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.

SAN plot: A graphical representation of the signal, noise, and artifacts content of spectra.

The signal-to-noise ratio is an important property of NMR spectra. It allows to compare the sensitivity of experiments, the performance of hardware, etc. Its measurement is usually done in a rudimentary manner involving manual operation of selecting separately a region of the spectrum with signal and noise, respectively, applying some operation and returning the signal-to-noise ratio. We introduce here a simple method based on the analysis of the distribution of point intensities in one- and two-dimensional spectra. The signal/artifact/noise plots, (SAN plots) allows one to present in a graphical manner qualitative and quantitative information about spectra. It will be shown that besides measuring signal and noise levels, SAN plots are also quite useful to visualize and compare artifacts within a series of spectra. Some basic properties of the SAN plots are illustrated with simple application.

Everything you wanted to know about phase and reference frequency in one- and two-dimensional NMR spectroscopy.

The fundamental concept of phase discussed in this tutorial aimed at providing students with an explanation of the delays and processing parameters they may find in nuclear magnetic resonance (NMR) pulse programs. We consider the phase of radio-frequency pulses, receiver, and magnetization and how all these parameters are related to phases and offsets of signals in spectra. The impact of the off-resonance effect on the phase of the magnetization is discussed before presenting an overview of how adjustment of the time reference of the free induction decay avoids first-order correction of the phase of spectra. The main objective of this tutorial is to show how the relative phase of a pulse and the receiver can be used to change the reference frequency along direct and indirect dimensions of NMR experiments. Unusual of phase incrementation with non-90° angles will be illustrated on one- and two-dimensional NMR spectra.

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.

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. Prod. Rep., 2018, DOI: .

Homonuclear decoupling in the 13 C indirect dimension of HSQC experiments for 13 C-enriched compounds.

The two most compelling methods for broadband homonuclear decoupling currently available, Zangger-Sterk (ZS) and pure shift yielded by chirp excitation (PSYCHE), were successfully adapted and tested on the 13 C isotope. When applied during the indirect carbon evolution in the HSQC experiment, they both entirely eliminated the extended carbon-carbon multiplet structures observed in this dimension of a non-decoupled HSQC spectrum of 13 C-enriched cholesterol. The optimized selective pulse modulated using novel non-equidistant scheme for multisite refocusing (ZS) and the small flip angle saltire chirps (PSYCHE) both proved to be robust and efficient in providing decoupled spectra with a sensitivity of about 25% that of the non-decoupled HSQC spectra with improved quality compared to earlier results.

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.

Targeted Isolation of Monoterpene Indole Alkaloids from Palicourea sessilis.

Phytochemical investigation of the alkaloid extract of Palicourea sessilis by LC-HRMS/MS using molecular networking and an in silico MS/MS fragmentation approach suggested the presence of several new monoterpene indole alkaloids. These compounds were isolated by semipreparative HPLC, and their structures confirmed by means of HRMS, NMR, and ECD measurements as 4-N-methyllyaloside (3), 4-N-methyl-3,4-dehydrostrictosidine (4), 4ß-hydroxyisodolichantoside (6), and 4α-hydroxyisodolichantoside (7), as well as the known alkaloids alline (1), N-methyltryptamine (2), isodolichantoside (5), and 5-oxodolichantoside (8). In addition, the acetylcholinesterase inhibitory activity of the compounds was evaluated up to 50 µM.

Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd.

Characterization of dimethylsulfoxide/glycerol mixtures: a binary solvent system for the study of "friction-dependent" chemical reactivity.

The properties of binary mixtures of dimethylsulfoxide and glycerol, measured using several techniques, are reported. Special attention is given to those properties contributing or affecting chemical reactions. In this respect the investigated mixture behaves as a relatively simple solvent and it is especially well suited for studies on the influence of viscosity on chemical reactivity. This is due to the relative invariance of the dielectric properties of the mixture. However, special caution must be taken with specific solvation, as the hydrogen-bonding properties of the solvent change with the molar fraction of glycerol.

Reconstruction of full high-resolution HSQC using signal split in aliased spectra.

Resolution enhancement is a long-sought goal in NMR spectroscopy. In conventional multidimensional NMR experiments, such as the (1) H-(13) C HSQC, the resolution in the indirect dimensions is typically 100 times lower as in 1D spectra because it is limited by the experimental time. Reducing the spectral window can significantly increase the resolution but at the cost of ambiguities in frequencies as a result of spectral aliasing. Fortunately, this information is not completely lost and can be retrieved using methods in which chemical shifts are encoded in the aliased spectra and decoded after processing to reconstruct high-resolution (1) H-(13) C HSQC spectrum with full spectral width and a resolution similar to that of 1D spectra. We applied a new reconstruction method, RHUMBA (reconstruction of high-resolution using multiplet built on aliased spectra), to spectra obtained from the differential evolution for non-ambiguous aliasing-HSQC and the new AMNA (additional modulation for non-ambiguous aliasing)-HSQC experiments. The reconstructed spectra significantly facilitate both manual and automated spectral analyses and structure elucidation based on heteronuclear 2D experiments. The resolution is enhanced by two orders of magnitudes without the usual complications due to spectral aliasing.

Exploiting the phase of NMR signals to carry useful information. Application to the measurement of chemical shifts in aliased 2D spectra.

Taking advantage of the phase of nuclear magnetic resonance (NMR) signals to encode NMR information is not easy because of their low precision and their sensitivity to nearby signals. We nevertheless demonstrated that the phase in indirect dimension of (1) H-(13) C heteronuclear single quantum coherence (HSQC) signals could provide carbon chemical shifts at low, but sufficient precision to resolve the ambiguities of the chemical shifts in aliased spectra. This approach, we called phase-encoding of the aliasing order Na (PHANA), only requires inserting a constant delay during the t1 evolution time to obtain spectra where signals with mixed phases can be decoded at the processing to reconstruct full spectra with a 15-fold increase in resolution.

1D†NMR Homodecoupled (1)H†Spectra with Scalar Coupling Constants from 2D†NemoZS-DIAG Experiments.

A two-dimensional liquid-state NMR experiment cleanly separating chemical shifts and scalar couplings information is introduced. This DIAG experiment takes advantage of a drastic reduction of the spectral window in the indirect dimension to be quickly recorded and of a new non-equidistant modulation of the selective pulse to improve the sensitivity of the broadband homodecoupling Zangger-Sterk sequence element by one order of magnitude. A simple automatic analysis results in 1D spectra displaying singlets and lists of the scalar couplings for first-order multiplets. This facilitates the analysis of 1D spectra by resolving multiplets based on their differences in chemical shifts and coupling structures.

A toolbox of HSQC experiments for small molecules at high 13C-enrichment. Artifact-free, fully 13C-homodecoupled and JCC-encoding pulse sequences.

A set of modified HSQC experiments designed for the study of (13)C-enriched small molecules is introduced. It includes an improved sensitivity-enhanced HSQC experiment eliminating signal artifacts because of high-order (13)C magnetization terms generated at high (13)C enrichment. A broadband homonuclear (13)C decoupling sequence based on Zangger and Sterk's method simplifies the complex (13)C-(13)C multiplet structure in the F1 dimension of HSQC. When recording spectra at high resolution, the combination with a multiple-site modulation of the selective pulse outperforms the constant-time HSQC in terms of sensitivity and reliability. Finally, two pulse sequences reintroducing selected J(CC) couplings with selective pulses facilitate their assignments and measurements either in the splitting of the resulting doublets or by modulation of the signal amplitude. A sample of uniformly 92% (13)C-enriched cholesterol is used as an example.

NASCA-HMBC, a new NMR methodology for the resolution of severely overlapping signals: application to the study of agathisflavone.

INTRODUCTION: Standard NMR 2D heteronuclear HMBC spectra have a low resolution in the indirect carbon dimension, making it very difficult to assign signals to individual carbons when their chemical shifts are < 0.3 ppm apart. OBJECTIVE: To establish spectral aliasing for HMBC experiments to improve the resolution in the carbon dimension without increasing the total experimental time and avoiding ambiguities in the observed chemical shifts. METHODOLOGY: The NASCA-HMBC (Non-ambiguous Assignment by Superposition of Coupled Aliased HMBC) methodology combines a pair of HMBC spectra recorded with slightly different carbon windows to provide typically one order of magnitude increase in the resolution and unambiguous chemical shifts. RESULTS: The application of this methodology to a biflavonoid found in Ouratea gilgiana resulted in spectra with a sufficiently high resolution to make the assignment straightforward and report, for the first time, the full assignment of agathisflavone. CONCLUSION: The methodology should find many applications in dimeric and oligomeric compounds such as peptides, carbohydrates, polyketides and other cases where signal clustering is expected.

Combination of homonuclear decoupling and spectral aliasing to increase the resolution in the (1)H dimension of 2D NMR experiments.

Broadband homonuclear decoupling (BBHD) in the indirect (1)H dimension of 2D experiments can be obtained using a modified Zangger and Sterk combination of a selective pulse with a pulsed-field gradient. The coupling structure of signals is reduced to a singlet along the F1 dimension at the cost of a sensitivity loss. With the classical sampling in F1, the full resolving power of BBHD-experiments requires very long acquisition times. Spectral aliasing can reduce the number of time increments accessing the top resolution of homodecoupled spectra of small molecules by two orders of magnitude. The TOCSY spectra of androst-4-ene-3,17-dione are shown as an example.

An efficient method for the production of isotopically enriched cholesterol for NMR.

(13)C-Cholesterol was produced with high efficiency by a genetically engineered yeast strain. The method produces ∼ 1 mg of cholesterol per gram of glucose using 100 ml of culture medium. Uniform 94% enrichment where the most abundant product is the fully enriched isotopomer (u-(13)C(27)) is obtained using (u-(13)C(6), 99%) glucose medium. High enrichment is very important for relaxation experiments, but for NMR applications where carbon-carbon couplings are measured, this is problematic. A good compromise between sensitivity and cost consists in diluting (u-(13)C(6), 25%) with natural-abundance glucose. With a 2:3 ratio, the maximal amount of singlets can be obtained in 1 dimensional (D) carbon and 2D heteronuclear single-quantum correlation (HSQC) spectra with 6× intensity increase relative to natural-abundance samples. The use of (1-(13)C(1)-glucose, 99%) or (2-(13)C(1)-glucose, 99%) as isotope sources allows the labeling of the cholesterol in multiple mostly nonvicinal positions and reach 45× intensity increase. As an alternative, the dilution of (u-(13)C(6), 99%) glucose can be used to simultaneously enrich eleven pairs of (13)C up to ∼ 1,000× natural-abundance probability, which should be very beneficial to double-quantum NMR experiments including the INADEQUATE and related pulse sequences. The flexibility of the method and the potential to adapt the culture protocol to specific needs should find many applications in chemistry and biology and in different fields of NMR and MS.

Schizanthines N, O, and P, tropane alkaloids from the aerial parts of Schizanthus tricolor.

Three tropane alkaloids, named schizanthines N, O, and P (1-3), have been isolated from the crude alkaloid extract of the endemic Chilean plant Schizanthus tricolor. On the basis of extensive NMR studies and MS fragmentation analysis, their structures were determined to be 3α-(E)-4-hydroxysenecioyloxy-6ß-angeloyloxytropane (1), 3α-(E)-4-hydroxysenecioyloxy-6ß-senecioyloxytropane (2), and 3α-mesaconyloxy-6ß-senecioyloxytropane (3). Compounds 1 and 2 are the first isomeric alkaloids in the tropane series possessing a hydroxysenecioyl substituent as an esterifying moiety.