Covariance NMR: Theoretical concerns, practical considerations, contemporary applications and related techniques

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.

Enhanced spectral resolution for correlated spectroscopic imaging using inner-product and covariance transform: a pilot analysis of metabolites and lipids in breast cancer in vivo

Acquisition duration of correlated spectroscopy in vivo can be longer due to a large number of t1 increments along the indirect (F1) dimension. Limited number of t1 increments on the other hand leads to poor spectral resolution along F1. Covariance transformation (CT) instead of Fourier transform along t1 is an alternative way of increasing the resolution of the 2D COSY spectrum. Prospectively undersampled five-dimensional echo-planar correlated spectroscopic imaging (EP-COSI) data from ten malignant patients and ten healthy women were acquired and reconstructed using compressed sensing. The COSY spectrum at each voxel location was then generated using FFT, CT and a variant of CT called Inner Product (IP). Metabolite and lipid ratios were computed with respect to water from unsuppressed one-dimensional spectrum. The effects of t1-ridging artifacts commonly seen with FFT were not observed with CT/IP. Statistically significant differences were observed in the fat cross peaks measured with CT/IP/FFT. Spectral resolution was increased ~ 8.5 times (~ 19.53 Hz in FFT, ~ 2.32 Hz in CT/IP) without affecting the spectral width along F1 was possible with CT/IP. CT and IP enabled substantially increased F1 resolution effectively with significant gain in scan time and reliable measure of unsaturation index as a biomarker for malignant breast cancer.

Quantitative stray-field T1 relaxometry with the matrix pencil method

The matrix pencil method (MPM) is tested as an approach to quantitatively process multiexponential low-field nuclear magnetic resonance T₁ relaxometry data. The data is obtained by measuring T₁ saturation recovery curves in the highly inhomogeneous magnetic field of a stray-field sensor. 0.9% brine solutions, doped with different concentrations of a Gd³⁺ containing contrast agent, serve as test liquids. Relaxation-times as a function of contrast-agent concentration along with the T₁ relaxation curves for combinations of multiple different test liquids are measured, and the results from processing using MPM as well as inverse Laplace transformation as a benchmark are compared. The relaxation-time resolution limits of both procedures are probed by gradually reducing the difference between the relaxation-times of two liquids measured simultaneously. The sensitivity to quantify the relative contribution of each component to the magnetization build-up curve is explored by changing their volume ratio. Furthermore, the potential to resolve systems with more than two components is tested. For the systems under test, MPM shows superior performance in separating two or three relaxation components, respectively and effectively quantifying the time constants.

NMR Fingerprints of Formyl Phloroglucinol Meroterpenoids and Their Application to the Investigation of Eucalyptus gittinsii subsp. gittinsii

NMR fingerprints provide powerful tools to identify natural products in complex mixtures. Principal component analysis and machine learning using ¹H and ¹³C NMR data, alongside structural information from 180 published formyl phloroglucinols, have generated diagnostic NMR fingerprints to categorize subclasses within this group. This resulted in the reassignment of 167 NMR chemical shifts ascribed to 44 compounds. Three pyrano-diformyl phloroglucinols, euglobal In-1 and psiguadiols E and G, contained ¹H and ¹³C NMR data inconsistent with their predicted phloroglucinol subclass. Subsequent reinterpretation of their 2D NMR data combined with DFT ¹³C NMR chemical shift and ECD calculations led to their structure revisions. Direct covariance processing of HMBC data permitted ¹H resonances for individual compounds in mixtures to be associated, and analysis of their ¹H/¹³C HMBC correlations using the fingerprint tool further classified components into phloroglucinol subclasses. NMR fingerprinting HMBC data obtained for six eucalypt flower extracts identified three subclasses of pyrano-acyl-formyl phloroglucinols from Eucalyptus gittinsii subsp. gittinsii. New, eucalteretial F and (+)-eucalteretial B, and known, (-)-euglobal VII and eucalrobusone C, compounds, each belonging to predicted subclasses, were isolated and characterized. Staphylococcus aureus and Plasmodium falciparum screening revealed eucalrobusone C as the most potent antiplasmodial formyl phloroglucinol to date.

1H NMR-based metabolic profile and chemometric analysis for the discrimination of Passiflora species genotypic variations

The species of the genus Passiflora (Passifloraceae family) have been used as food, cosmetic and traditional herbal. As a result, the Passiflora species are widely cultivated and has an economic, medicinal and ornamental importance. The popular designation as "passion fruit" and chemical profile of several Passiflora species remains unknown. The lack of chemical information contributes to the erroneous classification and adulteration. In recent years, special attention has been paid to the bioactivity and phytochemical profiles of several Passiflora species extracts. In this research, ¹H NMR-based metabolic profiling coupled with chemometric tools was used to characterize and distinguish extracts obtained from different wild Passiflora species (P. alata, P. cincinnata, and P. setacea) and genetic varieties (P. alata var. BRS Pérola do Cerrado, P. cincinnata var. BRS Sertão Forte, and P. setacea var. BRS Pérola do Cerrado). Fourteen metabolites were identified by 1D and 2D NMR experiments, highlighting the presence of fatty acids, carbohydrates, saponins, alkaloids, and mainly C-glycosidic flavones. Principal components analysis (PCA) allowed discrimination of Passiflora extracts, which the quadranguloside, oleanolic acid-3-sophoroside, α-glucose, β-glucose, and vitexin-2-O"-rhamnoside were relevant in the differentiation of P. alata and P. alata var. BRS Pérola do Cerrado, while the flavones isovitexin and isovitexin-2-O"-xyloside were dominant in the grouping of P. setacea and P. setacea var. BRS Pérola do Cerrado, and finally P. cincinnata and P. cincinnata var. BRS Sertão Forte grouped by the influence of the fatty acids, sucrose, flavones (isoorientin and vitexin-2-O"-xyloside), and trigonelline. The varieties of P. setacea, and P. cincinnata are chemically equivalent to the original Passiflora species. However, the PCA analysis showed that the genetic variety of P. alata occupied a different position in the scores plot provoked mainly by the presence of oleanolic acid-3-sophoroside. The ¹H NMR metabolic profile can be efficient for quality control evaluation, and can contribute to the investigation of new alternatives for official Passiflora herbal medicines.

Benchtop nuclear magnetic resonance spectroscopy in forensic chemistry

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique well known for its ability to elucidate structures and analyse mixtures and its quantitative nature. However, the cost and maintenance of high field NMR instruments prevent its widespread use by forensic chemists. The introduction of benchtop NMR spectrometers to the market operating at 40-80 MHz have a small footprint, are easy to use and cost much less than high field instruments, which makes them well suited to meet the needs of forensic chemists. These modern low field spectrometers are often capable of running multiple nuclei including ¹ H, ¹³ C, ¹⁹ F and ³¹ P; 2D NMR experiments and advanced experiments such as solvent suppression and diffusion-ordered spectroscopy (DOSY) are possible. This has resulted in a number of publications in the area of forensic chemistry using benchtop NMR spectroscopy in the last 5 years that was previously missing from the literature. This mini review summarises this research including examples of benchtop NMR being used to identify and quantify compounds relevant to forensics and some advanced methods that may be used to overcome some of the limitations of these instruments for forensic analysis. Further validation and automation are likely required for widespread uptake of benchtop NMR in industry; however, it has been demonstrated as a useful complement to other analytical techniques commonplace of forensic laboratories.

Continuing progress in the field of two-dimensional correlation spectroscopy (2D-COS), part II. Recent noteworthy developments

This comprehensive survey review compiles noteworthy developments and new concepts of two-dimensional correlation spectroscopy (2D-COS) for the last two years. It covers review articles, books, proceedings, and numerous research papers published on 2D-COS, as well as patent and publication trends. 2D-COS continues to evolve and grow with new significant developments and versatile applications in diverse scientific fields. The healthy, vigorous, and diverse progress of 2D-COS studies in many fields strongly confirms that it is well accepted as a powerful analytical technique to provide an in-depth understanding of systems of interest.

Continuing progress in the field of two-dimensional correlation spectroscopy (2D-COS): Part III. Versatile applications

In this review, the comprehensive summary of two-dimensional correlation spectroscopy (2D-COS) for the last two years is covered. The remarkable applications of 2D-COS in diverse fields using many types of probes and perturbations for the last two years are highlighted. IR spectroscopy is still the most popular probe in 2D-COS during the last two years. Applications in fluorescence and Raman spectroscopy are also very popularly used. In the external perturbations applied in 2D-COS, variations in concentration, pH, and relative compositions are dramatically increased during the last two years. Temperature is still the most used effect, but it is slightly decreased compared to two years ago. 2D-COS has been applied to diverse systems, such as environments, natural products, polymers, food, proteins and peptides, solutions, mixtures, nano materials, pharmaceuticals, and others. Especially, biological and environmental applications have significantly emerged. This survey review paper shows that 2D-COS is an actively evolving and expanding field.

Metabolite profiling analysis of hepatitis B virus-induced liver cirrhosis patients with minimal hepatic encephalopathy using gas chromatography-time-of-flight mass spectrometry and ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry

This study used gas chromatography-time-of-flight mass spectrometry (GC-TOFMS) and ultra-performance liquid chromatography-quadrupole TOFMS (UPLC-QTOFMS) metabonomic analytical techniques in combination with bioinformatics and pattern recognition analysis methods to analyze the serum metabolite profiling of hepatitis B virus (HBV)-induced liver cirrhosis patients with minimal hepatic encephalopathy (MHE), to find the specific biomarkers of MHE, to reveal the pathogenesis of MHE, and to determine a promising approach for early diagnosis of MHE. Serum samples of 100 normal controls (NC group), 29 HBV-induced liver cirrhosis patients with MHE (MHE group), and 24 HBV-induced liver cirrhosis patients without MHE [comprising 12 cases of compensated cirrhosis (CS group) and 12 cases of decompensated cirrhosis (DS group)] were collected and employed into GC-TOFMS and UPLC-QTOFMS platforms for serum metabolite detection; the outcome data were then analyzed using principal component analysis and orthogonal partial least squares-discriminant analysis (OPLS-DA). There were no significant differential metabolites between the NC group and the CS group. A series of key differential metabolites were detected. According to the variable influence in projection values and P-values, 60 small-molecule metabolites were considered to be dysregulated in the MHE group (compared to the NC group); 27 of these 60 dysregulated differential metabolites were considered to be the potential biomarkers (see Table 4, marked in bold); 66 small-molecule metabolites were considered to be dysregulated in the DS group (compared to the NC group); 34 of these 66 dysregulated differential metabolites were considered to be the potential biomarkers (see Table 5, marked in bold). According to the fold-change values, 9 of these 27 metabolites, namely valine, oxalic acid, erythro-sphingosine, 4,7,10,13,16,19-docosahexaenoic acid, isoleucine, allo-isoleucine, thyroxine, rac-octanoyl carnitine, and tocopherol (vitamin E), were downregulated in the MHE group (compared to the NC group); the other 18, namely adenine, glycochenodeoxycholic acid, fucose, allothreonine, glycohyocholic acid, glycoursodeoxycholic acid, tyrosine, taurocheno-deoxycholate, phenylalanine, 2-hydroxy-3-methyl-butanoic acid, hydroxyacetic acid, taurocholate, sorbitol, rhamnose, tauroursodeoxycholate, tolbutamide, pyroglutamic acid, and malic acid, were upregulated; 6 of these 34 metabolites were downregulated in the DS group (compared to the NC group), and the other 28 were upregulated, as shown in Table 5. (a) GC-TOFMS and UPLC-QTOFMS metabonomic analytical platforms can detect a range of metabolites in the serum; this might be of great help to study the pathogenesis of MHE and may provide a new approach for the early diagnosis of MHE. (b) Metabonomics analysis in combination with pattern recognition analysis might have great potential to distinguish the HBV-induced liver cirrhosis patients who have MHE from the normal healthy population and HBV-induced liver cirrhosis patients without MHE.

Minimizing Pervasive Artifacts in 4D Covariance Maps for Protein Side Chain NMR Assignments

Nuclear magnetic resonance (NMR) is a mainstay of biophysical studies that provides atomic level readouts to formulate molecular mechanisms. Side chains are particularly important to derive mechanisms involving proteins as they carry functional groups, but NMR studies of side chains are often limited by challenges in assigning their signals. Here, we designed a novel computational method that combines spectral derivatives and matrix square-rooting to produce reliable 4D covariance maps from routinely acquired 3D spectra and facilitates side chain resonance assignments. Thus, we generate two 4D maps from 3D-HcccoNH and 3D-HCcH-TOCSY spectra that each help overcome signal overlap or sensitivity losses. These 4D maps feature HC-HSQCs of individual side chains that can be paired to assigned backbone amide resonances of individual aliphatic signals, and both are obtained from a single modified covariance calculation. Further, we present 4D maps produced using conventional triple resonance experiments to easily assign asparagine side chain amide resonances. The 4D covariance maps encapsulate the lengthy manual pattern recognition used in traditional assignment methods and distill the information as correlations that can be easily visualized. We showcase the utility of the 4D covariance maps with a 10 kDa peptidyl carrier protein and a 52 kDa cyclization domain from a nonribosomal peptide synthetase.