Deuterium isotope effects in carbohydrates revisited. Cryoprobe studies of the anomerization and NH to ND deuterium isotope induced 13C NMR chemical shifts of acetamidodeoxy and aminodeoxy sugars

Complete ¹H and ¹³C NMR chemical shift assignments have been generated from a series of acetamidodeoxy and aminodeoxy sugar derivatives. For free sugars, the enhanced sensitivity of an NMR cryoprobe allowed simple 1D and 2D NMR spectra to be obtained from essentially single anomers, before significant mutarotation had occurred. The NMR assignments have been used to characterize deuterium isotope effects on ¹³C chemical shifts measured under conditions of slow NH to ND exchange in single solutions. Within a range of 0 to −0.138 ppm, β, γ, δ, and ζ deuterium isotope effects have been observed, thus providing additional reference data for assignment of the ¹³C NMR spectra of nitrogenous saccharides.     

Structural analysis and properties of dextran produced by Leuconostoc mesenteroides NRRL B-640

A water-soluble dextran was produced by purified dextransucrase from Leuconostoc mesenteroides NRRL B-640. The dextran was purified by alcohol precipitation. The structure of dextran was determined by FT-IR, ¹H NMR, ¹³C NMR and 2-dimensional NMR spectroscopic techniques. NMR techniques (1D ¹H, ¹³C and 2D HMQC) were used to fully assign the ¹H and ¹³C spectra. All the spectral data showed that the dextran contains d-glucose residues in a linear chain with consecutive α(1 → 6) linkages. No branching was observed in the dextran structure. The viscosity of dextran solution decreased with the increase in shear rate exhibiting a typical non-Newtonian pseudoplastic behavior. The surface morphology of dried and powdered dextran studied using Scanning electron microscopy revealed the cubical porous structure.     

Chemical constituents from Celastrus aculeatus Merr.

Phytochemical investigation of Celastrus aculeatus Merr. led to the isolation of nine compounds. Their structures were identified to be dulcitol (1), β-sitosterol (2), n-tritriacontane (3), nimbidiol (4), pristimerin (5), p-hydroxybenzoic acid (7), vanillic acid (8), 3, 5-dimethoxy-4-hydroxybenzoic acid (9) and a new compound named pristimerol (6) on the basis of mass and NMR spectra. This is the first report of phenolic acids (compounds 7–9) from C. aculeatus Merr. We present the HR-MS, 1D NMR (¹H, ¹³C NMR, DEPT) and 2D NMR (HMBC) data of the new compound (6).     

4D Non-uniformly sampled C,C-NOESY experiment for sequential assignment of 13C,15N-labeled RNAs

¹³C spin diluted protein samples can be produced using [1-¹³C] and [2-¹³C]-glucose (Glc) carbon sources in the bacterial growth medium. The ¹³C spin dilution results in favorable ¹³C spectral resolution and polarization transfer behavior. We recently reported the combined use of [1-¹³C]- and [2-¹³C]-Glc labeling to facilitate the structural analysis of insoluble and non-crystalline biological systems by solid-state NMR (ssNMR), including sequential assignment, detection of long-range contacts and structure determination of macromolecular assemblies. In solution NMR the beneficial properties of sparsely labeled samples using [2-¹³C]-glycerol (¹³C labeled Cα sites on a ¹²C diluted background) have recently been exploited to provide a bi-directional assignment method (Takeuchi et al. in J Biomol NMR 49(1):17–26, 2011 ). Inspired by this approach and our own recent results using [2-¹³C]-Glc as carbon sources for the simplification of ssNMR spectra, we present a strategy for a bi-directional sequential assignment of solid-state NMR resonances and additionally the detection of long-range contacts using the combination of ¹³C spin dilution and 3D NMR spectroscopy. We illustrate our results with the sequential assignment and the collection of distance restraints on an insoluble and non-crystalline supramolecular assembly, the Salmonella typhimurium type III secretion system needle.     

Conformation and dynamics changes of bacteriorhodopsin and its D85N mutant in the absence of 2D crystalline lattice as revealed by site-directed C NMR

¹³C NMR spectra of [3-¹³C]Ala- and [1-¹³C]Val-labeled D85N mutant of bacteriorhodopsin (bR) reconstituted in egg PC or DMPC bilayers were recorded to gain insight into their secondary structures and dynamics. They were substantially suppressed as compared with those of 2D crystals, especially at the loops and several transmembrane α_II-helices. Surprisingly, the ¹³C NMR spectra of [3-¹³C]Ala-D85N turned out to be very similar to those of [3-¹³C]Ala-bR in lipid bilayers, in spite of the presence of globular conformational and dynamics changes in the former as found from 2D crystalline preparations. No further spectral change was also noted between the ground (pH 7) and M-like state (pH 10) as far as D85N in lipid bilayers was examined, in spite of their distinct changes in the 2D crystalline state. This is mainly caused by that the resulting ¹³C NMR peaks which are sensitive to conformation and dynamics changes in the loops and several transmembrane α_II-helices of the M-like state are suppressed already by fluctuation motions in the order of 10⁴-10⁵ Hz interfered with frequencies of magic angle spinning or proton decoupling. However, ¹³C NMR signal from the cytoplasmic α-helix protruding from the membrane surface is not strongly influenced by 2D crystal or monomer. Deceptively simplified carbonyl ¹³C NMR signals of the loop and transmembrane α-helices followed by Pro residues in [1-¹³C]Val-labeled bR and D85N in 2D crystal are split into two peaks for reconstituted preparations in the absence of 2D crystalline lattice. Fortunately, ¹³C NMR spectral feature of reconstituted [1-¹³C]Val and [3-¹³C]Ala-labeled bR and D85N was recovered to yield characteristic feature of 2D crystalline form in gel-forming lipids achieved at lowered temperatures.     

Two alkaloids from Narcissus requienii

The aerial part of Narcissus requienii (Amaryllidaceae) was found to contain pseudolycorine as the major alkaloid, and two new phenolic bases: 2-O-acetylpseudolycorine and 1-O-acetylpseudolycorine. The present communication reports the complete assignments of the NMR spectra of pseudolycorine, and the structure elucidation of the other comnounds by means of 2D ¹H-¹H and ¹H-¹³C NMR chemical shift correlation experiments.     

Chemical constituents from the fruits of Melia azedarach (Meliaceae)

A new apotirucallane-type triterpenoid, 3α-benzoate triterpenoid A (1), along with six known triterpenoids (2–7), one aromatic ester (8) and eight lignans (9–16), were isolated from the fruits of Melia azedarach Linn. The structure of 1 was determined by spectral analyses, including HR-ESI-MS, 1D NMR (¹H NMR and ¹³C NMR) and 2D NMR (HSQC and HMBC) analyses. 10, 11 and 16 were reported for the first time from the family Meliaceae, 8 was identified from the genus Melia for the first time, and 2, 3, 5, 7, 9 and 12–15 were obtained from M. azedarach for the first time. The chemotaxonomic significance of these compounds is discussed.     

(3, 2)D <Superscript>1</Superscript>H, <Superscript>13</Superscript>C BIRD<Superscript>r,X</Superscript>-HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates

Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of ¹H chemical shifts; larger dispersion of ¹³C chemical shifts is often used to reduce this overlap, while still providing the proton–proton correlation information e.g. in the form of a 2D ¹H, ¹³C HSQC-TOCSY experiment. For this methodology to work, ¹³C chemical shift must be resolved. In case of ¹³C chemical shifts overlap, ¹H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D ¹H, ¹³C BIRD^r,X-HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F₁ dimension. The required high-resolution in the ¹³C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.     

In vivo enzymology: 13C NMR measurement of a kinetic isotope effect for methanol oxidation in Methylosinus trichosporium OB3b

The competitive oxidation of ¹³CH₃OH and ¹³CD₃OH has been observed using in vivo ¹³C NMR spectroscopy. Simultaneous ¹H and ²H decoupling gave isotopically shifted ¹³C singlets for the two methanol isotopomers. The measured enzymic isotope effect, kH/kD is approx. 1.8, indicating that CH bond cleavage is not rate-determining.     

13C NMR Spectra of some D:A-friedo-oleananes

The ¹³C NMR signals of D:A-friedo-olean-7-one, putranjivadione, D:A-friedo-olean-22-one, D:A-friedo-olean-3,22-dione, and Salacia triterpene R have been assigned using off-resonance decoupling and lanthanide induced shift techniques. ¹³C NMR data provide further evidence for the boat-boat conformation for the D and E rings of D:A-friedo-oleananes in solution.     

Bulbophyllanthrin,a phenanthrene of the orchid Bulbophyllum leopardium

Bulbophyllanthrin, a novel phenanthrene derivative from the orchid Bulbophyllum leopardium, was shown to have the structure 1a mainly on the basis of spectral evidence including ¹³C and 2D NMR spectra.     

Triterpenoid saponins from Piptadeniastrum africanum (Hook. f.) Brenan

One new triterpenoid saponin, named piptadeniaoside (1), along with two known saponins (2–3) have been isolated from the stem bark of Piptadeniastrum africanum. After previous isolation of flavone derivatives from this plant, new phytochemical investigations were performed for its saponin content. Their structures were established by direct interpretation of their spectral data, mainly HRESIMS, 1D NMR (¹H, ¹³C NMR, DEPT) and 2D NMR (COSY, NOESY, HSQC and HMBC), and by comparison with the literature data.     

A fast NMR method for resonance assignments: application to metabolomics

We present a new method for rapid NMR data acquisition and assignments applicable to unlabeled (¹²C) or ¹³C-labeled biomolecules/organic molecules in general and metabolomics in particular. The method involves the acquisition of three two dimensional (2D) NMR spectra simultaneously using a dual receiver system. The three spectra, namely: (1) G-matrix Fourier transform (GFT) (3,2)D [¹³C, ¹H] HSQC–TOCSY, (2) 2D ¹H–¹H TOCSY and (3) 2D ¹³C–¹H HETCOR are acquired in a single experiment and provide mutually complementary information to completely assign individual metabolites in a mixture. The GFT (3,2)D [¹³C, ¹H] HSQC–TOCSY provides 3D correlations in a reduced dimensionality manner facilitating high resolution and unambiguous assignments. The experiments were applied for complete ¹H and ¹³C assignments of a mixture of 21 unlabeled metabolites corresponding to a medium used in assisted reproductive technology. Taken together, the experiments provide time gain of order of magnitudes compared to the conventional data acquisition methods and can be combined with other fast NMR techniques such as non-uniform sampling and covariance spectroscopy. This provides new avenues for using multiple receivers and projection NMR techniques for high-throughput approaches in metabolomics.     

Innovations in Generation and Analysis of 2D [C,H] COSY NMR Spectra for Metabolic Flux Analysis Purposes

2D [¹³C,¹H] COSY NMR is used by the metabolic engineering community for determining ¹³C–¹³C connectivities in intracellular compounds that contain information regarding the steady-state fluxes in cellular metabolism. This paper proposes innovations in the generation and analysis of these specific NMR spectra. These include a computer tool that allows accurate determination of the relative peak areas and their complete covariance matrices even in very complex spectra. Additionally, a method is introduced for correcting the results for isotopic non-steady-state conditions. The proposed methods were applied to measured 2D [¹³C,¹H] COSY NMR spectra. Peak intensities in a one-dimensional section of the spectrum are frequently not representative for relative peak volumes in the two-dimensional spectrum. It is shown that for some spectra a significant amount of additional information can be gained from long-range ¹³C–¹³C scalar couplings in 2D [¹³C,¹H] COSY NMR spectra. Finally, the NMR resolution enhancement by dissolving amino acid derivatives in a nonpolar solvent is demonstrated.     

NMR studies of the conformation of the natural sweetener rebaudioside A

Rebaudioside A is a natural sweetener from Stevia rebaudiana in which four β-d-glucopyranose units are attached to the aglycone steviol. Its ¹H and ¹³C NMR spectra in pyridine-d₅ were assigned using 1D and 2D methods. Constrained molecular dynamics of solvated rebaudioside using NMR constraints derived from ROESY cross peaks yielded the orientation of the β-d-glucopyranose units. Hydrogen bonding was examined using the temperature coefficients of the hydroxyl chemical shifts, ROESY and long-range COSY spectra, and proton-proton coupling constants.     

Triterpenoid saponins from Albizia boromoensis Aubrév. & Pellegr

As part of our search of new bioactive saponins from Cameroonian medicinal plants, phytochemical investigation of the roots of Albizia boromoensis led to the isolation of four new oleanane-type saponins, named boromoenosides A–D (1–4). Their structures were established by direct interpretation of their spectral data, mainly HRESIMS, 1D NMR (¹H, ¹³C NMR, and DEPT) and 2D NMR (COSY, NOESY, HSQC and HMBC), and by comparison with the literature data. All isolated saponins were assayed for their cytotoxicity against U-87 MG human glioblastoma cell lines and TG1 glioblastoma stem-like cells with no positive activity detected.     

Novel metabolites from the roots of Cadaba natalensis

From an extract of the roots of Cadaba natalensis Sond. the novel macrocyclic dibenzo-diazacyclododecanedione 1 was isolated together with (S)-2-ethyl-2-methyloxazolidin-5-one (2a). In addition, the five known compounds were obtained. Of these, (R)-5-ethyl-5-methyloxazolidin-2-one (3) is reported as a natural product for the first time. The structures of the isolated compounds were elucidated by analysis of the spectral data, 1D NMR (¹H, ¹³C, and DEPT), 2D NMR (COSY, HMQC, HMBC, and NOESY), and HRESIMS, as well as by the comparison with previously reported data.     

Fungal macrolides: Structure determination and biosynthesis of achaetolide,a lactone from Achaetomium cristalliferum

The structure of a new ten-membered lactone, achaetolide, isolated from cultures of Achaetomium cristalliferum is deduced from its mass and NMR spectra and from the study ofsomederivatives. The ¹³C NMR spectra of achaetolide enriched with [1-¹³C], [2-¹³C] and [1, 2-¹³C] acetate established its formation from eight intact acetate units via a precursor octaketide chain.     

Synthesis and conformational analysis of carbasugar bioisosteres of α-l-iduronic acid and its methyl glycoside

The synthesis of two novel carbasugar analogues of α-l-iduronic acid is described in which the ring-oxygen is replaced by a methylene group. In analogy with the conformational equilibrium described for α-l-IdopA, the conformation of the carbasugars was investigated by ¹H and ¹³C NMR spectroscopy. Hadamard transform NMR experiments were utilised for rapid acquisition of ¹H,¹³C-HSQC spectra and efficient measurements of heteronuclear long-range coupling constants. Analysis of ¹H NMR chemical shifts and J_H,H coupling constants extracted by a total-lineshape fitting procedure in conjunction with J_H,C coupling constants obtained by three different 2D NMR experiments, viz., ¹H,¹³C-HSQC-HECADE, J-HMBC and IPAP-HSQC-TOCSY-HT, as well as effective proton-proton distances from 1D ¹H,¹H T-ROE and NOE experiments showed that the conformational equilibrium ⁴C₁?²S_5a?¹C₄ is shifted towards ⁴C₁ as the predominant or exclusive conformation. These carbasugar bioisosteres of α-l-iduronic acid do not as monomers show the inherent flexibility that is anticipated to be necessary for biological activity.     

3-Oxo-friedelan-20α-OIC acid from gymnosporia emarginata

3-Oxo-friedelan-20α-oic acid, named as maytenonic (polpunonic) acid, has been isolated along with β-amyrin and sitosterol from Gymnosporia emarginata. ¹H and ¹³C NMR signals have been assigned for the structure. X-ray analysis of the single crystal confirmed that the carboxylic acid is α-oriented at C-20 and the D/E rings of this D:A-friedo-oleanane are in chair-chair conformation. ¹³C NMR data of the present compound also enabled the assignment of the C-20α- and β-methyl carbons in friedelin.