High-resolution NMR spectroscopy in inhomogeneous fields

Tracking Metabolite Variations during the Degradation of Vegetables in Rice Bran Bed with Intact-State Nuclear Magnetic Resonance Spectroscopy

Fermentation-a process of compound degradation by microorganisms-is a traditional food processing method utilized worldwide for the long-term preservation of fresh foods. In recent years, fermented foods have gained attention as health foods. Fermentation increases the nutritional value of ingredients, producing complex flavors and aromas. To identify unknown components in fermented foods, it is necessary to analyze compounds and conditions nondestructively and comprehensively. We performed intact-state nuclear magnetic resonance (NMR) spectroscopy using intermolecular single quantum coherence (iSQC) to detect the degradation of vegetables directly and nondestructively. We used two types of vegetables and a rice bran bed (nukazuke), which is used for traditional vegetable fermentation in Japan. Major metabolites such as saccharides, organic acids, and amino acids were identified in iSQC-sliced spectra. Comparing NMR signal intensities during degradation revealed the transition of metabolites characteristic of lactic acid fermentation. A pathway-based network analysis showed pathways involved in amino acid metabolism and lactic acid fermentation. Our analytical approach with intact-state NMR spectroscopy using iSQC demonstrated that it may be effective in other experimental systems, allowing for the evaluation of phenomena that have been conventionally overlooked in their true state.

Restore High-Resolution Nuclear Magnetic Resonance Spectra from Inhomogeneous Magnetic Fields Using a Neural Network

High-resolution nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical tool with wide applications. However, the conventional shim technique may not guarantee the homogeneity of the magnetic field when the experimental conditions are unfavorable. In this study, we proposed a data postprocessing method called Restore High-resolution Unet (RH-Unet), which uses a convolutional neural network to restore distorted NMR spectra that have been acquired in inhomogeneous magnetic fields. The method generates feature-label pairs from singlet peak regions and ideal Lorentzian line shapes and trains a RH-Unet model to map low-resolution spectra to high-resolution spectra. The method was applied to different samples and showed superior performance than the reference deconvolution method incorporated in Bruker Topspin software. The proposed method provides a simple and fast way to obtain high-resolution NMR spectra in inhomogeneous fields that can facilitate the application of NMR spectroscopy in various fields.

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.

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.

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.

Flow-based in vivo NMR spectroscopy of small aquatic organisms

NMR applied to living organisms is arguably the ultimate tool for understanding environmental stress responses and can provide desperately needed information on toxic mechanisms, synergistic effects, sublethal impacts, recovery, and biotransformation of xenobiotics. To perform in vivo NMR spectroscopy, a flow cell system is required to deliver oxygen and food to the organisms while maintaining optimal line shape for NMR spectroscopy. In this tutorial, two such flow cell systems and their constructions are discussed: (a) a single pump high-volume flow cell design is simple to build and ideal for organisms that do not require feeding (i.e., eggs) and (b) a more advanced low-volume double pump flow cell design that permits feeding, maintains optimal water height for water suppression, improves locking and shimming, and uses only a small recirculating volume, thus reducing the amount of xenobiotic required for testing. In addition, key experimental aspects including isotopic enrichment, water suppression, and 2D experiments for both ¹³ C enriched and natural abundance organisms are discussed.

Boosting resolution in NMR spectroscopy by chemical shift upscaling

Resolution is an essential challenge in NMR spectroscopy. Narrow chemical shift range and extensive signal splittings due to scalar couplings often give rise to spectral congestion and even overlap in NMR spectra. Magnetic field strength is directly responsible for spectral resolution as higher magnetic field strength offers better signal dispersion. However, the process of further increasing magnetic field strength of NMR instruments is slow and expensive. Methodology aimed at resolution issue has long been developing. Here, we present a chemical shift upscaling method, in which chemical shifts are upscaled by a given factor while scalar couplings are unchanged. As a result, signal dispersion and hence the resolution are improved. Therefore, it is possible to separate multiplets which originally overlap with each other and to extract their integrals for quantitative analysis. Improved signal dispersion and the preservation of scalar couplings also facilitate multiplet analysis and signal assignment. Chemical shift upscaling offers a method for enhancing resolution limited by magnetic field strength.

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.

Enabling High Spectral Resolution of Liquid Mixtures in Porous Media by Antidiagonal Projections of Two-Dimensional 1H NMR COSY Spectra

The noninvasive, in situ chemical identification of liquid mixtures confined in porous materials is experimentally challenging. NMR is chemically resolved and applicable to optically opaque systems but suffers from a significant loss in spectral resolution in the presence of the magnetic field inhomogeneities typical of porous media. In this work, we introduce a method of analysis of conventional two-dimensional (2D) ¹H NMR correlation spectroscopy (COSY) spectra based on the extraction of 1D antidiagonal projections, which are free from line-broadening effects and can therefore be used for chemical species identification. Here, we show the application of the technique to the measurement of linear n-alkanes where the cross-to-diagonal peak ratios are shown to follow a power-law curve as a function of the chain length. This calibration enables quantifying mixtures of linear hydrocarbons confined in any porous material independently of temperature or inter-molecular dynamics. Thus, this is a promising tool for quantitative chemical reaction monitoring studies in heterogeneous systems under operando experimental conditions.

High-resolution two-dimensional 1H J-resolved MRS measurements on in vivo samples

Magnetic resonance spectroscopy (MRS) provides a noninvasive tool for metabolite characterization of in vivo biological samples. Conventional MRS measurements on biological samples generally suffer from field inhomogeneity caused by intrinsic magnetic susceptibility variations inside samples. Compared to one-dimensional MRS, two-dimensional (2D) J-resolved spectroscopy enables resolving J couplings along one of the spectral dimension and benefits to metabolite identification and analyses. Intermolecular double-quantum coherences (iDQC) has been proven to be insensitive to magnetic field inhomogeneity, herein we propose a MRS approach based on iDQC evolution and optimal echo sampling scheme to achieve high-resolution 2D J-resolved measurements on biological samples. The applicability of the proposed method is evaluated with experiments on an ex vivo pig brain tissue and an in vivo rat brain tissue. Compared to conventional MRS method which is sensitive to field inhomogeneity inside investigated biological tissues, the proposed method holds immunity to this field inhomogeneity and the quality of resulting spectra may not be influenced by localized voxel size variation. The signal to noise ratio enhancement of the proposed method benefitting from the optimal echo signal sampling is verified with a solution experiment. The new method provides a promising way for high-resolution MRS measurements on biological samples. In combination with fast acquisition strategy, it may find some promising biomedical applications.

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

A family of high-resolution NMR methods share the common concept of acquiring in parallel different sub-experiments in different spatial regions of the NMR tube. These spatial encoding and spatial selection methods were for the most part introduced independently from each other and serve different purposes, but they share common ingredients, often derived from magnetic resonance imaging, and they all benefit from a greatly improved time-efficiency. This review article provides a description of several spatial encoding and spatial selection methods, including single-scan multidimensional experiments (ultrafast 2D NMR, DOSY, Z spectroscopy, inversion recovery and Laplace NMR), pure shift and selective refocusing experiments (including Zangger-Sterk decoupling, G-SERF and PSYCHE), a Z filter, and fast-pulsing slice-selective experiments. Some key elements for spatial parallelisation are introduced and when possible a common framework is used for the analysis of each method. Sensitivity considerations are discussed, and a selection of applications is analysed to illustrate which questions can be answered thanks to spatial encoding and spatial selection methods, and discuss the perspectives for future developments and applications.

A Single-Scan Inhomogeneity-Tolerant NMR Method for High-Resolution Two-Dimensional J-Resolved Spectroscopy

OBJECTIVE

A robust and general single-scan NMR method, SGEN-J, is proposed for real-time recording high-resolution two-dimensional (2D) homonuclear J-resolved spectra under inhomogeneous magnetic fields.

METHODS

This proposed NMR method is designed based on the combination of a selective gradient encoding module to encode chemical shifts with spatial positions, and a J-modulation decoding module to reveal encoded structural information. Multi-band SGEN-J is further implemented to effectively enhance spectral sensitivity with a sustained tolerance of field inhomogeneity.

RESULTS

The SGEN-J provides an effective way to rapidly recover chemical shifts, J coupling constants, and multiplet patterns under inhomogeneous magnetic fields. Experiments on various chemical solutions were performed to demonstrate the feasibility and effectiveness of SGEN-J. Experiments on pig marrow tissues were performed to further investigate the applicability of SGEN-J to biological samples with intrinsic susceptibility variations.

CONCLUSION

Based on intrinsic advantages, SGEN-J serves as a helpful complement to existing 2D J-resolved methodologies in molecular structure elucidation and biomedical study, and offer bright perspectives for real-time analyzing in vivo biological systems and monitoring in situ chemical reactions.

Environmental Nuclear Magnetic Resonance Spectroscopy: An Overview and a Primer

NMR spectroscopy is a versatile tool for the study of structure and interactions in environmental media such as air, soil, and water as well as monitoring the metabolic responses of living organisms to an ever changing environment. Part review, part perspective, and part tutorial, this Feature is aimed at nonspecialists who are interested in learning more about the potential and impact of NMR spectroscopy in environmental research.

Analyzing the special PFG signal attenuation behavior of intermolecular MQC via the effective phase shift diffusion equation method

Inter-molecular multiple quantum coherence (iMQC) has important applications in NMR and MRI. However, the current theoretical methods still have some difficulties in analyzing the behavior of iMQC signal attenuation of pulsed field gradient diffusion experiments. In this paper, the iMQC diffusion experiments were analyzed by an effective phase shift diffusion equation (EPSDE) method, which is based on the idea that the accumulating phase shift (APS) can be viewed as the result of a diffusion process in virtual phase space (VPS) with effective diffusion coefficient K(2)(t) D (rad(2)/s) where K(t)=∫0 (t)γg(t')dt' is a wavenumber and D is the physical diffusion coefficient of the spin carrier in the real space. The term K(t(tot)) z1 needs to be added to the APS when K(t(tot)) is not zero. Most of the time, K(t(tot)) equals zero. However, in iMQC experiments, the condition K(t(tot)) equaling zero or being non-zero for each spin depends on the gradient pulse setting. The signal attenuations of these two types of iMQC, zero or non-zero K(t(tot)), were analyzed in detail for free and restricted diffusions, which shows that there are significant differences between these two types of iMQC. Particularly, if an apparent diffusion coefficient D(app) is used to analyze the signal attenuation, it equals nD for zero K(t(tot)) which agrees with current theoretical and experimental reports, while for non-zero K(t(tot)), it equals (2n - 1) D which agrees with experimental results from the literature; there are no similar theoretical results reported for comparison. The result that D(app) equals (2n - 1) D is important because the higher value of D(app) means that non-zero K(t(tot)) iMQC can potentially provide more contrast and measure slower diffusion rates than zero K(t(tot)) iMQC. The EPSDE method provides a new way to analyze iMQC diffusion experiments.