Dimensional Nuclear Magnetic Resonance Research Articles

A Joint Inversion Method Algorithm for T2-Pc two Dimensional NMR based on Logistic Functions

Data processing is a key step in the analysis of nuclear magnetic resonance (NMR) experimental data, and efficient and accurate computer inversion algorithms are the core of the T2-Pc two-dimensional NMR experiment. T2-Pc two-dimensional NMR experiment is an advanced experimental method that characterizes reservoir connectivity through two dimensions: relaxation time and capillary pressure, and can obtain irreducible water saturation under different pressure differences. However, the algorithm currently used for T2-Pc two-dimensional spectrum inversion uses a mutation kernel function, resulting in low accuracy of calculation results. This paper uses the Logistic function as the two-dimensional inversion kernel function, rewrites the inversion algorithm, and obtains more accurate inversion results. Numerical simulations have proven that the T2-Pc two-dimensional map obtained by this method not only has higher resolution, but also has greater applicability in the case of low signal-to-noise ratio and a small number of centrifugal echo groups. Practice has found that the proposed method can reduce the number of centrifugations during the experiment and significantly improve the efficiency of T2-Pc two-dimensional nuclear magnetic resonance experiments.

Recovery time reduction to decrease experimental duration (R2D2): A simple and universal method to accelerate NMR experiments

Acceleration techniques for one dimensional Nuclear Magnetic Resonance (1D NMR) are very useful, both for NMR enthusiasts and for chemists that use NMR for structural elucidation. To the latter, such techniques need to be straightforward. Recovery time Reduction to Decrease the experimental Duration (R2D2) relies on the incremental reduction of a pulse sequence's Recycle Time (TR). A pseudo-2D spectrum is acquired and after two Fourier transform, extraction and addition of the central rows, a 1D spectrum is obtained. Not only can it be applied to any pulse sequence that contains a TR, but it also requires only a list of recovery times and 2D processes to operate. With this method, we were able to easily reduce the experimental time by a factor of 2 and up to 4 using single-pulse, APT and DEPT 13C sequences. Moreover, R2D2 has the potential to be used on other low abundance nuclei (such as 15N or 2H) and numerous other pulse sequences.

Chemical constituents from Ficus sur Forssk (Moraceae).

Phytochemical investigation of the aerial roots of Ficus sur, a Cameroonian medicinal plant, resulted in apreviously undescribed cerebroside, suroside (1), in addition to its aglycon congener suramide (2). Moreover, six known natural products including alpinumisoflavone (3), wighteone metabolite (4), oleanolic acid (5), β-sitosterol (6), β-sitosterol-3-O-β-D-glucopyranoside (7), and epi-ѱ-taraxastanolone (8) were identified. The structures of thepreviously undescribed compounds were determined by analysis of 1D and 2D-NMR (One and two dimensional nuclear magnetic resonance), mass spectrometry, chemical conversion, and by comparison of these data with those from the literature. Wighteone metabolite (4) exhibited a weak cytotoxic activity against the human HepG2 hepatocellular carcinoma cells with an IC50 value of 51.9µM.

A Multi-Omics Analysis Reveals Anti-Osteoporosis Mechanism of Four Components from Crude and Salt-Processed Achyranthes bidentata Blume in Ovariectomized Rats.

The root of Achyranthes bidentata Blume (AB) is a well-known traditional Chinese medicine for treating osteoporosis. Plenty of studies focused on the pharmacological mechanism of the whole extract; however, the contribution of different components to the anti-osteoporosis effect remains unknown. The aim of this study is to explore the anti-osteoporosis mechanism of different components of crude and salt-processed AB under the guidance of network pharmacology, metabolomics, and microbiomics. First, network pharmacology analysis was applied to constructing the compound-target-disease network of AB to provide a holistic view. Second, the anti-osteoporosis effects of the four components were evaluated in female Wistar rats. The subjects were divided into a normal group, a model group, a 17α-estradiol (E2)-treated group, a polysaccharide-component-treated groups, and a polysaccharide-knockout-component-treated groups. All the serum, urine, and feces samples of the six groups were collected after 16 weeks of treatment. Biochemical and microcomputed tomography (μCT) parameters were also acquired. Coupled with orthogonal partial least-squares discrimination analysis, one dimensional nuclear magnetic resonance (NMR) was used to monitor serum metabolic alterations. A total of twenty-two biomarkers, including lipids, amino acids, polyunsaturated fatty acids, glucose, and so on were identified for the different components-treated groups. Through pathway analysis, it is indicated that glyoxylate and dicarboxylate metabolism, glycine, serine, and threonine metabolism, alanine, aspartate, and glutamate metabolism, d-glutamine, and d-glutamate metabolism were the major intervened pathways. Levels of these biomarkers shifted away from the model group and were restored to normal after treatment with the four components. In addition, 16S rDNA sequencing demonstrated that the abundance of Anaerofilum, Rothia, and Turicibacter bacteria was positively correlated with an anti-osteoporosis effect, whereas the abundance of Oscillospira was negatively correlated. The osteoprotective effect of the polysaccharide components of crude and salt-processed AB is related to the regulation of the abundance of these gut microbiota.

Isolation and identification of polyphenol monomers from celery leaves and their structure-antioxidant activity relationship

This study aimed to isolate, purify and identify phenols from the celery leaves and further evaluate the antioxidant activities of the monomers in chemical system. Seven polyphenol monomers (a-g) were identified by HPLC-ESI-MS/MS after being separated by D101 macroporous resin, semi-preparative reversed-phase high-performance liquid chromatography (RP-HPLC) and sephadex LH-20. Interestingly, chrysoeriol 7-O-glucoside was identified from celery leaves by UV, IR, one dimensional nuclear magnetic resonance (NMR) and two-dimensional NMR for the first time. In addition, these polyphenol monomers manifested desirable DPPH• scavenging capacity (EC50: 39.55 ± 1.43–612 ± 8.45 μM) and ABTS+• scavenging capacity (EC50: 32.12 ± 0.58–512 ± 25.12 μM), respectively. Among them, the polyphenol monomers (a and b) with two hydroxyl groups (-OH) on the B ring in flavone skeleton had the strongest antioxidant activities. Moreover, the analysis of the structure-activity relationship showed that the position and quantity of -OH on the B-ring and the methylation degree of 3-OH played an important role in regulating antioxidant activities.

Bioactive Compounds with Significant Anti- Rheumatoid Arthritis Effect Isolated for the First time from Leaves of Bougainvillea spectabilis.

The aim of this work is to identify and purify bioactive compounds from 70℅ aqueous methanolic extract (AME) of B. spectabilis leaves collected in Cairo, Egypt and assessed their rheumatoid arthritis activity. The methanolic extract of B. spectabilis leaves was fractionated and subjected to different chromatographic techniques to isolate pure new compounds which were identified by one dimensional and two dimensional nuclear magnetic resonance (NMR) spectroscopic analyses and mass spectrometric methods. The isolated compounds were evaluated for their anti-inflammatory activity on adjuvant induced chronic rheumatoid arthritis. Seven bioactive compounds were purified and identified for the first time from the methanolic extract of Bougainvillea spectabilis leaves; secologanin dimethyl acetal, α- and β-amyrin, α- and β-amyrin acetate, Kaempferol and kaempferol-3-O-rhamnoside. The previously mentioned compounds had a significant effect against rheumatoid arthritis. The seven compounds isolated from the methanolic extract of B. spectabilis leaves showed strong anti-rheumatoid arthritis activity.

Isolation and identification of soft resins from Humulus lupulus L

Humulus lupulus L. is abundantly cultivated worldwide for commercial use as raw material in the brewing industry since it adds bitterness and aromatic flavors to the beer. These characteristics are mainly ascribed to hop’s soft resins. However, its soft resin components are rarely studied and the structures of their derivatives remain unclear. This paper aimed to study the chemical diversity of the apolar part of hop extract. Consequently, twenty previously undescribed α-acid derivatives, humulunine A − T (1 − 20), and twenty-nine known compounds (21 − 49) were obtained from hops. Their planar structures were established based on the comprehensive investigations of the one dimensional nuclear magnetic resonance (1D NMR), 2D NMR and high resolution electrospray ionization mass spectrometry (HR-ESI-MS) data. The absolute configurations of compounds 1 − 3, 5 − 7, 11, 13, 16 and 17 were determined by comparing chemical shifts of their chiral carbon atoms and the experimental electronic circular dichroism (ECD) spectra with calculated (calcd) ones. This assignment aimed to acquire further chemical information on hops, which might provide deeper insights into material basis of Hummulus lupulus L.

Tracking oxidation-induced alterations in fibrin clot formation by NMR-based methods

Plasma fibrinogen is an important coagulation factor and susceptible to post-translational modification by oxidants. We have reported impairment of fibrin polymerization after exposure to hypochlorous acid (HOCl) and increased methionine oxidation of fibrinogen in severely injured trauma patients. Molecular dynamics suggests that methionine oxidation poses a mechanistic link between oxidative stress and coagulation through protofibril lateral aggregation by disruption of AαC domain structures. However, experimental evidence explaining how HOCl oxidation impairs fibrinogen structure and function has not been demonstrated. We utilized polymerization studies and two dimensional-nuclear magnetic resonance spectrometry (2D-NMR) to investigate the hypothesis that HOCl oxidation alters fibrinogen conformation and T2 relaxation time of water protons in the fibrin gels. We have demonstrated that both HOCl oxidation of purified fibrinogen and addition of HOCl-oxidized fibrinogen to plasma fibrinogen solution disrupted lateral aggregation of protofibrils similarly to competitive inhibition of fibrin polymerization using a recombinant AαC fragment (AαC 419–502). DOSY NMR measurement of fibrinogen protons demonstrated that the diffusion coefficient of fibrinogen increased by 17.4%, suggesting the oxidized fibrinogen was more compact and fast motion in the prefibrillar state. 2D-NMR analysis reflected that water protons existed as bulk water (T2) and intermediate water (T2i) in the control plasma fibrin. Bulk water T2 relaxation time was increased twofold and correlated positively with the level of HOCl oxidation. However, T2 relaxation of the oxidized plasma fibrin gels was dominated by intermediate water. Oxidation induced thinner fibers, in which less water is released into the bulk and water fraction in the hydration shell was increased. We have confirmed that T2 relaxation is affected by the self-assembly of fibers and stiffness of the plasma fibrin gel. We propose that water protons can serve as an NMR signature to probe oxidative rearrangement of the fibrin clot.

Aramatosides C and D, 2 Previously Undescribed Triterpene Glycosides Isolated From the Roots of Aralia armata

The 2 new oleanane-type triterpene glycosides, 23-hydroxyoleanolic acid-[28- O- β-D-glucopyranosyl]-3- O-{ β-D-glucopyranosyl-(1→2)-[ β-D-glucopyranosyl-(1→3)]- β-D-galactopyranoside}, (1) and oleanolic acid-[28- O- β-D-glucopyranosyl]-3- O-{ β-D-glucopyranosyl-(1→2)-[ β-D-glucopyranosyl-(1→3)]- β-D-galactopyranoside} (2) were isolated from the roots of Aralia armata. Their chemical structures were elucidated by using a combination of high resolution electrospray ionization mass spectrometry (HR-ESI-MS), 1 dimensional (1D), and 2 dimensional (2D) nuclear magnetic resonance spectral data, as well as by comparison with the previous literature. Compounds 1 and 2 displayed weak cytotoxic activity toward KB and HepG2 cell lines with IC50 values of 25.1 ± 1.2 and 23.7 ± 0.9 µM (for 1) and 29.5 ± 1.3 and 23.9 ± 0.7 µM (for 2), respectively, compared to that of the positive control compound, ellipticine (IC50: 1.3 ± 0.1 and 1.6 ± 0.1 µM, respectively) in in vitro assay.

Comprehensive Overview on the Chemistry and Biological Activities of Selected Alkaloid Producing Marine-Derived Fungi as a Valuable Reservoir of Drug Entities.

Marine-associated fungal strains act as a valuable reservoir of bioactive diverse secondary metabolites including alkaloids which are highly popular by their biological activities. This review highlighted the chemistry and biology of alkaloids isolated from twenty-six fungal genera associated with marine organisms and marine sea sediments. The selected fungi are from different marine sources without focusing on mangroves. The studied fungal genera comprises Acrostalagmus, Arthrinium, Chaetomium, Cladosporium, Coniothyrium, Curvularia, Dichotomomyces, Eurotium, Eutypella, Exophiala, Fusarium, Hypocrea, Microsphaeropsis, Microsporum, Neosartorya, Nigrospora, Paecilomyces, Penicillium, Pleosporales, Pseudallescheria, Scedosporium, Scopulariopsis, Stagonosporopsis, Thielavia, Westerdykella, and Xylariaceae. Around 347 alkaloid metabolites were isolated and identified via chromatographic and spectroscopic techniques comprising 1D and 2D NMR (one and two dimensional nuclear magnetic resonance) which were further confirmed using HR-MS (high resolution mass spectrometry) and Mosher reactions for additional ascertaining of the stereochemistry. About 150 alkaloids showed considerable effect with respect to the tested activities. Most of the reported bioactive alkaloids showed considerable biological activities mainly cytotoxic followed by antibacterial, antifungal, antiviral, antioxidant; however, a few showed anti-inflammatory and antifouling activities. However, the rest of the compounds showed weak or no activity toward the tested biological activities and required further investigations for additional biological activities. Thus, alkaloids isolated from marine-associated fungi can afford an endless source of new drug entities that could serve as leads for drug discovery combating many human ailments.

Automated metabolic assignment: Semi-supervised learning in metabolic analysis employing two dimensional Nuclear Magnetic Resonance (NMR)

Metabolomics is an expanding field of medical diagnostics since many diseases cause metabolic reprogramming alteration. Additionally, the metabolic point of view offers an insight into the molecular mechanisms of diseases. Due to the complexity of metabolic assignment dependent on the 1D NMR spectral analysis, 2D NMR techniques are preferred because of spectral resolution issues. Thus, in this work, we introduce an automated metabolite identification and assignment from 1H-1H TOCSY (total correlation spectroscopy) using real breast cancer tissue. The new approach is based on customized and extended semi-supervised classifiers: KNFST, SVM, third (PC3) and fourth (PC4) degree polynomial. In our approach, metabolic assignment is based only on the vertical and horizontal frequencies of the metabolites in the 1H–1H TOCSY. KNFST and SVM show high performance (high accuracy and low mislabeling rate) in relatively low size of initially labeled training data. PC3 and PC4 classifiers showed lower accuracy and high mislabeling rates, and both classifiers fail to provide an acceptable accuracy at extremely low size (≤9% of the entire dataset) of initial training data. Additionally, semi-supervised classifiers were implemented to obtain a fully automatic procedure for signal assignment and deconvolution of TOCSY, which is a big step forward in NMR metabolic profiling. A set of 27 metabolites were deduced from the TOCSY, and their assignments agreed with the metabolites deduced from a 1D NMR spectrum of the same sample analyzed by conventional human-based methodology.

Chemical composition, antimycobacterial and anti-inflammatory activities of iridoids and triterpene from Psychotria suterella (Rubiaceae)

Background: Psychotria species are known for their medicinal properties and psychoactive activities. Extracts of Psychotria suterella showed anti-tuberculosis (TB) activity; however, the substances related to this activity are unknown. Objectives: The objective was to study on the chemical constituents of the leaves of plant and evaluate the anti-TB and anti-inflammatory activity. Materials and Methods: Solvent extraction, partition, and column chromatography were used to separate the compounds. The structures of these compounds were determined by extensive one dimensional-and two dimensional-Nuclear Magnetic Resonance, infrared and mass spectrometry spectroscopic analyses. Some compounds were evaluated for their in vitro activity against Mycobacterium tuberculosis and their ability to inhibit nitric oxide (NO) production by lipopolysaccharide-stimulated macrophages. Results: This study led to the isolation and characterization of a new iridoid, named epi-geniposidic acid (1), together with nine known compounds: geniposidic acid (2), 3-O-acethyloleanolic acid (3), pomolic acid (4), spinolic acid (5), maslinic acid (6), tormentic acid (7), methyl oleanolate (8), lyalosidic acid (9), and strictosidinic acid (10). Triterpene 3-O-acethyloleanolic acid (3) was found to display antimycobacterial activity against M. tuberculosis H37Rv strain and hypervirulent strain (minimum inhibitory concentration 6.7 ± 0.1 and 89.1 ± 1.3 μg/mL, respectively). Epi-geniposidic acid (1), geniposidic acid (2), and 3-O-acethyloleanolic acid (3) showed promising inhibitory activities against NO production (IC50 range 4.12–5.12 μg/mL). The iridoid mixture showed no cytotoxicity against RAW 264.7 macrophages up to a concentration of 100 μg/mL. Conclusion: P. suterella presents relevant biological properties and should be considered for further in vivo studies using a pulmonary TB model.

Fast two-dimensional nuclear magnetic resonance resolution enhancement by use of a Laplacian estimator

A simple and fast data processing algorithm for the resolution enhancement of two dimensional (2 D) nuclear magnetic resonance spectra is proposed. It is based on a modified 2 D Laplacian operator and can be used as a standalone algorithm or embedded within peak picking routines. It can also be combined with other processing techniques such as linear prediction filling or covariance.

A New Chlorinated Phenolic Compound From the Antarctic Lichen, Pertusaria dactylina

A new chlorinated phenolic compound, methyl-3-chloro-2-hydroxy-4-methoxy-6-pentylbenzoate (1) and 4 known compounds (2-5) were isolated from the Antarctic lichen, Pertusaria dactylina ( Pertusariaceae). The structure of the new compound was determined by means of One-dimensional and two dimensional nuclear magnetic resonance (1D and 2D NMR) and high-resolution fast atom bombardment mass spectrometry (HRFABMS) experiments. The antimicrobial activities of compounds 1 to 5 against Staphylococcus aureus and Candida albicans were evaluated. The results showed that compound 1 exhibited a weak inhibitory effect against C. albicans with an IC50 value of 67 ± 7 μg/mL.

English

Ocimum lamiifolium is a well known medicinal plant in Ethiopia. Fresh leaves of the plant are squeezed and sniffed to treat colds and coughs and as an eye rinse for eye infections, while crushed leaves are used to arrest nose bleeding. In this study phytochemical investigation on the methanol extracts of this plant collected from Addis Ketema subcity, Addis Ababa. A triterpene, namely ursolic acid, was isolated using column chromatography over silica gel. The structure of this compound was identified using one dimensional Nuclear Magnetic Resonance (NMR) spectroscopic techniques such as proton NMR (1H NMR), carbon-13 NMR (13C NMR) and distortionless enhancement by polarization transfer (DEPT), two dimensional NMR spectroscopic method such as HMBC, HMQC and COSY and literature survaye. Key words: Ocimum lamiifolium, Ethiopia, phytochemical investigation, ursolic acid, Nuclear Magnetic Resonance (NMR) spectroscopy.

LAMA-1: A Cerebroside Isolated from the Deep-Sea-Derived Fungus Penicillium chrysogenum.

Chemical investigation of the ethyl acetate extract of Penicillium chrysogenum strain S003, a fungus isolated from Red Sea deep sediment, led to the isolation of a cerebroside molecular species LAMA (1) along with three other known compounds, ergosterol (2), epidioxyergosterol (3), and kojic acid (4). The structures of the isolated compounds were elucidated by interpretation of spectral data, including detailed 1D and 2D NMR (One and two dimensional Nuclear Magnetic Resonance) and mass spectrometry. The cytotoxic activities of isolated compounds 1–4 against five human carcinoma cells were evaluated using sulforhodamine B (SRB) assay. Compounds 2 and 3 displayed promising cytotoxic profiles against lung cancer (A-549), prostate (DU-145), breast adenocarcinoma (MCF-7), and hepatocellular (HepG2) cell lines, with IC50 values of 21.26, 19.3; 1.50, 6.10; 16.95, 13.6; and 2.89, 3.07 µM, respectively, while they were inactive against HeLa cells. Compounds 1 and 4 showed weak cytotoxic profiles against all cell lines under investigation.

A Rare Triterpenoidal Saponin Isolated and Identified fromTetraena simplex(L.) Beier &Thulin (Syn.Zygophyllum simplexL.)

AbstractTetraena simplex(L.) Beier & Thulin (syn.Zygophyllum simplexL.) is an annual, succulent plant belonging to family Zygophyllaceae. The plant grows in harsh environmental conditions and it is traditionally used as an analgesic and anti‐inflammatory agent. This study aims to isolate and identify phytochemical constituents of then‐butanol fraction of its aerial parts that was repeatedly chromatographed on Diaion HP‐20 and silica gel columns to yield a rare triterpenoidal saponin, 3‐O‐[β‐D‐glucopyranosyl‐(1→2)‐β‐D‐glucopyranosyl] quinovic acid‐28‐O‐β‐D‐glucopyranosyl ester (1) along with three other known triterpenoidal compounds namely; 3‐O‐methoxy‐quinovic acid (2), quinovic acid (3), and 3‐O‐β‐D‐glucopyranosyl‐quinovic acid (4). Moreover, quercetin 3‐O‐α‐L‐rhamnoside (5) was isolated from this fraction. Different spectroscopic techniques including one dimensional (1D) and two dimensional (2D) NMR (Nuclear Magnetic Resonance) spectroscopy allowed the unambiguous structure elucidation of the isolated compounds.

$N$-Dimensional Tensor Completion for Nuclear Magnetic Resonance Relaxometry

This paper deals with tensor completion for the solution of multidimensional inverse problems arising in nuclear magnetic resonance (NMR) relaxometry. We study the problem of reconstructing an approximately low-rank tensor from a small number of noisy linear measurements. New recovery guarantees, numerical algorithms, nonuniform sampling strategies, and parameter selection methods are developed in this context. In particular, we derive a fixed point continuation algorithm for tensor completion and prove its convergence. A restricted isometry property-based tensor recovery guarantee is proved. Probabilistic recovery guarantees are obtained for sub-Gaussian measurement operators and for measurements obtained by nonuniform sampling from a Parseval tight frame. The proposed algorithm is then applied to the setting of nuclear magnetic resonance relaxometry, for both simulated and experimental data. We compare our results with basis pursuit as well as with the state-of-the-art nonsubsampled data acquisition and reconstruction approach. Our experiments indicate that tensor recovery promises to significantly accelerate $N$-dimensional NMR relaxometry and related experiments, enabling previously impractical experiments to be performed. Our methods could also be applied to other similar inverse problems arising in machine learning, signal and image processing, and computer vision.

Structural Characterization and Antioxidant Activity of Milled Wood Lignin from Xylose Residue and Corncob.

Xylose residue (XR), after diluted acid treatment of corncob, consists of cellulose and lignin. However, structural changes of XR lignin have not been investigated comprehensively, and this has seriously hindered the efficient utilization of lignin. In this study, corncob milled wood lignin (CC MWL), and xylose residue milled wood lignin (XR MWL) were isolated according to the modified milled wood lignin (MWL) method. The structural features of two lignin fractions were thoroughly investigated via fourier transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), thermogravimetric analysis (TGA) and two dimensional nuclear magnetic resonance (2D NMR) spectroscopy techniques. XR MWL with higher yield and lower bound carbohydrate contents presented more phenolic OH contents than CC MWL due to partial cleavage of β-O-4. Furthermore, the molecular weights of XR MWL were increased, possibly because of condensation of the lignin during the xylose production. A study on antioxidant activity showed that XR lignin had better radical scavenging ability than that of 2,6-Di-tert-butyl-4-methyl-phenol (BHT) and CC MWL. The results suggested that the lignin in xylose residue, showing great antioxidant properties, has potential applications in food additives.

Screening of Azaphilone Derivatives From Monascus pilosus-Fermented Rice (Red Yeast Rice) and Their Evaluation as Nonsteroidal Androgen Receptor Antagonists

Monascus pilosus BCRC 38093 is a mutant strain of M. pilosus BCRC 38072. The 95% ethanol extract of red yeast rice fermented by M. pilosus BCRC 38093 showed 4 major signals on high performance liquid chromatography (HPLC) examination. The extraction of metabolites and chromatography of the ethyl acetate crude extract on silica gel yielded 2 azaphilone derivatives, monascin (1) and monascinol (2), and 2 monacolin-type derivatives, acid-form monacolin K (3) and lactone-form monacolin K (4). Their structural characterization was elucidated by spectroscopic techniques ultraviolet-visible (UV), infrared spectroscopy (IR), and two dimensional-nuclear magnetic resonance (2D-NMR) and mass spectrometry. These compounds were assayed for their anti-androgen activity; monascinol (2) exhibited strong activity.