NMReDATA: Tools and applications.

The nuclear magnetic resonance extracted data (NMReDATA) format has been proposed as a way to store, exchange, and disseminate nuclear magnetic resonance (NMR) data and physical and chemical metadata of chemical compounds. In this paper, we report on analytical workflows that take advantage of the uniform and standardized NMReDATA format. We also give access to a repository of sample data, which can serve for validating software packages that encode or decode files in NMReDATA format.

Ascorbigen A-NMR identification.

The connectivities of all atoms in ascorbigen A, an important metabolite, were determined unambiguously for the first time. The connectivity between carbon atoms was established by 2D INADEQUATE, and one-bond 13 C-13 C coupling constants were determined for all pairs of directly connected carbon atoms except for two strongly coupled carbon pairs. The 13 C-13 C coupling in one of the pairs was proved by a modification of standard INADEQUATE; however, the signals from the other pair were too weak to be observed. The connectivity within the two strongly coupled C-C pairs was confirmed by a combination of COSY and gHSQC; the latter experiment also identified all C-H bonds. The proton nuclear magnetic resonance (1 H NMR) spectra in dry dimethyl sulfoxide allowed identification and assignment of the signals due to NH and OH protons. The derived structure, 3-((1H-indol-3-yl)methyl)-3,3a,6-trihydroxytetrahydrofuro[3,2-b]furan-2(5H)-one, agrees with the structure suggested for ascorbigen A in 1966. The density functional theory (DFT) calculations showed that among 16 possible stereoisomers, only two complied with the almost zero value of the measured 3 J(H6-H6a). Of the two stereoisomers, 3S,3aS,6S,6aR and 3R,3aR,6R,6aS, the latter was excluded on synthetic grounds. The nuclear Overhauser effect measurements unveiled close proximity between H2' proton of the indole and the H6a proton of the tetrahydrofuro[3,2-b]furan part. Detailed structural interpretation of the measured NMR parameters by means of DFT NMR was hampered by rotational flexibility of the indole and tetrahydrofuro[3,2-b]furan parts and inadequacy of Polarizable Continuum Model (PCM) solvent model.

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases.

Identification of tentative marker in Corvina and Primitivo wines with CMC-se.

This paper introduces CMC-se-a program for computer-assisted structure elucidation. In the experimental part, the combination of modern analytical methods (LC-SPE-NMR/MS) and structure elucidation software is used for the identification of tentative markers in red wines.

Isoflavonoids and coumarins from Glycyrrhiza uralensis: antibacterial activity against oral pathogens and conversion of isoflavans into isoflavan-quinones during purification.

Phytochemical investigation of a supercritical fluid extract of Glycyrrhiza uralensis has led to the isolation of 20 known isoflavonoids and coumarins, and glycycarpan (7), a new pterocarpan. The presence of two isoflavan-quinones, licoriquinone A (8) and licoriquinone B (9), in a fraction subjected to gel filtration on Sephadex LH-20 is due to suspected metal-catalyzed oxidative degradation of licoricidin (1) and licorisoflavan A (2). The major compounds in the extract, as well as 8, were evaluated for their ability to inhibit the growth of several major oral pathogens. Compounds 1 and 2 showed the most potent antibacterial activities, causing a marked growth inhibition of the cariogenic species Streptococcus mutans and Streptococcus sobrinus at 10 µg/mL and the periodontopathogenic species Porphyromonas gingivalis (at 5 µg/mL) and Prevotella intermedia (at 5 µg/mL for 1 and 2.5 µg/mL for 2). Only 1 moderately inhibited growth of Fusobacterium nucleatum at the highest concentration tested (10 µg/mL).