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.

Application of multiplet structure deconvolution to extract scalar coupling constants from 1D nuclear magnetic resonance spectra.

Multiplet structure deconvolution provides a robust method to determine the values of the coupling constants in first-order 1D nuclear magnetic resonance (NMR) spectra. Functions simplifying the coupling structure for partners with spin larger than 1/2 and for doublets with unequal amplitudes were introduced. The chemical shifts of the coupling partners causing mild second-order effects can, in favourable cases, be calculated from the slopes measured in doublet structures. Illustrations demonstrate that deconvolution can straightforwardly analyse multiplet posing difficulties to humans and, in some cases, extract coupling constants from unresolved multiplets.

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.

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: .

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.

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.

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.

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.

Elimination of signals tilting caused by B0 field inhomogeneity using 2D-lineshape reference deconvolution.

An efficient approach for reference deconvolution of two-dimensional spectra aiming at the correction of static field inhomogeneity was established. In comparison to known techniques, a great improvement was achieved using the cross-section along the diagonal of the reference peak instead of its full 2D line shape. The method is termed pseudo-2D diagonal deconvolution. The approach developed allows suppressing the two-dimensional peaks tilting caused by the magnetic field inhomogeneity, while keeping the signal-to-noise ratio constant. Long-known method of 2D reference deconvolution (true-2D reference deconvolution) was also applied for comparison. The neutral and resolution-enhancing pseudo-2D deconvolutions were successfully applied for the resolution of complex overlapping multiplets and for measuring small scalar coupling constants. The new algorithm for the elimination of shape distortion of two-dimensional peaks showed to be promising in the perspective of an automated analysis of 2D correlation NMR spectra.

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.

Discrimination of hexabromocyclododecane from new polymeric brominated flame retardant in polystyrene foam by nuclear magnetic resonance.

Hexabromocyclododecane (HBCDD) is a brominated flame retardant (BFR) and major additive to polystyrene foam thermal insulation that has recently been listed as a persistent organic pollutant by the Stockholm Convention. During a 2013/2014 field analytical survey, we measured HBCDD content ranging from 0.2 to 2.4% by weight in 98 polystyrene samples. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analyses indicated that expandable (EPS) and extruded (XPS) polystyrene foams significantly differed in the α/γ HBCDD isomer ratio, with a majority of α and γ isomers in XPS and EPS, respectively. Interestingly, this technique indicated that some recent materials did not contain HBCDD, but demonstrated bromine content when analysed with X-ray fluorescence (XRF). Further investigation by Nuclear Magnetic Resonance (NMR) was able to discriminate between the BFRs present. In addition to confirming the absence or presence of HBCDD in polystyrene samples, high-field NMR spectroscopy provided evidence of the use of brominated butadiene styrene (BBS) as copolymer in the production of polystyrene. Use of this alternative flame retardant is expected to cause fewer health and environmental concerns. Our results highlight a trend towards the use of copolymerized BFRs as an alternative to HBCDD in polystyrene foam boards. In addition to providing a rapid NMR method to identify polymeric BFR, our analytical approach is a simple method to discriminate between flame-retardants in polystyrene foam insulating materials.

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.

New prostaglandin analog formulation for glaucoma treatment containing cyclodextrins for improved stability, solubility and ocular tolerance.

Latanoprost is a practically insoluble prostaglandin F2α analog considered a first-line agent for glaucoma treatment. From a pharmaceutical point of view, latanoprost is challenging to be formulated as an eye drop due to its poor water solubility and the presence of an ester bond that needs to be cleaved in vivo but maintained unchanged during storage. Cyclodextrins (CDs) are known to form complexes with hydrophobic drugs, influencing their stability, availability, solubility, and tolerance in a non-predictable manner. A variety of CDs including native α, ß, and γCDs as well as substituted hydroxypropylßCD, hydroxypropylγCD, dimethylßCD, sulphatedßCD, and propylaminoßCD were screened and the most appropriate CD for the formulation of latanoprost for an ocular topical application was selected. Among the tested CDs, propylaminoßCD had the best trade-off between latanoprost stability and availability, which was confirmed by its complex constant value of 3129M(-1). Phase-solubility and NMR investigations demonstrated that the propylaminoßCD effectively formed a complex involving the ester group of latanoprost providing protection to its ester bond, while ensuring proper latanoprost solubilization. Furthermore, in vivo experiments demonstrated that the latanoprost-propylaminoßCD formulation led to lower ocular irritation than the commercial latanoprost formulation used as a reference. The latanoprost-propylaminoßCD formulation was demonstrated to successfully address the main stability, solubility, and tolerance limitations of topical ocular latanoprost therapy for glaucoma.

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.