Charge‐assisted N—H·I and C—H·I hydrogen bonding in (1R,2S)‐1‐(ferrocenylmethyl)‐2‐(methoxymethyl)pyrrolidinium iodide

In the title compound, [Fe(C₅H₅)(C₁₂H₁₉NO)]I, the ferrocene moiety has an eclipsed conformation, with mean Fe—C bond lengths of 2.031 (4) and 2.020 (6) Å for the substituted and unsubstituted cyclo­penta­dienyl rings. The pyrrolidinium heterocycle adopts an envelope conformation and has its 1‐ and 2‐substituents in a relative trans disposition. Strong (+/−)‐charge‐assisted N—H·I and C—H·I hydrogen bonds are present. The crystal structure is also stabilized by weak C—H·O interactions.     

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).     

(1R,3S)‐Camphoramic acid

The title chiral compound, 3‐amino­carbonyl‐1,2,2‐tri­methyl­cyclo­pentane‐1‐carboxylic acid, C₁₀H₁₇NO₃, was prepared from (1R,3S)‐camphoric acid. The five‐membered ring adopts a conformation which is intermediate between a twist and an envelope. Elongations of the C—C bonds and contractions of the C—C—C bond angles are observed within the five‐membered ring. A ¹H NMR spectrum was recorded to assist in distinguishing the amide group from the carboxyl group.     

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).     

5‐Methyl‐2′‐deoxy‐4′‐thio‐α‐uridine (R)‐­S‐oxide

The pyrimidine ring of the title compound, C₁₀H₁₄N₂O₅S, is planar to within 0.024 (1) Å and makes an angle of 75.46 (10)° with the mean plane of the thio­sugar ring. In terms of standard nucleoside nomenclature, this ring has the C3′‐endo conformation. The O5′—C5′—C4′—C3′ torsion angle is 166.5 (3)° and the glycosidic torsion angle S4′—C1′—N1—C2 is ?52.1 (2)° (syn).     

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.     

Synthesis and crystal structures of C24‐epimeric 20(R)‐ocotillol‐type saponins

Ocotillol‐type saponins have a wide spectrum of biological activities. Previous studies indicated that the configuration at the C24 position may be responsible for their stereoselectivity in pharmacological action and pharmacokinetics. Natural ocotillol‐type saponins share a 20(S)‐form but it has been found that the 20(R)‐stereoisomers have different pharmacological effects. The semisynthesis of 20(R)‐ocotillol‐type saponins has not been reported and it is therefore worthwhile clarifying their crystal structures. Two C24 epimeric 20(R)‐ocotillol‐type saponins, namely (20R,24S)‐20,24‐epoxydammarane‐3β,12β,25‐triol, C₃₀H₅₂O₄, (III), and (20R,24R)‐20,24‐epoxydammarane‐3β,12β,25‐triol monohydrate, C₃₀H₅₂O₄·H₂O, (IV), were synthesized, and their structures were elucidated by spectral studies and finally confirmed by single‐crystal X‐ray diffraction. The (Me)C—O—C—C(OH) torsion angle of (III) is 146.41 (14)°, whereas the corresponding torsion angle of (IV) is −146.4 (7)°, indicating a different conformation at the C24 position. The crystal stacking in (III) generates an R₄⁴(8) motif, through which the molecules are linked into a one‐dimensional double chain. The chains are linked via nonclassical C—H…O hydrogen bonds into a two‐dimensional network, and further stacked into a three‐dimensional structure. In contrast to (III), epimer (IV) crystallizes as a hydrate, in which the water molecules act as hydrogen‐bond donors linking one‐dimensional chains into a two‐dimensional network through intermolecular O—H…O hydrogen bonds. The hydrogen‐bonded chains extend helically along the crystallographic a axis and generate a C₄⁴(8) motif.     

Hydro­gen‐bonded dimers of 1,8,10‐trihydroxy‐10‐(prop‐2‐enyl)­anthracen‐9(10H)‐one: S(6), R(10) and R(14) motifs

The central ring of the anthrone system in the title compound, C₁₇H₁₄O₄, has a shallow envelope conformation, and each of the two outer rings is inclined at an angle of 17.41 (3)°. In the solid state, the mol­ecules exist as centrosymmetrically related O—H⃛O hydrogen‐bonded dimers. Two intramolecular O—H⃛O hydrogen bonds, involving the central carbonyl O atom and having a graph‐set motif of S(6), are observed. These intramolecular interactions lead co‐operatively to an O—H⃛O⃛H—O pattern that has a binary graph‐set motif of (10).     

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°].     

An unusual conformation of gabapentin (Gpn) in Pyr‐Gpn‐NH‐NH‐Pyr stabilized by weak interactions

The crystal structure of N‐[(1‐{2‐oxo‐2‐[2‐(pyrazin‐2‐ylcarbonyl)hydrazin‐1‐yl]ethyl}cyclohexyl)methyl]pyrazine‐2‐carboxamide monohydrate (Pyr‐Gpn‐NN‐NH‐Pyr·H₂O), C₁₉H₂₃N₇O₃·H₂O, reveals an unusual trans–gauche (tg⁻) conformation for the gabapentin (Gpn) residue around the C^γ—C^β (θ₁) and C^β—C^α (θ₂) bonds. The molecular conformation is stabilized by intramolecular N—H...N hydrogen bonds and weak C—H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N—H...O and O—H...O hydrogen bonds together with weak C—H...O and π–π inteactions.     

O‐Ethyl and O‐methyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d‐glucopyranosyl)thiocarbamate

In both the title structures, O‐ethyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d ‐gluco­pyran­osyl)­thio­carbam­ate, C₁₇H₂₅NO₁₀S, and O‐methyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d ‐gluco­pyran­osyl)­thiocar­bam­ate, C₁₆H₂₃NO₁₀S, the hexo­pyran­osyl ring adopts the ⁴C₁ conformation. All the ring substituents are in equatorial positions. The acetoxy­methyl group is in a gauche–gauche conformation. The S atom is in a synperi­planar conformation, while the C—N—C—O linkage is antiperiplanar. N—H?O intermolecular hydrogen bonds link the mol­ecules into infinite chains and these are connected by C—H?O interactions.     

6,6′‐Di­methoxy‐2,2′‐[(1R,2R)‐cyclo­hexane‐1,2‐diyl­bis­(nitrilo­methyl­idyne)]­diphenol: three C—H⃛O hydrogen bonds generate a three‐dimensional framework

Molecules of the title compound, alternatively called (R,R)‐N,N′‐bis(3‐methoxysalicylidene)‐trans‐cyclohexane‐1,2‐diamine, C₂₂H₂₆N₂O₄, contain two intramolecular O—H⃛N hydrogen bonds and adopt a conformation with approximate twofold rotational symmetry. The mol­ecules are linked by three C—H⃛O hydrogen bonds [H⃛O = 2.45–2.55 Å, C⃛O = 3.329 (2)–3.398 (2) Å and C—H⃛O = 142–172°] into a continuous framework.     

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.     

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.     

Head‐to‐head dimers in the zwitterion of 1‐hydroxy‐1‐phosphono‐3‐(1‐piperidino)propylidene‐1‐phosphonate (PHPBP)

The title compound, C₈H₁₉NO₇P₂, is a member of the bis­phosphonate family of therapeutic compounds. PHPBP has inner‐salt character, consisting of a negatively charged PO₃ group and a positively charged N atom. The six‐membered piperidine ring adopts an almost‐perfect chair conformation. The hydroxyl group and the N atom have gauche and trans conformations in relation to the O—C—C—C—N backbone, respectively. Hydrogen bonding is the main contributor to the packing in the crystal, which consists of head‐to‐head dimers formed through phosphonyl–phosphonyl hydrogen bonds, while O—H⋯O and N—H⋯O interactions join the dimers into a plane parallel to crystallographic b and c axes.     

(2R*,4S*)‐2‐(Pyridin‐3‐yl)‐2,3,4,5‐tetrahydro‐1H‐1‐benzazepin‐4‐ol: a three‐dimensional framework built from O—H...N,C—H...O and C—H...π(arene) hydrogen bonds

The title compound, C₁₅H₁₆N₂O, crystallizes in the space group P2₁2₁2₁ with Z′ = 1. The seven‐membered ring adopts a chair‐type conformation with the hydroxy and pyridyl substituents in equatorial sites. Molecules are linked into a three‐dimensional framework structure by a combination of O—H...N, C—H...O and C—H...π(arene) hydrogen bonds, but N—H...O and N—H...π(arene) interactions are absent from the structure. Comparisons are made with some related compounds.     

Carbonyl–carbonyl and carbonyl–π interactions as directing motifs in the supramolecular structure of carbonyl(3‐oxopenta‐1,4‐diene‐1,5‐diyl)[tris(3,5‐dimethyl‐1H‐pyrazol‐1‐yl‐κN2)methane]iridium(III) trifluoromethanesulfonate

In the title complex salt, [Ir(C₅H₄O)(C₁₆H₂₂N₆)(CO)](CF₃O₃S), the Ir^III centre adopts a distorted octahedral geometry with a facial coordination of the tris(3,5‐dimethyl‐1H‐pyrazol‐1‐yl)methane ligand. The C—C distances of the iridacycle are in agreement with its iridacyclohexa‐2,5‐dien‐4‐one nature, which presents a nonsymmetric boat‐like conformation with the C—Ir—C vertex more bent than the C—C(=O)—C vertex. The supramolecular architecture is mainly directed by CO...CO and CO...π and Csp³—H...O interactions, the arrangement of which depends on the anion.     

(1R,2S)‐2‐[N‐Methyl‐N‐(4‐toluene­sulfonyl)amino]‐1‐phenylpropan‐1‐ol

In the title compound, C₁₇H₂₁NO₃S, the S atom is in a distorted tetrahedral geometry and the N atom exhibits sp² character. The antiperiplanar conformation is observed for the N and hydroxyl‐O atoms and the torsion angle around the N—C linkage is ?136.3 (2)°. The mol­ecules are linked by O—H?O intermolecular hydrogen bonds to form an infinite one‐dimensional chains along the c axis.     

24(R)‐Acetyl­oxy‐1α,2α‐epoxy­cholesta‐4,6‐dien‐3‐one hydrate

In the title compound, C₂₉H₄₂O₄·H₂O, cyclo­hexane rings A and B are in the sofa conformation, ring C is in a chair conformation and the five‐membered ring D is in an envelope conformation. The structure is stabilized by inter‐ and intramolecular C—H?O and O—H?O hydrogen bonds.