The Advantage of Automatic Peer-Reviewing of 13C-NMR Reference Data Using the CSEARCH-Protocol.

A systematic investigation of the experimental 13C-NMR spectra published in Molecules during the period of 1996 to 2015 with respect to their quality using CSEARCH-technology is described. It is shown that the systematic application of the CSEARCH-Robot-Referee during the peer-reviewing process prohibits at least the most trivial assignment errors and wrong structure proposals. In many cases, the correction of the assignments/chemical shift values is possible by manual inspection of the published tables; in certain cases, reprocessing of the original experimental data might help to clarify the situation, showing the urgent need for a public domain repository. A comparison of the significant key numbers derived for Molecules against those of other important journals in the field of natural product chemistry shows a quite similar level of quality for all publishers responsible for the six journals under investigation. From the results of this study, general rules for data handling, data storage, and manuscript preparation can be derived, helping to increase the quality of published NMR-data and making these data available as validated reference material.

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.

A Critical Evaluation of the Quality of Published 13C NMR Data in Natural Product Chemistry.

Nuclear Magnetic Resonance spectroscopy contributes very efficiently to the structure elucidation process in organic chemistry. Carbon-13 NMR spectroscopy allows direct insight into the skeleton of organic compounds and therefore plays a central role in the structural assignment of natural products. Despite this important contribution, there is no established and well-accepted workflow protocol utilized during the first steps of interpreting spectroscopic data and converting them into structural fragments and then combining them, by considering the given spectroscopic constraints, into a final proposal of structure. The so-called "combinatorial explosion" in the process of structure generation allows in many cases the generation of reasonable alternatives, which are usually ignored during manual interpretation of the measured data leading ultimately to a large number of structural revisions. Furthermore, even when the determined structure is correct, problems may exist such as assignment errors, ignoring chemical shift values, or assigning lines of impurities to the compound under consideration. An extremely large heterogeneity in the presentation of carbon NMR data can be observed, but, as a result of the efficiency and precision of spectrum prediction, the published data can be analyzed in substantial detail.This contribution presents a comprehensive analysis of frequently occurring errors with respect to 13C NMR spectroscopic data and proposes a straightforward protocol to eliminate a high percentage of the most obvious errors. The procedure discussed can be integrated readily into the processes of submission and peer-reviewing of manuscripts.

Iridoids as chemical markers of false ipecac (Ronabea emetica), a previously confused medicinal plant.

ETHNOPHARMACOLOGICAL RELEVANCE: Several roots or rhizomes of rubiaceous species are reportedly used as the emetic and antiamoebic drug ipecac. True ipecac (Carapichea ipecacuanha) is chemically well characterized, in contrast to striated or false ipecac derived from the rhizomes of Ronabea emetica (syn. Psychotria emetica). Besides its previous use as substitute of ipecac, the latter species is applied in traditional medicine of Panama and fruits of its relative Ronabea latifolia are reported as curare additives from Colombia. MATERIALS AND METHODS: Compounds of Ronabea emetica were isolated using standard chromatographic techniques, and structurally characterized by NMR spectroscopy and mass spectrometry. Organ specific distribution in Ronabea emetica as well as in Ronabea latifolia was further assessed by comparative HPLC analysis. RESULTS: Four iridoid-glucosides, asperuloside (1), 6α-hydroxygeniposide (2), deacetylasperulosidic acid (3) and asperulosidic acid (4) were extracted from leaves of Ronabea emetica. Rhizomes, used in traditional medicine, were dominated by 3. HPLC profiles of Ronabea latifolia were largely corresponding. These results contrast to the general tendency of producing emetine-type and indole alkaloids in species of Psychotria and closely related genera and merit chemotaxonomic significance, characterizing the newly delimited genus Ronabea. CONCLUSIONS: The aim of the work was to resolve the historic problem of adulteration of ipecac by establishing the chemical profile of Ronabea emetica, the false ipecac, as one of its less known sources. The paper demonstrates that different sources of ipecac can be distinguished by their phytochemistry, thus contributing to identifying adulterations of true ipecac.

Xanthones, biflavanones and triterpenes from Pentadesma grandifolia (Clusiaceae): structural determination and bioactivity.

Stem bark, roots, leaves and fruits of Pentadesma grandifolia Baker f. (Clusiaceae) have been analyzed for the presence of xanthones, biflavonoids and triterpenoids. Isolated and identified structures include the xanthones cowagarcinone B (1) and alpha-mangostin (2), further the two biflavanones 3,8"-binaringenin (3) and the corresponding 3,6"-binaringenin (4), which is here reported as natural constituent for the first time. Structures were determined by NMR and mass spectrometry, as well as by 13C-NMR CSEARCH and SPECINFO database systems. The triterpenes lupeol (5), beta-amyrin (6) and betulin (7) were also encountered. Compounds 2 - 4 exhibited antifungal activity against Cladosporium sphaerospermum. Results are discussed in context to organ-specific accumulation and to other bioactivities that may relate to the ethnomedicinal uses of this species.

Prenylated flavanones and flavanonols as chemical markers in Glycosmis species (Rutaceae).

Fifteen prenylated or geranylated flavanones and flavanonols were isolated from the leaf extracts of different Glycosmis species collected in Thailand and Malaysia. All structures were elucidated by spectroscopic methods, especially 1D and 2D NMR. Six compounds were described for the first time and two were only known so far as synthetic products. The chemotaxonomic significance of flavanoid accumulation within the genus Glycosmis is highlighted.

(13)C-NMR spectra of santalol derivatives: a comparison of DFT-based calculations and database-oriented prediction techniques.

A systematic investigation of a series of santalol and epi-santalol derivatives by means of ab initio and density functional theory (DFT) calculations together with database-oriented prediction methods leads to a configurational reassignment within this compound class. The DFT calculations as well as the HOSE-code and neural network-based predictions allow deriving a general rule set for unambiguous assignment within this compound class. The methyl group in position 2' serves as an indication for the configuration at this stereocenter allowing easy differentiation between santalol derivatives and their diastereomers belonging to the epi-santalol series.