Naphthoquinone dimers and trimers from Euclea natalensis

The naphthoquinone dimers natalenone, 8′-hydroxydiospyrin and euclanone and the trimers galpinone and a compound with MW 562 were isolated from E. natalensis roots. Natalenone is a dehydrodimer of 7-methyl- juglone with the two moieties linked by two CC bonds to give a fused tetracyclic structure, one ring bearing a methylene bridge. Galpinone is a 7-methyljuglone linear trimer, the three units probably being linked C-8-C-6′and C-3′-C-3″. Euclanone is a new dimer of 7-methyljuglone and methylnaphthazarin, isomeric with 8′-hydroxydiospyrin.     

Conformational analysis of levanbiose by molecular mechanics.

A relaxed conformational energy map for levanbiose, O-beta-D-fructofuranosyl-(2----6)-beta-D-fructofuranoside, was computed with the molecular mechanics program MM2(87). All torsion angles of the three linkage bonds were driven by 30 degrees increments while two primary alcohol groups were held at three staggered forms. The steric energy of all other parameters was optimized. The side groups were retained at the same relative positions on the two rings in this first part of the study so our results are directly applicable to the study of polymeric levan with identical repeating units. The low-energy dimers did not lead to viable polymers. The interresidue linkage torsion angles defined by C-6-O-2'-C-2'-C-1' (phi) and O-5-C-5-C-6-O-2' (omega) have minima at +60 degrees and -60 degrees, respectively, with accessible minima at other staggered forms. As observed in inulobiose, the preferred torsion angle at central linkage bond defined by C-5-C-6-O-2'-C-2' (psi) was antiperiplanar. An analysis of all conformations of staggered side groups showed that the C-1 and C-1' groups had little effect but the C-6' group showed a preference for chi-6'(O-5'-C-5'-C-6'-O-6') = -60 degrees. The fructofuranose rings were started at the low-energy 4(3)T conformation (angle of pseudorotation, phi 2 = 265 degrees) that was retained except when the linkage conformations created severe inter-residue conflict.     

Using simple 13C NMR linewidth and relaxation measurements to make detailed chemical shift assignments in triacylglycerols and related compounds

Two simple experiments measuring the ¹³C linewidths ν_1/2 and spin–lattice relaxation times T₁ of each of the signals in the spectrum of trilinolein indicate that the ν_1/2 and T₁ values are consistent with the different degrees of motional freedom expected for the various ¹³C nuclei. However, for each chain, the ν_1/2 and T₁ measurements indicate a small reversal in mobility at C-10 relative to C-9 before motional freedom again steadily increases on each chain starting at C-11. The T₁ experiment allows unambiguous assignments of the C-8 signal and C-14 signal, which differ by only 0.010 ppm. Measurements of ¹³C ν_1/2 and T₁ values on tripalmitin provide secure assignments for the C-5 and C-6 signals, for which conflicting assignments have been reported. The T₁ measurements also show that among the tightly clustered C-8 through C-12 signals, the C-11 signals are the most downfield, while the C-12 signals are the most upfield, again contrary to a previous report. Similar measurements of ¹³C ν_1/2 and T₁ values on other triacylglycerols or related compounds may prove equally useful in making chemical shift assignments and detecting any discontinuities in motional freedom along a chain. The benefits and possible limitations of ultrahigh field NMR for studying triacylglycerols and related compounds are discussed.     

Conformational analysis of inulobiose by molecular mechanics

Conformational energies for inulobiose [beta-D-fructofuranosyl-(2----1)-beta-D-fructofuranoside], a model for inulin, were computed with the molecular mechanics program MMP2(85). The torsion angles of the three linkage bonds were driven in 20 degree increments, and the steric energy of all other parameters was minimized. The linkage torsion angles defined by C-1'-C-2'-O-C-1 (phi) and O-C-1-C-2-O-2 (omega) have minima at +60 degrees and -60 degrees, respectively, regardless of side group orientation; accessible minima exist at other staggered conformations. The torsion angle at the central bond C-2'-O-1-C-1-C-2 (psi) was approximately 180 degrees in all the low-energy conformers. This appears to be generally true for rings linked by three bonds. The fructofuranose rings initially had low-energy 4/3T conformations (angle of pseudorotation, phi 2 = 265 degrees) that were retained except when the linkage conformations created severe inter-residue conflicts. In those cases, almost all puckerings of the furanose rings were found.     

Comparison of the glycosaminoglycans isolated from the skin and head cartilage of Gould's arrow squid (Nototodarus gouldi)

The glycosaminoglycans from the skin and head cartilage of the squid Nototodarus gouldi have been isolated and characterised by constituent disaccharide and neutral sugar analysis, ¹³C nuclear magnetic resonance (NMR) spectroscopy, anion exchange and size exclusion chromatography. The glycosaminoglycans from both tissues are chondroitin sulphate species. The skin consists principally of unsulphated but relatively highly glycosylated material. The chondroitin sulphate from the head cartilage is more highly sulphated, predominantly C-4,6diS (chondroitin sulphate E), with a higher molecular weight than the skin derived material but somewhat less highly glycosylated. To provide a standard for the assignment of the ¹³C NMR spectrum, C-4,6diS was chemically prepared from bovine tracheal chondroitin sulphate. This showed that it is not possible to distinguish between a mixture of the monosulphates, C-4S and C-6S, and the C-4,6diS by one-dimensional and simple two-dimensional ¹³C NMR techniques.     

Hydroxyl Radical-Induced Reactions in Polyadenylic Acid as Studied by Pulse Radiolysis: Part I. Transformation Reactions of Two Isomeric OH-Adducts

The absorption spectra of polyadenylic acid (polyA) radicals in N₂0 saturated aqueous solution have been measured as a function of time (up to 15 s) following an 0.4μS electron pulse. The spectra and their changes were analysed by comparison with those from monomeric adenine derivatives (nucleosides and nucleotides) which had been studied by Steenken.¹

The reaction of OH^· radicals with the adenine moiety in poly A results in the formation of two hvdroxvl adducts at the positions C-4 [polyA40H^·] and C-8 [polyA80H^·]. Each OH-adduct undergoes a unimol-ecular transformation reaction before any bimolecular or other unimolecular decay occurs. These reactions are characterized by different rate constants and _pH dependencies. The polyA40H^· adduct undergoes a dehydration reaction to yield a neutral N⁶ centered radical (rate constant K_deh= 1.4 × 10⁴s^-1 at ^pH7.3). This reaction is strongly inhibited by H⁺. In comparison with the analogous reactions in adenosine phosphates, the kinetic _pK value for its inhibition is two ^pH units higher. This shift is the result of the counter ion condensation or double-strand formation. The polyA80H^· adduct undergoes an imidazole ring opening reaction to yield an enol type of formamidopyrimidine radical with the resulting base damage (k^r.o. = 3.5 × 10⁴ s ^-1 at pH7.3). This reaction in contrast is strongly catalysed by H⁺and OH^-, similar as for adenosine but different compared to the nucleotides.     

The dimerization of protochlorophyll pigments in non-polar solvents

The infrared, visible and nuclear magnetic resonance spectra of protochlorophyll a and vinylprotochlorophyll a in dry non-polar solvents (carbon tetrachloride, chloroform, cyclohexane) are presented and interpreted in terms of dimer interaction.

The infrared spectra in the 1600–1800 cm⁻¹ region clearly show the existence of a coordination interaction between the C-9 ketone oxygen function of one molecule and the central magnesium atom of another molecule. Infrared spectra in the OH stretching region (3200–3800 cm⁻¹) provide a valuable test of the water content in the samples.

The analysis of the absorption and circular dichroism spectra of protochlorophyll a and vinylprotochlorophyll a in carbon tetrachloride demonstrates the existence of a monomer-dimer equilibrium in the concentration range from 10⁻⁶ to 5 · 10⁻⁴ M. The dimerization constants are (6±2) · 10⁵ 1 · M⁻¹ for protochlorophyll a and (4.5±2) · 10⁵ 1 · M⁻¹ for vinylprotochlorophyll a at 20 °C. The deconvolution of visible spectra in the red region has been performed in order to obtain quantitative information on the dimer structure. Two models involving a parallel or a perpendicular arrangement of the associated molecules are considered.

From ¹H NMR spectra, it appears that the region of overlap occurs near ring V, in agreement with the interpretation of the infrared spectra.     

X-ray crystal structure of galabiose, O-alpha-D-galactopyranosyl-(1---4)-D-galactopyranose

O-alpha-D-Galactopyranosyl-(1---4)-D-galactopyranose, C12H22O11, Mr = 342.30, crystallises in the orthorhombic space group P2(1)2(1)2(1), and has alpha = 5.826(1), b = 13.904(3), c = 17.772(4) A, Z = 4, and Dx = 1.579 g.cm-3. Intensity data were collected with a CAD4 diffractometer. The structure was solved by direct methods and refined to R = 0.063 and Rw = 0.084 for 2758 independent reflections. The glycosidic linkage is of the type 1-axial-4-axial with torsion angles phi O-5' (O-5'-C-1'-O-1'-C-4) = 98.1(2) degrees, psi C-3 (C-3-C-4-O-1'-C-1') = -81.9(3) degrees, phi H (H-1'-C-1'-O-1'-C-4) = -18 degrees, and psi H (H-4-C-4-O-1'-C-1') = 35 degrees. The conformation is stabilised by an O-3 . . . O-5' intramolecular hydrogen-bond with length 2.787(3) A and O-3-H . . . O-5' = 162 degrees. The glycosidic linkage causes a folding of the molecule with an angle of 117 degrees between the least-square planes through the pyranosidic rings. The crystal investigated contained 56(1)% of alpha- and 44(1)% of beta-galabiose as well as approximately 70% of the gauche-trans and approximately 30% of the trans-gauche conformers about the exocyclic C-5'-C-6' and C-5-C-6 bonds. The crystal packing is governed by hydrogen bonding that engages all oxygen atoms except the intramolecular acceptor O-5' and the glycosidic O-1' oxygen atoms.     

Flavan-3-ols from the rhizomes of Drynaria fortunei

One monomer flavan-3-ol, 4α-carboxymethyl-(+)-catechin methyl ester, two monomer flavan-3-ol glycosides, (+)-afzelechin-3-O-β-allopyranoside, (+)-afzelechin-6-C-β-glucopyranoside, two dimer flavan-3-ols, (-)-epiafzelechin-(4β→8)-4β-carboxymethyl-(-)-epicatechin methyl ester, and -(-)-epiafzelechin-(4β→8)-4α-carboxymethyl-(-)epiafzelechin ethyl ester, and one trimer flavan-3-ol, (-)-epiafzelechin-(4β→8)-(-)-epiafzelechin-(4β→8)-4β-carboxymethyl-(-)-epiafzelechin methyl ester, together with thirteen known flavan-3-ols were isolated from the rhizomes of Drynaria fortunei (Kunze) J.Sm (Polypodiaceae). The structures were established by analysis of their HRESIMS, 1D, 2D NMR spectroscopic, and CD data. In order to obtain improved resolution, the high-resolution NMR spectra of the dimers and trimer were measured at -40 °C.     

Analysis of the biosynthetic process of cellulose and curdlan using C-labeled glucoses

In order to elucidate the biosynthetic process of cellulose and curdlan, ¹³C-labeled polysaccharides were biosynthesized by Acetobacter xylinum (IFO 13693) and Agrobacterium sp. (ATCC 31749), from culture media containing -(1-¹³C)glucose, -(2-¹³C)glucose, -(4-¹³C)glucose, or -(6-¹³C)glucose as the carbon source, and their structures were determined by ¹³C NMR spectroscopy. The labeling was mainly found in the original position, indicating direct polymerization of introduced glucoses. In addition, the transfer of labeling from C-2 to C-1, C-3 and C-5, from C-4 to C-1, C-2 and C-3, and from C-6 to C-1 was found in celluloses. In curdlan, the transfer of labeling from C-1 to C-3, from C-2 to C-1 and C-3, from C-4 to C-1, C-2 and C-3, and from C-6 to C-1 and C-3 was observed. From analysis of this labeling, the biosynthetic process of cellulose and curdlan was explained as involving six routes. The percentages of each route via which cellulose or curdlan is biosynthesized were estimated for upper (C-1 to C-3) and lower portions (C-4 to C-6) of glucosidic units in the polysaccharides. It is noted that very few polysaccharides are formed via the Embden-Meyerhof pathway. The lower half (C-4 to C-6) structure of introduced glucoses is well preserved in the polysaccharides.     

Structures of the two 3D domain-swapped RNase A trimers

When concentrated in mildly acidic solutions, bovine pancreatic ribonuclease (RNase A) forms long-lived oligomers including two types of dimer, two types of trimer, and higher oligomers. In previous crystallographic work, we found that the major dimeric component forms by a swapping of the C-terminal beta-strands between the monomers, and that the minor dimeric component forms by swapping the N-terminal alpha-helices of the monomers. On the basis of these structures, we proposed that a linear RNase A trimer can form from a central molecule that simultaneously swaps its N-terminal helix with a second RNase A molecule and its C-terminal strand with a third molecule. Studies by dissociation are consistent with this model for the major trimeric component: the major trimer dissociates into both the major and the minor dimers, as well as monomers. In contrast, the minor trimer component dissociates into the monomer and the major dimer. This suggests that the minor trimer is cyclic, formed from three monomers that swap their C-terminal beta-strands into identical molecules. These conclusions are supported by cross-linking of lysyl residues, showing that the major trimer swaps its N-terminal helix, and the minor trimer does not. We verified by X-ray crystallography the proposed cyclic structure for the minor trimer, with swapping of the C-terminal beta-strands. This study thus expands the variety of domain-swapped oligomers by revealing the first example of a protein that can form both a linear and a cyclic domain-swapped oligomer. These structures permit interpretation of the enzymatic activities of the RNase A oligomers on double-stranded RNA.     

Nuclear magnetic resonance spectroscopy of 3 beta,7 beta-dihydroxy-5-cholen-24-oic acid multi-conjugates: unusual bile acid metabolites in human urine

Complete ¹H and ¹³C resonance assignments were made for a new type of 3β,7β-dihydroxy-5-cholen-24-oic acid doubly conjugated with sulfuric acid at C-3 and N-acetylglucosamine at C-7 and its glycine- and taurine-amidated triple-conjugates by the combined use of several homonuclear and heteronuclear shift-correlated 2D NMR techniques. The effects of sulfation at C-3, N-acetylglucosaminidation at C-7, and aminoacyl amidation at C-24 on the ¹H and ¹³C chemical shifts and signal multiplicity were clarified. The shielding data serving to characterize each of the bile acid multi-conjugates are also discussed.     

Mode of cleavage of the c-c bonds in methyl pento- and hexo-pyranosides with periodate

The course of oxidation reactions of three methyl pentopyranosides and five methyl hexopyranosides with periodate was studied by simultaneous determination of the conjugated aldehydes in the products. It was found that the C-3-C-4 bonds in all of these glycosides were cleaved rapidly, but the velocity of subsequent cleavage of the C-2-C-3 bonds depended on the configuration of the substituent groups on the pyranose ring. Equatorial C-1 methoxyl and C-2 hydroxyl groups favored cleavage of the C-2-C-3 bonds more than did the corresponding axial groups, whereas the equatorial C-5 hydroxymethyl group suppressed C-2-C-3-bond-cleavage. The 4-isomeric glycosides were oxidized at the same rate, without regard to the configuration at C-4.     

The effect of temperature on the primary reaction of chloroplast Photosystem II Evidence for a temperature-dependent back reaction

The primary reaction of Photosystem II has been studied over the temperature range from −196 to −20 °C. The photooxidation of the reaction-center chlorophyll (P680) was followed by the free-radical electron paramagnetic resonance signal of P680⁺, and the photoreduction of the Photosystem II primary electron acceptor was monitored by the C-550 absorbance change.

At temperatures below −100 °C, the primary reaction of Photosystem II is irreversible. However, at temperatures between −100 and −20 °C a back reaction that is insensitive to 3-(3′,4′-dichlorophenyl)-1,1′-dimethylurea (DCMU) occurs between P680⁺ and the reduced acceptor.

The amount of reduced acceptor and P680⁺ present under steady-state illumination at temperatures between −100 and −20 °C is small unless high light intensity is used to overcome the competing back reaction. The amount of reduced acceptor present at low light intensity can be increased by adjusting the oxidation-reduction potential so that P680⁺ is reduced by a secondary electron donor (cytochrome b₅₅₉) before P680⁺ can reoxidize the reduced primary acceptor. The photooxidation of cytochrome b₅₅₉ and the accompanying photoreduction of C-550 are inhibited by DCMU. The inhibition of C-550 photoreduction by DCMU, the dependence of P680 photooxidation and C-550 photoreduction on light intensity, and the effect of the availability of reduced cytochrome b₅₅₉ on C-550 photoreduction are unique to the temperature range where the Photosystem II primary reaction is reversible and are not observed at lower temperatures.     

Cyclic tetranuclear half-sandwich ruthenium(II) complexes with 4,7-phenanthroline and hydroxo bridges: crystal structure, solution behaviour and binding to nucleosides

The reaction between [(η⁶-p-cymene)Ru(H₂O)₃]X₂ and 4,7-phenanthroline (phen) leads to the formation of the rectangular tetranuclear complexes [(η⁶-p-cymene)₄Ru₄(μ-4,7-phen-N⁴,N⁷)₂(μ-OH)₄]X₄ (X = NO₃, 1a; SO₃CF₃, 1b) which have been structurally characterised by X-ray crystallography. ¹H NMR spectroscopic studies suggest the presence of a partially dissociated dinuclear species of type [(η⁶-p-cymene)₂Ru₂(μ-4,7-phen-N⁴,N⁷)(solv)₄]⁴⁺ in equilibrium with the tetranuclear cyclic species found in the solid state. The temperature effect for this equilibrium was studied by variable temperature ¹H NMR experiments in D₂O and MeOD. The results reveal that the proportion of the tetranuclear species increases with the polarity of the solvent which favour stacking interactions between the phenanthroline moieties. In addition, the reactivity of the tetranuclear species towards the nucleosides guanosine (Guo), cytidine (Cyt), 2′-deoxythymidine (Thy) and 2′-deoxyadenosine (dAdo) has been monitored by ¹H NMR as a potential model for the interaction of the 1 species with the probable DNA target. The results reveal that the 1 systems are able to bind the nucleobases endocyclic nitrogen atoms of Guo Cyt, and dAdo.     

C andH NMR spectroscopy as a tool in the configurational analysis of iridoid glucosides

The ¹³C NMR data of 51 iridoid glucosides or glucoside acetates are tabulated. The collection includes 20 pairs of C-6, C-7 or C-8 epimers. Three parameters in using the data for the configurational assignment of 6-O-substituents are given. The chemical shift for C-9 in a range of substituted compounds is shown to be numerically related to the stereochemistry at C-8. This allows the determination of the configuration at this centre for most types of substitution patterns by calculation of the C-9 shift using increments for each substituent. Such increments are given for 25 substituents in three different solvents. A method for simulation of spectra of unknown iridoid glucosides is presented. By this method, the structures of five novel iridoid glucosides have been elucidated, and that of tecomoside has been revised. The methods used to assign the configurations to C-6 and C-8 epimeric iridoid glucosides by ¹H NMR spectroscopy are discussed and a table with selected data is presented. It is suggested that the structures in the literature for ajugol and myoporoside should be interchanged. Consequently, Horeau's method has failed in these instances. Finally, the differences in the ¹³C NMR spectra of pairs of C-6 and C-8 epimeric iridoid glucosides have been interpreted as originating from cis/trans-interactions.     

Mg-activated double-stranded DNA cleavage by [(bpy)2(OH2)Ru---O---Ru(H2O) (bpy)2]

The reaction of the title complex with DNA has been examined. Addition of [(bpy)₂(OH₂)RuORu(OH₂) (bpy)₂]⁴⁺ to DNA leads to the reduction of the complex to Ru(bpy)₂(OH₂)₂²⁺, as indicated by absorption spectroscopy and cyclic voltammetry. The reaction is accelerated by Mg²⁺. The combined evidence points to a mechanism where the oxo-bridged dimer is hydrolyzed to a monomeric Ru(III) complex that is capable of oxidizing DNA to effect strand scission. Gel electrophoresis demonstrates nicking of supercoiled /gfX174 DNA by [(bpy)₂(OH₂)RuORu(OH₂) (bpy)₂]⁴⁺, and double-stranded cleavage is observed in the presence of Mg²⁺. Linearization of the plasmid prior to treatment with the complex does not lead to further fragmentation, suggesting that supercoiling is required to realize double-stranded cleavage.     

Structural studies of gum arabic, the exudate polysaccharide from Acacia senegal

A 25.182-MHz ¹³C-n.m.r. spectrum of gum arabic allows unambiguous characterisation of all the C-1 resonances. These assignments have been confirmed by correlation of the modification of the intensities of these signals after controlled acid hydrolysis and characterisation of the released fragments. The resonances of the other carbons have been assigned through partial relaxed T₁ spectra of the polysaccharides obtained by graded degradation of the gum. These results indicate gum arabic to consist mainly of a (1→3)-β- -galactan core with (1→6)-β- -galacto-pyranosyl branches and with - -arabinofuranosyl-(1→3)-- -arabinofuranosyl and - -rhamnopyranosyl-(1→4)-β- -glucopyranosyluronic acid groups attached to positions 3 and 6, respectively, of the branch units.     

Biosynthesis of C-labeled branched polysaccharides by pestalotiopsis from C-labeled glucoses and the mechanism of formation

Biosynthesis of branched glucan by Pestalotiopsis from media containing D-(1-¹³C)glucose, D-(2-¹³C)glucose, D-(4-¹³C)glucose, D-(6-¹³C)glucose or a mixture of D-(1-¹³C)glucose and D-(2-¹³C)glucose was carried out to elucidate biosynthetic mechanism of branched polysaccharides. ¹³C NMR spectra of the labeled polysaccharides were determined and assigned. Analysis of ¹³C NMR spectra of glucitol acetates obtained from hydrolysates of the labeled branched polysaccharides indicated that transfer of labeling from C-1 to C-3 and C-6 carbons, from C-2 to C-1, C-3 and C-5 carbons, and from C-6 to C-1 carbon. From the results the percentages of routes via which the polysaccharide is biosynthesized are estimated. They show that the biosynthesis of the polysaccharide via the Embden-Meyerhof pathway and that from lipids and proteins are more active, and the pentose cycle is less active, than in the biosynthesis of cellulose and curdlan. As for the results, labeling at C-6 carbon in the branched polysaccharide cultured from D-(6-¹³C)glucose was low, compared to that of cellulose and curdlan.     

C-H-deprotonation mediated by a remote syn-axial acetoxy group--an unprecedented double bond formation upon cyanation of the dimer from L-fucal

Replacement of the anomeric acetate by a cyanide group in the dimer of di-O-acetyl-L-fucal by the action of mild Lewis acid [Hg(CN)(2)-HgBr(2)-Me(3)SiCN], resulted not only in the desired transformation but also in the introduction of an additional double bond between C-2A and C-3A. Due to its configuration, the remote C-4A acetoxy group may facilitate the deprotonation by functioning as an internal base. 1H NMR spectroscopy and X-ray crystallography indicate that the conformations of both rings A and B and their relative orientation in the resulting C-linked disaccharidic glycosyl cyanide, 4-O-acetyl-2-C-(4-O-acetyl-2,3-dideoxy-alpha-L-threo-hex-2-enopyranosyl)-2,3-dideoxy-2-eno-alpha-L-fucopyranosyl cyanide, in solution are virtually identical to the crystal structure.