Application Of NMR Research Articles

Beyond traditional magnetic resonance processing with artificial intelligence

Smart signal processing approaches using Artificial Intelligence are gaining momentum in NMR applications. In this study, we demonstrate that AI offers new opportunities beyond tasks addressed by traditional techniques. We developed and trained artificial neural networks to solve three problems that until now were deemed “impossible”: quadrature detection using only Echo (or Anti-Echo) modulation from the traditional Echo/Anti-Echo scheme; accessing uncertainty of signal intensity at each point in a spectrum processed by any given method; and defining a reference-free score for quantitative access of NMR spectrum quality. Our findings highlight the potential of AI techniques to revolutionize NMR processing and analysis.

Pure Shift NMR in Continuous Flow.

Flow NMR is an expanding analytical approach with applications that include in-line analysis for process control and optimisation, and real-time reaction monitoring. The samples monitored by flow NMR are typically mixtures that yield complex 1D1H spectra. "Pure shift" NMR is a powerful approach to simplifying1H NMR spectra, but its standard implementation is not compatible with continuous flow because of interference between sample motion and the position-dependent spin manipulations that are required in pure shift NMR. Here we show that pure shift NMR spectra can be successfully collected for continuously flowing samples, thanks to an adapted acquisition scheme, robust solvent suppression, and a velocity-compensation strategy. The resulting method is used to collect ultrahigh resolution reaction monitoring data. Pure shift NMR spectra are expected to benefit many applications of flow NMR.

19F NMR relaxation of buried tryptophan side chains suggest anisotropic rotational diffusion of the protein RfaH.

The recent application of 19F NMR in the study of biomolecular structure and dynamics has made it a potentially attractive probe to complement traditional 15N/13C labelled probes for backbone and sidechain dynamics, albeit with some complications. The utility of 15N relaxation rates of rigid backbone amide groups to determine the rotational diffusion tensor of proteins is well established. Here we show that the measured 19F relaxation rates of two buried and possibly immobile 19F labelled tryptophan sidechains for the multidomain protein RfaH, in its closed conformation, are in reasonable agreement with the calculated values, only when anisotropic rotational diffusion of the protein is considered. While the sparsity of 19F relaxation data from a limited number of probes precludes the experimental determination of the rotational diffusion tensor here, these results demonstrate the influence of rotational diffusion anisotropy of proteins on 19F NMR relaxation of rigid tryptophan sidechains, while adding to the expanding literature of 19F NMR relaxation data sets in biomolecules.

Nanomolar Hg2+ detection via phenothiazine fluorogenic chemosensor: Applications in water analysis and intracellular imaging

A Knoevenagel condensation reaction paved the way for the development of the PTZ-BCN probe namely (z)-2-(1H-benzo[d]imidazole-2-yl)-3-(10-ethyl-10H-phenothiazin-3-yl) acrylonitrile. PTZ-BCN’s spectral characteristics were verified through the application of IR, 1H NMR, 13C NMR, and HRMS techniques. The PTZ-BCN probe showed a high selectivity and sensitivity toward Hg2+ ions over other interfering competing metal ions in CH3CN: HEPES buffer (9:1, v/v) system. The addition of Hg2+ results in a notable redshift and fluorescence quenching of the PTZ-BCN probe. An examination of the interaction between the PTZ-BCN probe and Hg2+ involved recoding 1H NMR titration spectra, HRMS, DFT analysis, and Job’s plot respectively. Quantification of the lowest detectable Hg2+ concentration at 2.3 nM, exhibiting a correlation coefficient of R2 = 0.9985. PTZ-BCN probe has proven effective in quantitatively determining the existence of Hg2+ in real-time water samples, test strips, solid state, and Hela living cells.

33S NMR: Recent Advances and Applications.

The purpose of this review is to present advances and applications of 33S NMR, which is an underutilized NMR spectroscopy. Experimental NMR aspects in solution, chemical shift tendencies, and quadrupolar relaxation parameters will be briefly summarized. Emphasis will be given to advances and applications in the emerging fields of solid-state and DFT computations of 33S NMR parameters. The majority of the examples were taken from the last twenty years and were selected on the basis of their importance to provide structural, electronic, and dynamic information that is difficult to obtain by other techniques.

Cellular Applications of DNP Solid-State NMR - State of the Art and a Look to the Future.

Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within their native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality and further discuss the type of structural information that can presently be garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broader adoption namely due a lack of sensitivity and spectral resolution. We also explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.

Decorating phenylalanine side-chains with triple labeled 13C/19F/2H isotope patterns.

We present an economic and straightforward method to introduce 13C-19F spin systems into the deuterated aromatic side chains of phenylalanine as reporters for various protein NMR applications. The method is based on the synthesis of [4-13C, 2,3,5,6-2H4] 4-fluorophenylalanine from the commercially available isotope sources [2-13C] acetone and deuterium oxide. This compound is readily metabolized by standard Escherichia coli overexpression in a glyphosate-containing minimal medium, which results in high incorporation rates in the corresponding target proteins.

1H NMR and UV-Vis as Analytical Techniques to Evaluate Biodiesel Conversion and Oxidative Stability

The present study evaluated the applicability of 1H NMR and UV-Vis spectroscopies as analytical techniques for the characterization and determination of biodiesel conversion and for monitoring the oxidative stability of biodiesel samples with antioxidants. For this study, safflower and babassu biodiesels were obtained through transesterification, and physicochemical properties confirmed the success of both reactions. A bench-top accelerated oxidation system was used as an alternative to the Rancimat® method, with samples of 6.0 g heated at 110 ± 5 °C and collected every 2 h for 12 h. The agreement for biodiesel conversions was good, with divergences between 2% and 0.4% for safflower biodiesel and 1.9% for babassu biodiesel. As for UV-Vis spectroscopy, the technique showed the same trend as the Rancimat® method, showing efficiency in evaluating the oxidative stability of safflower biodiesel and in the performance of antioxidants BHT and DMP-30. The accuracy of NMR signals integration for mixtures of safflower oil and safflower biodiesel and the use of UV-Vis spectroscopy associated with a bench-top accelerated oxidation system to investigate the performance of phenolic and amine antioxidants in safflower and babassu biodiesel were explored for the first time, showing results close to the standard methods. Therefore, 1H NMR and UV-Vis spectroscopies could be applied as alternatives to the GC and Rancimat® methods to determine conversion and monitor the oxidative stability of biodiesel rapidly and practically.

Slice through the water-Exploring the fundamental challenge of water suppression for benchtop NMR systems.

Benchtop NMR provides improved accessibility in terms of cost, space, and technical expertise. In turn, this encourages new users into the field of NMR spectroscopy. Unfortunately, many interesting samples in education and research, from beer to whole blood, contain significant amounts of water that require suppression in 1H NMR in order to recover sample information. However, due to the significant reduction in chemical shift dispersion in benchtop NMR systems, the sample signals are much closer to the water resonance compared to those in a corresponding high-field NMR spectrum. Therefore, simply translating solvent suppression experiments intended for high-field NMR instruments to benchtop NMR systems without careful consideration can be problematic. In this study, the effectiveness of several popular water suppression schemes was evaluated for benchtop NMR applications. Emphasis is placed on pulse sequences with no, or few, adjustable parameters making them easy to implement. These fall into two main categories: (1) those based on Pre-SAT including Pre-SAT, PURGE, NOESY-PR, and g-NOESY-PR and (2) those based on binomial inversion including JRS and W5-WATERGATE. Among these schemes, solvent suppression sequences based on Pre-SAT offer a general approach for easy solvent suppression for samples with higher analyte concentrations (sucrose standard and Redbull™). However, for human urine, binomial-like sequences were required. In summary, it is demonstrated that highly efficient water suppression approaches can be implemented on benchtop NMR systems in a simple manner, despite the limited spectral dispersion, further illustrating the potential for widespread implementation of these approaches in education and research.

High-throughput calculations and machine learning modeling of 17O NMR in non-magnetic oxides.

The only NMR-active oxygen isotope, oxygen-17 (17O), serves as a sensitive probe due to its large chemical shift range, the electric field gradient at the oxygen site, and the quadrupolar interaction. Consequently, 17O solid-state NMR offers unique insights into local structures and finds significant applications in the studies of disorder, reactivity, and host-guest chemistry. Despite recent advances in sensitivity enhancement, isotopic labeling, and NMR crystallography, the application of 17O solid-state NMR is still hindered by low natural abundance, costly enrichment, and challenges in handling spectrum signals. Density functional theory calculations and machine learning techniques offer an alternative approach to mapping the local crystal structures to NMR parameters. However, the lack of high-quality data remains a challenge, despite the establishment of some datasets. In this study, we implement and execute a high-throughput workflow combining AiiDA and CASTEP to evaluate the NMR parameters. Focusing on non-magnetic oxides, we have chosen over 7100 binary, ternary, and quaternary compounds from the Materials Project database and performed calculations. Furthermore, using various descriptors for the local crystalline environments, we model the 17O NMR parameters using machine learning techniques, further enhancing our ability to predict and understand 17O NMR parameters in oxide crystals.

Recent advances in the NMR of fuel: a brief overview

Present review covers the most recent advances in the NMR studies of oil refining products - light fractions, different types of fuels, heavy fractions, and crude oil itself. By no means does it discuss NMR applications in this field in detail providing only a brief overview of different NMR methods used for structural elucidation of the oil refining products together with crude oil with particular emphasis on recent achievements and advances in this field.<br> The bibliography includes 48 references.

NMR spectroscopy can help accelerate antiviral drug discovery programs

Small molecule drugs have an important role to play in combating viral infections, and biophysics support has been central for contributing to the discovery and design of direct acting antivirals. Perhaps one of the most successful biophysical tools for this purpose is NMR spectroscopy when utilized strategically and pragmatically within team workflows and timelines. This report describes some clear examples of how NMR applications contributed to the design of antivirals when combined with medicinal chemistry, biochemistry, X-ray crystallography and computational chemistry. Overall, these multidisciplinary approaches allowed teams to reveal and expose compound physical properties from which design ideas were spawned and tested to achieve the desired successes. Examples are discussed for the discovery of antivirals that target HCV, HIV and SARS-CoV-2.

Applicability of NMR in combination with chemometrics for the characterization and differentiation of oil-resin extracted from Copaifera langsdorffii and Copaifera spp.

Copaiba oil-resin is a natural product widely used in popular medicine and as raw material for pharmaceutical and cosmetic industry. Differences between species or extraction sites can cause changes in the product composition, which highlights the importance of its quality control regarding purity and identification of the Copaifera species from which the oil-resin was extracted. Thus, this work proposes to use the NMR technique associated with chemometric to differentiate and characterize samples of copaiba oil-resin obtained from different species and regions of Brazil. For this, 1H and 13C NMR spectra of 26 samples of copaiba oil-resin were acquired and submitted to chemometric analysis, which allows the recognition of patterns between the samples, as well as indicate the main variables responsible for the clustering. Based on these results, two-dimensional NMR experiments were carried out to identify the structure of the molecules that can be used as chemical markers to differentiate the oil-resin extracted from the Copaifera langsdorffii from other Copaifera species (Copaifera spp.). The structural elucidation of three terpenes (hardwickic acid, caryophyllene oxide, and kaurenoic acid) was successfully achieved, thus showing a decisive role in distinguishing the Copaifera langsdorffii samples.

Solubilization of progesterone into Gemini surfactant solutions: 2D ROESY spectroscopy

We investigate the capabilities of micellar systems, specifically their role as solubilizing agents for hydrophobic substances. Our focus is on interaction of a Gemini surfactant of 14-6-14,2Br− with progesterone, a hydrophobic bioactive compound. Through the application of 1H NMR and 2D ROESY spectroscopic techniques, we provide a detailed analysis of the proton environments within the surfactant and their spatial organization within the micellar structure. Our results indicate that the integration of progesterone into the system does not significantly disrupt the micellar structure, highlighting the stability of the 14-6-14,2Br− micelles. Additionally, we present compelling evidence suggesting that progesterone is situated near the micellar surface, a critical insight into the positioning of solubilized molecules within micellar structures. The structural fingerprint and electron density map of progesterone further support this conclusion, indicating a potential interaction between the acetyl group of progesterone and the positively charged -N(CH3)2 headgroups of the surfactant near the micelle surface. This study enhances our understanding of micellar systems and their potential use in the solubilization of hydrophobic compounds, paving the way for advancements in drug delivery systems and related fields.

Characterization of Nanoprecipitated PET Nanoplastics by 1H NMR and Impact of Residual Ionic Surfactant on Viability of Human Primary Mononuclear Cells and Hemolysis of Erythrocytes.

Manufactured nanoplastic particles (NPs) are indispensable for in vitro and in vivo testing and a health risk assessment of this emerging environmental contaminant is needed. The high surface area and inherent hydrophobicity of plastic materials makes the production of NPs devoid of any contaminants very challenging. In this study, we produced nanoprecipitated polyethylene terephthalate (PET) NPs (300 nm hydrodynamic diameter) with an overall yield of 0.76%. The presence of the ionic surfactant sodium dodecyl sulfate (SDS) was characterized by 1H NMR, where the relative ratio of NP/surfactant was monitored on the basis of the chemical shifts characteristic of PET and SDS. For a wide range of surfactant/NP ratios (17:100 to 1.2:100), the measured zeta potential changed from -42.10 to -34.93 mV, but with an NP concentration up to 100 μg/mL, no clear differences were observed in the cellular assays performed in protein-rich media on primary human cells. The remaining impurities contributed to the outcome of the biological assays applied in protein-free buffers, such as human red blood cell hemolysis. The presence of SDS increased the NP-induced hemolysis by 1.5% in protein-rich buffer and by 7.5% in protein-free buffer. As the size, shape, zeta potential, and contaminants of NPs may all be relevant parameters for the biological effects of NPs, the relative quantification of impurities exemplified in our work by the application of 1H NMR for PET NPs and the ionic surfactant SDS could be a valuable auxiliary method in the quality control of manufactured NPs.

Application of response surface methodology and quantitative NMR for the optimum extraction, characterization, and quantitation of Antrodia cinnamomea triterpenoids

Antrodia cinnamomea (AC) is a treasured Asian medicinal mushroom, which has attracted attention due to recent research on its effectiveness in targeting a variety of serious ailments such as cancer and liver diseases. Among different A. cinnamomea constituents, triterpenoids are regarded as the most therapeutically attractive components because of their anti-inflammatory and cytotoxic activities. In the present study, we proposed a mathematical and statistical extraction protocol to evaluate the concentrations of total ergostane and lanostane triterpenoid derivatives from the ethanolic extract of the wild fruiting bodies of A. cinnamomea (EEAC) by utilizing response surface methodology (RSM) and quantitative NMR (qNMR) approaches. The optimum response surface model showed that the variations of the investigated response variables reached more than 90%, suggesting that the developed model is accurate in explaining response variability. Furthermore, the EEAC major characteristic triterpenoids were quantified through the comparison of the HPLC-tandem MS results with those of the qNMR results. The precision of the used techniques was also evaluated. The experimental design of the EEAC optimum extraction procedure obtained by using RSM and qNMR enabled accurate characterization and quantitation of A. cinnamomea triterpenoids.

Rhabdastrellosides A and B: Two New Isomalabaricane Glycosides from the Marine Sponge Rhabdastrella globostellata, and Their Cytotoxic and Cytoprotective Effects.

Investigation of the Vietnamese marine sponge Rhabdastrella globostellata led to the isolation of two new polar isomalabaricanes: rhabdastrellosides A (1) and B (2). Their structures and stereochemistry were elucidated with the application of 1D and 2D NMR, HRESIMS, and HRESIMS/MS methods, as well as chemical modifications and GC-MS analysis. Metabolites 1 and 2 are the first isomalabaricanes with non-oxidized cyclopentane ring in the tricyclic core system. Moreover, having a 3-O-disaccharide moiety in their structures, they increase a very rare group of isomalabaricane glycosides. We report here a weak cytotoxicity of 1 and 2 toward human neuroblastoma SH-SY5Y cells and normal rat H9c2 cardiomyocytes, as well as the cytoprotective activity of rhabdastrelloside B (2) at 1 µM evaluated using CoCl2-treated SH-SY5Y and H9c2 cells.

Application of NMR and Chemometric Analyses to Better Understand the Quality Attributes in pH and Thermally Degraded Monoclonal Antibodies

PurposeNuclear magnetic resonance (NMR) spectroscopy provides the sensitivity and specificity to probe the higher order structure (HOS) of monoclonal antibodies (mAbs) for potential changes. This study demonstrates an application of chemometric tools to measure differences in the NMR spectra of mAbs after forced degradation relative to the respective unstressed starting materials.MethodsSamples of adalimumab (Humira, ADL-REF) and trastuzumab (Herceptin, TRA-REF) were incubated in three buffer-pH conditions at 40°C for 4 weeks to compare to a control sample that was left unstressed. Replicate 1D 1H and 2D 1H-13C HMQC NMR spectra were collected on all samples. Chemometric analyses such as Easy Comparability of HOS (ECHOS), PROtein FIngerprinting by Lineshape Enhancement (PROFILE), and Principal Component Analysis (PCA) were applied to capture and quantitate differences between the spectra.ResultsVisual and statistical inspection of the 2D 1H-13C HMQC spectra of adalimumab and trastuzumab after forced degradation conditions shows no changes in the spectra relative to the unstressed material. Chemometric analysis of the 1D 1H NMR spectra shows only minor changes in the spectra of adalimumab after forced degradation, but significant differences in trastuzumab.ConclusionThe chemometric analyses support the lack of statistical differences in the structure of pH-thermal stressed adalimumab, however, it reveals conformational changes or chemical modifications in trastuzumab after forced degradation. Application of chemometrics in comparative NMR studies enables HOS characterization and showcases the sensitivity and specificity in detecting differences in the spectra of mAbs after pH-thermal forced degradation with respect to local and global protein structure.

In situ monitoring multi-carbon alcohol oxidation by combined electrochemistry with spatially selective NMR spectroscopy

In situ electrochemical nuclear magnetic resonance (EC-NMR) plays a pivotal role in electrochemical observation on liquid fuel cells, but its applications are generally trapped by insufficient spectral resolution caused by spatiotemporal variations of magnetic fields. Herein, we develop a general spectroelectrochemistry protocol to address this problem and facilitate real-time electrooxidation analyses. This protocol enables the direct extraction of well-resolved and undistorted NMR signals from standard NMR instruments, thus it is commonly applicable to in situ electrochemical studies. The effectiveness for electrooxidation mechanism investigations on multi-carbon alcohols is validated by 1-butanol electrooxidation. It is verified that the direct oxidation of 1-butanol to butyric acid becomes more significant along with higher potentials on Pt/C at 60 °C, while 1-butanol oxidation is more likely to yield gaseous products (mainly CO2) at lower potentials. Additionally, this protocol reveals that Pt/C rather than PtRu/C is inclined to accomplish the β -C–H bond breaking process for CO2 generation at a high potential of 1.2 V (vs. SCE) . Therefore, this study provides a promising paradigm for electrooxidation investigations on fuel cells, and it may take a meaningful step toward wider electrochemical studies and NMR applications.

A thermosensitive gel matrix for bioreactor-assisted in-cell NMR of nucleic acids and proteins

Introducing the flow through the bioreactor has revolutionized in-cell NMR spectroscopy by prolonging the measurement time available to acquire spectral information about biomacromolecules in metabolically active cells. Bioreactor technology relies on immobilizer matrices, which secure cells in the active volume of the NMR coil and enable uniform perfusion of the growth medium, supplying fresh nutrients to the cells while removing toxic byproducts of their metabolism. The main drawbacks of commonly used matrices include the inability to recover intact cells post-measurement for additional analyses and/or requirements for specific operating temperatures. Here, we report on the development and characterization of a set of thermosensitive and nontoxic triblock copolymers based on poly(D,L-lactide)-b-poly(ethylene glycol)-b-poly(D,L-lactide) (PLA-PEG-PLA). Here, we show for the first time that these copolymers are suitable as immobilizer matrices for the acquisition of in-cell NMR spectra of nucleic acids and proteins over a commonly used sample temperature range of 15–40 °C and, importantly, allow recovery of cells after completion of in-cell NMR spectra acquisition. We compared the performances of currently used matrices in terms of cell viability (dye exclusion assays), cellular metabolism (1D 31P NMR), and quality of in-cell NMR spectra of two model biomacromolecules (hybrid double-stranded/i-motif DNA and ubiquitin). Our results demonstrate the suitability and advantages of PLA-PEG-PLA copolymers for application in bioreactor-assisted in-cell NMR.