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.     

The effect of hydrogen bonding on the conformations of 2‐(1H‐indol‐3‐yl)‐2‐oxoacetamide and 2‐(1H‐indol‐3‐yl)‐N,N‐dimethyl‐2‐oxoacetamide

In the title compounds, C₁₀H₈N₂O₂, (I), and C₁₂H₁₂N₂O₂, (II), the two carbonyl groups are oriented with torsion angles of −149.3 (3) and −88.55 (15)°, respectively. The single‐bond distances linking the two carbonyl groups are 1.528 (4) and 1.5298 (17) Å, respectively. In (I), the molecules are linked by an elaborate system of N—H...O hydrogen bonds, which form adjacent R²₂(8) and R⁴₂(8) ring motifs to generate a ladder‐like construct. Adjacent ladders are further linked by N—H...O hydrogen bonds to build a three‐dimensional network. The hydrogen bonding in (II) is far simpler, consisting of helical chains of N—H...O‐linked molecules that follow the 2₁ screw of the b axis. It is the presence of an elaborate hydrogen‐bonding system in the crystal structure of (I) that leads to the different torsion angle for the orientation of the two adjacent carbonyl groups from that in (II).     

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.     

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).     

3‐Bromo‐1‐(2‐deoxy‐β‐d‐erythro‐pento­furan­osyl)‐1H‐pyrazolo­[3,4‐d]­pyrimidine‐4,6‐di­amine: a nucleoside which strongly enhances DNA duplex stability

The title compound, C₁₀H₁₃BrN₆O₃, exhibits an anti gly­cosylic bond conformation, with an O—C—N—C torsion angle of −105.0 (6)°. The pseudorotation phase angle and the amplitude [P = 5.8 (5)° and τ_m = 30.0 (3)°, respectively] indicate N‐type sugar puckering (³T₂).     

Helical supramolecular assembly of N2,N2′‐bis[3‐(morpholin‐4‐yl)propyl]‐N1,N1′‐(1,2‐phenylene)dioxalamide dimethyl sulfoxide monosolvate

In the title compound, C₂₄H₃₆N₆O₆·C₂H₆OS, the carbonyl groups are in an antiperiplanar conformation, with O=C—C=O torsion angles of 178.59 (15) and −172.08 (16)°. An intramolecular hydrogen‐bonding pattern is depicted by four N—H...O interactions, which form two adjacent S(5)S(5) motifs, and an N—H...N interaction, which forms an S(6) ring motif. Intermolecular N—H...O hydrogen bonding and C—H...O soft interactions allow the formation of a meso‐helix. The title compound is the first example of a helical 1,2‐phenylenedioxalamide. The oxalamide traps one molecule of dimethyl sulfoxide through N—H...O hydrogen bonding. C—H...O soft interactions give rise to the two‐dimensional structure.     

Strong hydrogen‐bonded amino acid dimers in l‐alanine alaninium nitrate

The title compound, C₃H₇NO₂·C₃H₈NO₂⁺·NO₃^?, contains l ‐alanine–alaninium dimers bonded via the carboxyl groups by a strong asymmetric hydrogen bond with an O?O distance of 2.4547 (19) Å. The neutral alanine mol­ecule exists as a zwitterion, where the carboxyl group is dissociated and the amino group is protonated. The alaninium cation has both groups in their acidic form. The alanine mol­ecule and the alaninium cation differ only slightly in their conformation, having an N—C_α—C=O torsion angle close to ?25°. The dimers and the nitrate anion are joined through a three‐dimensional hydrogen‐bond network, in which the full hydrogen‐bonding capabilities of the amino groups of the two alanine moieties are realised.     

Molecular structure of WO2Br2

Molecular structure of WO₂Br₂ has been studied by electron diffractometry. Structural parameters for the molecule with C_2v symmetry are: r_α(W=O)=1.710(6) Å, r_α(W?Br)=2.398(5) Å, r_α(O?O)=2.815(30) Å, r_α(Br?Br)=4.021(16) Å, r_α(O?Br)=3.347(10) Å. The OWO and BrWBr bond angles are close to tetrahedral:L _αOWO=110.8(2.0)°, L_αBrWBr=113.9(1.0)°. The W=O bond was found to be characteristic in the series of tungsten dioxyhalides.     

4‐Iodo­anilinium 3‐nitro­phthalate(1–): tripartite sheets built from O—H...O and N—H...O hydrogen bonds

In the title compound, 4‐iodoanilinium 2‐carboxy‐6‐nitrobenzoate, C₆H₇IN⁺·C₈H₄NO₆⁻, the anions are linked by an O—H...O hydrogen bond [H...O = 1.78 Å, O...O = 2.614 (3) Å and O—H...O = 171°] into C(7) chains, and these chains are linked by two two‐centre N—H...O hydrogen bonds [H...O = 1.86 and 1.92 Å, N...O = 2.700 (3) and 2.786 (3) Å, and N—H...O = 153 and 158°] and one three‐centre N—H...(O)₂ hydrogen bond [H...O = 2.02 and 2.41 Å, N...O = 2.896 (3) and 2.789 (3) Å, N—H...O = 162 and 105°, and O...H...O = 92°], thus forming sheets con­taining R(6), R(8), R(13) and R(18) rings.     

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.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

S‐(4‐Nitrophenyl) 4‐nitrobenzenethiosulfonate

The title compound, C₁₂H₈N₂O₆S₂, (I), is a positional isomer of S‐(2‐nitrophenyl) 2‐nitrobenzenethiosulfonate [Glidewell, Low & Wardell (2000). Acta Cryst. B 56 , 893–905], (II). The most obvious difference between the two isomers is the rotation of the nitro groups with respect to the planes of the adjacent aryl rings. In (I), the nitro groups are only slightly rotated out of the plane of the adjacent aryl ring [2.4 (6) and 6.7 (7)°], while in (II) the nitro groups are rotated by between 37 and 52°, in every case associated with S—S—C—C torsion angles close to 90°. Other important differences between the isomers are the C—S—S(O₂)—C torsion angle [78.39 (2)° for (I) and 69.8 (3)° for (II) (mean)] and the dihedral angles between the aromatic rings [12.3 (3)° for (I) and 28.6 (3)° for (II) (mean)]. There are two types of C—H...O hydrogen bond in the structure [C...O = 3.262 (7) Å and C—H...O = 144°; C...O = 3.447 (7) Å and C—H...O = 166°] and these link the molecules into a two‐dimensional framework. The hydrogen‐bond‐acceptor properties differ between the two isomers.     

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′‐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.     

The molecular structure of cis- and trans-bicyclo [4.2.0]-octane in the gas phase as studied by electron diffraction and molecular mechanics

The molecular structure of Cis- and trans-bicyclo[4.2.0]octane in the gas phase was studied. Molecular mechanics calculations applying Boyd's force Held were used for constraining differences between structural parameters during least squares analysis and for calculating vibrational amplitudes. The cyclohexane ring was found to have a distorted chair conformation, the ring in the cis isomer being flattened along the junction and more twisted in the other part. For the trans compound the reverse is true. The following structural parameters were obtained (r_a-structure):cis: r(C-C)_av. = 1.535 Å. Cyclohexane ring: average bond angle 112.9°; average torsional angle 48°. Cyclobutane ring: average bond angle 88.9°; puckering 157°. The dihedral angle between the bisecting planes of the C(2)-C(1)-C(6)-C(5) and C(8)-C(1)-C(6)-C(7) torsional angles, is 119° - the “connection angle” of the two rings.trans: r(C-C)_av.= 1.532 Å. Cyclohexane ring: average bond angle 110.4° ; average torsional angle 57°. Cyclobutane ring: average bond angle 87.3°; puckering 145°. The “connection angle” is 180° (C₂ symmetry).Comparison is made with structures of related compounds.     

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.     

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‐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.