Use of carbon-13 NMR to identify known natural products by querying a nuclear magnetic resonance database-An assessment.

The quick identification of known organic low molecular weight compounds, also known as structural dereplication, is a highly important task in the chemical profiling of natural resource extracts. To that end, a method that relies on carbon-13 nuclear magnetic resonance (NMR) spectroscopy, elaborated in earlier works of the author's research group, requires the availability of a dedicated database that establishes relationships between chemical structures, biological and chemical taxonomy, and spectroscopy. The construction of such a database, called acd_lotus, was reported earlier, and its usefulness was illustrated by only three examples.

nuclear magnetic resonance experiments for chemical reaction monitoring under spin diffusion conditions.

osity-enhanced spectroscop () offers a new way to analyze complex mixtures of time-varying composition. This communication reports the use of the viscous binary solvent DMSO-/water to induce NMR spin diffusion for chemical reaction monitoring and real-time characterization of a 3-substituted 4-hydroxycoumarin derivative and its side-product.

Sherlock-A Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR Data.

The structure elucidation of small organic molecules (<1500 Dalton) through 1D and 2D nuclear magnetic resonance (NMR) data analysis is a potentially challenging, combinatorial problem. This publication presents Sherlock, a free and open-source Computer-Assisted Structure Elucidation (CASE) software where the user controls the chain of elementary operations through a versatile graphical user interface, including spectral peak picking, addition of automatically or user-defined structure constraints, structure generation, ranking and display of the solutions. A set of forty-five compounds was selected in order to illustrate the new possibilities offered to organic chemists by Sherlock for improving the reliability and traceability of structure elucidation results.

Use of Diethanolamine as a Viscous Solvent for Mixture Analysis by Multidimensional Heteronuclear NMR Experiments.

Diethanolamine/DMSO- as a viscous binary solvent is first reported for the individualization of low-polarity mixture components by multidimensional heteronuclear NMR experiments under spin diffusion conditions. Solvent viscosity induces the slowing down of molecular tumbling, hence promoting magnetization transfer by dipolar longitudinal cross-relaxation. As a result, all H nuclei resonances within the same molecule may correlate in a 2D nuclear Overhauser effect spectroscopy (NOESY) spectrum, giving access to mixture analysis.

Virtual decoupling to break the simplification versus resolution trade-off in nuclear magnetic resonance of complex metabolic mixtures.

The heteronuclear single quantum correlation (HSQC) experiment developed by Bodenhausen and Ruben (1980) in the early days of modern nuclear magnetic resonance (NMR) is without a doubt one of the most widely used experiments, with applications in almost every aspect of NMR including metabolomics. Acquiring this experiment, however, always implies a trade-off: simplification versus resolution. Here, we present a method that artificially lifts this barrier and demonstrate its application towards metabolite identification in a complex mixture.

ViscY NMR experiments in phosphoric acid as a viscous solvent for individualization of small molecules within mixtures by spin diffusion.

The analysis of small molecules within complex mixtures is a particularly difficult task when dealing with the study of metabolite mixtures or chemical reaction media. This issue has fostered in recent years an active search for effective and practical solutions. In this context, the ViscY NMR approach has been recently proposed.

Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation.

The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR.

13C NMR Dereplication Using MixONat Software: A Practical Guide to Decipher Natural Products Mixtures.

The growing use of herbal medicines worldwide requires ensuring their quality, safety, and efficiency to consumers and patients. Quality controls of vegetal extracts are usually undertaken according to pharmacopeial monographs. Analyses may range from simple chemical experiments to more sophisticated but more accurate methods.

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.

The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of (C. Presl) J.F. Macbr. as a Preliminary Test Case.

The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication.

H-NMR metabolomics profiling of zebra mussel (Dreissena polymorpha): A field-scale monitoring tool in ecotoxicological studies.

Biomonitoring of aquatic environments requires new tools to characterize the effects of pollutants on living organisms. Zebra mussels (Dreissena polymorpha) from the same site in north-eastern France were caged for two months, upstream and downstream of three wastewater treatment plants (WWTPs) in the international watershed of the Meuse (Charleville-Mézières "CM" in France, Namur "Nam" and Charleroi "Cr" in Belgium). The aim was to test H-NMR metabolomics for the assessment of water bodies' quality.

Dereplication of Natural Extracts Diluted in Glycerin: Physical Suppression of Glycerin by Centrifugal Partition Chromatography Combined with Presaturation of Solvent Signals in C-Nuclear Magnetic Resonance Spectroscopy.

For scientific, regulatory, and safety reasons, the chemical profile knowledge of natural extracts incorporated in commercial cosmetic formulations is of primary importance. Many extracts are produced or stabilized in glycerin, a practice which hampers their characterization. This article proposes a new methodology for the quick identification of metabolites present in natural extracts when diluted in glycerin.

Multiple solvent signal presaturation and decoupling artifact removal in C{H} nuclear magnetic resonance.

The analysis by proton-decoupled carbon-13 nuclear magnetic resonance spectroscopy of samples dissolved in solvents presenting strong multiple resonances can be facilitated by the suppression of these resonances by multisite presaturation. The advantage drawn from this operation is the elimination of the possible artifacts that arise from the solvent signals in non-optimized decoupling conditions. Solvent presaturation was implemented on glycerol, 1,2-propanediol, 1,3-propanediol, 1,2-butanediol, and 1,3-butanediol with at least 94 % on-resonance efficiency and a bandwidth of less than 50  measured at 50 % signal intensity decrease.

Abundant Extractable Metabolites from Temperate Tree Barks: The Specific Antimicrobial Activity of Extracts.

Tree barks are mainly considered as wood wastes from forestry activities, but represent valuable resources as they may contain antimicrobial compounds. Here, we aimed to evaluate the possible antimicrobial activities of bark extracts and to characterize the chemical composition of the most active extract. Ten methanol bark extracts were tested in vitro against 17 bacterial strains and 5 yeast strains, through minimum inhibitory concentration (MIC) and minimum bactericidal (or fungicidal) concentration (MBC/MFC) assays.

Mixture Analysis in Viscous Solvents by NMR Spin Diffusion Spectroscopy: ViscY. Application to High- and Low-Polarity Organic Compounds Dissolved in Sulfolane/Water and Sulfolane/DMSO- Blends.

The sulfolane/water and sulfolane/DMSO- binary NMR solvents are reported for the individualization of mixture components by spin diffusion when molecular tumbling is slow due to solvent viscosity, thus strongly favoring magnetization transfer by dipolar cross-relaxation. All H nuclei resonances within the same molecule tend then to correlate in a 2D NOESY spectrum, opening the way to mixture analysis. Till now, analysis of organic compounds by NMR spin diffusion in viscous solvents involved H, C, N, and F.

Investigation of the glucosinolates in Hesperis matronalis L. and Hesperis laciniata All.: Unveiling 4'-O-β-d-apiofuranosylglucomatronalin.

The glucosinolate (GSL) profiles of wild-growing plants from the genus Hesperis, i.e. Hesperis laciniata All.

Glucosinolates of L. (Brassicaceae) from Croatia.

The glucosinolate (GSL) profiles (inflorescence, stem, root, and fruit) of the wild-growing plant L. (Brassicaceae) from Croatia was established by LC-MS analysis. During this investigation, we confirmed the presence of benzyl- (), 3-methoxybenzyl- (), 4-hydroxybenzyl- (), 4-methoxyindol-3-ylmethyl- () GSLs and reported for the first time in the plant the presence of (2 )-hydroxybut-3-enyl- (), (2)-hydroxybut-3-enyl- (), but-3-enyl- (), and 2-phenylethyl- () GSLs.

Polar mixture analysis by NMR under spin diffusion conditions in viscous sucrose solution and agarose gel.

The use of two new viscous solvents, sucrose solution and agarose gel, is reported for the first time for giving access to the individual NMR spectra of polar and potentially bioactive compounds in a mixture. Under viscous conditions, the tumbling rate of small and mid-sized molecules reduces in solution, so that the longitudinal cross-relaxation encourages the observation of spin diffusion. As a result, all of the resonances of the 1H nuclei within the same molecule tend to correlate together in a 2D NOESY spectrum, thus paving the way to mixture analysis.

Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat.

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Glucosinolate turnover in Brassicales species to an oxazolidin-2-one, formed via the 2-thione and without formation of thioamide.

Glucosinolates are found in plants of the order Brassicales and hydrolyzed to different breakdown products, particularly after tissue damage. In Barbarea vulgaris R.Br.

Structural characterization and pro-tumor properties of a highly conserved matrikine.

Elastin-derived peptides (EDPs) exert protumor activities by increasing tumor growth, migration and invasion. A number of studies have highlighted the potential of VGVAPG consensus sequence-derived elastin-like polypeptides whose physicochemical properties and biocompatibility are particularly suitable for applications, such as drug delivery and tissue engineering. However, among the EDPs, the influence of elastin-derived nonapeptides (xGxPGxGxG consensus sequence) remains unknown.