Complete 1H NMR Assignments Research Articles

Isolation of an anti-HIV diprenylated bibenzyl from Glycyrrhiza lepidota

The organic soluble extract from the leaves of Glycyrrhiza lepidota showed moderate activity in the US National Cancer Institute in vitro anti-HIV-1 bioassay. Chromatographic separation of this extract resulted in the identification of a new diprenylated bibenzyl as the compound responsible for the observed anti-viral activity. Extensive spectroscopic experiments provide the complete 1H NMR and 13C NMR spectral assignments to support the proposed structure. Known compounds glepidotin B and glepidotin A were also isolated from the extract and shown to be inactive in the anti-viral assay.

Structure elucidation of three new acetylated flavonoid glycosides from Centaurium spicatum

AbstractThree new acetylated flavonol glycosides, quercetin 3‐O‐(2,3,4‐triacetyl‐α‐rhamnopyranosyl)‐(1 → 6)‐β‐galactopyranoside, quercetin 3‐O‐[(2,3,4‐triacetyl‐α‐rhamnopyranosyl)‐(1 → 6)]‐3‐acetyl‐β‐galactopyranoside and quercetin 3‐O‐[(2,3,4‐triacetyl‐α‐rhamnopyranosyl)‐(1 → 6)]‐4‐acetyl‐β‐galactopyranoside, were isolated from Centaurium spicatum (L.) Fritsch (Gentianaceae). Structure elucidation, especially the localization of the acetyl groups, and complete 1H and 13C NMR assignments of these biologically active compounds were carried out using one‐ and two‐dimensional NMR methods, including 1H and 13C NMR, DEPT‐135 and DEPT‐90 and gradient‐assisted experiments such as DQF‐COSY, TOCSY, HSQC and HMBC experiments. Copyright © 2001 John Wiley & Sons, Ltd.

ISOLATION AND STRUCTURAL ANALYSIS OF NEW FRUCTANS PRODUCED BY CHICORY

This report describes a new series of oligosaccharides, which is formed in chicory roots under forcing conditions and during in vitro experiments using purified chicory 1-FFT (fructan:fructan 1-fructosyl transferase). It was demonstrated that the three smallest members of this new series (disaccharide, trisaccharide and tetrasaccharide) contain exclusively β-D-fructosyl residues after hydrolysis. The present data demonstrate that the smallest compound is levanbiose and that the other oligomers of this new series of fructans do not belong to the linear 2→6 linked levan-oligosaccharides nor to the linear 2→1 linked inulo-oligosaccharides. A combination of several chromatographic techniques yielded a fraction that contained only the compound with degree of polymerisation (DP) 2 (levanbiose, β-D-fructofuranosyl-(2→6)-D-fructofuranose), and a mixture of DP 3 of the new series and 1-kestose. Using homonuclear and heteronuclear 2D NMR experiments the complete 1H and 13C NMR assignments of levanbiose and DP 3 were obtained. From High Performance Anion Exchange Chromatography (HPAEC) and NMR experiments of DP 3 of the new series it was concluded that the molecule contains a β-D-fructofuranosyl residue 2→1 linked to the non-reducing moiety of levanbiose, and thus has to be named β-D-fructofuranosyl-(2→1)-β-D-fructofuranosyl-(2→6)-D-fructofuranose. The simple and regular pattern of the HPAEC retention times of the new oligosaccharides suggests that it is a homologous series of oligomers build by 2→1 elongation with β-D-fructofuranosyl residues at the non-reducing residue of levanbiose.

Complete 1H and 13C NMR assignments of chamigrenes from Aplysia dactilomela

AbstractStereochemical evaluation and complete 1H and 13C NMR assignment of the chamigrenes johnstonol (1), pacifenediol (2), pacifidiene (3), pacifenol (4), isolated from the Brazilian mollusc Aplysia dactilomela, were performed using 2D NMR techniques including COSY, NOESY, HSQC and HMBC, combined with AMI calculations and 1H NMR spectrum simulations. Copyright © 2001 John Wiley & Sons, Ltd.

Complete 1H and 13C NMR assignment of mono-sulfated galactosylceramides with four types of ceramides from human kidney

The full assignment of 1H and 13C NMR signals of galactosylceramide 3-sulfate (galactosyl sulfatide) and 1H signals of galactosylceramide 6-sulfate was achieved by using 1H– 1H DQF-COSY and 1H– 13C heteronuclear COSY. Analyses were performed on a mixture of galactosyl sulfatides with four representative ceramide types consisting of a combination of non-hydroxy or 2-hydroxy fatty acids and sphingenine or 4 D-hydroxysphinganine (trihydroxysphinganine) as the long-chain bases. The 1H and 13C NMR parameters of galactosyl sulfatide with 4-hydroxysphinganine as well as 13C signals of complex lipids with 4-hydroxysphinganine were elucidated for the first time. Not only sulfation of the galactosyl residue, but also modification of the aglycon, including hydroxylation of fatty acids and hydration of the double bond in sphingoid bases, altered the chemical shifts substantially. In addition, the unique long-range coupling constants, 4 J H,H and 5 J H,H, in the galactosyl residue of galactosyl sulfatide could be determined.

NMR spectroscopy, molecular dynamics, and conformation of a synthetic octasaccharide fragment of the O-specific polysaccharide of Shigella dysenteriae type 1

A synthetic octasaccharide fragment ( 2) of the O-specific polysaccharide ( 1) of Shigella dysenteriae type 1 has been studied as its methyl glycoside by one- and two-dimensional homo- and heteronuclear NMR spectroscopy. Complete 1H and 13C NMR assignments have been generated, and the 13C spin–lattice relaxation times have been measured for the octasaccharide 2. A congener ( 6) of this octasaccharide containing one d-galactose residue with a specific 13C label at C-1 has been synthesized and used to measure interglycosidic 13C– 1H coupling by the 2D J-resolved 1H NMR method. From the NMR data, three types of conformational restraints were developed: (a) 29 inter-residue, distance restraints; (b) 48 intra-residue, ring atom dihedral angle restraints, and (c) one heteronuclear, inter-residue dihedral angle restraint. The use of these restraints in a restrained molecular dynamics computation with simulated annealing yielded a conformation resembling a short, irregular spiral, with methyl substituents on the exterior.

NMR studies on synthesized diosgenyl saponin analogs

The identification of six synthesized diosgenyl saponin analogs with up to five sugars was accomplished by NMR studies. A combination of homo- and heteronuclear two-dimensional NMR techniques was utilized to achieve the complete 1H and 13C NMR assignments. Copyright © 2000 John Wiley & Sons, Ltd.

Molecular structure and 1H, 13C NMR assignments of 1,3,5-tris(imidazol-1-ylmethyl)-2,4,6-trimethylbenzene

The molecule 1,3,5-tris(imidazol-1-ylmethyl)-2,4,6-trimethylbenzene (titmb) crystallizes as a monohydrate in the monoclinic space group C2/c with a = 20.888(4), b = 13.220(2), c = 14.385(2) A, β = 90.36(1)°. Two of three imidazole groups are on one side of the central benzene ring, and the other one is on the opposite side. The crystal packing of titmb is stabilized by O-H--N hydrogen bonding between the water molecule and nitrogen atoms of the imidazole group. The complete 1H and 13C NMR assignments for titmb were carried out by 2D NMR spectral measurements.

NMR and molecular modeling studies on two glycopeptides from the carbohydrate-protein linkage region of connective tissue proteoglycans.

Complete 1H and 13C NMR assignments are reported for two glycopeptides representing the carbohydrate-protein linkage region of connective tissue proteoglycans. These glycopeptides are the octasaccharide hexapeptide, Ser(GlcpAbeta(1-->3) Galpbeta(1-->3)Galpbeta(1-->4)Xylpbeta)-Gly-Ser-Gly-Se r (GlcpAbeta(1-->3)Galpbeta(1-->3)Galpbeta(1-->4)Xylp beta)-Gly (1), and the tetrasaccharide dipeptide, Ser(GlcpAbeta(1-->3)Galpbeta(1-->3)Galpbeta(1-->4)X ylpbeta)-Gly (2). The vicinal coupling constant data show that the monosaccharide residues adopt4 C 1 chair conformations. Distance geometry/simulated annealing calculations using 2D NOESY derived distance constraints yielded a single family of structures for the tetrasaccharide moiety, with well defined interglycosidic linkage conformations. The straight phi torsion angles of the glycosidic C1'-O1 bonds showed a strict preference for the -sc range whereas the psi torsion angles (O1-Cn) exhibited dependence upon the interglycosidic linkage position (-ac for beta(1-->3) linkage, +ac for beta(1-->4) linkage). The predominant conformation about the glycopeptide bond is straight phi = -sc and psi = +ac. The presence of strong daN (i, i+1) NOE contacts, and the general absence of dNN (i, i+1) contacts (except for a weak Ser-5/Gly-6 dNN contact) and the dbN (i, i+1) contacts (except for Ser-1/Gly-2) in the ROESY spectrum, suggest that the backbone for 1 is predominantly in an extended conformation. A comparison of the ROESY data for 1 with those obtained from the unglycosylated hexapeptide (3) of the same sequence suggests that glycosylation has only a marginal influence on the backbone conformation of the hexapeptide.

Complete1H and13C NMR assignments of stephalic acid

In addition to 1D NMR methods and 2D shift-correlated NMR techniques (COSY and HETCOR), spin–spin simulation and MMX calculations, to obtain the minimum energy conformation structure, were used for the complete 1H and 13C NMR assignments of stephalic acid. Copyright © 1999 John Wiley & Sons, Ltd.

Conversion dependence of the structural units and the degree of branching of a hyperbranched polyester based on 4,4-bis-(4′-hydroxyphenyl)pentanoic acid determined by NMR spectroscopy

The hyperbranched polyester based on 4,4-bis-(4′-hydroxyphenyl)pentanoic acid was synthesized with different DP's. A complete 1H and 13C NMR assignment of the oligomers was carried out. Six different structural units were quantified by NMR analysis. The conversion dependence of the content of these structural units and of the degree of branching DB follows the theoretically derived equations. Furthermore, six different diads were quantified by 13C NMR spectroscopy. The conversion dependence of the diads was calculated and again the measured data agree well with the theory. The good fit between theoretical and measured data proves that the polycondensation of the 4,4-bis-(4′-hydroxyphenyl)pentanoic acid follows a random growth of the different units with equal reaction rates of all reaction steps. Finally, spin-lattice relaxation times (T1C) and nuclear Overhauser enhancements (NOE) were determined and discussed.

Complete spectroscopic structural characterization of novobiocin, isonovobiocin, decarbamylnovobiocin, 2″‐(o‐Carbamyl)novobiocin, and novobiocin‐2″,3″‐carbonate

AbstractThe rigorous structural characterization of novobiocin, is reported using mass spectrometric, infrared and nmr spectroscopic analysis. Complete nmr assignments are reported. Previous reports in the literature had left some quaternary carbon resonances unassigned. Isonovobiocin and decarbamylnovobiocin, although known in the literature for a number of years, have never been completely characterized. Mass spectrometric fragmentation pathways and complete 1H and 13C nmr assignments are reported for these congeners for the first time. The mass spectral fragmentation pathway and nmr assignments are also reported for 2″‐(O‐carbamyl)novobiocin although the nmr assignments at lower field were reported previously. The structural characterization of novobiocin‐2″,3″‐carbonate observed in the Test Assay procedure used for Novobiocin is reported for the first time.

Complete isomer-specific 1H and 13C NMR assignments of the heme resonances of rat liver outer mitochondrial membrane cytochrome b5.

Singly and doubly labeled delta-aminolevulinic acid derivatives were used to prepare rat liver outer mitochondrial membrane (OM) cytochrome b5 containing a 13C-labeled heme active site. A variety of NMR experiments, including HMBC and INADEQUATE in conjunction with the more commonly used HMQC, NOESY, and COSY, were conducted to make unambiguous assignments of protonated carbons and the quaternary pyrrole-alpha and -beta carbons in both isomeric forms of the paramagnetic active center of OM cytochrome b5. Because the long interpulse delays in the HMBC experiment have a detrimental effect on the detectability of fast relaxing paramagnetically affected resonances. INADEQUATE is proposed as the experiment of choice for assigning quaternary carbons in paramagnetic hemes with carefully chosen macrocycle labeling patterns. Furthermore, the applicability of the INADEQUATE experiment to paramagnetic heme active sites should be facilitated greatly by the availability of biosynthetic methods for producing isotopically labeled b-hemes and, more recently, isotopically labeled c-hemes.

Complete 1H and 13C NMR assignments of diosgenyl saponins

The complete assignments of 1H and 13C NMR data for a series of synthesized diosgenyl saponin analogs are described, viz. diosgenyl β-D-glucopyranoside (1), diosgenyl α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranoside (2), diosgenyl α-L-rhamnopyranosyl-(1→3)-β-D-glucopyranoside (3), diosgenyl α-L-rhamnopyranosyl-(1→2)-α-L-rhamnopyranosyl-(1→3)-β-D-glucopyranoside (4), α-L-rhamnopyranosyl-(1→2)-β-D-xylopyranosyl-(1→3)-β-D-glucopyranoside (5), α-L-rhamnopyranosyl-(1→2)-β-L-arabinofuranosyl-(1→3)-β-D-glucopyranoside (6) and α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranosyl-(1→3)-β-D-glucopyranoside (7). The assignments were achieved using homo- and heteronuclear two-dimensional NMR techniques. Copyright © 1999 John Wiley & Sons, Ltd.

Complete 1H and 13C NMR assignments of four caesalpin furanoditerpenes of Caesalpinia bonducella

Four cassane furanoditerpenes, including the known α-caesalpin and caesalpin F, were isolated from the roots of Caesalpinia boducella. The 1H and 13C NMR spectra of all four compounds were completely assigned by using a combination of 2D NMR experiments, which included 1H–1H COSY, HMQC, HMBC and NOESY sequences. © 1998 John Wiley & Sons, Ltd.

Sequence-specific 1H assignment and secondary structure of the bacteriocin AS-48 cyclic peptide.

The bacteriocin AS-48 is a cationic peptide (7149 Da) having a broad antimicrobial spectrum, encoded by the 68 kb conjugative plasmid pMB2 from Enterococcus faecalis S-48. It is a unique peptide since it has a cyclic structure, which is achieved by the formation of a tail-head peptide bond after ribosomal synthesis (Gálvez et al., 1989; Martínez-Bueno et al., 1994; Samyn et al., 1994). Preliminary CD and calorimetric studies (data not shown) pointed towards a highly helical and very stable three dimensional structure. All the information gathered until now indicates that the target of AS-48 is the cytoplasmic membrane in which it opens channels or pores, leading to dissipation of the proton motive force and cell death, which in some cases is also followed by bacterial lysis (Gálvez et al., 1991). This peptide is a suitable tool for studying protein-membrane interactions, and it also offers promising perspectives for biotechnological applications. Knowledge of the 3D structure of AS-48 is a first step in the conduct of further structure-function studies. Here we report the complete 1H NMR assignment of its proton resonances together with the resulting secondary structure pattern as prerequisites for the determination of a high-resolution 3D solution structure.

Confirmation and complete 1H and 13C NMR assignment of the structure of peptidoglycan from Sarcina ventriculi, a highly adaptable Gram-positive bacterium

The structure of peptidoglycan extracted from the Gram-positive bacterium Sarcina ventriculi grown at pH 3 was characterized by amino acid analysis, mass spectrometry, and two-dimensional NMR spectroscopy. The basic muropeptide subunit consisted of an N-acetylglucosamine- β-1,4- N-acetylmuramic acid disaccharide substituted with an oligopeptide with the sequence Ala- isoGln-A 2pm(-Gly)-Ala. The dimeric muropeptide was also characterized as a cross-linked bis-disaccharide-penta-hexapeptide with the structure, GlcNAc-MurNAc-Ala- isoGln-A 2pm(-Gly)-Ala → GlcNAc-MurNAc-Ala- isoGln-A 2(-Gly)-Ala-Ala. These results are consistent with a structure proposed based on enzymatic degradation and chemical modifications but with no use of spectroscopic information [O. Kandler, D. Claus, and A. Moore, Arch. Mikrobiol., 82 (1972) 140–146]. The cell wall of this organism is very tightly cross-linked and is much more rigid than that of most other Gram-positive bacteria. There is, however, a large degree of conservation in the general structure compared to peptidoglycan in other bacteria that are not well adaptable to extremes, indicating that the membrane plays a more important role in adaptation.

Structural NMR Studies on Aryl-Substitutedπ-Allyl-Pd(II) Complexes by Concerted Use ofGradient-Based Experiments

Complete 1H and 13C NMR assignments of several aryl-substituted π-allyl–Pd(II) complexes were achieved using modern gradient-based 1D and 2D experiments. In addition, unambiguous 31P assignments were readily made using an improved gradient-enhanced 1H–31P HMBC experiment from which the regiochemistry of cationic complexes containing asymmetric bidentate ligands could also be elucidated. The effect of the nature of the substituent on allylic proton and carbon chemical shifts is briefly evaluated. Finally, a partial π–σ–π isomerization mechanism is proposed taking into account some observed dynamic NMR processes which are largely dependent on the ligand nature of these complexes. © 1997 by John Wiley & Sons, Ltd.

Full 1H NMR assignment and detailed O-acetylation patterns of capsular polysaccharides from Neisseria meningitidis used in vaccine production

We report essentially complete 1H NMR assignments for the capsular polysaccharides from Neisseria meningitidis serotypes A, C, W-135, and Y. These polysaccharides are components of current polysaccharide vaccines against meningococcal infection and of the polysaccharide-protein conjugate vaccines under development. From these NMR data the pattern of O-acetylation was determined. O-Acetylation of the W-135 polysaccharide is reported for the first time. We also show that, for the Types C and W-135 polysaccharides, a migration of O-acetyl groups occurs during storage in solution, and demonstrate that high field 1H NMR represents a simple and sensitive method to define the O-acetylation pattern of individual batches of these polysaccharides.

1H and13C NMR Assignments of Some Green Tea Polyphenols

Complete and unequivocal 1H and 13C NMR assignments for a range of green tea polyphenols [epiafzelechin, catechin, epicatechin, gallocatechin, epigallocatechin, catechin-3-O-gallate, epicatechin-3-O-gallate, gallocatechin-3-O-gallate, epigallocatechin-3-O-gallate and epigallocatechin-3-O-(3′-O-methyl)-gallate] in acetone-d6 solvent have been achieved using the 2D proton–carbon correlation experiments HMQC and HMBC and also 1D NOE difference spectroscopy.