface areas. The benzene ring which occupies the centre of the molecule forms π–π interactions to the equivalent benzene ring at a perpendicular distance of 3.32 (1) Å. Centrosymmetric dimers formed in this way are interconnected by intermolecular C—H...π interactions with a rather short H...CgA distance of 2.51 Å (CgA is the centroid of the central benzene ring). The molecules are arranged in regular parallel sheets. Within a sheet, molecules are interconnected via C—H...O interactions where all carbonyl O atoms participate in weak hydrogen bonds as hydrogen‐bond acceptors. Neighbouring sheets are connected through the above‐mentioned π–π and C—H...π interactions.     

3‐Deoxy‐β‐d‐ribo‐hexopyranose (3‐deoxy‐β‐d‐glucopyranose)

The β‐pyranose form, (III), of 3‐deoxy‐d ‐ribo‐hexose (3‐deoxy‐d ‐glucose), C₆H₁₂O₅, crystallizes from water at 298 K in a slightly distorted ⁴C₁ chair conformation. Structural analyses of (III), β‐d ‐glucopyranose, (IV), and 2‐deoxy‐β‐d ‐arabino‐hexopyranose (2‐deoxy‐β‐d ‐glucopyranose), (V), show significantly different C—O bond torsions involving the anomeric carbon, with the H—C—O—H torsion angle approaching an eclipsed conformation in (III) (−10.9°) compared with 32.8 and 32.5° in (IV) and (V), respectively. Ring carbon deoxygenation significantly affects the endo‐ and exocyclic C—C and C—O bond lengths throughout the pyranose ring, with longer bonds generally observed in the monodeoxygenated species (III) and (V) compared with (IV). These structural changes are attributed to differences in exocyclic C—O bond conformations and/or hydrogen‐bonding patterns superimposed on the direct (intrinsic) effect of monodeoxygenation. The exocyclic hydroxymethyl conformation in (III) (gt) differs from that observed in (IV) and (V) (gg).     

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).     

Influence of fluorine substitution on the molecular conformation of 3′‐deoxy‐3′‐fluoro‐5‐methyluridine

Fluorine substitutions on the furanose ring of nucleosides are known to strongly influence the conformational properties of oligonucleotides. In order to assess the effect of fluorine on the conformation of 3′‐deoxy‐3′‐fluoro‐5‐methyluridine (^RT^F), C₁₀H₁₃FN₂O₅, we studied its stereochemistry in the crystalline state using X‐ray crystallography. The compound crystallizes in the chiral orthorhombic space group P2₁2₁2₁ and contains two symmetry‐independent molecules (A and B) in the asymmetric unit. The furanose ring in molecules A and B adopts conformations between envelope (²E, 2′‐endo, P = 162°) and twisted (²T₃, 2′‐endo and 3′exo, P = 180°), with pseudorotation phase angles (P) of 164.3 and 170.2°, respectively. The maximum puckering amplitudes, ν_max, for molecules A and B are 38.8 and 36.1°, respectively. In contrast, for 5‐methyluridine (^RT^OH), the value of P is 21.2°, which is between the ³E (3′‐endo, P = 18.0°) and ³T₄ (3′‐endo and 4′‐exo, P = 36°) conformations. The value of ν_max for ^RT^OH is 41.29°. Molecules A and B of ^RT^F generate respective helical assemblies across the crystallographic 2₁‐screw axis through classical N—H…O aand O—H…O hydrogen bonds supplemented by C—H…O contacts. Adjacent parallel helices of both molecules are linked to each other via O—H…O and O…π interactions.     

6,6′‐Dimethoxygossypolone

6,6′‐Dimethoxygossypolone (systematic name: 7,7′‐dihydroxy‐5,5′‐diisopropyl‐6,6′‐dimethoxy‐3,3′‐dimethyl‐1,1′,4,4′‐tetraoxo‐2,2′‐binaphthalene‐8,8′‐dicarbaldehyde), C₃₂H₃₀O₁₀, is a dimeric molecule formed by oxidation of 6,6′‐dimethoxygossypol. When crystallized from acetone, 6,6′‐dimethoxygossypolone has monoclinic (P2₁/c) symmetry, and there are two molecules within the asymmetric unit. Of the four independent quinoid rings, three display flattened boat conformations and one displays a flattened chair/half‐chair conformation. The angles between the planes of the two bridged naphthoquinone structures are fairly acute, with values of about 68 and 69°. The structure has several intramolecular O—H...O and C—H...O hydrogen bonds and several weak intermolecular C—H...O hydrogen bonds, but no intermolecular O—H...O hydrogen bonds.     

Cocrystallization of adamantane‐1,3‐dicarboxylic acid and 4,4′‐bipyridine

The cocrystallization of adamantane‐1,3‐dicarboxylic acid (adc) and 4,4′‐bipyridine (4,4′‐bpy) yields a unique 1:1 cocrystal, C₁₂H₁₆O₄·C₁₀H₈N₂, in the C2/c space group, with half of each molecule in the asymmetric unit. The mid‐point of the central C—C bond of the 4,4′‐bpy molecule rests on a center of inversion, while the adc molecule straddles a twofold rotation axis that passes through two of the adamantyl C atoms. The constituents of this cocrystal are joined by hydrogen bonds, the stronger of which are O—H...N hydrogen bonds [O...N = 2.6801 (17) Å] and the weaker of which are C—H...O hydrogen bonds [C...O = 3.367 (2) Å]. Alternate adc and 4,4′‐bpy molecules engage in these hydrogen bonds to form zigzag chains. In turn, these chains are linked through π–π interactions along the c axis to generate two‐dimensional layers. These layers are neatly packed into a stable crystalline three‐dimensional form via weak C—H...O hydrogen bonds [C...O = 3.2744 (19) Å] and van der Waals attractions.     

Synthesis,Crystal Structure and Hydrolysis of a Novel Anhydrogalactosucrose: 2′‐Methoxyl‐O‐1′,4′:3′,6′‐dianhydro‐β‐D‐fructofuranosyl 3,6‐anhydro‐4‐chloro‐4‐deoxy‐α‐D‐galactopyranoside

A novel anhydrogalactosucrose derivative 2′‐methoxyl‐O‐1′,4′:3′,6′‐dianhydro‐β‐D‐fructofuranosyl 3,6‐anhydro‐4‐chloro‐4‐deoxy‐α‐D‐galactopyranoside ( 4 ) was prepared from 3,6:1′,4′:3′,6′‐trianhydro‐4‐chloro‐4‐deoxy‐galactosucrose ( 3 ) via a facile method and characterized by ¹H NMR, ¹³C NMR and 2D NMR spectra. The single crystal X‐ray diffraction analysis shows that the title molecule forms a two thee‐dimensional network structure by two kinds of hydrogen bond interactions [O(2) H(2)···O(7), O(5) H(5)···O(8)]. Its stability was investigated by acid hydrolysis reaction treated with sulfuric acid, together with the formation of 1,6‐Di‐O‐methoxy‐4‐chloro‐4‐deoxy‐β‐D‐galactopyranose ( 5 ) and 2,2‐Di‐C‐methoxy‐1,4:3,6‐dianhydromannitol ( 6 ). According to the result, the relative stability of the ether bonds in the structure is in the order: C(1) O C(5)≈C(3′) O C(6′)≈C(1′) O C(4′)>C(3) O C(6)≈C(1) O C(2′)>C(2′) O C(5′).     

The double‐stranded ladder‐like structure of poly[[bis(μ2‐acetato‐κ2O:O′)bis(acetato‐κO)bis(μ‐4,4′‐bipyridine‐κ2N:N′)dicopper(II)] 4‐nitrophenol disolvate tetrahydrate]

The reaction of 4,4′‐bipyridine with copper acetate in the presence of 4‐nitrophenol led to the formation of the title compound, {[Cu(CH₃COO)₂(C₁₀H₈N₂)]·C₆H₅NO₃·2H₂O}_n. The complex forms a double‐stranded ladder‐like coordination polymer extending along the b axis. The double‐stranded polymers are separated by 4‐nitrophenol and water solvent molecules. The two Cu^II centres of the centrosymmetric Cu₂O₂ ladder rungs have square‐pyramidal coordination environments, which are formed by two acetate O atoms and two 4,4′‐bipyridine N atoms in the basal plane and another acetate O atom at the apex. The ladder‐like double strands are separated from each other by one unit‐cell length along the c axis, and are connected by the water and 4‐nitrophenol molecules through a series of O—H...O and C—H...O hydrogen‐bonding interactions and two unique intermolecular π–π interactions.     

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′‐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.     

A new one‐dimensional nickel metal–organic framework: catena‐poly[[[diaquabis(4‐{[(1‐phenyl‐1H‐tetrazol‐5‐yl)sulfanyl]methyl}benzoato‐κO)nickel(II)]‐μ‐4,4′‐bipyridine‐κ2N:N′] monohydrate]

The title complex, {[Ni(C₁₅H₁₁N₄O₂S)₂(C₁₀H₈N₂)(H₂O)₂]·H₂O}_n, was synthesized by the reaction of nickel chloride, 4‐{[(1‐phenyl‐1H‐tetrazol‐5‐yl)sulfanyl]methyl}benzoic acid (HL) and 4,4′‐bipyridine (bpy) under hydrothermal conditions. The asymmetric unit contains two half Ni^II ions, each located on an inversion centre, two L⁻ ligands, one bpy ligand, two coordinated water molecules and one unligated water molecule. Each Ni^II centre is six‐coordinated by two monodentate carboxylate O atoms from two different L⁻ ligands, two pyridine N atoms from two different bpy ligands and two terminal water molecules, displaying a nearly ideal octahedral geometry. The Ni^II ions are bridged by 4,4′‐bipyridine ligands to afford a linear array, with an Ni...Ni separation of 11.361 (1) Å, which is further decorated by two monodentate L⁻ ligands trans to each other, resulting in a one‐dimensional fishbone‐like chain structure. These one‐dimensional fishbone‐like chains are further linked by O—H...O, O—H...N and C—H...O hydrogen bonds and π–π stacking interactions to form a three‐dimensional supramolecular architecture. The thermal stability of the title complex was investigated via thermogravimetric analysis.