NOAH: NMR Supersequences for Small Molecule Analysis and Structure Elucidation

SimpleNMR: An interactive graph network approach to aid constitutional isomer verification using standard 1D and 2D NMR experiments

Despite progress in computer automated solutions, constitutional isomer verification by NMR using one- and two-dimensional data sets is still, in the main, a manual, user-intensive activity that is challenging for a number of reasons. These include the problem of simultaneously keeping track of the information from a number of separate NMR experiments and the difficulty of another researcher subsequently verifying the assignments made without having to independently repeat the whole analysis. This paper describes a graphical interactive approach that overcomes some of these problems. By using concepts used to visualise graph networks, we have been able to represent the NMR data in a manner that highlights directly the link between the different NMR experiments and the molecule of interest. Furthermore, by making the graph networks interactive, a user can easily validate and correct the assignment and understand the decisions made in arriving at the solution. We have developed a usable proof-of-concept computer program, 'simpleNMR', written in Python to illustrate the ideas and approach.

Overcoming NMR line broadening of nitrogen containing compounds: A simple solution

This study presents a straightforward solution to the challenge of elucidating the structures of nitrogen containing compounds undergoing isomerization. When spectral line broadening occurs related to isomerization, be it prototropic tautomerism or bond rotations, this poses a significant obstacle to structural elucidation. By adding acids, we demonstrate a simple approach to overcome this issue and effectively sharpen NMR signals for acid stable prototropic tautomers as well as the conformational isomers containing a morpholine or piperazine ring.

Exploring the Significance, Extraction, and Characterization of Plant-Derived Secondary Metabolites in Complex Mixtures

Secondary metabolites are essential components for the survival of plants. Secondary metabolites in complex mixtures from plants have been adopted and documented by different traditional medicinal systems worldwide for the treatment of various human diseases. The extraction strategies are the key components for therapeutic development from natural sources. Polarity-dependent solvent-selective extraction, acidic and basic solution-based extraction, and microwave- and ultrasound-assisted extraction are some of the most important strategies for the extraction of natural products from plants. The method needs to be optimized to isolate a specific class of compounds. Therefore, to establish the mechanism of action, the characterization of the secondary metabolites, in a mixture or in their pure forms, is equally important. LC-MS, GC-MS, and extensive NMR spectroscopic strategies are established techniques for the profiling of metabolites in crude extracts. Various protocols for the extraction and characterization of a wide range of classes of compounds have been developed by various research groups and are described in this review. Additionally, the possible means of characterizing the compounds in the mixture and their uniqueness are also discussed. Hyphenated techniques are crucial for profiling because of their ability to analyze a vast range of compounds. In contrast, inherent chemical shifts make NMR an indispensable tool for structure elucidation in complex mixtures.

Single-Scan Ultraselective NMR Experiments with Preserved Sensitivity

Selective NMR experiments provide rapid access to important structural information, and are essential to tackle the analysis of large molecules and complex mixtures. Single-scan ultraselective experiments are particularly useful, as they can rapidly select signals that overlap with other signals. Here, we describe a novel type of single-scan ultraselective NMR experiments that is robust against the effects of translational molecular diffusion, and thus make it possible to improve significantly the sensitivity of the experiment. This will largely broaden the applicability of this powerful class of experiments.

NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER

Carbohydrate structures containing alkyl groups as aglycones are useful for investigating enzyme activity and glycan-protein interactions. Moreover, linker-containing oligosaccharides with a spacer group are commonly used to print glycan microarrays or to prepare protein-conjugates as vaccine candidates. The structural accuracy of these synthesized glycans are essential for interpretation of results from biological experiments in which the compounds have been used and NMR spectroscopy can unravel and confirm their structures. An approach for efficient 1H and 13C NMR chemical shift assignments employed a parallel NOAH-10 measurement followed by NMR spin-simulation to refine the 1H NMR chemical shifts, as exemplified for a disaccharide with an azidoethyl group as an aglycone, the NMR chemical shifts of which have been used to enhance the quality of CASPER (http://www.casper.organ.su.se/casper/). The CASPER program has been further developed to aid characterization of linker-containing oligo- and polysaccharides, either by chemical shift prediction for comparison to experimental NMR data or as structural investigation of synthesized glycans based on acquired unassigned NMR data. The ability of CASPER to elucidate structures of linker-containing oligosaccharides is demonstrated and comparisons to assigned or unassigned NMR data show the utility of CASPER in supporting a proposed oligosaccharide structure. Prediction of NMR chemical shifts of an oligosaccharide, corresponding to the repeating unit of an O-antigen polysaccharide, having a linker as an aglycone and a non-natural substituent derivative thereof are presented to exemplify the diversity of structures handled. Furthermore, NMR chemical shift predictions of synthesized polysaccharides, corresponding to bacterial polysaccharides, containing a linker are described showing that in addition to oligosaccharide structures also polysaccharide structures having an aglycone spacer group can be analyzed by CASPER.

J-filter: An experiment to simplify and isolate specific signals in 1 H NMR spectra of complex mixtures based on scalar coupling constants

One-dimensional selective NMR experiments relying on a J-filter element are proposed to isolate specific signals in crowded 1 H spectral regions. The J-filter allows the edition or filtering of signals in a region of interest of the spectrum by exploiting the specific values of their 1 H-1 H coupling constants and certain parameters of protons coupled to them that appear in less congested parts of the spectrum (chemical shifts and coupling constants). The new experiments permitted the isolation of specific peaks of phytosterol components in a sample obtained from a liquid nutraceutical recommended for lowering blood cholesterol levels in regions with complete overlap in the 1 H spectrum.

Paramagnetic Relaxation Agents for Enhancing Temporal Resolution and Sensitivity in Multinuclear FlowNMR Spectroscopy

Sensitivity in FlowNMR spectroscopy for reaction monitoring often suffers from low levels of pre-magnetisation due to limited residence times of the sample in the magnetic field. While this in-flow effect is tolerable for high sensitivity nuclei such as 1 H and 19 F, it significantly reduces the signal-to-noise ratio in 31 P and 13 C spectra, making FlowNMR impractical for low sensititvity nuclei at low concentrations. Paramagnetic relaxation agents (PRAs), which enhance polarisation and spin-lattice relaxation, could eliminate the adverse in-flow effect and improve the signal-to-noise ratio. Herein, [Co(acac)3 ], [Mn(acac)3 ], [Fe(acac)3 ], [Cr(acac)3 ], [Ni(acac)2 ]3, [Gd(tmhd)3 ] and [Cr(tmhd)3 ] are investigated for their effectiveness in improving signal intensity per unit time in FlowNMR applications under the additional constraint of chemical inertness towards catalytically active transition metal complexes. High-spin Cr(III) acetylacetonates emerged as the most effective compounds, successfully reducing 31 P T1 values four- to five-fold at PRA concentrations as low as 10 mM without causing adverse line broadening. Whereas [Cr(acac)3 ] showed signs of chemical reactivity with a mixture of triphenylphosphine, triphenylphosphine oxide and triphenylphosphate over the course of several hours at 80° C, the bulkier [Cr(tmhd)3 ] was stable and equally effective as a PRA under these conditions. Compatibility with a range of representative transition metal complexes often used in homogeneous catalysis has been investigated, and application of [Cr(tmhd)3 ] in significantly improving 1 H and 31 P{1 H} FlowNMR data quality in a Rh-catalysed hydroformylation reaction has been demonstrated. With the PRA added, 13 C relaxation times were reduced more than six-fold, allowing quantitative reaction monitoring of substrate consumption and product formation by 13 C{1 H} FlowNMR spectroscopy at natural abundance.

NMR as a tool for compound identification in mixtures

INTRODUCTION

Natural products and metabolomics are intrinsically linked through efforts to analyze complex mixtures for compound annotation. Although most studies that aim for compound identification in mixtures use MS as the main analysis technique, NMR has complementary advances that are worth exploring for enhanced structural confidence.

OBJECTIVE

This review aimed to showcase a portfolio of the main tools available for compound identification using NMR.

MATERIALS AND METHODS

COLMAR, SMART-NMR, MADByTE, and NMRfilter are presented using examples collected from real samples from the perspective of a natural product chemist. Data are also made available through Zenodo so that readers can test each case presented here.

CONCLUSION

The acquisition of ¹ H NMR, HSQC, TOCSY, HSQC-TOCSY, and HMBC data for all samples and fractions from a natural products study is strongly suggested. The same is valid for MS analysis to create a bridged analysis between both techniques in a complementary manner. The use of NOAH supersequences has also been suggested and demonstrated to save NMR time.

Simultaneous recoupling of chemical shift tensors of two nuclei by R-symmetry sequences

Chemical shift tensors (CSTs) are sensitive probes of structure and dynamics. R-symmetry pulse sequences (RNCSA) can efficiently recouple CSTs of varying magnitudes in magic angle spinning (MAS) NMR experiments, for a broad range of conditions and MAS frequencies. Herein, we introduce dual-channel R-symmetry pulse sequences for simultaneously recording CSTs of two different nuclei in a single experiment (DORNE-CSA). We demonstrate the performance of DORNE-CSA sequences for simultaneous measurement of 13C and 15N CSTs, on a U-13C,15N-labeled microcrystalline l-histidine. We show that the DORNE-CSA method is robust, provides accurate CST parameters, and takes only half of the measurement time compared to a pair of RNCSA experiments otherwise required for recording the CSTs of individual nuclei. DORNE-CSA approach is broadly applicable to a wide range of biological and inorganic systems.

Synthesis of Sterically Encumbered Alkaline-Earth Metal Amides Applying the In Situ Grignard Reagent Formation

Magnesium and calcium are too inert to deprotonate amines directly. For the synthesis of bulky amides alternative strategies are required and in the past, N-bound trialkylsilyl groups have been used to ease metalation reactions. The in situ Grignard reagent formation in stirred suspensions of magnesium or calcium with hydryl halide and imine in THF allows the synthesis of a plethora of amides with bulky silyl-free substituents. Ball milling protocols partially favor competitive side reactions such as aza-pinacol coupling reactions. Calcium is the advantageous choice for the in situ Grignard reagent formation and subsequent addition onto the imines yielding bulky calcium bis(amides) whereas the stronger reducing heavier alkaline-earth metals strontium and barium are less selective and hence, the aza-pinacol coupling reaction becomes competitive. Exemplary, the solid-state molecular structures of [(Et₂ O)Mg(N(Ph)(CHPh₂ )₂ ] and [(Et₂ O)₂ Ca(N(Ph)(CHPh₂ )₂ ] have been determined.

Primary Structure of Glycans by NMR Spectroscopy

Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a ¹H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.

Practical Aspects of NMR-Based Metabolomics

While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for >40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5-10 years.

NMR methods for the analysis of mixtures

NMR spectroscopy is a powerful approach for the analysis of mixtures. Its usefulness arises in large part from the vast landscape of methods, and corresponding pulse sequences, that have been and are being designed to tackle the specific properties of mixtures of small molecules. This feature article describes a selection of methods that aim to address the complexity, the low concentrations, and the changing nature that mixtures can display. These notably include pure-shift and diffusion NMR methods, hyperpolarisation methods, and fast 2D NMR methods such as ultrafast 2D NMR and non-uniform sampling. Examples or applications are also described, in fields such as reaction monitoring and metabolomics, to illustrate the relevance and limitations of different methods.

Leveraging the HMBC to Facilitate Metabolite Identification

The accuracy and ease of metabolite assignments from a complex mixture are expected to be facilitated by employing a multispectral approach. The two-dimensional (2D) 1H-13C heteronuclear single quantum coherence (HSQC) and 2D 1H-1H-total correlation spectroscopy (TOCSY) are the experiments commonly used for metabolite assignments. The 2D 1H-13C HSQC-TOCSY and 2D 1H-13C heteronuclear multiple-bond correlation (HMBC) are routinely used by natural products chemists but have seen minimal usage in metabolomics despite the unique information, the nearly complete 1H-1H and 1H-13C and spin systems provided by these experiments that may improve the accuracy and reliability of metabolite assignments. The use of a 13C-labeled feedstock such as glucose is a routine practice in metabolomics to improve sensitivity and to emphasize the detection of specific metabolites but causes severe artifacts and an increase in spectral complexity in the HMBC experiment. To address this issue, the standard HMBC pulse sequence was modified to include carbon decoupling. Nonuniform sampling was also employed for rapid data collection. A dataset of reference 2D 1H-13C HMBC spectra was collected for 94 common metabolites. 13C-13C spin connectivity was then obtained by generating a covariance pseudo-spectrum from the carbon-decoupled HMBC and the 1H-13C HSQC-TOCSY spectra. The resulting 13C-13C pseudo-spectrum provides a connectivity map of the entire carbon backbone that uniquely describes each metabolite and would enable automated metabolite identification.

NMR-Based Chromatography Readouts: Indispensable Tools to “Translate” Analytical Features into Molecular Structures

Gaining structural information is a must to allow the unequivocal structural characterization of analytes from natural sources. In liquid state, NMR spectroscopy is almost the only possible alternative to HPLC-MS and hyphenating the effluent of an analyte separation device to the probe head of an NMR spectrometer has therefore been pursued for more than three decades. The purpose of this review article was to demonstrate that, while it is possible to use mass spectrometry and similar methods to differentiate, group, and often assign the differentiating variables to entities that can be recognized as single molecules, the structural characterization of these putative biomarkers usually requires the use of NMR spectroscopy.

In Situ Grignard Metalation Method for the Synthesis of Hauser Bases

The in situ Grignard Metalation Method (iGMM) is a straightforward one‐pot procedure to quickly produce multigram amounts of Hauser bases R₂N‐MgBr which are valuable and vastly used metalation reagents and novel electrolytes for magnesium batteries. During addition of bromoethane to a suspension of Mg metal and secondary amine at room temperature in an ethereal solvent, a smooth reaction yields R₂N‐MgBr under evolution of ethane within a few hours. A Schlenk equilibrium is operative, interconverting the Hauser bases into their solvated homoleptic congeners Mg(NR₂)₂ and MgBr₂ depending on the solvent. Scope and preconditions are studied, and side reactions limiting the yield have been investigated. DOSY NMR experiments and X‐ray crystal structures of characteristic examples clarify aggregation in solution and the solid state.

NOAH-(15N/13C)-CEST NMR supersequence for dynamics studies of biomolecules

An NMR supersequence is introduced for the rapid acquisition of ¹⁵N-CEST and methyl-¹³C-CEST experiments in the same pulse sequence for applications to proteins. The high sensitivity and accuracy allows the simultaneous quantitative characterization of backbone and side-chain dynamics on the millisecond timescale ideal for routine screening for alternative protein states.

PHRONESIS: a one-shot approach for sequential assignment of protein resonances by ultrafast MAS solid-state NMR spectroscopy

Solid‐state NMR (ssNMR) spectroscopy has emerged as the method of choice to analyze the structural dynamics of fibrillar, membrane‐bound, and crystalline proteins that are recalcitrant to other structural techniques. Recently, ¹H detection under fast magic angle spinning and multiple acquisition ssNMR techniques have propelled the structural analysis of complex biomacromolecules. However, data acquisition and resonance‐specific assignments remain a bottleneck for this technique. Here, we present a comprehensive multi‐acquisition experiment (PHRONESIS) that simultaneously generates up to ten 3D ¹H‐detected ssNMR spectra. PHRONESIS utilizes broadband transfer and selective pulses to drive multiple independent polarization pathways. High selectivity excitation and de‐excitation of specific resonances were achieved by high‐fidelity selective pulses that were designed using a combination of an evolutionary algorithm and artificial intelligence. We demonstrated the power of this approach with microcrystalline U‐¹³C,¹⁵N GB1 protein, reaching 100 % of the resonance assignments using one data set of ten 3D experiments. The strategy outlined in this work opens up new avenues for implementing novel ¹H‐detected multi‐acquisition ssNMR experiments to speed up and expand the application to larger biomolecular systems.

Studying Metabolism by NMR-Based Metabolomics

During the past few decades, the direct analysis of metabolic intermediates in biological samples has greatly improved the understanding of metabolic processes. The most used technologies for these advances have been mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. NMR is traditionally used to elucidate molecular structures and has now been extended to the analysis of complex mixtures, as biological samples: NMR-based metabolomics. There are however other areas of small molecule biochemistry for which NMR is equally powerful. These include the quantification of metabolites (qNMR); the use of stable isotope tracers to determine the metabolic fate of drugs or nutrients, unravelling of new metabolic pathways, and flux through pathways; and metabolite-protein interactions for understanding metabolic regulation and pharmacological effects. Computational tools and resources for automating analysis of spectra and extracting meaningful biochemical information has developed in tandem and contributes to a more detailed understanding of systems biochemistry. In this review, we highlight the contribution of NMR in small molecule biochemistry, specifically in metabolic studies by reviewing the state-of-the-art methodologies of NMR spectroscopy and future directions.

Mechanistic analysis by NMR spectroscopy: A users guide

A 'principles and practice' tutorial-style review of the application of solution-phase NMR in the analysis of the mechanisms of homogeneous organic and organometallic reactions and processes. This review of 345 references summarises why solution-phase NMR spectroscopy is uniquely effective in such studies, allowing non-destructive, quantitative analysis of a wide range of nuclei common to organic and organometallic reactions, providing exquisite structural detail, and using instrumentation that is routinely available in most chemistry research facilities. The review is in two parts. The first comprises an introduction to general techniques and equipment, and guidelines for their selection and application. Topics include practical aspects of the reaction itself, reaction monitoring techniques, NMR data acquisition and processing, analysis of temporal concentration data, NMR titrations, DOSY, and the use of isotopes. The second part comprises a series of 15 Case Studies, each selected to illustrate specific techniques and approaches discussed in the first part, including in situ NMR (^1/2H, ^10/11B, ¹³C, ¹⁵N, ¹⁹F, ²⁹Si, ³¹P), kinetic and equilibrium isotope effects, isotope entrainment, isotope shifts, isotopes at natural abundance, scalar coupling, kinetic analysis (VTNA, RPKA, simulation, steady-state), stopped-flow NMR, flow NMR, rapid injection NMR, pure shift NMR, dynamic nuclear polarisation, ¹H/¹⁹F DOSY NMR, and in situ illumination NMR.

Synergy and sensitivity-balance in concatenating experiments in NO relaxation delay NMR (NORD)

The NMR experiment design strategy of NO Relaxation Delay (NORD), introduced mostly as an idealized theoretical approach, is extended and put to practical use by considering synergy and sensitivity-balance in concatenation of experiments. It is illustrated by a novel experiment, NORD {HMBC}-{HSQC}-{TOCSY}, where magnetization of non-¹³C attached protons effectively is channeled from the TOCSY spectrum toward primarily the least sensitive spectrum of HMBC. The experiment is expected to find its place as a full-package NMR method for metabolomics, carbohydrates, peptides and small-molecules in general.

Correction of field instabilities in biomolecular solid-state NMR by simultaneous acquisition of a frequency reference

With the advent of faster magic-angle spinning (MAS) and higher magnetic fields, the resolution of biomolecular solid-state nuclear magnetic resonance (NMR) spectra has been continuously increasing. As a direct consequence, the always narrower spectral lines, especially in proton-detected spectroscopy, are also becoming more sensitive to temporal instabilities of the magnetic field in the sample volume. Field drifts in the order of tenths of parts per million occur after probe insertion or temperature change, during cryogen refill, or are intrinsic to the superconducting high-field magnets, particularly in the months after charging. As an alternative to a field-frequency lock based on deuterium solvent resonance rarely available for solid-state NMR, we present a strategy to compensate non-linear field drifts using simultaneous acquisition of a frequency reference (SAFR). It is based on the acquisition of an auxiliary 1D spectrum in each scan of the experiment. Typically, a small-flip-angle pulse is added at the beginning of the pulse sequence. Based on the frequency of the maximum of the solvent signal, the field evolution in time is reconstructed and used to correct the raw data after acquisition, thereby acting in its principle as a digital lock system. The general applicability of our approach is demonstrated on 2D and 3D protein spectra during various situations with a non-linear field drift. SAFR with small-flip-angle pulses causes no significant loss in sensitivity or increase in experimental time in protein spectroscopy. The correction leads to the possibility of recording high-quality spectra in a typical biomolecular experiment even during non-linear field changes in the order of 0.1 ppm h- 1 without the need for hardware solutions, such as stabilizing the temperature of the magnet bore. The improvement of linewidths and peak shapes turns out to be especially important for 1 H-detected spectra under fast MAS, but the method is suitable for the detection of carbon or other nuclei as well.

Modular Pulse Program Generation for NMR Supersequences

NMR supersequences allow multiple 2D NMR data sets to be acquired in greatly reduced experiment durations through tailored detection of NMR responses within concatenated modules. In NOAH (NMR by Ordered Acquisition using ¹H detection) experiments, up to five modules can be combined (or even more when parallel modules are employed), which in theory leads to thousands of plausible supersequences. However, constructing a pulse program for a supersequence is highly time-consuming, requires specialized knowledge, and is error-prone due to its complexity; this has prevented the true potential of the NOAH concept from being fully realized. We introduce here an online tool named GENESIS (GENEration of Supersequences In Silico), available via https://nmr-genesis.co.uk, which systematically generates pulse programs for arbitrary NOAH supersequences compatible with Bruker spectrometers. The GENESIS website provides a unified “one-stop” interface where users may obtain customized supersequences for specific applications, together with all associated acquisition and processing scripts, as well as detailed instructions for running NOAH experiments. Furthermore, it enables the rapid dissemination of new developments in NOAH sequences, such as new modules or improvements to existing modules. Here, we present several such enhancements, including options for solvent suppression, new modules based on pure shift NMR, and improved artifact reduction in HMBC and HMQC modules.

Parallel NMR Supersequences: Ten Spectra in a Single Measurement

The principles employed in parallel NMR and MRI are applied to NMR supersequences yielding as many as ten 2D NMR spectra in one measurement. We present a number of examples where two NOAH (NMR by Ordered Acquisition using 1H-detection) supersequences are recorded in parallel, thus dramatically increasing the information content obtained in a single NMR experiment. The two parallel supersequences entangled by time-sharing schemes (IPAP-seHSQC, HSQC-COSY, and HSQC-TOCSY) incorporate also modified (sequential and/or interleaved) conventional pulse schemes (modules), including HMBC, TOCSY, COSY, CLIP-COSY, NOESY, and ROESY. Such parallel supersequences can be tailored for specific applications, for instance, the analysis and characterization of molecular structure of complex organic molecules from a single measurement. In particular, the CASPER software was used to establish the structure of a tetrasaccharide, β-LNnTOMe, with a high degree of confidence from a single measurement involving a parallel NOAH-5 supersequence.

Elusive Toxin in Cleistanthus collinus Causing Vasoconstriction and Myocardial Depression: Detailed NMR Analyses and Biological Studies of Cleistanthoside A

Cleistanthus collinus leaf extracts are consumed for suicidal purposes in southern India. The boiled decoction is known to be more toxic than the fresh leaf juice. Although several compounds have been isolated and their toxicity tested, controversy remains as to which compounds are responsible for the high level of toxicity of C. collinus. We report herein that cleistanthoside A is the major toxin in the boiled aqueous extract of fresh leaves and causes death in rats in small doses. The toxicity of the boiled extract prepared in the manner described can be attributed entirely to cleistanthoside A. Cleistanthin A could also be isolated from the boiled extract, albeit in trace amounts. As hypotension not responding to vasoconstrictors is the cause of death in patients who have consumed the boiled extract, effects of cleistanthoside A on the determinants of blood pressure, namely, force of cardiac contraction and vascular resistance, were tested in isolated organ experiments. Cleistanthoside A has a direct vasoconstrictor effect; however, it inhibits ventricular contractility. Therefore, the notion that the shock in C. collinus poisoning is of vascular origin must be considered carefully, and the possibility of cardiogenic shock must be studied. We present the crystal structure of cleistanthin A and show the potency of fast NMR methods (NOAH4-BSCN-NUS) in the full spectral assignment of cleistanthoside A as a real-world sample of a natural product. We also compare the results of the NOAH4-BSCN-NUS NMR experiments with conventional NMR methods.

Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules

The sensitivity-enhanced HSQC, as well as HSQC-TOCSY, experiments have been modified for incorporation into NOAH (NMR by Ordered Acquisition using ¹H detection) supersequences, adding diversity for ¹³C and ¹⁵N modules. Importantly, these heteronuclear modules have been specifically tailored to preserve the magnetisation required for subsequent acquisition of other heteronuclear or homonuclear modules in a supersequence. In addition, we present protocols for optimally combining HSQC and HSQC-TOCSY elements within the same supersequences, yielding high-quality 2D spectra suitable for structure characterisation but with greatly reduced experiment durations. We further demonstrate that these time savings can translate to increased detection sensitivity per unit time.

(DiMeIHeptCl)Pd: A Low-Load Catalyst for Solvent-Free (Melt) Amination

(DiMeIHept^Cl)Pd, a hyper-branched N-aryl Pd NHC catalyst, has been shown to be efficient at performing amine arylation reactions in solvent-free ("melt") conditions. The highly lipophilic environment of the alkyl chains flanking the Pd center serves as lubricant to allow the complex to navigate through the paste-like environment of these mixtures. The protocol can be used on a multi-gram scale to make a variety of aniline derivatives, including substrates containing alcohol moieties.

NORD: NO Relaxation Delay NMR Spectroscopy

The novel concept of NORD (NO relaxation delay) NMR spectroscopy is introduced. The idea is to design concatenated experiments in a way that the magnetization used in the first relaxes toward equilibrium during the second and vice versa, thus saving instrument time. Applications include complete well‐resolved ¹H‐¹H and ¹H‐¹³C one‐bond and long‐range correlation maps of an 80 mM solution of a trisaccharide recorded in less than two minutes and hydrocortisone with extensive spectral overlap.

Multiplexing experiments in NMR and multi-nuclear MRI

Multiplexing NMR experiments by direct detection of multiple free induction decays (FIDs) in a single experiment offers a dramatic increase in the spectral information content and often yields significant improvement in sensitivity per unit time. Experiments with multi-FID detection have been designed with both homonuclear and multinuclear acquisition, and the advent of multiple receivers on commercial spectrometers opens up new possibilities for recording spectra from different nuclear species in parallel. Here we provide an extensive overview of such techniques, designed for applications in liquid- and solid-state NMR as well as in hyperpolarized samples. A brief overview of multinuclear MRI is also provided, to stimulate cross fertilization of ideas between the two areas of research (NMR and MRI). It is shown how such techniques enable the design of experiments that allow structure elucidation of small molecules from a single measurement. Likewise, in biomolecular NMR experiments multi-FID detection allows complete resonance assignment in proteins. Probes with multiple RF microcoils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems, effectively reducing the cost of NMR analysis and increasing the information content at the same time. Solid-state NMR experiments have also benefited immensely from both parallel and sequential multi-FID detection in a variety of multi-dimensional pulse schemes. We are confident that multi-FID detection will become an essential component of future NMR methodologies, effectively increasing the sensitivity and information content of NMR measurements.

Investigation of protein-ligand complexes by ligand-based NMR methods

Molecular recognition is at the base of all biological events and its knowledge at atomic level is pivotal in the development of new drug design approaches. NMR spectroscopy is one of the most widely used technique to detect and characterize transient ligand-receptor interactions in solution. In particular, ligand-based NMR approaches, including NOE-based NMR techniques, diffusion experiments and relaxation methods, are excellent tools to investigate how ligands interact with their receptors. Here we describe the key structural information that can be achieved on binding processes thanks to the combined used of advanced NMR and computational methods. Saturation Transfer Difference NMR (STD-NMR), WaterLOGSY, diffusion- and relaxation-based experiments, together with tr-NOE techniques allow, indeed, to investigate the ligand behavior when bound to a receptor, determining, among others, the epitope map of the ligand and its bioactive conformation. The combination of these NMR techniques with computational methods, including docking, molecular dynamics and CORCEMA-ST analysis, permits to define and validate an accurate 3D model of protein-ligand complexes.

Expedited Nuclear Magnetic Resonance Assignment of Small- to Medium-Sized Molecules with Improved HSQC-CLIP-COSY Experiments

Resonance assignment is a pivotal step for any nuclear magnetic resonance (NMR) analysis, such as structure elucidation or the investigation of protein-ligand interactions. Both ¹H-¹³C heteronuclear single quantum correlation (HSQC) and ¹H-¹H correlation spectroscopy (COSY) two-dimensional (2D) experiments are invaluable for ¹H NMR assignment, by extending the high signal dispersion of ¹³C chemical shifts onto ¹H resonances and by providing a high amount of through-bond ¹H-¹H connectivity information, respectively. The recently introduced HSQC-CLIP(Clean In-Phase)-COSY method combines these two experiments, providing COSY correlations along the high-resolution ¹³C dimension with clean in-phase multiplets. However, two experiments need to be recorded to unambiguously identify COSY cross-peaks. Here, we propose novel variants of the HSQC-CLIP-COSY pulse sequence that edit cross-peak signs so that direct HSQC responses can be distinguished from COSY relay peaks, and/or the multiplicities of the ¹³C nuclei are reflected, allowing the assignment of all the peaks in a single experiment. The advanced HSQC-CLIP-COSY variants have the potential to accelerate and simplify the NMR structure-elucidation process of both synthetic and natural products and to become valuable tools for high-throughput computer-assisted structure determination.

Sensitivity enhancement by sequential data acquisition for 13C-direct detection NMR

¹³C-direct detection NMR has several advantages compared to proton detection, including a tendency to relax slower and wider chemical shift range. However, the sensitivity of ¹³C-direct detection is much lower than that of proton detection because of its lower gyromagnetic ratio. In addition, a virtual decoupling procedure is often performed to remove peak splitting in the ¹³C-direct detection axis, which further reduces the sensitivity to 1/√2. In this study, to enhance the sensitivity of ¹³C-direct detection experiments, we developed a HCACO-type new pulse sequence in which anti-phase (AP) and in-phase (IP) signals are acquired sequentially in a single scan. The developed experiment was tested on an amino acid (valine) and two proteins (streptococcal protein G B1 domain (GB1) and α-synuclein). The AP and IP spectra were successfully obtained in all cases. Using these spectra, IPAP virtual decoupling was performed, and peak splitting was successfully removed. The sensitivity of the experiment was increased by 1.43, 1.26 and 1.26 times for valine, GB1 and α-synuclein, respectively, compared to the conventional HCACO experiment. In addition, we developed another HCACO-type pulse sequence, where AP and IP signals are simultaneously acquired in a single FID. The sensitivity of the experiment was increased by 1.40 and 1.35 times for valine and GB1, respectively. These methods are potentially applicable to other ¹³C-direct detection experiments that measure one-bond correlations and will further extend the utility of the ¹³C-direct detection method, especially for structural analyses of intrinsically disordered proteins.

Double and adiabatic BANGO for concatenating two NMR experiments relying on the same pool of magnetization

It is shown how the same pool of magnetization can be tapped twice in two different concatenations of three experiments into a single pulse sequence with only one relaxation delay. This is accomplished by using the BANGO pulse sequence element twice for independent rotations of ¹H magnetization attached or not attached to ¹³C and it includes a refinement of BANGO with an adiabatic ¹³C inversion pulse resulting in improved tolerance to a spread in ¹J_CH coupling constants that translates directly into improved sensitivity of the modular experiment relying on ¹H magnetization attached to ¹³C. The two new pulse sequences are SEA XLOC-HMBC-H2OBC/2BOB and SEA XLOC(ZQ)-SEA XLOC(2Q)-H2OBC/2BOB which both represent a rapid route to complete heteronuclear one-bond and long-range J_CH correlation maps for small molecules, as is demonstrated on ibuprofen and prednisolone.

Fast time-resolved NMR with non-uniform sampling

NMR spectroscopy is a versatile tool for studying time-dependent processes: chemical reactions, phase transitions or macromolecular structure changes. However, time-resolved NMR is usually based on the simplest among available techniques - one-dimensional spectra serving as "snapshots" of the studied process. One of the reasons is that multidimensional experiments are very time-expensive due to costly sampling of evolution time space. In this review we summarize efforts to alleviate the problem of limited applicability of multidimensional NMR in time-resolved studies. We focus on techniques based on sparse or non-uniform sampling (NUS), which lead to experimental time reduction by omitting a significant part of the data during measurement and reconstructing it mathematically, adopting certain assumptions about the spectrum. NUS spectra are faster to acquire than conventional ones and thus better suited to the role of "snapshots", but still suffer from non-stationarity of the signal i.e. amplitude and frequency variations within a dataset. We discuss in detail how these instabilities affect the spectra, and what are the optimal ways of sampling the non-stationary FID signal. Finally, we discuss related areas of NMR where serial experiments are exploited and how they can benefit from the same NUS-based approaches.

Searching for Small Molecules with an Atomic Sort

The discovery of biologically active small molecules requires sifting through large amounts of data to identify unique or unusual arrangements of atoms. Here, we develop, test and evaluate an atom-based sort to identify novel features of secondary metabolites and demonstrate its use to evaluate novelty in marine microbial and sponge extracts. This study outlines an important ongoing advance towards the translation of autonomous systems to identify, and ultimately elucidate, atomic novelty within a complex mixture of small molecules.

Proton-detected polarization optimized experiments (POE) using ultrafast magic angle spinning solid-state NMR: Multi-acquisition of membrane protein spectra

Proton-detected solid-state NMR (ssNMR) spectroscopy has dramatically improved the sensitivity and resolution of fast magic angle spinning (MAS) methods. While relatively straightforward for fibers and crystalline samples, the routine application of these techniques to membrane protein samples is still challenging. This is due to the low sensitivity of these samples, which require high lipid:protein ratios to maintain the structural and functional integrity of membrane proteins. We previously introduced a family of novel polarization optimized experiments (POE) that enable to make the best of nuclear polarization and obtain multiple-acquisitions from a single pulse sequence and one receiver. Here, we present the ¹H-detected versions of POE using ultrafast MAS ssNMR. Specifically, we implemented proton detection into our three main POE strategies, H-DUMAS, H-MEIOSIS, and H-MAeSTOSO, achieving the acquisition of up to ten different experiments using a single pulse sequence. We tested these experiments on a model compound N-Acetyl-Val-Leu dipeptide and applied to a six transmembrane acetate transporter, SatP, reconstituted in lipid membranes. These new methods will speed up the spectroscopy of challenging biomacromolecules such as membrane proteins.

All-in-one NMR spectroscopy of small organic molecules: complete chemical shift assignment from a single NMR experiment

A new class of NOAH NMR experiments (NOAH-AST and NOAH-AST_PS), with the abbreviations, A: 1,1-ADEQUATE, S: sensitivity improved version of multiplicity-edited (ME)-HSQC, T: TOCSY, and T_PS: pure shift TOCSY, are reported to obtain complete chemical shift assignments of small organic molecules from a single NMR experiment. While NOAH-AST provides ¹³C–¹³C, ¹H–¹³C, and ¹H–¹H connectivities for molecules with well resolved chemical shifts, NOAH-AST_PS experiments discern ¹H–¹H connectivities even in complex organic molecules such as steroids at ultra-high resolution. These methods are very flexible and allow to record data through non-uniform-sampling, which reduces the experimental time to a great extent. In order to make these methods friendly to non-NMR experts (especially organic chemists and natural product scientists), python scripts have been developed and they help researchers in using these methods.

All-in-one NOAH-AST/NOAH-AST_PS provides complete chemical shift information (¹³C–¹³C/¹H–¹³C/¹H–¹H) of small organic molecules from a single NMR experiment.

Triplet NOAH supersequences optimised for small molecule structure characterisation

A series of NMR supersequences are presented for the time-efficient structure characterisation of small molecules in the solution state. These triplet sequences provide HMBC, HSQC, and one homonuclear correlation experiment of choice according to the NMR by Ordered Acquisition using ¹ H detection principle. The experiments are demonstrated to be compatible with non-uniform sampling schemes and may be acquired and processed under full automation.

New NOAH modules for structure elucidation at natural isotopic abundance

We introduce several new NOAH modules designed for NMR supersequences that allow structure elucidation of small organic molecules from a single measurement. We show that double isotope filters (ZZ-filters) increase the flexibility of module permutation within the NMR supersequences, optimising combinations exploiting ¹⁵N and ¹³C nuclides. The time-shared 2BOB module combined with the ZZ-HMBC module (yielding NOAH-2 BO) provides an example of extending the NMR supersequences with parallel experiments (here 2BOB) that are incompatible with sequential implementation. Finally, the PANSY-COSY module combined with the HSQC sequence (yielding NOAH-2 SC²) provides an example of incorporating multiple receiver experiments into NMR supersequences opening new avenues for designing information rich NMR experiments. The new NOAH supersequences were utilized in computer assisted structure elucidation (CASE) study accomplished using the CMCse software.

Natural Products as a Foundation for Drug Discovery

Many natural products have been used as drugs for the treatment of diverse indications. Although most U.S. pharmaceutical companies have reduced or eliminated their in-house natural-product research over the years, new approaches for compound screening and chemical synthesis are resurrecting interest in exploring the therapeutic value of natural products. The aim of this commentary is to review emerging strategies and techniques that have made natural products a viable strategic choice for inclusion in drug discovery programs. Published 2019. U.S. Government.

Experiments with direct detection of multiple FIDs

Pulse schemes with direct observation of multiple free induction decays (FIDs) offer a dramatic increase in the spectral information content of NMR experiments and often yield substantial improvement in measurement sensitivity per unit time. Availability of multiple receivers on the state-of-the-art commercial spectrometers allows spectra from different nuclear species to be recorded in parallel routinely. Experiments with multi-FID detection have been designed with both, homonuclear and multinuclear acquisition. We provide a brief overview of such techniques designed for applications in liquid- and solid- state NMR as well as in hyperpolarized samples. Here we show how these techniques have led to design of experiments that allow structure elucidation of small molecules and resonance assignment in proteins from a single measurement. Probes with multiple RF micro-coils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems. Solid-state NMR experiments have also benefited immensely from both parallel and simultaneous FID acquisition in a variety of multi-dimensional pulse schemes. We believe that multi-FID detection will become an essential component of the future NMR methodologies effectively increasing the information content of NMR experiments and reducing the cost of NMR analysis.

NMR Spectroscopy for Metabolomics Research

Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.