Crystal and molecular structure of 1′,2:4,6-di-O-isopropyl-idenesucrose tetra-acetate: a unique example of a d-fructofuranosyl ring in a sucrose derivative puckered at oxygen

Crystals of the title compound are monoclinic, space group P2₁, with cell dimensions: a = 11.260(5), b = 8.841(7), c = 15.605(6) Å, β = 102.25(7)°, and Z = 2; 2888 independent reflections, measured on a diffractometer, have been refined to R = 0.055 in the molecule, the pyranosyl ring has the expected ⁴C₁ conformation. However, the conformation of the d-fructofuranosyl ring is unexpected [P = 277.1°] with O-2′ exo to C-6′ furthest from the ring plane. The reason for this conformation, previously unknown in sucrose-related molecules, is not readily apparent from the crystal structure the eight-membered ring, however, has the expected boat-chair conformation.     

Crystal structure of trisodium β-d-fructofuranose 1,6-diphosphate octahydrate

Trisodium β-d-fructose 1,6-diphosphate octahydrate crystallises in the monoclinic space group P2₁ with unit-cell dimensions a = 13.289(2), b = 11.643(3), c = 7.092(1) Å, and β = 102.32(2)°. The unit cell contains two symmetry-related molecules. The structure has been determined by direct methods, and refined to an R value of 0.035 and an R_w value of 0.049. The puckering of the furanose ring is C-3-exo, corresponding to an E₃ conformation slightly distorted towards ⁴T₃. The sodium atoms are hexaco-ordinated. The crystal packing involves alternating charged layers and a network of hydrogen bonds which links the molecules belonging to the same layer and to adjacent layers.     

Cytldlne Cyclic (3′, 5′) Monophosphate: Cyclic Nucleotide With a Non-Characteristic Ribose Ring Conformation

Abstract

Cytidine 3′,-5′-cyclic phosphate (cCMP) occurs in nature and has growth stimulatory activity on L-1210 cells. The initiation of cell growth by cCMP, under conditions where CAMP, cGMP and cUMP delay the onset of proliferation suggests that cCMP may play a regulatory role in the cell metabolism. It has been reported that in 3′,5′-cyclic nucleotides, the phosphate ring fused to the furanose ring resuicts the conformation of the furanose ring to the twist form C(3′) endo C(4′) exo (³T₄), in contrast to the C(2′) endo C(3′) endo (²T₃) and C(3′) endo C(2′) exo (³T₂) twist forms normally found in nucleotides and nucleosides. We have carried out an accurate crystal structure of cCMP and found that the furanose ring in cCMP has the C(3′) endo C(2′) exo conformation (³T₂), with a pseudo rotation amplitude (P) of 44° and phase angle τ_m of 12°. cCMP is in low anti conformation (X_CN = 15.4°) and O(5′) has the fixed g conformation. The phosphate ring is constrained to the chair conformation, as in other cyclic nucleotides. The two exocyclic P-O bond distances are short (1.489, 1.476Å) and the ring angle at N(3) is large (125.2°) suggesting that the molecule in the solid state is a zwitterion with a plus charge on N(3). The crystals are hydrated and highly unstable. The three water molecules are highly disordered in ten locations. The crystals of cCMP 3H₂O are hexagonal, a = 16.294(3), b = c = 11.099(4)Å, space group P6₁, final R value is 0.067 for 1620 reflections 230.     

The crystal structure of d-glucose 6-(sodium hydrogen-phosphate)

The title compound, when recrystallised from water, is monoclinic, space group P2₁, with a = 5.774(4), b = 7.189(5), c = 12.69(1) Å, β = 106.66(5)°, and Z = 2. The crystal structure was determined from three-dimensional X-ray diffraction data taken on an automatic diffractometer with CuKα, and refined by least-squares techniques to R = 0.034 for 977 reflexions. The pyranose ring adopts the ⁴C₁ conformation. The conformation about the exocyclic C-5-C-6 bond is gauche-trans [the torsion angles O-6-C-6-C-5-O-5 and O-6-C-6-C-5-C-4 are 64.2(8) and ?175.6(7)°, respectively], which is significantly different from the gauche-gauche geometry in d-glucose 6-(barium phosphate). The phosphate ester bond, P-O-6, is 1.584(3) Å. All of the oxygen-bonded hydrogen atoms are involved in intermolecular hydrogen-bonds.     

X-ray crystal structure of maltitol (4-O-α-d-glucopyranosyl-d-glucitol

Maltitol, crystallised from aqueous solution, has m.p. 146.5–147°, [α]_d + 106.5° (water), and is orthorhombic with the space group P2₁2₁2₁ and Z = 4, and with cell dimensions a = 8.166(5), b = 12.721(9), and c = 13.629(6) Å. The molecule shows a fully extended conformation with no intramolecular hydrogen-bonds. All nine hydroxyl groups are involved in intermolecular hydrogen-bond networks and in bifurcated, finite chains. The d-glucopyranosyl moiety has the ⁴C₁ conformation, and the conformation about the C-5–C-6 bond is gauche-gauche. The d-glucitol residue has the bent [ap, Psc, Psc (APP)] conformation. The empirical formula for the solubility in water is C = 119.1 + 1.204 T + 4.137 × 10^?2 T² ? 7.137 × 10^?4 T³ + 7.978 × 10^?6 T⁴. The thermal properties are as follows: ΔH_f = 13.5 kcal.mol^?1, and Q = ?5.57 kcal.mol^?1.     

Determination of the molecular conformation of beta-D-O2,2'-cyclouridine in aqueous solution by proton magnetic resonance spectroscopy

The solution conformation of β-D -O²,2′-cyclouridine has been determined at 27 and 88°C in D₂O by proton magnetic resonance spectroscopy. The conformation is described in terms of a fixed syn-like sugar-base torsional angle, a type S furanose ring conformation (similar to 2′-endo), and a temperature-dependent exocyclic C(4)′–C(5′) rotamer population containing approximately 50% of the gauche-gauche form at 27°C. β-D -O²,2′-Cyclouridine 5′-phosphate likewise possesses a type S furanose ring conformation.     

Bioactive peptides: Conformational studies of [TYR4] cyclolinopeptide A

The solid state conformational analysis of [Tyr⁴] cyclolinopeptide A has been carried out by x-ray diffraction studies. The crystal structure of the monoclinic form, grown from a dioxane-water mixture [a = 9.849 (5) Å, b = 20.752 (4) Å, c = 16.728 (5) Å, β = 98.83 (3)°, space group P2₁, Z = 2], shows the presence of five intramolecular N-H? O?C hydrogen bonds, with formation of one C₁₇ ring structure, one α-turn (C₁₃), one inverse γ-turn (C₇), and two β-turns (C₁₀, one of type III and one of type 1). The Pro¹-Pro² peptide unit is cis (ω = 5°) all others are trans. The structure is almost superimposable with that of cyclolinopeptide A. The rms deviation for the atoms of the backbones is on the average 0.33 Å. © 1995 John Wiley & Sons, Inc.     

Strukturanalyse der methyl-2,3,6-tridesoxy-2-C-[2-hydroxy-1,1-(Äthylendithio)Äthyl]-α-l-threo-hexopyranosid-4-ulo-22,4-pyranose

Methyl 2,3,6-trideoxy-2-C-[2-hydroxy-1,1-(ethylenedithio)ethyl]-α-l-threo-hexopyranosid-4-ulo-2²,4-pyranose (1) crystallizes in a rhombic space group P2₁2₁2₁ with four molecules in the elementary unit. The structure was refined to an R-value of 0.057. The aldopyranose ring adopts a ¹C₄ conformation with an axial side-chain forming a hemiacetal ring to the keto group at C-4. Both six-membered rings connected in the 2,7-dioxabicyclo[3.3.1]nonane system differ only slightly from the ¹C₄ chair conformation. The spirocyclic dithiolane ring adopts a nearly ideal envelope form with a deviation of C-21 from the plane S-1-C-7-S-2-C-22. The dihedral angle O-5-C-1 O-1-C-11 of 59.1° is an agreement with the exo-anomeric effect.     

Kinetic and equilibrium studies of cyclomalto-octaose (γ-cyclodextrin)-methyl orange inclusion complexes

Measurements of the equilibrium and temperature-jump u.v., visible, and induced c.d. spectra of Methyl Orange (MO) in the presence of cyclomalto-octaose (γ-cyclodextrin, γ-CD) have been carried out. Three mechanistic steps were detected through the temperature-jump data (25.0°):

where K₁, K₂, and K₃ are 45 (±7), 2.0 (±1.1) × 10⁶, and 6.1 (±2.5) × 10³ dm³.mol^?1, respectively, k₂ = 9.4 (±5.1) × 10⁹ dm³.mol^?1.s^?1, and k_?2 = 4.8 (±0.8) × 10³ s^?1. The equilibrium u.v./visible data are also consistent with this reaction scheme. The high stability of the dimer inclusion complex (MO)₂ · γ-CD compared to that of the monomer inclusion complex MO · γ-CD appears to be related to the annular diameter of γ-CD and demonstrates a degree of selectivity in cyclodextrin inclusion complexes. The (MO)₂ · (γ-CD)₂ complex also contains a dimer, included by both γ-CD molecules.     

Synthesis,crystal structure,and conformation of 3-O-(6-O-acetyl-2,3-anhydro-4-deoxy-α-l-ribo-hexopyranosyl)-1,2:5,6-di-O-isopropylidene-α-d-glucofuranose

3-O-(6-O-Acetyl-2,3-anhydro-4-deoxy-α-l-ribo-hexopyranosyl)-1,2:5,6-di-O-isopropylidene-α-d-glucofuranose has been synthesised and its monocrystal investigated by X-ray diffraction methods. The compound crystallises in the orthorhombic system, space group P2₁2₁2₁, with cell constants a = 8.790(7), b = 11.678(4), and c = 21.457(10) Å. The intensity data were collected with a four-circle CAD-4 diffractometer. From a total of 1684 intensities, 1275 were of I > 2σ_I. The structure was solved by direct methods and refined by the full-matrix, least-squares procedure, resulting in R 0.057. The 4-deoxy-2,3-anhydropyranose ring is characterised by a sofa conformation (₅E), the 1,2-O-isopropylidene ring has a hybrid conformation (E + T), and the 5,6-O-isopropylidene and the α-d-glucofuranose rings have twist (T) conformations. The φ and ψ torsion angles for the glycosidic linkage are 54(4)° and 29(4)°, respectively.     

On the stereochemistry of 2,3-dihydroxy fatty acids of fungi sphingolipids. Resolution and configuration analysis of erythro-2,3-dihydroxyoctadecanoic acid

DL-erythro-2,3-dihydroxyoctadecanoic acid, synthesized according to Palameta and Pro?tenik (Tetrahedron, 19 (1969) 1463) was converted to the R(+)-1-phenylethylamide and the obtained diastereomers resolved by chromatography on silica gel. The enantiomeric erythro-2,3-dihydroxyoctadecanoic acids were recovered by acidic hydrolysis (m.p., 117°, [α]_D²² = ±3.28°, [M_D²² = ±10.38°). A comparison of the chromatographic mobility of R- and S-1-phenylethylamides and the optical rotation of 2,3-dihydroxy fatty acids from fungi sphingo-lipids shows that the natural occurring enantiomer has (+)D-erythro configuration.     

Effects of carbohydrate-structure changes on induced shifts in differential isotope-shift 13C-N.M.R.

Deuterium-induced, ¹³C-isotope shifts are shown to vary considerably from the initially predicted values calculated for ordinary pyranose and furanose sugars, when minor structural changes are introduced into the carbohydrate ring. Both substitution of C-OH groups or reduction of C-OH to CH₂ permitted the evaluation of γ effects of OD without the contribution of β-OD-induced shifting. The observed γ-shift values for these modified structures were twice as large as those previously noted. This difference is most probably due to favored salvation. Substitution of OH at C-6 led to the predicted loss of differential isotope-shift (d.i.s.) at C-6 because of its isolation from all β and γ OD groups. The ³¹P resonances of d-glucose 6-phosphate show downfield deuterium shifts. Based on d.i.s. values, new ¹³C-shift assignments are proposed for isomaltose and 2-amino-2-deoxy-α-d-glucose. A study of acidic carbohydrates has demonstrated that isotope shifts are somewhat larger for sp²-hybridized carbon atoms whose OH groups are acidic. Relaxation times for sp² carbon atoms isolated from dipolar interaction with protons were very long in D₂O relative to their relaxation time in the H₂O environment.     

Conformational studies of per-O-trimethylsilyl derivatives of D-fructoses and oligosaccharides containing β-D-fructofuranose residues by 220- and 300-MHz P.M.R. spectroscopy

The interpretation of 220- and 300-MHz P.M.R. spectra and the accurate chemical shifts and coupling constants of a number of per-O-trimethylsilyl-(TMS-) D-fructose derivatives and TMS-oligosaccharides containing β-D-fructofuranose residues are presented. On the basis of calculations with an adapted Karplus equation it is concluded that TMS-α- and -β-D-fructopyranose occur in the ²C₅(D) chair conformation whereas the D-glucopyranose rings in the oligosaccharides adopt the usual ⁴C₁(D) chair conformation. The structure of the latter units is very similar to that of TMS-α-_D-glucopyranose. The ⁴E(D) envelope and ⁴T₅(D) twist are the principal conformations of the D-fructofuranose rings. The conformation of the furanose ring depends on the number and kind of monosaccharide units attached thereto. The calculated, preferred conformation of the C-5-CH₂OTMS group of the D-fructofuranose moieties correlates with the time-averaged displacement of C-4 above the plane of C-2, C-3, and O-5.     

Production of ginsenosides Rg1 and Rh1 by hydrolyzing the outer glycoside at the C-6 position in protopanaxatriol-type ginsenosides using β-glucosidase from Pyrococcus furiosus

The specific activity of a recombinant β-glucosidase from Pyrococcus furiosus for protopanaxatriol (PPT)-type ginsenosides followed the order Rf > R₁ > Re > R₂ > Rg₂, which were converted to Rh₁, Rg₁, Rg₁, Rh₁, and Rh₁, respectively. No activity was observed with Rg₁ and Rh₁. Thus, P. furiosus β-glucosidase hydrolyzed the outer glycoside at the C-6 position in PPT-type ginsenosides whereas the enzyme did not hydrolyze the inner glucoside at the C-6 position and the glucoside at the C-20 position. The activity for Rf was optimal at 95 °C, pH 5.5, 5 mM ginsenoside, and 32 U enzyme l^?1. Under these conditions, P. furiosus β-glucosidase completely converted from R₁ to Rg₁ after 10 h, with a productivity of 0.4 g l^?1 h^?1 and completely converted Rf to Rh₁ after 1.2 h, with a productivity of 2.74 g l^?1 h^?1.     

The crystal structure of 2-deoxy-β-d-arabino-hexopyranose at −150°

2-Deoxy-β-d-arabino-hexopyranose, C₆H₁₂O₅, is orthorhombic, P2₁2₁2₁, with cell dimensions at ?150° [20°], a = 6.484(2) [6.510(3)], b = 10.364(2) [10.427(4)], c = 11.134(3) [11.153(5)] Å, V = 748.2 [757.1] ų, Z = 4, D_x = 1.457 [1.440], and D_m = [1.455] g.cm^?3. The intensities of 1269 reflections were measured by using MoKα radiation. The structure was solved by direct methods, and refined by full-matrix least-squares, with anisotropic, thermal parameters for the carbon and oxygen atoms, and isotropic parameters for the hydrogen atoms. The pyranose has the ⁴C₁(d) conformation, with puckering parameters Q = 0.563 Å, θ = 3.9°, and ? = 350.3°. The departure from ideality is very small, and less than that in β-d-glucopyranose, Q = 0.584 Å and θ = 6.9°. The β-glycosidic, CO bond is short, 1.383(4) Å, and the OCOH torsion angle is ?87°, consistent with the anomeric effect. The hydrogen-bonding scheme consists of infinite chains, with side chains terminating at a ring-oxygen atom.     

Crystal structure of methyl 2,6-dichloro-2,6-dideoxy-3,4-O-isopropylidene-α-D-altropyranoside. A pyranoside system close to a skew-boat conformation

The crystal structure of methyl 2,6-dichloro-2,6-dideoxy-3,4-O-isopropylidene-α-D-altropyranoside (1) has been determined by X-ray diffraction. The compound crystallizes in the orthorhombic system, space group P2₁2₁2₁, with unit-cell dimensions a  7.932, b  8.133, and c  20.447 Å. The structure was solved by the heavy-atom method and refined by the least-squares technique to an R value of 0.047 by using 736 intensities measured on a diffractometer. The pyranoside ring is close to a skew-boat conformation, with C-2 and C-5 being maximally displaced from the least-squares plane through the remaining four atoms. The H-1H-2 dihedral angle of  158° is in agreement with the J_1,2 value of 4.5 Hz. Thus the solid-state conformation appears to correspond with the conformation in solution. The dioxolane ring is in a twist form, with O-4 and, C-8 puckered on opposite sides of the plane of the other ring atoms. The pyranose-ring substituents are in equatorial and pseudoequatorial orientations. The hydrogen atoms at C-3 and C-4 are in a cis arrangement. The orientations of both the methoxyl group and the chloromethyl group with respect to the ring are gauche—trans. The exocyclic anomeric C-1O-1 bond-distance (1.39 Å) is the shortest CO bond in the structure. The intracyclic CO bonds are significantly different, C-1O-5 being less than C-5O-5.     

Crystal structure of a new form of copper(II)—inosine 5′-monophosphate—2,2′-dipyridylamine ternary complex

Two crystalline forms of the [Cu(II) (IMP) (DPA) (H₂O)]₂·nH₂O (IMP=inosine 5′-monophosphate, DPA=2,2′-dipyridylamine) complex were obtained from aqueous solution at pH=6.2. The crystals of the two forms belong to the monoclinic system, space group P2₁. The cell parameters are: a=9.445(2), b=33.902(4), c=7.802(2) Å, β=90.48(2)°, Z= 2, D_c=1.69g cm⁻³ and μ(Mo Kα) = 10.49cm⁻¹ (form α, n=4), and a=7.828(2), b=18.552(3), c=17.378(3) Å, β=91.16(2)°, Z=2, D_c=1.66 g cm⁻³, μ(Mo Kα) = 10.40 cm⁻¹ (form β, n=3.62). Bau and coworkers reported the preparation of form α by vapor diffusion of CH₃CN into aqueous solution containing Cu(NO₃)₂, Na₂IMP and DPA in a 1:1:1 molar ratio and the analysis of the compound by single crystal X-ray diffraction [1].Intensities for 3412 reflections were collected from a crystal of form β in the present work. Graphite-monochromatized Mo Kα radiation was employed. The structure was refined to final R and R_w values of 0.1000 and 0.1115 respectively. The dimeric units contain two copper ions in square-pyramidal coordination polyhedra. Each polyhedron consists of two nitrogen atoms of DPA, two oxygen atoms from two phosphate groups and a water molecule in the axial position. A statistical disorder was found in a nucleotide moiety of the dimer. Two sets of atomic positions corresponding to the purine system were refined with site occupation factors of 0.62(1) and 0.38(1) respectively. Also the ribose ring shows a disorder with two possible conformations. The puckering mode of the prevailing conformation is C(3′)-endo. In the other nucleotide molecule of the dimer the furanose puckering mode is C(3′)-endo. The rotation around the glycosyl linkages can be described as ‘anti’ in the structure of form β. The C(4)N(9)C(1′)O(4′) torsion angle values are −97(2) and −94(3)° for the disordered nucleotide molecule and +91(2)^o for the other nucleotide moiety. Strong intermolecular DPADPA and purine-purine stacking interactions stabilize the crystal lattice. The differences on the nucleotide conformation between the structure of form α and form β can probably be ascribed to differences in the hydrogen bonds and stacking interactions.     

Dioxo-, oxothio- and dithio-tungsten(VI) and tungsten(V) complexes of the ligand N,N′-Dimethyl-N,N′-bis(2-mercaptophenyl)ethylenediamine

Synthesis of complexes cis,cis-W^VOXL (X=Cl, NCS), cis,trans-W^VOXL (X=Cl, OPh, SPh) and cis,trans-W^VIE₂L (E₂=O₂, OS, S₂) of the title ligand LH₂ are reported. cis,cis-W^VOCIL crystallises in space group P2₁/c with a=13.6541(9) Å, b=7.1555(11) Å, c=18.198(2) Å, β=95.294(6)°, V=1770.4(3) ų and Z=4 while the cis,trans isomer crystallises in space group P2₁/n with a=10.361(3) Å, b=14.141(4) Å, c=12.213(5) Å, β=102.56(3)°, V=1747(2) ų and Z=4. cis,trans-W^VIS₂L crystallises in space group P2₁/n with a=10.645(2) Å, b=13.929(2) Å, c=12.189(2) Å, β=103.14(2)°, V=1760(1) ų and Z=4. A short CH₃···Cl distance of 3.067(7) Å and an acute OWCl angle of 94.1(2)° are seen in cis,cis-W^VOClL, which converts to the cis,trans form on heating in MeCN. The latter isomer features a CH₃···Cl distance of 3.38(2) Å and an OWCl angle of 105.1(8)°. Electrochemical and EPR data are reported. In particular, cis,trans-W^VIE₂L may be reduced to [W^VE₂L]^–. EPR properties of these anions and those of complexes W^VOXL are discussed in the context of W^V centres in tungsten enzymes.