Spatial encoding and spatial selection methods in high-resolution NMR spectroscopy

Gut in Tube─Continuous Measurement of Metabolic Crosstalk between Cell Populations in Heterogeneous Samples by NMR Imaging

In complex living systems, such as the human gut, the interplay between the multiple cell types present is governed by the exchange of small molecule metabolites. However, at present, we lack techniques capable of monitoring this crosstalk in real time and with spatial resolution. Here, we present a model of the human gut in a 5 mm NMR tube that accounts for the intraluminal, mucosal, and colonocyte spaces. Cells are cultured in different spatial regions enabling metabolites, changes in pH, and the effects of exogenous molecules to be monitored exclusively using localized NMR techniques. Our model represents a high-throughput, readily available, and widely applicable approach to the study of living systems with multiple cell types on a molecular level. We used our model to explore the interplay between gut bacteria and colonocytes in the human large intestine and study the molecular concentration gradients naturally present in these systems. Such studies could help shed light on the crucial role played by the gut microbiota in maintaining gut homeostasis, modulating immune responses, metabolizing nutrients, and regulating host physiology.

Enhanced spectral reconstruction of ultrafast spatiotemporal encoded 2D NMR spectroscopy

BACKGROUND

Nuclear Magnetic Resonance (NMR) is extensively utilized in research as a non-invasive technique for investigating molecular structures and composite components. The spatiotemporal encoding (SPEN) technique effectively accelerates multi-dimensional NMR experiments. In ultrafast SPEN NMR, the acquired data are divided into odd and even segments corresponding to the positive and negative gradients during the decoding stage, respectively. However, the interlaced Fourier transform (FT) method used to reconstruct a full-width spectrum from these segments often suffers from severe noise contamination, necessitating the development of a more effective spectrum reconstruction method.

RESULTS

In this work, we analyze the noise amplification effect of the interlaced FT and find that the noise is most significant in two edge regions of the spectrum along the indirect dimension due to the relatively small time offset differences between odd and even segments in those regions. Consequently, we develop an iterative optimization method to obtain the full-width spectrum while mitigating the noise. The proposed method incorporates the odd and even data segments into an objective function with sparsity regularization to simplify the spectrum, which is then refined iteratively during the optimization. As a result, the reconstructed spectrum is significantly cleaner and maintains the full spectral width. Experimental results demonstrate a remarkable improvement in the readability and interpretability of SPEN data, evidenced by clearer signal peaks and reduced background noise.

SIGNIFICANCE

The proposed reconstruction method provides a reliable approach for processing SPEN 2D NMR data, effectively addressing the low sensitivity issue in the joint reconstruction on odd and even segments. Combining SPEN's ultrafast data acquisition with the proposed high-sensitivity spectrum reconstruction method enhances the utility of NMR for more accurate molecular structure analysis and component identification in composite samples, particularly promoting NMR research in rapid reaction systems.

Ultrafast Nuclear Magnetic Resonance as a Tool to Detect Rapid Chemical Change in Solution

Ultrafast nuclear magnetic resonance (NMR) uses spatial encoding to record an entire two-dimensional data set in just a single scan. The approach can be applied to either Fourier-transform or Laplace-transform NMR. In both cases, acquisition times are significantly shorter than traditional 2D/Laplace NMR experiments, which allows them to be used to monitor rapid chemical transformations. This Perspective outlines the principles of ultrafast NMR and focuses on examples of its use to detect fast molecular conversions in situ with high temporal resolution. We discuss how this valuable tool can be applied in the future to study a much wider variety of novel reactivity.

Improving the analysis of phase-separated bio-fuel samples with slice-selective total correlation NMR spectroscopy

Separated samples are a particular challenge for NMR experiments. The boundary is severely detrimental to high-resolution spectra and normal NMR experiments simply add the two spectra of the two layers together. Pyrolysis bio-oils represent an increasingly important alternative fuel resource yet readily separate, whether due to naturally high water content or due to blending, a common practice for producing a more viable fuel. Slice-selective NMR, where the NMR spectrum of only a thin slice of the total sample is acquired, is extended here and improved, with slice-selective two-dimensional correlation experiments used to resolve the distinct chemical spectra of the various components of the phase-separated blended fuel mixtures. Analysis of how the components of any blended biofuel samples partition between the two layers is an important step towards understanding the separation process and may provide insight into mitigating the problem.

Catalytic Upcycling of Polyolefins

The large production volumes of commodity polyolefins (specifically, polyethylene, polypropylene, polystyrene, and poly(vinyl chloride)), in conjunction with their low unit values and multitude of short-term uses, have resulted in a significant and pressing waste management challenge. Only a small fraction of these polyolefins is currently mechanically recycled, with the rest being incinerated, accumulating in landfills, or leaking into the natural environment. Since polyolefins are energy-rich materials, there is considerable interest in recouping some of their chemical value while simultaneously motivating more responsible end-of-life management. An emerging strategy is catalytic depolymerization, in which a portion of the C-C bonds in the polyolefin backbone is broken with the assistance of a catalyst and, in some cases, additional small molecule reagents. When the products are small molecules or materials with higher value in their own right, or as chemical feedstocks, the process is called upcycling. This review summarizes recent progress for four major catalytic upcycling strategies: hydrogenolysis, (hydro)cracking, tandem processes involving metathesis, and selective oxidation. Key considerations include macromolecular reaction mechanisms relative to small molecule mechanisms, catalyst design for macromolecular transformations, and the effect of process conditions on product selectivity. Metrics for describing polyolefin upcycling are critically evaluated, and an outlook for future advances is described.

CTCOSY-JRES: A high-resolution three-dimensional NMR method for unveiling J-couplings

Two-dimensional (2D) J-resolved spectroscopy provides valuable information on J-coupling constants for molecular structure analysis by resolving one-dimensional (1D) spectra. However, it is challenging to decipher the J-coupling connectivity in 2D J-resolved spectra because the J-coupling connectivity cannot be directly provided. In addition, 2D homonuclear correlation spectroscopy (COSY) can directly elucidate molecular structures by tracking the J-coupling connectivity between protons. However, this method is limited by the problem of spectral peak crowding and is only suitable for simple sample systems. To fully understand the intuitive coupling relationship and coupling constant information, we propose a three-dimensional (3D) COSY method called CTCOSY-JRES (Constant-Time COrrelation SpectroscopY and J-REsolved Spectroscopy) in this paper. By combining the J-resolved spectrum with the constant-time COSY technique, a doubly decoupled COSY spectrum can be provided while preserving the J-coupling constant along an additional dimension, ensuring high-resolution analysis of J-coupling connectivity and J-coupling information. Moreover, compression sensing and fold-over correction techniques are introduced to accelerate experimental acquisition. The CTCOSY-JRES method has been successfully validated in a variety of sample systems, including industrial, agricultural, and biopharmaceutical samples, revealing complex coupling interactions and providing deeper insights into the resolution of molecular structures.

Spatially Resolved Anisotropic Natural Abundance Deuterium 2D-NMR Spectroscopy Using Bimesophasic Lyotropic Chiral Systems

In this paper, we describe, for the first time, the combined and original use of spatially resolved anisotropic natural abundance deuterium (ANAD) 2D-NMR experiments and bimesophasic lyotropic chiral systems to extract two independent sets of anisotropic parameters such as 2H-RQCs from a single NMR sample. As a pioneering example, we focus on a mixture of immiscible polypeptides (PBLG) and polyacetylene helical polymers (L-MSP) dissolved in weakly polar organic solvents (chloroform). Nondeuterated (D)-(+)-camphor is used as a model chiral solute. By providing two series of 2H-RQCs, this new analytical approach paves the way for applications in 3D structure elucidation with increased reliability and also opens up original investigations in terms of spectral enantiomeric discriminations and mixing of helical polymers.

Spatially encoded pure-shift diffusion-ordered NMR spectroscopy yielded by chirp excitation

Spatially-encoded diffusion-ordered NMR spectroscopy (SPEN-DOSY) has emerged as a new time-efficient tool for the analysis of mixtures of small molecules in solution. Time efficiency is achieved using the concept of spatial parallelization of the effective gradient area, instead of the sequential incrementation used in conventional diffusion experiments. The data acquired with such sequences are then usually processed to extract diffusion coefficients, but cases when peak overlap in the 1H spectrum are difficult to address. Such limitation in conventional diffusion experiments is addressed via using the Pure Shift Yielded by CHirp Excitation (PSYCHE)-iDOSY sequence. Here we have adapted the PSYCHE-iDOSY sequence by using echo planar spectroscopic imaging (EPSI) to acquire SPEN-DOSY data. The pure shift mode of PSYCHE separates the overlapped components and a modified Stejskal-Tanner equation is used to extract the corresponding diffusion coefficient. The primary results obtained with the above-mentioned mixtures seem to open the possibility of separating complex mixtures in less time than PSYCHE-iDOSY.

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.

Solution-State 2D NMR Spectroscopy of Mixtures HyperpolarizedUsing Optically Polarized Crystals

The HYPNOESYS method (Hyperpolarized NOE System), which relies on the dissolution of optically polarized crystals, has recently emerged as a promising approach to enhance the sensitivity of NMR spectroscopy in the solution state. However, HYPNOESYS is a single-shot method that is not generally compatible with multidimensional NMR. Here we show that 2D NMR spectra can be obtained from HYPNOESYS-polarized samples, using single-scan acquisition methods. The approach is illustrated with a mixture of terpene molecules and a benchtop NMR spectrometer, paving the way to a sensitive, information-rich and affordable analytical method.

Efficient method for in situ agitation of liquids directly inside NMR spectrometer

The objective of the method is to allow agitation and fast homogenization of liquid systems in NMR tubes, directly inside the NMR spectrometer. The setup makes it possible to record spectra of samples that are macroscopically not stable, as dispersions of large particles. It makes also possible to fasten the homogeneization of liquid during a reaction or a phase transition. In the present paper, the method has been evaluated using homogeneous liquid extraction (HLLE). This configuration can also be used to introduce gases in different systems to perform various types of experiments. The set up consists in a Teflon tube inserted in the NMR tube bringing gas that yields agitation by bubbling. The gas flow is tuned using an electronically operated valve connected to gas line and to the NMR console. The method details how to reach proper homogenization without any perturbation, as liquid leaks.•An easy method for agitation of liquids inside NMR spectrometers.•The set up can be used for the insertion of gases in the NMR tube inside the spectrometer.•The method allows the study of the mixing of biphasic systems by NMR techniques.

Recovering sensitivity lost through convection in pure shift NMR

Practical pure shift NMR experiments, especially on instruments equipped with cryoprobes, can sometimes give very disappointing results. Here we show for the first time that this is a consequence of signal loss due to sample convection, and demonstrate a simple adjustment to common pure shift NMR experiments that restores the lost signal.

Cutting without a Knife: A Slice-Selective 2D 1H-13C HSQC NMR Sequence for the Analysis of Inhomogeneous Samples

Nuclear magnetic resonance (NMR) is a powerful technique with applications ranging from small molecule structure elucidation to metabolomics studies of living organisms. Typically, solution-state NMR requires a homogeneous liquid, and the whole sample is analyzed as a single entity. While adequate for homogeneous samples, such an approach is limited if the composition varies as would be the case in samples that are naturally heterogeneous or layered. In complex samples such as living organisms, magnetic susceptibility distortions lead to broad 1H line shapes, and thus, the additional spectral dispersion afforded by 2D heteronuclear experiments is often required for metabolite discrimination. Here, a novel, slice-selective 2D, 1H-13C heteronuclear single quantum coherence (HSQC) sequence was developed that exclusively employs shaped pulses such that only spins in the desired volume are perturbed. In turn, this permits multiple volumes in the tube to be studied during a single relaxation delay, increasing sensitivity and throughput. The approach is first demonstrated on standards and then used to isolate specific sample/sensor elements from a microcoil array and finally study slices within a living earthworm, allowing metabolite changes to be discerned with feeding. Overall, slice-selective NMR is demonstrated to have significant potential for the study of layered and other inhomogeneous samples of varying complexity. In particular, its ability to select subelements is an important step toward developing microcoil receive-only arrays to study environmental toxicity in tiny eggs, cells, and neonates, whereas localization in larger living species could help better correlate toxin-induced biochemical responses to the physical localities or organs involved.

Benchtop NMR-Based Metabolomics: First Steps for Biomedical Application

Nuclear magnetic resonance (NMR)-based metabolomics is a valuable tool for identifying biomarkers and understanding the underlying metabolic changes associated with various diseases. However, the translation of metabolomics analysis to clinical practice has been limited by the high cost and large size of traditional high-resolution NMR spectrometers. Benchtop NMR, a compact and low-cost alternative, offers the potential to overcome these limitations and facilitate the wider use of NMR-based metabolomics in clinical settings. This review summarizes the current state of benchtop NMR for clinical applications where benchtop NMR has demonstrated the ability to reproducibly detect changes in metabolite levels associated with diseases such as type 2 diabetes and tuberculosis. Benchtop NMR has been used to identify metabolic biomarkers in a range of biofluids, including urine, blood plasma and saliva. However, further research is needed to optimize the use of benchtop NMR for clinical applications and to identify additional biomarkers that can be used to monitor and manage a range of diseases. Overall, benchtop NMR has the potential to revolutionize the way metabolomics is used in clinical practice, providing a more accessible and cost-effective way to study metabolism and identify biomarkers for disease diagnosis, prognosis, and treatment.

Determining the Physico-Chemical Composition of Biomolecular Condensates from Spatially-Resolved NMR

Liquid-Liquid phase separation has emerged as fundamental process underlying the formation of biomolecular condensates. Insights into the composition and structure of biomolecular condensates is, however, complicated by their molecular complexity and dynamics. Here, we introduce an improved spatially-resolved NMR experiment that enables quantitative analysis of the physico-chemical composition of multi-component biomolecular condensates in equilibrium and label-free. Application of spatially-resolved NMR to condensates formed by the Alzheimer's disease-associated protein Tau demonstrates decreased water content, exclusion of the molecular crowding agent dextran, presence of a specific chemical environment of the small molecule DSS, and ≈150-fold increased concentration of Tau inside the condensate. The results suggest that spatially-resolved NMR can have a major impact in understanding the composition and physical chemistry of biomolecular condensates.

Theoretical analysis of flow effects in spatially encoded diffusion NMR

The measurement of translational diffusion coefficients by nuclear magnetic resonance (NMR) spectroscopy is essential in a broad range of fields, including organic, inorganic, polymer, and supramolecular chemistry. It is also a powerful method for mixture analysis. Spatially encoded diffusion NMR (SPEN DNMR)" is a time efficient technique to collect diffusion NMR data, which is particularly relevant for the analysis of samples that evolve in time. In many cases, motion other than diffusion is present in NMR samples. This is, for example, the case of flow NMR experiments, such as in online reaction monitoring and in the presence of sample convection. Such motion is deleterious for the accuracy of DNMR experiments in general and for SPEN DNMR in particular. Limited theoretical understanding of flow effects in SPEN DNMR experiments is an obstacle for their broader experimental implementation. Here, we present a detailed theoretical analysis of flow effects in SPEN DNMR and of their compensation, throughout the relevant pulse sequences. This analysis is validated by comparison with numerical simulation performed with the Fokker-Planck formalism. We then consider, through numerical simulation, the specific cases of constant, laminar, and convection flow and the accuracy of SPEN DNMR experiments in these contexts. This analysis will be useful for the design and implementation of fast diffusion NMR experiments and for their applications.

Metabolomics and NMR

The purpose of this manuscript will be to convince the reader to dive deeper into NMR spectroscopy and prevent the technique from being just another "black-box" in the lab. We will try to concisely highlight interesting topics and supply additional references for further exploration at each stage. The advantages of delving into the technique will be shown. The secondary objective, i.e., avoiding common problems before starting, will hopefully then become clear. Lastly, we will emphasize the spectrometer information needed for manuscript reporting to allow reproduction of results and confirm findings.

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.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

A one-shot double-slice selection NMR method for biphasic systems

We propose a new and robust one-shot double-slice selection experiment to detect 1H NMR signals of biphasic systems simultaneously. The resultant spectrum contains opposite-phased peaks representing the chemical species from the two phases, respectively.

Ultrafast 2D NMR for the analysis of complex mixtures

2D NMR is extensively used in many different fields, and its potential for the study of complex biochemical or chemical mixtures has been widely demonstrated. 2D NMR gives the ability to resolve peaks that overlap in 1D spectra, while providing both structural and quantitative information. However, complex mixtures are often analysed in situations where the data acquisition time is a crucial limitation, due to an ongoing chemical reaction or a moving sample from a hyphenated technique, or to the high-throughput requirement associated with large sample collections. Among the great diversity of available fast 2D methods, ultrafast (or single-scan) 2D NMR is probably the most general and versatile approach for complex mixture analysis. Indeed, ultrafast NMR has undergone an impressive number of methodological developments that have helped turn it into an efficient analytical tool, and numerous applications to the analysis of mixtures have been reported. This review first summarizes the main concepts, features and practical limitations of ultrafast 2D NMR, as well as the methodological developments that improved its analytical potential. Then, a detailed description of the main applications of ultrafast 2D NMR to mixture analysis is given. The two major application fields of ultrafast 2D NMR are first covered, i.e., reaction/process monitoring and metabolomics. Then, the potential of ultrafast 2D NMR for the analysis of hyperpolarized mixtures is described, as well as recent developments in oriented media. This review focuses on high-resolution liquid-state 2D experiments (including benchtop NMR) that include at least one spectroscopic dimension (i.e., 2D spectroscopy and DOSY) but does not cover in depth applications without spectral resolution and/or in inhomogeneous fields.

Rapid analytical CEST spectroscopy of competitive host-guest interactions using spatial parallelization with a combined approach of variable flip angle, keyhole and averaging (CAVKA)

A serious limitation of high resolution ¹²⁹Xe chemical exchange saturation transfer (CEST) NMR spectroscopy for comparing competitive host-guest interactions from different samples is the long acquisition time due to step-wise encoding of the chemical shift dimension. A method of optimized use of ¹²⁹Xe spin magnetization to enable the accelerated and simultaneous acquisition of CEST spectra from multiple samples or regions in a setup is described. The method is applied to investigate the host-guest system of commercially available cucurbit[7]uril (CB7) and xenon with competing guests: cis-1,4-bis(aminomethyl)cyclohexane, cadaverine, and putrescine. Interactions with the different guests prove that the observed CEST signal is from a CB6 impurity and that CB7 itself does not produce a CEST signal. Instead, rapid interactions between xenon and CB7 manifest in the spectrum as a broad saturation response that could be suppressed by cis-1,4-bis(aminomethyl)cyclohexane. This guest prevents interactions at the CB7 portals. The suggested method represents a type of spectroscopic imaging that is capable of capturing the exchange kinetics information of systems that otherwise suffer from shortened T₂ times and yields multiple spectra for comparing exchange conditions with a reduction of >95% in acquisition time. The spectral quality is sufficient to perform quantitative analysis and quantifications relative to a CB6 standard as well as relative to a known blocker concentration (putrescine) that both reveal an unexpectedly high CB6 impurity of ca. 8%.

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.

Temporal and spatial characterisation of protein liquid-liquid phase separation using NMR spectroscopy

Liquid-liquid phase separation (LLPS) of protein solutions is increasingly recognised as an important phenomenon in cell biology and biotechnology. However, opalescence and concentration fluctuations render LLPS difficult to study, particularly when characterising the kinetics of the phase transition and layer separation. Here, we demonstrate the use of a probe molecule trifluoroethanol (TFE) to characterise the kinetics of protein LLPS by NMR spectroscopy. The chemical shift and linewidth of the probe molecule are sensitive to local protein concentration, with this sensitivity resulting in different characteristic signals arising from the dense and lean phases. Monitoring of these probe signals by conventional bulk-detection ¹⁹F NMR reports on the formation and evolution of both phases throughout the sample, including their concentrations and volumes. Meanwhile, spatially-selective ¹⁹F NMR, in which spectra are recorded from smaller slices of the sample, was used to track the distribution of the different phases during layer separation. This experimental strategy enables comprehensive characterisation of the process and kinetics of LLPS, and may be useful to study phase separation in protein systems as a function of their environment.

Improved design of frequency-swept pulse sequences

Frequency-swept pulses are extensively used in magnetic resonance spectroscopic techniques for the robust manipulation of spins across wide ranges of offset frequencies in the presence of B₁ field variations. Nevertheless, designing pulse sequences consisting of multiple frequency-swept pulses can be challenging, as they often require specific timings and parameter tweaking. In the present work we discuss a simple and general approach for constructing such sequences. We present new and improved pulse sequences for applications including broadband B₁-tolerant CPMG (CHORUS-CPMG), broadband chirped excitation with suppression of homonuclear J-modulation (PROCHORUS), and the further compression of frequency-swept pulse sequences by superposition of pulses which reduces pulse sequence durations by 25-40%. All sequence design strategies are accompanied by mathematical presentations, experimental results, and supporting simulations.

Quadratic spacing of the effective gradient area for spatially encoded diffusion NMR

Diffusion NMR experiments rely on the measurement of signal attenuation as a function of the area of diffusion-encoding pulsed magnetic-field gradients. In conventional experiments, arbitrary series of gradient values can be used, and different gradient spacing strategies have different advantages. Ultrafast diffusion NMR relies on the spatial parallelisation of effective gradient area values to collect full 2D diffusion data sets in a single scan. Until recently, only linear spacing was available. We have shown that quadratic spacing can be achieved using a tailored frequency swept pulse. Here we describe the design of the pulse and validate it with numerical spin simulations, that make it possible to check the effect of the quadratic spacing pulse at different stages of the pulse sequence. We also show that quadratic spacing makes it possible to use a recently reported analysis method for diffusion NMR, the Matrix Pencil Method. We describe the results obtained with the MPM and those obtained with the direct exponential curve resolution algorithm (DECRA), which also requires quadratic gradient spacing. Overall, these developments open new opportunities for applications of spatially encoded diffusion experiments, such as ultrafast DOSY NMR and ultrafast Laplace NMR.

Optimisation of spatially-encoded diffusion-ordered NMR spectroscopy for the analysis of mixtures

Diffusion-ordered NMR spectroscopy (DOSY NMR) is a widely used method for the analysis of mixtures. It can be used to separate the spectra of a mixture's components and to analyse interactions. The classic implementation of DOSY experiments, based on an incrementation of the diffusion-encoding gradient area, requires several minutes or more to collect a 2D data set. Spatially-encoded (SPEN) DOSY makes it possible to collect a complete data set in less than 1 s, by spatial parallelisation of the effective gradient area. While several short descriptions of SPEN DOSY experiments have been reported, a thorough characterisation of its features and its practical use is missing, and this hinders the use of the method. Here, we present the unusual principles and implementation of the SPEN DOSY experiment, an understanding of which is useful to make optimal use of the method. The encoding and acquisition steps are described, and the parameter relations that govern the setup of SPEN DOSY experiments are discussed. The influence of key parameters, including on sensitivity, is illustrated experimentally on mixtures of small molecules. This study should be useful for the setup of SPEN DOSY experiments, which are particularly useful for systems that evolve in time.

Optimal control gradient precision trade-offs: Application to fast generation of DeepControl libraries for MRI

We have recently demonstrated supervised deep learning methods for rapid generation of radiofrequency pulses in magnetic resonance imaging (https://doi.org/10.1002/mrm.27740, https://doi.org/10.1002/mrm.28667). Unlike the previous iterative optimization approaches, deep learning methods generate a pulse using a fixed number of floating-point operations - this is important in MRI, where patient-specific pulses preferably must be produced in real time. However, deep learning requires vast training libraries, which must be generated using the traditional methods, e.g., iterative quantum optimal control methods. Those methods are usually variations of gradient descent, and the calculation of the gradient of the performance metric with respect to the pulse waveform can be the most numerically intensive step. In this communication, we explore various ways in which the calculation of gradients in quantum optimal control theory may be accelerated. Four optimization avenues are explored: truncated commutator series expansions at zeroth and first order, a novel midpoint truncation scheme at first order, and the exact complex-step method. For the spin systems relevant to MRI, the first-order midpoint truncation is found to be sufficiently accurate, but also significantly faster than the machine precision gradient. This makes the generation of training databases for the machine learning methods considerably more realistic.

In Vitro Spatio-Temporal NMR Metabolomics of Living 3D Cell Models

Three-dimensional cell cultures are of growing importance in biochemical research as they represent tissue features more accurately than standard two-dimensional systems, but to investigate these challenging new models an adaptation of established analytical techniques is required. Spatially resolved data for living organoids are needed to gain insight into transport processes and biochemical characteristics of domains with different nutrient supply and waste product removal. Within this work, we present an NMR-based approach to obtain dynamically radial metabolite profiles for cell spheroids, one of the most frequently used 3D models. Our approach combines an easy to reproduce custom-made measurement design, maintaining physiological conditions without inhibition of the NMR experiment, with spatially selective NMR pulse sequences. To overcome the inherently low sensitivity of NMR spectroscopy we excited slices instead of smaller cube-like voxels in combination with an efficient interleaved measurement approach and employed a commercially available cryogenic NMR probe. Finally, radial metabolite profiles could be obtained via double Abel inversion of the measured one-dimensional intensity profiles. Applying this method to Ty82 cancer cell spheroids demonstrates the achieved spatial resolution, for instance confirming exceedingly high lactic acid and strongly decreased glucose concentrations in the oxygen-depleted core of the spheroid. Furthermore, our approach can be employed to investigate fast and slow metabolic changes in single spheroids simultaneously, which is shown as an example of a spheroid degrading over several days after stopping the nutrient supply.

Ultrafast methods for relaxation and diffusion

Relaxation and diffusion NMR measurements offer an approach to studying rotational and translational motion of molecules non-invasively, and they also provide chemical resolution complementary to NMR spectra. Multidimensional experiments enable the correlation of relaxation and diffusion parameters as well as the observation of molecular exchange phenomena through relaxation or diffusion contrast. This review describes how to accelerate multidimensional relaxation and diffusion measurements significantly through spatial encoding. This so-called ultrafast Laplace NMR approach shortens the experiment time to a fraction and makes even single-scan experiments possible. Single-scan experiments, in turn, significantly facilitate the use of nuclear spin hyperpolarization methods to boost sensitivity. The ultrafast Laplace NMR method is also applicable with low-field, mobile NMR instruments, and it can be exploited in many disciplines. For example, it has been used in studies of the dynamics of fluids in porous materials, identification of intra- and extracellular metabolites in cancer cells, and elucidation of aggregation phenomena in atmospheric surfactant solutions.

Practical dissolution dynamic nuclear polarization

This review article intends to provide insightful advice for dissolution-dynamic nuclear polarization in the form of a practical handbook. The goal is to aid research groups to effectively perform such experiments in their own laboratories. Previous review articles on this subject have covered a large number of useful topics including instrumentation, experimentation, theory, etc. The topics to be addressed here will include tips for sample preparation and for checking sample health; a checklist to correctly diagnose system faults and perform general maintenance; the necessary mechanical requirements regarding sample dissolution; and aids for accurate, fast and reliable polarization quantification. Herein, the challenges and limitations of each stage of a typical dissolution-dynamic nuclear polarization experiment are presented, with the focus being on how to quickly and simply overcome some of the limitations often encountered in the laboratory.

The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science

The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.

Use of Spectroscopic Methods and Their Clinical Applications in Drug Abuse: A Review

Assurance of substance abuse in plasma and different parts of the body is vital in clinical and legal toxicology. Detection techniques are evaluated for their appropriateness in scientific and clinical sciences, where extraordinary prerequisites must be met. Recognition and affirmation are for the most part done by gas chromatography-Mass spectrometry (GC-MS) or liquid chromatography (LC-MS), Surface-enhanced Raman spectroscopy (SERS), Magnetic resonance imaging, Positron Emission Tomography, Infrared Spectroscopy, and UV Spectroscopy. Progressed spectroscopic techniques provided helpful quantitative or qualitative data about the natural chemistry and science of exploited substances. These spectroscopic techniques are assumed as quick, precise, and some of them are non-damaging investigation apparatus that may be assumed as a substitution for previously used compound investigation. Spectroscopy with its advances in technology is centralized to novel applications in the detection of abused drug substances and clinical toxicology. These techniques have attracted growing interest as forensic tools for the early detection and monitoring of exploited drugs. This review describes the principle, role, and clinical application of various spectroscopic techniques which are utilized for the identification of drug abuse like morphine, cocaine, codeine, alcohol, amphetamines, and their metabolites in whole blood, plasma, hair, and nails.

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.

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.

Ultrafast diffusion-based unmixing of 1H NMR spectra

We show that the NMR spectra of components in a mixture can be separated using 2D data acquired in less than one second, and an algorithm that is executed in just a few seconds. This NMR unmixing method is based on spatial encoding of the translational diffusion coefficients of the mixture's components, with multivariate processing of the data. This requires a new frequency swept pulse, which is designed and implemented to obtain quadratic spacing of the spatially parallelised gradient dimension. Ultrafast NMR unmixing may help in the analysis of mixtures that evolve in time.

-Frequency-swept pulses for ultrafast spatially encoded NMR

Ultrafast NMR based on spatial encoding yields arbitrary multidimensional spectra in a single scan. The dramatic acceleration afforded by spatial parallelisation makes it possible to capture transient species and processes, and has notably been applied to the monitoring of reactions and the analysis of hyperpolarised species. At the heart of ultrafast NMR lies the spatially sequential manipulation of nuclear spins. This is virtually always achieved by combining a swept radio-frequency pulse with a magnetic field gradient pulse. The dynamics of nuclear spins during these pulse sequence elements is key to understand and design ultrafast NMR experiments, and can often be described by surprisingly simple models. This article describes the spatial encoding of relaxation, chemical shift and diffusion in a common framework and discusses directions for future developments.

NMR as a "Gold Standard" Method in Drug Design and Discovery

Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.

Gradient-based pulse sequences for benchtop NMR spectroscopy

Benchtop NMR spectroscopy has been on the rise for the last decade, by bringing high-resolution NMR in environments that are not easily compatible with high-field NMR. Benchtop spectrometers are accessible, low cost and show an impressive performance in terms of sensitivity with respect to the relatively low associated magnetic field (40-100 MHz). However, their application is limited by the strong and ubiquitous peak overlaps arising from the complex mixtures which are often targeted, often characterized by a great diversity of concentrations and by strong signals from non-deuterated solvents. Such limitations can be addressed by pulse sequences making clever use of magnetic field gradient pulses, capable of performing efficient coherence selection or encoding chemical shift or diffusion information. Gradients pulses are well-known ingredients of high-field pulse sequence recipes, but were only recently made available on benchtop spectrometers, thanks to the introduction of gradient coils in 2015. This article reviews the recent methodological advances making use of gradient pulses on benchtop spectrometers and the applications stemming from these developments. Particular focus is made on solvent suppression schemes, diffusion-encoded, and spatially-encoded experiments, while discussing both methodological advances and subsequent applications. We eventually discuss the exciting development and application perspectives that result from such advances.

Spin dynamics during chirped pulses: applications to homonuclear decoupling and broadband excitation

Swept-frequency pulses have found applications in a wide range of areas including spectroscopic techniques where efficient control of spins is required. For many of these applications, a good understanding of the evolution of spin systems during these pulses plays a vital role, not only in describing the mechanism of techniques, but also in enabling new methodologies. In magnetic resonance spectroscopy, broadband inversion, refocusing, and excitation using these pulses are among the most used applications in NMR, ESR, MRI, and in vivo MRS. In the present survey, a general expression for chirped pulses will be introduced, and some numerical approaches to calculate the spin dynamics during chirped pulses via solutions of the well-known Liouville-von Neumann equation and the lesser-explored Wei-Norman Lie algebra along with comprehensive examples are presented. In both cases, spin state trajectories are calculated using the solution of differential equations. Additionally, applications of the proposed methods to study the spin dynamics during the PSYCHE pulse element for broadband homonuclear decoupling and the CHORUS sequence for broadband excitation will be presented.

High-Resolution Magic Angle Spinning (HR-MAS) NMR-Based Fingerprints Determination in the Medicinal Plant Berberis laurina

Berberis laurina (Berberidaceae) is a well-known medicinal plant used in traditional medicine since ancient times; however, it is scarcely studied to a large-scale fingerprint. This work presents a broad-range fingerprints determination through high-resolution magical angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy, a well-established flexible analytical method and one of most powerful "omics" platforms. It had been intended to describe a large range of chemical compositions in all plant parts. Beyond that, HR-MAS NMR allowed the direct investigation of botanical material (leaves, stems, and roots) in their natural, unaltered states, preventing molecular changes. The study revealed 17 metabolites, including caffeic acid, and berberine, a remarkable alkaloid from the genus Berberis L. The metabolic pattern changes of the leaves in the course of time were found to be seasonally dependent, probably due to the variability of seasonal and environmental trends. This metabolites overview is of great importance in understanding plant (bio)chemistry and mediating plant survival and is influenceable by interacting environmental means. Moreover, the study will be helpful in medicinal purposes, health sciences, crop evaluations, and genetic and biotechnological research.

Spatial molecular-dynamically ordered NMR spectroscopy of intact bodies and heterogeneous systems

Noninvasive evaluation of the spatial distribution of chemical composition and diffusion behavior of materials is becoming possible by advanced nuclear magnetic resonance (NMR) pulse sequence editing. However, there is room for improvement in the spectral resolution and analytical method for application to heterogeneous samples. Here, we develop applications for comprehensively evaluating compounds and their dynamics in intact bodies and heterogeneous systems from NMR data, including spatial z-position, chemical shift, and diffusion or relaxation. This experiment is collectively named spatial molecular-dynamically ordered spectroscopy (SMOOSY). Pseudo-three-dimensional (3D) SMOOSY spectra of an intact shrimp and two heterogeneous systems are recorded to evaluate this methodology. Information about dynamics is mapped onto two-dimensional (2D) chemical shift imaging spectra using a pseudo-spectral imaging method with a processing tool named SMOOSY processor. Pseudo-2D SMOOSY spectral images can non-invasively assess the different dynamics of the compounds at each spatial z-position of the shrimp's body and two heterogeneous systems.

Use of dissolved hyperpolarized species in NMR: Practical considerations

Hyperpolarization techniques that can transiently boost nuclear spin polarization are generally carried out at low temperature - as in the case of dynamic nuclear polarization - or at high temperature in the gaseous state - as in the case of optically pumped noble gases. This review aims at describing the various issues and challenges that have been encountered during dissolution of hyperpolarized species, and solutions to these problems that have been or are currently proposed in the literature. During the transport of molecules from the polarizer to the NMR detection region, and when the hyperpolarized species or a precursor of hyperpolarization (e.g. parahydrogen) is introduced into the solution of interest, several obstacles need to be overcome to keep a high level of final magnetization. The choice of the magnetic field, the design of the dissolution setup, and ways to isolate hyperpolarized compounds from relaxation agents will be presented. Due to the non-equilibrium character of the hyperpolarization, new NMR pulse sequences that perform better than the classical ones will be described. Finally, three applications in the field of biology will be briefly mentioned.

High-Resolution Probing of Heterogeneous Samples by Spatially Selective Pure Shift NMR Spectroscopy

Liquid NMR spectroscopy generally encounters two major challenges for high-resolution measurements of heterogeneous samples, namely, magnetic field inhomogeneity caused by spatial variations in magnetic susceptibility and spectral congestion induced by crowded NMR resonances. In this study, we demonstrate a spatially selective pure shift NMR approach for high-resolution probing of heterogeneous samples by suppressing effects of field inhomogeneity and J coupling simultaneously. A Fourier phase encoding strategy is proposed and implemented for spatially selective pure shift experiments to enhance signal intensity and further boost the applicability. The spatially selective pure shift method can serve as an effective tool for high-resolution probing of heterogeneous samples, thus presenting interesting prospects for extensive applications in the fields of chemistry, physics, biology, and food science.

Acceleration of 3D DOSY NMR by Spatial Encoding of the Chemical Shift

Diffusion-ordered NMR spectroscopy (DOSY) is a powerful method for the analysis of solution mixtures. With 3D DOSY, the 2D NMR spectra of a mixture's components can be separated according to the translational diffusion coefficient of each component. The acquisition of 3D DOSY data is, however, very time-consuming because of the need to consecutively acquire scans for both the diffusion and the indirect spectral dimensions. We show that spatial encoding of the indirect spectral dimension, of the kind used in ultrafast 2D NMR, can accelerate 3D DOSY experiments by an order of magnitude or more. This is illustrated with homonuclear single-quantum (COSY) and double-quantum (DQS) correlation spectra. Implementations with concatenated and incorporated (iDOSY) diffusion blocks are compared and in both cases, 2D spectra are separated with less than 6 min of experiment time.

Ultrafast Maximum-Quantum NMR Spectroscopy for the Analysis of Aromatic Mixtures

Maximum-quantum (MaxQ) NMR experiments have been introduced to overcome issues related to peak overlap and high spectral density in the NMR spectra of aromatic mixtures. In MaxQ NMR, spin systems are separated on the basis of the highest-quantum coherence that they can form. MaxQ experiments are however time consuming and methods have been introduced to accelerate them. In this article, we demonstrate the ultrafast, single-scan acquisition of MaxQ NMR spectra using spatial encoding of the multiple-quantum dimension. So far, the spatial encoding methodology has been applied only for the encoding of up to double-quantum coherences, and here we show that it can be extended to higher coherence orders, to yield a massive reduction of the acquisition time of multi-quantum spectra of aromatic mixtures, and also to monitor chemical reactions.