Methyl β‐d‐fructopyranoside

In methyl β‐d ‐fructopyranoside, C₇H₁₄O₆, the thermodynamically most stable methyl glycoside of the ketose d ‐fructose, the pyranose ring is close to being an ideal ²C₅ chair. The compound forms bilayers involving a complex hydrogen‐bonding pattern of five independent hydrogen bonds. Graph‐set analysis was applied to distinguish the hydrogen‐bond patterns at unary and higher level graph sets.     

Divergent Synthesis of 3‐Deoxy‐d‐manno‐oct‐2‐ulosonic Acid (Kdo) Glycosides Containing α‐(2→4)‐Linked Kdo‐Kdo Unit

A convenient and divergent approach was developed to prepare diverse bacterial 3‐deoxy‐d ‐manno‐oct‐2‐ulosonic acid (Kdo) oligosaccharides containing a Kdo‐α‐(2→4)‐Kdo fragment. The orthogonal protected α‐(2→4) linked Kdo‐Kdo disaccharide 3 , serving as a common precursor, was divergently transformed into the corresponding 8‐, 8′‐, and 4′‐hydroxy disaccharides 5 , 7 , and 14 , respectively. Then, these alcohols were glycosylated, respectively, with the 5,7‐O‐di‐tert‐butylsilylene (DTBS) protected Kdo thioglycoside donors 1 or 2 in an α‐stereoselective and high‐yielding manner to afford a range of Kdo oligosaccharides. Finally, removal of all protecting groups of the newly formed glycosides resulted in the desired free Kdo oligomer.     

Methyl β‐d‐galactopyranosyl‐(1→4)‐β‐d‐allopyranoside tetrahydrate

The title compound, C₁₃H₂₄O₁₁·4H₂O, (I), crystallized from water, has an internal glycosidic linkage conformation having ϕ′ (O5_Gal—C1_Gal—O1_Gal—C4_All) = −96.40 (12)° and ψ′ (C1_Gal—O1_Gal—C4_All—C5_All) = −160.93 (10)°, where ring‐atom numbering conforms to the convention in which C1 denotes the anomeric C atom, C5 the ring atom bearing the exocyclic hydroxymethyl group, and C6 the exocyclic hydroxymethyl (CH₂OH) C atom in the βGalp and βAllp residues. Internal linkage conformations in the crystal structures of the structurally related disaccharides methyl β‐lactoside [methyl β‐d ‐galactopyranosyl‐(1→4)‐β‐d ‐glucopyranoside] methanol solvate [Stenutz, Shang & Serianni (1999). Acta Cryst. C 55 , 1719–1721], (II), and methyl β‐cellobioside [methyl β‐d ‐glucopyranosyl‐(1→4)‐β‐d ‐glucopyranoside] methanol solvate [Ham & Williams (1970). Acta Cryst. B 26 , 1373–1383], (III), are characterized by ϕ′ = −88.4 (2)° and ψ′ = −161.3 (2)°, and ϕ′ = −91.1° and ψ′ = −160.7°, respectively. Inter‐residue hydrogen bonding is observed between O3_Glc and O5_Gal/Glc in the crystal structures of (II) and (III), suggesting a role in determining their preferred linkage conformations. An analogous inter‐residue hydrogen bond does not exist in (I) due to the axial orientation of O3_All, yet its internal linkage conformation is very similar to those of (II) and (III).     

Methyl β‐allolactoside [methyl β‐d‐galactopyranosyl‐(1→6)‐β‐d‐glucopyranoside] monohydrate

Methyl β‐allolactoside [methyl β‐d ‐galactopyranosyl‐(1→6)‐β‐d ‐glucopyranoside], (II), was crystallized from water as a monohydrate, C₁₃H₂₄O₁₁·H₂O. The βGalp and βGlcp residues in (II) assume distorted ⁴C₁ chair conformations, with the former more distorted than the latter. Linkage conformation is characterized by ϕ′ (C2_Gal—C1_Gal—O1_Gal—C6_Glc), ψ′ (C1_Gal—O1_Gal—C6_Glc—C5_Glc) and ω (C4_Glc—C5_Glc—C6_Glc—O1_Gal) torsion angles of 172.9 (2), −117.9 (3) and −176.2 (2)°, respectively. The ψ′ and ω values differ significantly from those found in the crystal structure of β‐gentiobiose, (III) [Rohrer et al. (1980). Acta Cryst. B 36 , 650–654]. Structural comparisons of (II) with related disaccharides bound to a mutant β‐galactosidase reveal significant differences in hydroxymethyl conformation and in the degree of ring distortion of the βGlcp residue. Structural comparisons of (II) with a DFT‐optimized structure, (II_C), suggest a link between hydrogen bonding, pyranosyl ring deformation and linkage conformation.     

Methyl 4‐O‐β‐l‐galactopyranosyl‐β‐d‐glucopyranoside (methyl β‐l‐lactoside)

Methyl β‐l ‐lactoside, C₁₃H₂₄O₁₁, (II), is described by glycosidic torsion angles ϕ (O5_Gal—C1_Gal—O4_Glc—C4_Glc) and ψ (C1_Gal—O1_Gal—C4_Glc—C5_Glc) of 93.89 (13) and −127.43 (13)°, respectively, where the ring atom numbering conforms to the convention in which C1 is the anomeric C atom and C6 is the exocyclic hydroxy­methyl (CH₂OH) C atom in both residues (Gal is galactose and Glc is glucose). Substitution of l ‐Gal for d ‐Gal in the biologically relevant disaccharide, methyl β‐lactoside [Stenutz, Shang & Serianni (1999). Acta Cryst. C 55 , 1719–1721], (I), significantly alters the glycosidic linkage inter­face. In the crystal structure of (I), one inter‐residue (intra­molecular) hydrogen bond is observed between atoms H3O_Glc and O5_Gal. In contrast, in the crystal structure of (II), inter‐residue hydrogen bonds are observed between atoms H6O_Glc and O5_Gal, H6O_Glc and O6_Gal, and H3O_Glc and O2_Gal, with H6O_Glc serving as a donor with two intra­molecular acceptors.     

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).     

Methyl 4‐O‐β‐d‐galactopyranosyl α‐d‐mannopyranoside methanol 0.375‐solvate

Methyl β‐d ‐galactopyranosyl‐(1→4)‐α‐d ‐mannopyranoside methanol 0.375‐solvate, C₁₃H₂₄O₁₁·0.375CH₃OH, (I), was crystallized from a methanol–ethanol solvent system in a glycosidic linkage conformation, with ϕ′ (O5_Gal—C1_Gal—O1_Gal—C4_Man) = −68.2 (3)° and ψ′ (C1_Gal—O1_Gal—C4_Man—C5_Man) = −123.9 (2)°, where the ring is defined by atoms O5/C1–C5 (monosaccharide numbering); C1 denotes the anomeric C atom and C6 the exocyclic hydroxymethyl C atom in the βGalp and αManp residues, respectively. The linkage conformation in (I) differs from that in crystalline methyl α‐lactoside [methyl β‐d ‐galactopyranosyl‐(1→4)‐α‐d ‐glucopyranoside], (II) [Pan, Noll & Serianni (2005). Acta Cryst. C 61 , o674–o677], where ϕ′ is −93.6° and ψ′ is −144.8°. An intermolecular hydrogen bond exists between O3_Man and O5_Gal in (I), similar to that between O3_Glc and O5_Gal in (II). The structures of (I) and (II) are also compared with those of their constituent residues, viz. methyl α‐d ‐mannopyranoside, methyl α‐d ‐glucopyranoside and methyl β‐d ‐galactopyranoside, revealing significant differences in the Cremer–Pople puckering parameters, exocyclic hydroxymethyl group conformations and intermolecular hydrogen‐bonding patterns.     

Methyl 4‐O‐β‐d‐galacto­pyran­osyl α‐d‐gluco­pyran­oside (methyl α‐lactoside)

Methyl α‐lactoside, C₁₃H₂₄O₁₁, (I), is described by glycosidic torsion angles ϕ (O5_gal—C1_gal—O1_gal—C4_glc) and ψ (C1_gal—O1_gal—C4_glc—C5_glc), which have values of −93.52 (13) and −144.83 (11)°, respectively, where the ring atom numbering conforms to the convention in which C1 is the anomeric C atom and C6 is the exocyclic hydroxy­methyl (–CH₂OH) C atom in both residues. The linkage geometry is similar to that observed in methyl β‐lactoside methanol solvate, (II), in which ϕ is −88.4 (4)° and ψ is −161.3 (4)°. As in (II), an inter­molecular O3_glc—H⋯O5_gal hydrogen bond is observed in (I). The hydroxy­methyl group conformation in both residues is gauche–trans, with torsion angles ω_gal (O5_gal—C5_gal—C6_gal—O6_gal) and ω_glc (O5_glc—C5_glc—C6_glc—O6_glc) of 69.15 (13) and 72.55 (14)°, respectively. The latter torsion angle differs substantially from that found for (II) [−54.6 (2)°; gauche–gauche]. Cocrystallization of methanol, which is hydrogen bonded to O6_glc in the crystal structure of (II), presumably affects the hydroxy­methyl conformation in the Glc residue in (II).     

Methyl 2‐O‐β‐d‐glucopyranosyl‐α‐l‐rhamnopyranoside

The overall conformation of the title compound, C₁₃H₂₄O₁₀, is described by the glycosidic torsion angles ?_H (H1_g—C1_g—O2_r—C2_r) and ψ_H (C1_g—O2_r—C2_r—H2_r), which have values of 13.6 and 16.1°, respectively. The former is significantly different from the value predicted by consideration of the exo‐anomeric effect (?_H～ 60°) and from that in solution (?_H～ 50°), as determined previously by NMR spectroscopy. An intramolecular O3_r—H?O2_g hydrogen bond may help to stabilize the conformation in the solid state. The orientation of the hydroxy­methyl group of the glucose residue is gauche–gauche, with a torsion angle ω (O5_g—C5_g—C6_g—O6_g) of ?70.4 (4)°. Both pyranose rings are in their expected chair conformations, i.e.⁴C₁ for d ‐glucose and ¹C₄ for l ‐rhamnose.     

Methyl 3‐O‐β‐l‐fucopyranosyl α‐d‐glucopyranoside trihydrate

The water content of the title compound, C₁₃H₂₄O₁₀·3H₂O, creates an extensive hydrogen‐bonding pattern, with all the hydroxyl groups of the disaccharide acting as hydrogen‐bond donors and acceptors. The water molecules are arranged in columns along the crystallographic b axis and form, together with one of the hydroxyl groups, infinite hydrogen‐bonded chains. The conformation of the disaccharide is described by glycosidic torsion angles of −38 and 18°.     

1‐(β‐d‐Erythrofuranos­yl)cytidine (β‐erythrocytidine)

1‐(β‐d ‐Erythrofuranosyl)cytidine, C₈H₁₁N₃O₄, (I), a derivative of β‐cytidine, (II), lacks an exocyclic hydroxy­methyl (–CH₂OH) substituent at C4′ and crystallizes in a global conformation different from that observed for (II). In (I), the β‐d ‐erythrofuranosyl ring assumes an E₃ conformation (C3′‐exo; S, i.e. south), and the N‐glycoside bond conformation is syn. In contrast, (II) contains a β‐d ‐ribofuranosyl ring in a ³T₂ conformation (N, i.e. north) and an anti‐N‐glycoside linkage. These crystallographic properties mimic those found in aqueous solution by NMR with respect to furan­ose conformation. Removal of the –CH₂OH group thus affects the global conformation of the aldofuranosyl ring. These results provide further support for S/syn–anti and N/anti correlations in pyrimidine nucleosides. The crystal structure of (I) was determined at 200 K.     

Methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranoside dihydrate and methyl 2‐formamido‐2‐deoxy‐β‐d‐glucopyranoside

Methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glucopyranoside (β‐GlcNAcOCH₃), (I), crystallizes from water as a dihydrate, C₉H₁₇NO₆·H₂O, containing two independent molecules [denoted (IA) and (IB)] in the asymmetric unit, whereas the crystal structure of methyl 2‐formamido‐2‐deoxy‐β‐d ‐glucopyranoside (β‐GlcNFmOCH₃), (II), C₈H₁₅NO₆, also obtained from water, is devoid of solvent water molecules. The two molecules of (I) assume distorted ⁴C₁ chair conformations. Values of ϕ for (IA) and (IB) indicate ring distortions towards B_C2,C5 and ^C3,O5B, respectively. By comparison, (II) shows considerably more ring distortion than molecules (IA) and (IB), despite the less bulky N‐acyl side chain. Distortion towards B_C2,C5 was observed for (II), similar to the findings for (IA). The amide bond conformation in each of (IA), (IB) and (II) is trans, and the conformation about the C—N bond is anti (C—H is approximately anti to N—H), although the conformation about the latter bond within this group varies by ∼16°. The conformation of the exocyclic hydroxymethyl group was found to be gt in each of (IA), (IB) and (II). Comparison of the X‐ray structures of (I) and (II) with those of other GlcNAc mono‐ and disaccharides shows that GlcNAc aldohexopyranosyl rings can be distorted over a wide range of geometries in the solid state.     

Methyl 2‐O‐β‐l‐fucopyranosyl α‐d‐glucopyranoside monohydrate: a synchrotron study

The structure of the title compound, C₁₃H₂₄O₁₀·H₂O, is stabilized by hydrogen bonds situated adjacent to the glycoside linkage. A direct intramolecular hydrogen bond is present between the fucopyranosyl ring O atom and a glucopyranoside OH group, and a bridging water molecule mediates a hydrogen‐bond‐based interaction from a fucopyranosyl OH group to the methoxy O atom. The conformation of the disaccharide is described by the glycosidic torsion angles ϕ_H = −41° and ψ_H = −2°.     

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).     

1‐(β‐d‐Erythrofuranosyl)adenosine

The title compound, also known as β‐erythroadenosine, C₉H₁₁N₅O₃, (I), a derivative of β‐adenosine, (II), that lacks the C5′ exocyclic hydroxymethyl (–CH₂OH) substituent, crystallizes from hot ethanol with two independent molecules having different conformations, denoted (IA) and (IB). In (IA), the furanose conformation is ^OT₁–E₁ (C1′‐exo, east), with pseudorotational parameters P and τ_m of 114.4 and 42°, respectively. In contrast, the P and τ_m values are 170.1 and 46°, respectively, in (IB), consistent with a ²E–²T₃ (C2′‐endo, south) conformation. The N‐glycoside conformation is syn (+sc) in (IA) and anti (−ac) in (IB). The crystal structure, determined to a resolution of 2.0 Å, of a cocrystal of (I) bound to the enzyme 5′‐fluorodeoxyadenosine synthase from Streptomyces cattleya shows the furanose ring in a near‐ideal ^OE (east) conformation (P = 90° and τ_m = 42°) and the base in an anti (−ac) conformation.     

Disorder and conformational analysis of methyl β‐d‐galactopyranosyl‐(1→4)‐β‐d‐xylopyranoside

Methyl β‐d ‐galactopyranosyl‐(1→4)‐β‐d ‐xylopyranoside, C₁₂H₂₂O₁₀, (II), crystallizes as colorless needles from water with positional disorder in the xylopyranosyl (Xyl) ring and no water molecules in the unit cell. The internal glycosidic linkage conformation in (II) is characterized by a ϕ′ torsion angle (C2′_Gal—C1′_Gal—O1′_Gal—C4_Xyl) of 156.4 (5)° and a ψ′ torsion angle (C1′_Gal—O1′_Gal—C4_Xyl—C3_Xyl) of 94.0 (11)°, where the ring atom numbering conforms to the convention in which C1 denotes the anomeric C atom, and C5 and C6 denote the hydroxymethyl (–CH₂OH) C atoms in the β‐Xyl and β‐Gal residues, respectively. By comparison, the internal linkage conformation in the crystal structure of the structurally related disaccharide, methyl β‐lactoside [methyl β‐d ‐galactopyranosyl‐(1→4)‐β‐d ‐glucopyranoside], (III) [Stenutz, Shang & Serianni (1999). Acta Cryst. C 55 , 1719–1721], is characterized by ϕ′ = 153.8 (2)° and ψ′ = 78.4 (2)°. A comparison of β‐(1→4)‐linked disaccharides shows considerable variability in both ϕ′ and ψ′, with the range in the latter (∼38°) greater than that in the former (∼28°). Inter‐residue hydrogen bonding is observed between atoms O3_Xyl and O5′_Gal in the crystal structure of (II), analogous to the inter‐residue hydrogen bond detected between atoms O3_Glc and O5′_Gal in (III). The exocyclic hydroxymethyl conformations in the Gal residues of (II) and (III) are identical (gauche–trans conformer).     

Stereoselective Synthesis of α‐3‐Deoxy‐D‐manno‐oct‐2‐ulosonic Acid (α‐Kdo) Glycosides Using 5,7‐O‐Di‐tert‐butylsilylene‐Protected Kdo Ethyl Thioglycoside Donors

An efficient methodology for the synthesis of α‐Kdo glycosidic bonds has been developed with 5,7‐O‐di‐tert‐butylsilylene (DTBS) protected Kdo ethyl thioglycosides as glycosyl donors. The approach permits a wide scope of acceptors to be used, thus affording biologically significant Kdo glycosides in good to excellent chemical yields with complete α‐selectivity. The synthetic utility of an orthogonally protected Kdo donor has been demonstrated by concise preparation of two α‐Kdo‐containing oligosaccharides.     

Methyl 4‐O‐β‐l‐fucopyranosyl α‐­d‐­glucopyranoside hemihydrate

The crystal structure of methyl 4‐O‐β‐l ‐fuco­pyran­osyl α‐d ‐gluco­pyran­oside hemihydrate C₁₃H₂₄O₁₀·0.5H₂O is organized in sheets with antiparallel strands, where hydro­phobic interaction accounts for partial stabilization. Infinite hydrogen‐bonding networks are observed within each layer as well as between layers; some of these hydrogen bonds are mediated by water mol­ecules. The conformation of the disaccharide is described by the glycosidic torsion angles: ?_H = ?6.1° and ψ_H = 34.3°. The global energy minimum conformation as calculated by molecular mechanics in vacuo has ?_H = ?58° and ψ_H = ?20°. Thus, quite substantial changes are observed between the in vacuo structure and the crystal structure with its infinite hydrogen‐bonding networks.     

Biotransformation and metabolic profile of caudatin‐2,6‐dideoxy‐3‐O‐methy‐β‐d‐cymaropyranoside with human intestinal microflora by liquid chromatography quadrupole time‐of‐flight mass spectrometry

In our previous studies, caudatin‐2,6‐dideoxy‐3‐O‐methy‐β‐d‐ cymaropyranoside (CDMC) was for the first time isolated from Cynanchum auriculatum Royle ex Wightand and was reported to possess a wide range of biological activities. However, the routes and metabolites of CDMC produced by intestinal bacteria are not well understood. In this study, ultra‐performance liquid chromatography/quadrupole time‐of‐flight mass spectrometry (UPLC‐Q‐TOF‐MS) technique combined with Metabolynx^TMsoftware was applied to analyze metabolites of CDMC by human intestinal bacteria. The incubated samples collected for 48 h in an anaerobic incubator and extracted with ethyl acetate were analyzed by UPLC‐Q‐TOF‐MS within 12 min. Eight metabolites were identified based on MS and MS/MS data. The results indicated that hydrolysis, hydrogenation, demethylation and hydroxylation were the major metabolic pathways of CDMC in vitro. Seven strains of bacteria including Bacillus sp. 46, Enterococcus sp. 30 and sp. 45, Escherichia sp. 49A, sp. 64, sp. 68 and sp. 75 were further identified using 16S rRNA gene sequencing owing to their relatively strong metabolic capacity toward CDMC. The present study provides important information about metabolic routes of CDMC and the roles of different intestinal bacteria in the metabolism of CDMC. Moreover, those metabolites might influence the biological effect of CDMC in vivo, which affects the clinical effects of this medicinal plant. Copyright © 2015 John Wiley & Sons, Ltd.