Application Of Nuclear Magnetic Resonance Research Articles

Anisotropic NMR data acquisition with a prototype 400 MHz cryogen-free NMR spectrometer.

High-temperature superconducting (HTS) materials have recently been incorporated into the construction of HTS cryogen-free magnets for nuclear magnetic resonance (NMR) spectroscopy. These HTS NMR spectrometers do not require liquid cryogens, thereby providing significant cost savings and facilitating easy integration into chemistry laboratories. However, the optimal performance of these HTS magnets against standard cryogen NMR magnets must be evaluated, especially with demanding modern NMR applications such as NMR in anisotropic media. The stability of the HTS magnets over time and their performance with complex pulse sequence experiments are the main unknown factors of this new technology. In this study, we evaluate the utility of our prototype 400 MHz cryogen-free power-driven HTS NMR spectrometer, installed in the fumehood of a chemistry laboratory, for stereochemical analysis of three commercial natural products (artemisinin, artemether, and dihydroartemisinin) via measurement of anisotropic NMR data, in particular, residual dipolar couplings. The accuracy of measurement of the anisotropic NMR data with the HTS magnet spectrometer is evaluated through the CASE-3D fitting protocol, as implemented in the Mestrenova-StereoFitter software program.

A Method of Inverting Rock Grain Size Based on Nuclear Magnetic Resonance Logging Data and Application

Rock grain size parameter is the key parameter of reservoir rock physics analysis. The study found that the relationship between the NMR T 2 spectrum and rock grain size distribution curve is directly related to NMR T 2 distribution and grain size distribution of rock, so you can use T 2 to retrieve the size distribution of rock NMR spectral data. Based on the calculation of the rock core experiment results of grain size distribution by NMR T 2 distribution using the conversion method of piecewise nonlinear calibration for each core, adjusting the calibration parameters to make the grain size distribution calculated with the core analysis of grain size distribution approximation, the error is minimum to obtain each core scale parameter conversion. In the end, the core parameters are classified according to the parameters of pore and permeability. Finally, according to the actual NMR T 2 distribution curve inversion of underground rock granularity, the inversion results contrast with the core analysis results, and the reliability of the method is verified to provide accurate, continuous rock size distribution profile analysis of geological reservoir rock physics.

A fast and efficient tool for the structural characterization of marine dissolved organic matter: Nonuniform sampling 2D COSY NMR

AbstractAn in‐depth structural characterization of marine dissolved organic matter (DOM) is crucial for a better understanding of its connection to marine and global biogeochemical cycles. High‐field nuclear magnetic resonance (NMR) spectroscopy in general and two‐dimensional (2D) correlation spectroscopy (COSY) in particular are powerful tools for the molecular level structural analysis of marine DOM. These 2D NMR experiments demand prolonged experimental times of days to weeks per sample due to the requirement of a large number of experiments to record the second dimension (t1) of the 2D NMR experiment. Herein, we demonstrate the efficacy of nonuniform sampling (NUS) in 2D COSY, which (i) reduces the measurement time by half without compromising spectral quality and (ii) enhances the signal intensity for the given experiment time. This approach can lead to substantial progress in the structural analysis of previously poorly characterized marine DOM. NUS COSY has been exemplified on two solid‐phase extracted DOM samples from the surface and deep ocean at 800 MHz and 1.2 GHz instruments. A dramatic improvement in sensitivity and spectral resolution is observed in NUS COSY spectra recorded at 1.2 GHz instrument when compared to 800 MHz instrument. NUS COSY NMR is versatile and anticipated to have significant potential for uncovering the hidden molecular diversity of DOM from various aquatic environments within a reasonable timeframe. The introduction of NUS into the environmental sciences was long overdue, and our study now opens the door for a wide field of new applications of NMR in the marine and aquatic sciences.

Potential Application of Nuclear Magnetic Resonance to Infer In Situ Degree of Saturation in Tailings

Potential Application of Nuclear Magnetic Resonance to Infer In Situ Degree of Saturation in Tailings

Application of Benchtop NMR for Metabolomics Study Using Feces of Mice with DSS-Induced Colitis

Nuclear magnetic resonance (NMR)-based metabolomics, which comprehensively measures metabolites in biological systems and investigates their response to various perturbations, is widely used in research to identify biomarkers and investigate the pathogenesis of underlying diseases. However, further applications of high-field superconducting NMR for medical purposes and field research are restricted by its high cost and low accessibility. In this study, we applied a low-field, benchtop NMR spectrometer (60 MHz) employing a permanent magnet to characterize the alterations in the metabolic profile of fecal extracts obtained from dextran sodium sulfate (DSS)-induced ulcerative colitis model mice and compared them with the data acquired from high-field NMR (800 MHz). Nineteen metabolites were assigned to the 60 MHz 1H NMR spectra. Non-targeted multivariate analysis successfully discriminated the DSS-induced group from the healthy control group and showed high comparability with high-field NMR. In addition, the concentration of acetate, identified as a metabolite with characteristic behavior, could be accurately quantified using a generalized Lorentzian curve fitting method based on the 60 MHz NMR spectra.

Benchtop 19F nuclear magnetic resonance spectroscopy enabled kinetic studies and optimization of the synthesis of carmofur

Carmofur, a 5-fluorouracil (5-FU) derivative, was initially developed as an antineoplastic agent to treat colorectal cancer. Through drug repurposing efforts, it has been identified as a potent covalent inhibitor of the main protease of SARS-CoV-2 (Mpro), making it a promising therapeutic agent against COVID-19. However, previous synthetic procedures suffer from low yields or long reaction times. In this study, benchtop 19F nuclear magnetic resonance (NMR) spectroscopy enables the real-time quantitative monitoring and characterization of the synthesis of carmofur by providing kinetic insight. Furthermore, its proton lock capabilities no longer require the use of deuterated solvents and have enabled convenient and rapidly scalable synthesis of our compound. Here, we present the application of benchtop 19F NMR as an efficient method for optimizing the synthesis of carmofur and its future application in the synthesis of related 5-FU analogs.

Deep Learning Methodology for Obtaining Ultraclean Pure Shift Proton Nuclear Magnetic Resonance Spectra

Nuclear magnetic resonance (NMR) is one of the most powerful analytical techniques. In order to obtain high-quality NMR spectra, a real-time Zangger-Sterk (ZS) pulse sequence is employed to collect low-quality pure shift NMR data with high efficiency. Then, a neural network named AC-ResNet and a loss function named SM-CDMANE are developed to train a network model. The model with excellent abilities of suppressing noise, reducing line widths, discerning peaks, and removing artifacts is utilized to process the acquired NMR data. The processed spectra with noise and artifact suppression and small line widths are ultraclean and high-resolution. Peaks overlapped heavily can be resolved. Weak peaks, even hidden in the noise, can be discerned from noise. Artifacts, even as high as spectral peaks, can be removed completely while not suppressing peaks. Eliminating perfectly noise and artifacts and smoothing baseline make spectra ultraclean. The proposed methodology would greatly promote various NMR applications.

Reliable Surface Area Assessment of Wet and Dry Nonporous and Nanoporous Particles: Nuclear Magnetic Resonance Relaxometry and Gas Physisorption

The reliable assessment of surface area is extremely important for many applications, e.g., catalysis, separation, and energy storage/conversion. Within this context, major progress has been made concerning the textural characterization of porous materials in the gas/dry state, e.g., gas physisorption and mercury porosimetry. However, these methods are not sufficient for the characterization of wet materials utilized in liquid-phase processes. For this, the application of nuclear magnetic resonance (NMR) relaxometry has been considered, but a systematic and rigorous assessment of the applicability of NMR relaxometry for reliable surface and pore size characterization of nanoporous materials is missing. Hence, we present a systematic study in which we assess the applicability of NMR relaxometry for reliable surface area assessment utilizing for the first time true surface area benchmark data based on argon 87 K adsorption on nonporous particles (silica and carbon black) coupled with the development of an advanced methodology including the investigation of the choice of the probe molecule and the effect of its accessibility to the pore network. Our results show that the method provides a fast (a few minutes per measurement) and reliable surface area of silica and carbon black model materials immersed in a liquid phase. In addition, our work clearly demonstrates the potential of NMR relaxometry for the targeted surface area assessment of defined pore classes (here ultramicropores) and suggests a new methodology for the characterization of pore entrances (pore window size). Furthermore, we investigate the effect of wettability and suggest that NMR relaxometry could be developed into a unique tool for assessing the wetting characteristics of adsorbate phases on pore surfaces. This fundamental study can be considered a first major step in enabling NMR relaxometry for reliable surface area assessment for wet materials, particularly relevant for materials used in processes occurring in a liquid phase.

Fractal-Based Approaches to Pore Structure Investigation and Water Saturation Prediction from NMR Measurements: A Case Study of the Gas-Bearing Tight Sandstone Reservoir in Nanpu Sag

Pore space of tight sandstone samples exhibits fractal characteristics. Nuclear magnetic resonance is an effective method for pore size characterization. This paper focuses on fractal characteristics of pore size from nuclear magnetic resonance (NMR) of tight sandstone samples. The relationship between the fractal dimension from NMR with pore structure and water saturation is parameterized by analyzing experimental data. Based on it, a pore structure characterization and classification method for water-saturated tight sandstone and a water saturation prediction method in a gas-bearing sandstone reservoir have been proposed. To verify the models, the fractal dimension from NMR of 19 tight sandstone samples selected from the gas-bearing tight sandstone reservoir of Shahejie Formation in Nanpu Sag and that of 16 of them under different water saturation states are analyzed. The application result of new methods in the gas-bearing tight sandstone reservoir of Shahejie Formation in Nanpu Sag shows consistency with experimental data. This paper has facilitated the development of the NMR application by providing a non-electrical logging idea in reservoir quality evaluation and water saturation prediction. It provides a valuable scientific resource for reservoir engineering and petrophysics of unconventional reservoir types, such as tight sandstone, low porosity, and low permeability sandstone, shale, and carbonate rock reservoirs.

Real-time NMR analysis of polyhydroxyalkanoate synthase reaction that synthesizes block copolymer comprising glycolate and 3-hydroxybutyrate

The sequence-regulating polyhydroxyalkanoate (PHA) synthase PhaCAR spontaneously synthesizes the homo-random block copolymer, poly[3-hydroxybutyrate (3HB)]-b-poly[glycolate (GL)-ran-3HB]. In this study, a real-time in vitro chasing system was established using a high-resolution 800 MHz nuclear magnetic resonance (NMR) and 13C-labeled monomers to monitor the polymerization of GL-CoA and 3HB-CoA into this atypical copolymer. Consequently, PhaCAR initially consumed only 3HB-CoA and subsequently consumed both substrates. The structure of the nascent polymer was analyzed by extracting it with deuterated hexafluoro-isopropanol. In the primary reaction product, a 3HB-3HB dyad was detected, and GL-3HB linkages were subsequently formed. According to these results, the P(3HB) homopolymer segment is synthesized prior to the random copolymer segment. This is the first report of its kind which proposes the application of real-time NMR to a PHA synthase assay, paving the way for elucidating the mechanisms of PHA block copolymerization.

Reconversion of Parahydrogen Gas in Surfactant-Coated Glass NMR Tubes.

The application of parahydrogen gas to enhance the magnetic resonance signals of a diversity of chemical species has increased substantially in the last decade. Parahydrogen is prepared by lowering the temperature of hydrogen gas in the presence of a catalyst; this enriches the para spin isomer beyond its normal abundance of 25% at thermal equilibrium. Indeed, parahydrogen fractions that approach unity can be attained at sufficiently low temperatures. Once enriched, the gas will revert to its normal isomeric ratio over the course of hours or days, depending on the surface chemistry of the storage container. Although parahydrogen enjoys long lifetimes when stored in aluminum cylinders, the reconversion rate is significantly faster in glass containers due to the prevalence of paramagnetic impurities that are present within the glass. This accelerated reconversion is especially relevant for nuclear magnetic resonance (NMR) applications due to the use of glass sample tubes. The work presented here investigates how the parahydrogen reconversion rate is affected by surfactant coatings on the inside surface of valved borosilicate glass NMR sample tubes. Raman spectroscopy was used to monitor changes to the ratio of the (J: 0 → 2) vs. (J: 1 → 3) transitions that are indicative of the para and ortho spin isomers, respectively. Nine different silane and siloxane-based surfactants of varying size and branching structures were examined, and most increased the parahydrogen reconversion time by 1.5×-2× compared with equivalent sample tubes that were not treated with surfactant. This includes expanding the pH2 reconversion time from 280 min in a control sample to 625 min when the same tube is coated with (3-Glycidoxypropyl)trimethoxysilane.

The Application of HPLC-FLD and NMR in the Monitoring of Therapy Efficacy in Alpha-Mannosidosis.

Alpha-mannosidosis is a rare lysosomal storage disorder, caused by decreased activity of α-D-mannosidase. This enzyme is involved in the hydrolysis of mannosidic linkages in N-linked oligosaccharides. Due to the mannosidase defect, undigested mannose-rich oligosaccharides (Man2GlcNAc - Man9GlcNAc) accumulating in cells are excreted in large quantities in urine. In this work, we determined the levels of urinary mannose-rich oligosaccharides in a patient subjected to novel enzyme replacement therapy. Urinary oligosaccharides were extracted using solid phase extraction (SPE), labeled by fluorescent tag 2-aminobenzamide, and quantified by high-performance liquid chromatography (HPLC) with fluorescence detector (FLD). The identity of peaks was determined by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometry. In addition, the levels of urinary mannose-rich oligosaccharides were also quantified by 1H nuclear magnetic resonance (NMR) spectroscopy. The data were analyzed using one-tailed paired t-test and Pearson's correlation tests. Compared to levels before the administration of therapy, an approximately two-folds decrease in total mannose-rich oligosaccharides after one month of treatment was observed by NMR and HPLC. After four months, an approximately ten-folds significant decrease in total urinary mannose-rich oligosaccharides was detected, suggesting therapy effectiveness. A significant decrease in the levels of oligosaccharides with 7-9 mannose units was detected by HPLC. The application of both HPLC-FLD and NMR in quantification of oligosaccharide biomarkers is a suitable approach for monitoring of therapy efficacy in alpha-mannosidosis patients.

In-house fabrication of 1.3 to 7 mm MAS drive caps using desktop 3D printers

The 3D-printing technology has emerged as a well-developed method to produce parts with considerably low cost and yet with high precision (<100 μm). Recent literature has shown that the 3D-printing technology can be exploited to fabricate a magic-angle spinning (MAS) system in solid-state nuclear magnetic resonance (NMR) spectroscopy. In particular, it was demonstrated that advanced industry-grade 3D printers could fabricate 3.2 mm MAS drive caps with intricate features, and the caps were shown to spin > 20 kHz. Here, we show that not only lab-affordable benchtop 3D printers can produce 3.2 mm drive caps with a similar quality as the commercialized version, but also smaller 2.5 mm and 1.3 mm MAS drive caps—despite a slight compromise in performance. All in-house fabricated drive caps (1.3 to 7 mm) can be consistently reproduced (>90 %) and achieve excellent spinning performances. In summary, the > 3.2 mm systems have similar performances as the commercial systems, while the 2.5- and 1.3-mm caps can spin up to 26 kHz ± 2 Hz, and 46 kHz ± 1 Hz, respectively. The low-cost and fast in-house fabrication of MAS drive caps allows easy prototyping of new MAS drive cap models and, possibly, new NMR applications. For instance, we have fabricated a 4 mm drive cap with a center hole that could allow better light penetration or sample insertion during MAS. Besides, an added groove design on the drive cap allows an airtight seal suitable for probing air- or moisture-sensitive materials. Moreover, the 3D-printed cap was shown to be robust for low-temperature MAS experiments at ∼ 100 K, making it suitable for DNP experiments.

Expression of 2H, 13C, 15N-labeled NIST-Fab fragment in the methylotrophic yeast Komagataella phaffii for nuclear magnetic resonance studies

Labeling of proteins with deuterium is an essential tool in overcoming size limitations in the application of nuclear magnetic resonance (NMR) spectroscopy to proteins larger than 30 kilodaltons (kDa). A non-originator antigen-binding fragment (Fab) of NIST RM 8671 NISTmAb, so called yNIST-Fab, is a ~ 50 kDa protein, with 5 native disulfide linkages, that can be expressed in properly folded form in methylotrophic Komagataella phaffii (formerly Pichia pastoris). Further, the K. phaffii host can support the production of perdeuterated yNIST-Fab which is necessary to obtain well-resolved TROSY-based tripleresonance NMR spectra for chemical shift assignment of the peptide backbone resonances. Here, we examined growth conditions and effects of media composition to maximize biomass generation and expression yield of the 2H, 13C, 15N-enriched NIST-Fab fragment. Triple-labeled yNIST-Fab with ~93% deuteration reduced the 1HN, 15N and 13C-linewidths in the NMR spectra, allowing sequential NMR assignment of backbone resonance a key step toward sequence-specific structural and dynamic studies of Fab fragments and intact antibodies.

Multitype Noise Suppression in Magnetic Resonance Sounding Data Based on a Time–Frequency Fully Convolutional Neural Network

Magnetic resonance sounding (MRS) is one of the technical applications of nuclear magnetic resonance (NMR) used to directly detect and quantify groundwater content. MRS suffers from a low signal-to-noise ratio (SNR) due to the low amplitude of free induction decay (FID) signals and an inability to shield environmental noise. In this paper, a time-frequency fully convolutional neural network (TFCN) was proposed to suppress random, harmonic, and spike noise from MRS data. The TFCN parameters were trained with the time-frequency spectrum obtained by the short-time Fourier transform (STFT) of the MRS datasets as the input and the noise-free FID signals as the output. Based on the results of synthetic and field data experiments, the TFCN was compared with existing denoising methods. The results showed that the TFCN extracted the envelope of the FID signals from low-SNR random noise with higher accuracy than other methods. Moreover, the TFCN simultaneously suppressed multiple types of noise and exhibited high computational efficiency.

Ligands selectively tune the local and global motions of neurotensin receptor 1 (NTS1)

Nuclear magnetic resonance (NMR) studies have revealed that fast methyl sidechain dynamics can report on entropically-driven allostery. Yet, NMR applications have been largely limited to the super-microsecond motional regimes of G protein-coupled receptors (GPCRs). We use13Cε-methionine chemical shift-based global order parameters to test if ligands affect the fast dynamics of a thermostabilized GPCR, neurotensin receptor 1 (NTS1). We establish that the NTS1 solution ensemble includes substates with lifetimes on several, discrete timescales. The longest-lived states reflect those captured in agonist- and inverse agonist-bound crystal structures, separated by large energy barriers. We observe that the rapid fluctuations of individual methionine residues, superimposed on these long-lived states, respond collectively with the degree of fast, global dynamics correlating with ligand pharmacology. This approach lends confidence to interpreting spectra in terms of local structure and methyl dihedral angle geometry. The results suggest a role for sub-microsecond dynamics and conformational entropy in GPCR ligand discrimination.

In vivo singlet state filtered nuclear magnetic resonance: towards monitoring toxic responses inside living organisms.

In line with recent paradigm shifts in toxicity testing, in vivo nuclear magnetic resonance (NMR) is a powerful tool for studying the biological impacts and perturbations caused by toxicants in living organisms. However, despite the excellent molecular insights that can be obtained through this technique, in vivo NMR applications are hampered by considerable experimental challenges such as poor line shape and spectral overlap. Here, we demonstrate the application of singlet-filtered NMR to target specific metabolites and facilitate the study of metabolite fluxes in living Daphnia magna, an aquatic keystone species and model organism. Informed by mathematical simulations and experiments on ex vivo organisms, singlet state NMR is used to monitor the flux of metabolites such as d-glucose and serine in living D. magna, during the environmentally relevant processes of anoxic stress and reduced food availability. Overall, singlet state NMR is shown to have significant future potential for studying metabolic processes in vivo.

Methods for Structure Determination of SH2 Domain-Phosphopeptide Complexes by NMR.

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique to solve the structure of biomolecular complexes at atomic resolution in solution. Small proteins such as Src-homology 2 (SH2) domains have fast tumbling rates and long-lived NMR signals, making them particularly suited to be studied by standard NMR methods. SH2 domains are modular proteins whose function is the recognition of sequences containing phosphotyrosines. In this chapter, we describe the application of NMR to assess the interaction between SH2 domains and phosphopeptides and determine the structure of the resulting complexes.

A Generally Regularized Inversion for NMR Applications and Beyond

NMR (Nuclear Magnetic Resonance) technique presents a powerful analytical tool in the fields of chemistry, biology, and material science. The performance of the NMR technique highly relies on post-data processing methods, which are diverse according to different applications. In this paper, we propose a general processing method that can cover a wide range of applications from molecular dynamics study to biomedical engineering. We analyze the computation performance of the method by comparing it to other well-known algorithms and demonstrate its application in various NMR data processing problems, i.e., diffusion-ordered spectroscopy processing, under-sampled MRI (Magnetic Resonance Imaging) reconstruction, Laplace NMR inversion, and spectrum denoising. The results corroborate that the method performs effectively and efficiently compared to state-of-the-art methods. Moreover, we construct the method as a light toolbox, with which the users can perform various kinds of data processing tasks conveniently via graphic interfaces.

Challenges and advances in measuring sap flow in agriculture and agroforestry: A review with focus on nuclear magnetic resonance.

Sap flow measurement is one of the most effective methods for quantifying plant water use.A better understanding of sap flow dynamics can aid in more efficient water and crop management, particularly under unpredictable rainfall patterns and water scarcity resulting from climate change. In addition to detecting infected plants, sap flow measurement helps select plant species that could better cope with hotter and drier conditions. There exist multiple methods to measure sap flow including heat balance, dyes and radiolabeled tracers. Heat sensor-based techniques are the most popular and commercially available to study plant hydraulics, even though most of them are invasive and associated with multiple kinds of errors. Heat-based methods are prone to errors due to misalignment of probes and wounding, despite all the advances in this technology. Among existing methods for measuring sap flow, nuclear magnetic resonance (NMR) is an appropriate non-invasive approach. However, there are challenges associated with applications of NMR to measure sap flow in trees or field crops, such as producing homogeneous magnetic field, bulkiness and poor portable nature of the instruments, and operational complexity. Nonetheless, various advances have been recently made that allow the manufacture of portable NMR tools for measuring sap flow in plants. The basic concept of the portal NMR tool is based on an external magnetic field to measure the sap flow and hence advances in magnet types and magnet arrangements (e.g., C-type, U-type, and Halbach magnets) are critical components of NMR-based sap flow measuring tools. Developing a non-invasive, portable and inexpensive NMR tool that can be easily used under field conditions would significantly improve our ability to monitor vegetation responses to environmental change.