Fingerprinting analysis of Rhizoma chuanxiong of commercial types using 1H nuclear magnetic resonance spectroscopy and high performance liquid chromatography method.

PubMed

Qin, Hai-Lin; Deng, An-Jun; Du, Guan-Hua; Wang, Peng; Zhang, Jin-Lan; Li, Zhi-Hong

2009-06-01

The (1)H nuclear magnetic resonance ((1)H NMR) fingerprints of fractionated non-polar extracts (control substance for a plant drug (CSPD) A) from Rhizoma chuanxiong, the rhizomes of Ligusticum chuanxiong Hort., of seven specimens from different sources were measured on Fourier Transform (FT)-NMR spectrometer and assigned by comparing them with the (1)H NMR spectra of the isolated pure compounds. The (1)H NMR fingerprints showed exclusively characteristic resonance signals of the major special constituents of the plant. Although the differences in the relative intensity of the (1)H NMR signals due to a discrepancy in the ratio of the major constituents among these samples could be confirmed by high performance liquid chromatography analysis, the general features of the (1)H NMR fingerprint established for an authentic sample of the rhizomes of L. chuanxiong exhibited exclusive data from those special compounds and can be used for authenticating L. Chuanxiong species.

Genotype evaluation of cowpea seeds (Vigna unguiculata) using 1H qNMR combined with exploratory tools and solid-state NMR.

PubMed

Alves Filho, Elenilson G; Silva, Lorena M A; Teofilo, Elizita M; Larsen, Flemming H; de Brito, Edy S

2017-01-01

The ultimate aim of this study was to apply a non-targeted chemometric analysis (principal component analysis and hierarchical clustering analysis using the heat map approach) of NMR data to investigate the variability of organic compounds in nine genotype cowpea seeds, without any complex pre-treatment. In general, both exploratory tools show that Tvu 233, CE-584, and Setentão genotypes presented higher amount mainly of raffinose and Tvu 382 presented the highest content of choline and least content of raffinose. The evaluation of the aromatic region showed the Setentão genotype with highest content of niacin/vitamin B3 whereas Tvu 382 with lowest amount. To investigate rigid and mobile components in the seeds cotyledon, 13 C CP and SP/MAS solid-state NMR experiments were performed. The cotyledon of the cowpea comprised a rigid part consisting of starch as well as a soft portion made of starch, fatty acids, and protein. The variable contact time experiment suggests the presence of lipid-amylose complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C.

PubMed

Gaßmeyer, Sarah Katharina; Yoshikawa, Hiroyuki; Enoki, Junichi; Hülsemann, Nadine; Stoll, Raphael; Miyamoto, Kenji; Kourist, Robert

2015-06-23

Structure-guided protein engineering achieved a variant of the unique racemase AMDase G74C, with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. Substrate binding during catalysis was investigated by saturation-transfer-difference NMR (STD-NMR) spectroscopy. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose substitutions increased the activity of G74C. Single amino acid exchanges increased the activity moderately; structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.

PubMed

Collins, Katherine M; Oregioni, Alain; Robertson, Laura E; Kelly, Geoff; Ramos, Andres

2015-03-31

Defining the RNA target selectivity of the proteins regulating mRNA metabolism is a key issue in RNA biology. Here we present a novel use of principal component analysis (PCA) to extract the RNA sequence preference of RNA binding proteins. We show that PCA can be used to compare the changes in the nuclear magnetic resonance (NMR) spectrum of a protein upon binding a set of quasi-degenerate RNAs and define the nucleobase specificity. We couple this application of PCA to an automated NMR spectra recording and processing protocol and obtain an unbiased and high-throughput NMR method for the analysis of nucleobase preference in protein-RNA interactions. We test the method on the RNA binding domains of three important regulators of RNA metabolism. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comprehensive NMR analysis of compositional changes of black garlic during thermal processing.

PubMed

Liang, Tingfu; Wei, Feifei; Lu, Yi; Kodani, Yoshinori; Nakada, Mitsuhiko; Miyakawa, Takuya; Tanokura, Masaru

2015-01-21

Black garlic is a processed food product obtained by subjecting whole raw garlic to thermal processing that causes chemical reactions, such as the Maillard reaction, which change the composition of the garlic. In this paper, we report a nuclear magnetic resonance (NMR)-based comprehensive analysis of raw garlic and black garlic extracts to determine the compositional changes resulting from thermal processing. (1)H NMR spectra with a detailed signal assignment showed that 38 components were altered by thermal processing of raw garlic. For example, the contents of 11 l-amino acids increased during the first step of thermal processing over 5 days and then decreased. Multivariate data analysis revealed changes in the contents of fructose, glucose, acetic acid, formic acid, pyroglutamic acid, cycloalliin, and 5-(hydroxymethyl)furfural (5-HMF). Our results provide comprehensive information on changes in NMR-detectable components during thermal processing of whole garlic.

Reproducibility of NMR Analysis of Urine Samples: Impact of Sample Preparation, Storage Conditions, and Animal Health Status

PubMed Central

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Introduction. Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining 1H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. Methods. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after 1H NMR spectroscopy. Results. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at −20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Conclusion. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions. PMID:23865070

Reproducibility of NMR analysis of urine samples: impact of sample preparation, storage conditions, and animal health status.

PubMed

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining (1)H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after (1)H NMR spectroscopy. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at -20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions.

Multicomponent analysis of fat- and water-soluble vitamins and auxiliary substances in multivitamin preparations by qNMR.

PubMed

Eiff, Julia; Monakhova, Yulia B; Diehl, Bernd W K

2015-04-01

A nuclear magnetic resonance (NMR) spectroscopic method was tested to control 12 vitamins and accompanying substances in multivitamin preparations. The limits of detection (LODs) and limits of quantification (LOQs) varied in the 9.0-77.0 mg/kg and in the 34.5-93.5 mg/kg range, respectively. The coefficients of variation (CVs) ranged between 0.9% and 12%. The (1)H NMR spectra showed linearity for the 140-260 mg sample weight (R(2) > 0.918). The NMR spectra of multivitamin preparations showed the presence of different degradation products of ascorbic acid. The NMR method was applied to 13 different multivitamin preparations including tablets, capsules, and effervescent tablets with average recovery rates between 85% and 132%. A number of accompanying substances (citric acid, mannitol, saccharin, cyclamate, sum of steviol glycosides, and butylhydroxytoluene) were additionally identified and quantified. NMR was found to be suitable for the simultaneous qualitative measurement of water- and fat-soluble vitamins and accompanying substances and shows some promise for quantitative determination of at least 5 vitamins (B1, B3, B5, B6, and E) in multivitamin preparations.

Analysis of the interface variability in NMR structure ensembles of protein-protein complexes.

PubMed

Calvanese, Luisa; D'Auria, Gabriella; Vangone, Anna; Falcigno, Lucia; Oliva, Romina

2016-06-01

NMR structures consist in ensembles of conformers, all satisfying the experimental restraints, which exhibit a certain degree of structural variability. We analyzed here the interface in NMR ensembles of protein-protein heterodimeric complexes and found it to span a wide range of different conservations. The different exhibited conservations do not simply correlate with the size of the systems/interfaces, and are most probably the result of an interplay between different factors, including the quality of experimental data and the intrinsic complex flexibility. In any case, this information is not to be missed when NMR structures of protein-protein complexes are analyzed; especially considering that, as we also show here, the first NMR conformer is usually not the one which best reflects the overall interface. To quantify the interface conservation and to analyze it, we used an approach originally conceived for the analysis and ranking of ensembles of docking models, which has now been extended to directly deal with NMR ensembles. We propose this approach, based on the conservation of the inter-residue contacts at the interface, both for the analysis of the interface in whole ensembles of NMR complexes and for the possible selection of a single conformer as the best representative of the overall interface. In order to make the analyses automatic and fast, we made the protocol available as a web tool at: https://www.molnac.unisa.it/BioTools/consrank/consrank-nmr.html. Copyright © 2016 Elsevier Inc. All rights reserved.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

NASA Astrophysics Data System (ADS)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

Metabolic profiling of human lung cancer blood plasma using 1H NMR spectroscopy

NASA Astrophysics Data System (ADS)

Kokova, Daria; Dementeva, Natalia; Kotelnikov, Oleg; Ponomaryova, Anastasia; Cherdyntseva, Nadezhda; Kzhyshkowska, Juliya

2017-11-01

Lung cancer (both small cell and non-small cell) is the second most common cancer in both men and women. The article represents results of evaluating of the plasma metabolic profiles of 100 lung cancer patients and 100 controls to investigate significant metabolites using 400 MHz 1H NMR spectrometer. The results of multivariate statistical analysis show that a medium-field NMR spectrometer can obtain the data which are already sufficient for clinical metabolomics.

Facilitated Visual Interpretation of Scores in Principal Component Analysis by Bioactivity-Labeling of 1H-NMR Spectra-Metabolomics Investigation and Identification of a New α-Glucosidase Inhibitor in Radix Astragali.

PubMed

Liu, Yueqiu; Nyberg, Nils T; Jäger, Anna K; Staerk, Dan

2017-03-06

Radix Astragali is a component of several traditional medicines used for the treatment of type 2 diabetes in China. Radix Astragali is known to contain isoflavones, which inhibit α-glucosidase in the small intestines, and thus lowers the blood glucose levels. In this study, 21 samples obtained from different regions of China were extracted with ethyl acetate, then the IC50-values were determined, and the crude extracts were analyzed by 1H-NMR spectroscopy. A principal component analysis of the 1H-NMR spectra labeled with their IC50-values, that is, bioactivity-labeled 1H-NMR spectra, showed a clear correlation between spectral profiles and the α-glucosidase inhibitory activity. The loading plot and LC-HRMS/NMR of microfractions indicated that previously unknown long chain ferulates could be partly responsible for the observed antidiabetic activity of Radix Astragali. Subsequent preparative scale isolation revealed a compound not previously reported, linoleyl ferulate (1), showing α-glucosidase inhibitory activity (IC50 0.5 mM) at a level comparable to the previously studied isoflavones. A closely related analogue, hexadecyl ferulate (2), did not show significant inhibitory activity, and the double bonds in the alcohol part of 1 seem to be important structural features for the α-glucosidase inhibitory activity. This proof of concept study demonstrates that bioactivity-labeling of the 1H-NMR spectral data of crude extracts allows global and nonselective identification of individual constituents contributing to the crude extract's bioactivity.

Metabolite profiling of Clinacanthus nutans leaves extracts obtained from different drying methods by 1H NMR-based metabolomics

NASA Astrophysics Data System (ADS)

Hashim, Noor Haslinda Noor; Latip, Jalifah; Khatib, Alfi

2016-11-01

The metabolites of Clinacanthus nutans leaves extracts and their dependence on drying process were systematically characterized using 1H nuclear magnetic resonance spectroscopy (NMR) multivariate data analysis. Principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA) were able to distinguish the leaves extracts obtained from different drying methods. The identified metabolites were carbohydrates, amino acid, flavonoids and sulfur glucoside compounds. The major metabolites responsible for the separation in PLS-DA loading plots were lupeol, cycloclinacosides, betulin, cerebrosides and choline. The results showed that the combination of 1H NMR spectroscopy and multivariate data analyses could act as an efficient technique to understand the C. nutans composition and its variation.

Quantification of oil and water in preserved reservoir rock by NMR spectroscopy and imaging.

PubMed

Davies, S; Hardwick, A; Roberts, D; Spowage, K; Packer, K J

1994-01-01

Reservoir rock analysis by proton NMR requires separation of the response into brine and crude oil components. Tests on preserved core from a North Sea chalk reservoir show that spin-lattice relaxation time distributions can be used to distinguish the two fluids. NMR estimates of oil and water saturations for 1.5" diameter core examined in a 10 MHz Bruker Minispec spectrometer closely match fluid contents determined by distillation. The spin-lattice relaxation contrast mechanism developed for core samples can be applied in the quantitative analysis of NMR images. The relaxation data are compared with data from chemical shift imaging on the same core sample. The results indicate that it will be possible to monitor changes in fluid distributions, in this and similar systems, under dynamic conditions such as in a waterflood.

Biological variation of Vanilla planifolia leaf metabolome.

PubMed

Palama, Tony Lionel; Fock, Isabelle; Choi, Young Hae; Verpoorte, Robert; Kodja, Hippolyte

2010-04-01

The metabolomic analysis of Vanilla planifolia leaves collected at different developmental stages was carried out using (1)H-nuclear magnetic resonance (NMR) spectroscopy and multivariate data analysis in order to evaluate their variation. Ontogenic changes of the metabolome were considered since leaves of different ages were collected at two different times of the day and in two different seasons. Principal component analysis (PCA) and partial least square modeling discriminate analysis (PLS-DA) of (1)H NMR data provided a clear separation according to leaf age, time of the day and season of collection. Young leaves were found to have higher levels of glucose, bis[4-(beta-D-glucopyranosyloxy)-benzyl]-2-isopropyltartrate (glucoside A) and bis[4-(beta-D-glucopyranosyloxy)-benzyl]-2-(2-butyl)-tartrate (glucoside B), whereas older leaves had more sucrose, acetic acid, homocitric acid and malic acid. Results obtained from PLS-DA analysis showed that leaves collected in March 2008 had higher levels of glucosides A and B as compared to those collected in August 2007. However, the relative standard deviation (RSD) exhibited by the individual values of glucosides A and B showed that those compounds vary more according to their developmental stage (50%) than to the time of day or the season in which they were collected (19%). Although morphological variations of the V. planifolia accessions were observed, no clear separation of the accessions was determined from the analysis of the NMR spectra. The results obtained in this study, show that this method based on the use of (1)H NMR spectroscopy in combination with multivariate analysis has a great potential for further applications in the study of vanilla leaf metabolome. Copyright 2009 Elsevier Ltd. All rights reserved.

NMR, ESI/MS, and MALDI-TOF/MS analysis of pear juice polymeric proanthocyanidins with potent free radical scavenging activity.

PubMed

Es-Safi, Nour-Eddine; Guyot, Sylvain; Ducrot, Paul-Henri

2006-09-20

The structure of a polymeric proanthocyanidin fraction isolated from pear juice was characterized by NMR, ESI/MS, and MALDI-TOF/MS analyses, and its antioxidant activity was investigated using the DPPH free radical scavenging method. The results obtained from 13C NMR analysis showed the predominance of signals representative of procyanidins. Typical signals in the chemical shift region between 70 and 90 ppm demonstrated the exclusive presence of epicatechin units. The results obtained through negative ESI/MS analysis showed singly and doubly charged ions corresponding to the molecular mass of procyanidins with a degree of polymerization up to 22. The spectra obtained through MALDI-TOF/MS analysis revealed the presence of two series of tannin oligomers. Supporting the observations from NMR spectroscopy, the first series consists of well-resolved tannin identified as procyanidin polymers units with chain lengths of up to 25. A second series of monogalloyl flavan-3-ols polymers with polymerization degree up to 25 were also detected. This is the first mass spectrometric evidence confirming the existence of galloylated procyanidin oligomers in pear fruits. Within each of these oligomers, various signals exist suggesting the presence of several oligomeric tannins. The antioxidant properties of the polymeric fraction were investigated through reduction of the DPPH free radical, and the results obtained showed that the polymeric fraction exhibited a higher antioxidant power compared to those of (+)-catechin and B3 procyanidin dimer.

In Situ Flow MAS NMR Spectroscopy and Synchrotron PDF Analyses of the Local Response of the Brønsted Acidic Site in SAPO-34 during Hydration at Elevated Temperatures.

PubMed

Kalantzopoulos, Georgios N; Lundvall, Fredrik; Checchia, Stefano; Lind, Anna; Wragg, David S; Fjellvåg, Helmer; Arstad, Bjørnar

2018-02-19

In situ flow magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and synchrotron-based pair distribution function (PDF) analyses were applied to study water's interactions with the Brønsted acidic site and the surrounding framework in the SAPO-34 catalyst at temperatures up to 300 °C for NMR spectroscopy and 700 °C for PDF. 29 Si enrichment of the sample enabled detailed NMR spectroscopy investigations of the T-atom generating the Brønsted site. By NMR spectroscopy, we observed dehydration above 100 °C and a coalescence of Si peaks due to local framework adjustments. Towards 300 °C, the NMR spectroscopy data indicated highly mobile acidic protons. In situ total X-ray scattering measurements analyzed by PDF showed clear changes in the Al local environment in the 250-300 °C region, as the Al-O bond lengths showed a sudden change. This fell within the same temperature range as the increased Brønsted proton mobility. We suggest that the active site in this catalyst under industrial conditions comprises not only the Brønsted proton but also SiO 4 . To the best of our knowledge, this is the first work proposing a structural model of a SAPO catalyst by atomic PDF analysis. The combination of synchrotron PDF analysis with in situ NMR spectroscopy is promising in revealing the dynamic features of a working catalyst. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Studies on the biosynthesis of vitamin B sub 2 and vitamin B sub 12

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, H.C.

1988-01-01

Feeding experiments with Ashbya gossypii followed by NMR analysis of the resulting riboflavin showed incorporation of deuterium from D-(2-{sup 2}H)ribose at C-2{prime} and from D-(1-{sup 2}H)ribose in the pro-R position at C-1{prime} of the ribityl side chain. The results rule out an Amadori rearrangement mechanism for the reduction of the ribosylamino to the ribitylamino linkage and point to formation of a Schiff base that is reduced stereospecifically opposite to the face from which the oxygen has departed. As prerequisite for the analysis, the {sup 1}H NMR signals for the pro-R and pro-S hydrogens at C-1{prime} of riboflavin and its tetraacetatemore » were assigned with the aid of synthetic stereospecifically deuteriated samples. Feeding experiments with Propionibacterium shermianii followed by NMR analysis of the resulting vitamin B{sub 12} showed: (1) 5-methylbenzimidazole (5MBI) incorporated and only one regioisomer (B6-demethylcyanocobalamin)formed. (2) 8-demethylriboflavin incorporated and the same regioisomer was obtained as 5MBI experiment. (3) (1{prime}-{sup 13}C, 5-{sup 15}N)riboflavin incorporated and {sup 13}C-NMR showed that {sup 13}C at the B2 position of cyanocobalamin coupled to both adjacent nitrogen-15 atoms at about the same ratio.« less

Structural investigation of the capsular polysaccharide produced by a novel Klebsiella serotype (SK1). Location of O-acetyl substituents using NMR and MS techniques.

PubMed

Cescutti, P; Ravenscroft, N; Ng, S; Lam, Z; Dutton, G G

1993-06-21

The capsular polysaccharide of Klebsiella SK1 was investigated by methylation analysis, Smith degradation, and 1H NMR spectroscopy. The oligosaccharides (P1 and P2) obtained by bacteriophage phi SK1 degradation of the polymer were studied by methylation analysis, and 1D- and 2D-NMR spectroscopy. The resulting data showed that the parent repeating unit is a branched pentasaccharide having a structure identical to the revised structure recently proposed for Klebsiella serotype K8 capsular polysaccharide. [Formula: see text] The 2D-NMR data showed that one third of the glucuronic acid residues in the SK1 polymer are acetylated at O-2, O-3, or O-4. FABMS studies confirmed the presence of monoacetylated glucuronic acid residues. Thus, the relationship between the Klebsiella K8 and SK1 polymers is akin to that found for Klebsiella polysaccharides K30 and K33, which have been typed as serologically distinct yet their structures differ only in the degree of acetylation.

Chemical Characterization and Water Content Determination of Bio-Oils Obtained from Various Biomass Species using 31P NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, K.; Ben, H.; Muzzy, J.

2012-03-01

Pyrolysis is a promising approach to utilize biomass for biofuels. One of the key challenges for this conversion is how to analyze complicated components in the pyrolysis oils. Water contents of pyrolysis oils are normally analyzed by Karl Fischer titration. The use of 2-chloro-4,4,5,5,-tetramethyl-1,3,2-dioxaphospholane followed by {sup 31}P NMR analysis has been used to quantitatively analyze the structure of hydroxyl groups in lignin and whole biomass. Results: {sup 31}P NMR analysis of pyrolysis oils is a novel technique to simultaneously characterize components and analyze water contents in pyrolysis oils produced from various biomasses. The water contents of various pyrolysis oilsmore » range from 16 to 40 wt%. The pyrolysis oils obtained from Loblolly pine had higher guaiacyl content, while that from oak had a higher syringyl content. Conclusion: The comparison with Karl Fischer titration shows that {sup 31}P NMR could also reliably be used to measure the water content of pyrolysis oils. Simultaneously with analysis of water content, quantitative characterization of hydroxyl groups, including aliphatic, C-5 substituted/syringyl, guaiacyl, p-hydroxyl phenyl and carboxylic hydroxyl groups, could also be provided by {sup 31}P NMR analysis.« less

Nicotine Metabolite Ratio (3-hydroxycotinine/cotinine) in Plasma and Urine by Different Analytical Methods and Laboratories: Implications for Clinical Implementation

PubMed Central

Tanner, Julie-Anne; Novalen, Maria; Jatlow, Peter; Huestis, Marilyn A.; Murphy, Sharon E.; Kaprio, Jaakko; Kankaanpää, Aino; Galanti, Laurence; Stefan, Cristiana; George, Tony P.; Benowitz, Neal L.; Lerman, Caryn; Tyndale, Rachel F.

2015-01-01

Background The highly genetically variable enzyme CYP2A6 metabolizes nicotine to cotinine (COT) and COT to trans-3′-hydroxycotinine (3HC). The nicotine metabolite ratio (NMR, 3HC/COT) is commonly used as a biomarker of CYP2A6 enzymatic activity, rate of nicotine metabolism, and total nicotine clearance; NMR is associated with numerous smoking phenotypes, including smoking cessation. Our objective was to investigate the impact of different measurement methods, at different sites, on plasma and urinary NMR measures from ad libitum smokers. Methods Plasma (n=35) and urine (n=35) samples were sent to eight different laboratories, which employed similar and different methods of COT and 3HC measurements to derive the NMR. We used Bland-Altman analysis to assess agreement, and Pearson correlations to evaluate associations, between NMR measured by different methods. Results Measures of plasma NMR were in strong agreement between methods according to Bland-Altman analysis (ratios 0.82–1.16) and were highly correlated (all Pearson r>0.96, P<0.0001). Measures of urinary NMR were in relatively weaker agreement (ratios 0.62–1.71) and less strongly correlated (Pearson r values of 0.66–0.98, P<0.0001) between different methods. Plasma and urinary COT and 3HC concentrations, while weaker than NMR, also showed good agreement in plasma, which was better than in urine, as was observed for NMR. Conclusions Plasma is a very reliable biological source for the determination of NMR, robust to differences in these analytical protocols or assessment site. Impact Together this indicates a reduced need for differential interpretation of plasma NMR results based on the approach used, allowing for direct comparison of different studies. PMID:26014804

Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift.

PubMed

Kukić, Predrag; Farrell, Damien; Søndergaard, Chresten R; Bjarnadottir, Una; Bradley, John; Pollastri, Gianluca; Nielsen, Jens Erik

2010-03-01

pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural transitions in bovine beta-lactoglobulin (betaLG) by analyzing its NMR pH-titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in betaLG. The results show that around 20% of the amide nuclei CSPs in betaLG originate exclusively from "through-space" electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH-dependent structural transitions in betaLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH-dependent conformational change. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

PubMed

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time. Copyright © 2018 Elsevier Inc. All rights reserved.

Metabolic discrimination of sea buckthorn from different Hippophaë species by 1H NMR based metabolomics.

PubMed

Liu, Yue; Fan, Gang; Zhang, Jing; Zhang, Yi; Li, Jingjian; Xiong, Chao; Zhang, Qi; Li, Xiaodong; Lai, Xianrong

2017-05-08

Sea buckthorn (Hippophaë; Elaeagnaceae) berries are widely consumed in traditional folk medicines, nutraceuticals, and as a source of food. The growing demand of sea buckthorn berries and morphological similarity of Hippophaë species leads to confusions, which might cause misidentification of plants used in natural products. Detailed information and comparison of the complete set of metabolites of different Hippophaë species are critical for their objective identification and quality control. Herein, the variation among seven species and seven subspecies of Hippophaë was studied using proton nuclear magnetic resonance ( 1 H NMR) metabolomics combined with multivariate data analysis, and the important metabolites were quantified by quantitative 1 H NMR (qNMR) method. The results showed that different Hippophaë species can be clearly discriminated and the important interspecific discriminators, including organic acids, L-quebrachitol, and carbohydrates were identified. Statistical differences were found among most of the Hippophaë species and subspecies at the content levels of the aforementioned interspecific discriminators via qNMR and one-way analysis of variance (ANOVA) test. These findings demonstrated that 1 H NMR-based metabolomics is an applicable and effective approach for simultaneous metabolic profiling, species differentiation and quality assessment.

NMR signal analysis to attribute the components to the solid/liquid phases present in mixes and ice creams.

PubMed

Mariette, François; Lucas, Tiphaine

2005-03-09

The NMR relaxation signals from complex products such as ice cream are hard to interpret because of the multiexponential behavior of the relaxation signal and the difficulty of attributing the NMR relaxation components to specific molecule fractions. An attribution of the NMR relaxation parameters is proposed, however, based on an approach that combines quantitative analysis of the spin-spin and spin-lattice relaxation times and the signal intensities with characterization of the ice cream components. We have been able to show that NMR can be used to describe the crystallized and liquid phases separately. The first component of the spin-spin and spin-lattice relaxation describes the behavior of the protons of the crystallized fat in the mix. The amount of fat crystals can then be estimated. In the case of ice cream, only the spin-lattice relaxation signal from the crystallized fraction is relevant. However, it enables the ice protons and the protons of the crystallized fat to be distinguished. The spin-lattice relaxation time can be used to describe the mobility of the protons in the different crystallized phases and also to quantify the amount of ice crystals and fat crystals in the ice cream. The NMR relaxation of the liquid phase of the mix has a biexponential behavior. A first component is attributable to the liquid fraction of the fat and to the sugars, while a second component is attributable to the aqueous phase. Overall, the study shows that despite the complexity of the NMR signal from ice cream, a number of relevant parameters can be extracted to study the influence of the formulation and of the process stages on the ice fraction, the crystallized fat fraction, and the liquid aqueous fraction.

Structure of Ancient Glass by 29 Si Magic Angle Spinning NMR Spectroscopy.

PubMed

Bradford, Henry; Ryder, Amy; Henderson, Julian; Titman, Jeremy J

2018-05-23

29 Si magic angle spinning (MAS) NMR spectroscopy has been applied for the first time to the structural analysis of ancient glass samples obtained from archaeological excavations. The results show that it is possible to establish the distribution of Si environments in ancient glass by 29 Si MAS NMR, so long as the concentrations of magnetic impurities, such as Mn and Fe oxides, are low. In general, good agreement has been obtained with compositions determined by means of electron probe microanalysis. In addition, the 29 Si MAS NMR data reveal structural differences between glasses manufactured at separate ancient sites. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

PubMed

Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

2015-08-24

High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hao, Naijia; Bezerra, Tais Lacerda; Wu, Qiong

Pyrolysis is a promising method for converting biomass to biofuels. However, some of pyrolysis oil's physiochemical properties still limit its commercial applications. Here, the autohydrolysis pretreatment at 175 ± 3 °C for 40 min was conducted to improve the resulting pine pyrolysis oil’s properties as a fuel. During autohydrolysis, deacetylation and decomposition of hemicellulose was observed by ion-exchange chromatography and Fourier transform infrared spectroscopy (FT-IR). Additionally, the cleavage of lignin ether bonds was clearly determined by 13C cross-polarization/magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR). Phosphitylation followed by 31P NMR analysis of the heavy oils gave detailed structural information ofmore » the hydroxyl groups; the results revealed that autohydrolysis pretreatment led to a reduction of carboxyl acids in the heavy oils generated at all three pyrolysis temperatures (400, 500, and 600 °C). The 31P NMR analysis also revealed that autohydrolysis pretreatment led to a reduction of condensed phenolic hydroxyl groups in the heavy oils produced at 600 °C. 1H- 13C heteronuclear single-quantum correlation (HSQC) NMR analysis showed that at a pyrolysis temperature of 600 °C, the pretreated pine produced lower methoxy group constituents. In both 31P and HSQC NMR results indicated that autohydrolysis pretreatment increased levoglucosan yields in the bio-oils.« less

31P NMR spectroscopy studies of phospholipid metabolism in human melanoma xenograft lines differing in rate of tumour cell proliferation.

PubMed

Lyng, H; Olsen, D R; Petersen, S B; Rofstad, E K

1995-04-01

The concentration of phospholipid metabolites in tumours has been hypothesized to be related to rate of cell membrane turnover and may reflect rate of cell proliferation. The purpose of the study reported here was to investigate whether 31P NMR resonance ratios involving the phosphomonoester (PME) or phosphodiester (PDE) resonance are correlated to fraction of cells in S-phase or volume-doubling time in experimental tumours. Four human melanoma xenograft lines (BEX-t, HUX-t, SAX-t, WIX-t) were included in the study. The tumours were grown subcutaneously in male BALB/c-nu/nu mice. 31P NMR spectroscopy was performed at a magnetic field strength of 4.7 T. Fraction of cells in S-phase was measured by flow cytometry. Tumour volume-doubling time was determined by Gompertzian analysis of volumetric growth data. BEX-t and SAX-t tumours differed in fraction of cells in S-phase and volume-doubling time, but showed similar 31P NMR resonance ratios. BEX-t and WIX-t tumours showed significantly different 31P NMR resonance ratios but similar fractions of cells in S-phase. The 31P NMR resonance ratios were significantly different for small and large HUX-t tumours even though fraction of cells in S-phase and volume-doubling time did not differ with tumour volume. None of the 31P NMR resonance ratios showed significant increase with increasing fraction of cells in S-phase or significant decrease with increasing tumour volume-doubling time across the four xenograft lines.(ABSTRACT TRUNCATED AT 250 WORDS)

[Study on three different species tibetan medicine sea buckthorn by 1H-NMR-based metabonomics].

PubMed

Su, Yong-Wen; Tan, Er; Zhang, Jing; You, Jia-Li; Liu, Yue; Liu, Chuan; Zhou, Xiang-Dong; Zhang, Yi

2014-11-01

The 1H-NMR fingerprints of three different species tibetan medicine sea buckthorn were established by 1H-HMR metabolomics to find out different motablism which could provide a new method for the quality evaluation of sea buckthorn. The obtained free induction decay (FID) signal will be imported into MestReNova software and into divide segments. The data will be normalized and processed by principal component analysis and.partial least squares discriminant analysis to perform pattern recognition. The results showed that 25 metabolites belonging to different chemical types were detected from sea buckthorn,including flavonoids, triterpenoids, amino acids, carbohydrates, fatty acids, etc. PCA and PLS-DA analysis showed three different varietiest of sea buckthorn that can be clearly separated by the content of L-quebrachitol, malic acid and some unidentified sugars, which can be used as the differences metabolites of three species of sea buckthorn. 1H-NMR-based metabonomies method had a holistic characteristic with sample preparation and handling. The results of this study can offer an important reference for the species identification and quality control of sea buckthorn.

Comparative NMR and NIRS analysis of oxygen-dependent metabolism in exercising finger flexor muscles.

PubMed

Bendahan, David; Chatel, Benjamin; Jue, Thomas

2017-12-01

Muscle contraction requires the physiology to adapt rapidly to meet the surge in energy demand. To investigate the shift in metabolic control, especially between oxygen and metabolism, researchers often depend on near-infrared spectroscopy (NIRS) to measure noninvasively the tissue O 2 Because NIRS detects the overlapping myoglobin (Mb) and hemoglobin (Hb) signals in muscle, interpreting the data as an index of cellular or vascular O 2 requires deconvoluting the relative contribution. Currently, many in the NIRS field ascribe the signal to Hb. In contrast, 1 H NMR has only detected the Mb signal in contracting muscle, and comparative NIRS and NMR experiments indicate a predominant Mb contribution. The present study has examined the question of the NIRS signal origin by measuring simultaneously the 1 H NMR, 31 P NMR, and NIRS signals in finger flexor muscles during the transition from rest to contraction, recovery, ischemia, and reperfusion. The experiment results confirm a predominant Mb contribution to the NIRS signal from muscle. Given the NMR and NIRS corroborated changes in the intracellular O 2 , the analysis shows that at the onset of muscle contraction, O 2 declines immediately and reaches new steady states as contraction intensity rises. Moreover, lactate formation increases even under quite aerobic condition. Copyright © 2017 the American Physiological Society.

Crystallinity and compositional changes in carbonated apatites: Evidence from 31P solid-state NMR, Raman, and AFM analysis

NASA Astrophysics Data System (ADS)

McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M. Banaszak; Tecklenburg, Mary M. J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

2013-10-01

Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and 31P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse 31P NMR linewidth and inverse Raman PO43-ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3-10.3 wt% CO32- range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the 31P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals.

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy

PubMed Central

Kheddo, Priscilla; Cliff, Matthew J.; Uddin, Shahid; van der Walle, Christopher F.; Golovanov, Alexander P.

2016-01-01

ABSTRACT Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins. PMID:27589351

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy.

PubMed

Kheddo, Priscilla; Cliff, Matthew J; Uddin, Shahid; van der Walle, Christopher F; Golovanov, Alexander P

2016-10-01

Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1 H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins.

A self optimizing synthetic organic reactor system using real-time in-line NMR spectroscopy.

PubMed

Sans, Victor; Porwol, Luzian; Dragone, Vincenza; Cronin, Leroy

2015-02-01

A configurable platform for synthetic chemistry incorporating an in-line benchtop NMR that is capable of monitoring and controlling organic reactions in real-time is presented. The platform is controlled via a modular LabView software control system for the hardware, NMR, data analysis and feedback optimization. Using this platform we report the real-time advanced structural characterization of reaction mixtures, including 19 F, 13 C, DEPT, 2D NMR spectroscopy (COSY, HSQC and 19 F-COSY) for the first time. Finally, the potential of this technique is demonstrated through the optimization of a catalytic organic reaction in real-time, showing its applicability to self-optimizing systems using criteria such as stereoselectivity, multi-nuclear measurements or 2D correlations.

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

PubMed

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/.

Time-Domain Nuclear Magnetic Resonance (TD-NMR) and Chemometrics for Determination of Fat Content in Commercial Products of Milk Powder.

PubMed

Nascimento, Paloma Andrade Martins; Barsanelli, Paulo Lopes; Rebellato, Ana Paula; Pallone, Juliana Azevedo Lima; Colnago, Luiz Alberto; Pereira, Fabíola Manhas Verbi

2017-03-01

This study shows the use of time-domain (TD)-NMR transverse relaxation (T2) data and chemometrics in the nondestructive determination of fat content for powdered food samples such as commercial dried milk products. Most proposed NMR spectroscopy methods for measuring fat content correlate free induction decay or echo intensities with the sample's mass. The need for the sample's mass limits the analytical frequency of NMR determination, because weighing the samples is an additional step in this procedure. Therefore, the method proposed here is based on a multivariate model of T2 decay, measured with Carr-Purcell-Meiboom-Gill pulse sequence and reference values of fat content. The TD-NMR spectroscopy method shows high correlation (r = 0.95) with the lipid content, determined by the standard extraction method of Bligh and Dyer. For comparison, fat content determination was also performed using a multivariate model with near-IR (NIR) spectroscopy, which is also a nondestructive method. The advantages of the proposed TD-NMR method are that it (1) minimizes toxic residue generation, (2) performs measurements with high analytical frequency (a few seconds per analysis), and (3) does not require sample preparation (such as pelleting, needed for NIR spectroscopy analyses) or weighing the samples.

Ultralow field NMR spectrometer with an atomic magnetometer near room temperature

NASA Astrophysics Data System (ADS)

Liu, Guobin; Li, Xiaofeng; Sun, Xianping; Feng, Jiwen; Ye, Chaohui; Zhou, Xin

2013-12-01

We present a Cs atomic magnetometer with a sensitivity of 150 fT/Hz1/2 operating near room temperature. The nuclear magnetic resonance (NMR) signal of 125 μL tap water was detected at an ultralow magnetic field down to 47 nT, with the signal-to-noise ratio (SNR) of the NMR signal approaching 50 after eight averages. Relaxivity experiments with a Gd(DTPA) contrast agent in zero field were performed, in order to show the magnetometer's ability to measure spin-lattice relaxation time with high accuracy. This demonstrates the feasibility of an ultralow field NMR spectrometer based on a Cs atomic magnetometer, which has a low working temperature, short data acquisition time and high sensitivity. This kind of NMR spectrometer has great potential in applications such as chemical analysis and magnetic relaxometry detection in ultralow or zero fields.

NPK NMR Sensor: Online Monitoring of Nitrogen, Phosphorus, and Potassium in Animal Slurry.

PubMed

Sørensen, Morten K; Jensen, Ole; Bakharev, Oleg N; Nyord, Tavs; Nielsen, Niels Chr

2015-07-07

Knowledge of the actual content of nitrogen, phosphorus, and potassium (NPK) in animal slurry is highly important to optimize crop production and avoid environmental pollution when slurry is spread on agricultural fields. Here, we present a mobile, low-field nuclear magnetic resonance (NMR) sensor suitable for online monitoring of the NPK content in animal slurry as an alternative to crude estimates or tedious nonspecific, off-site laboratory analysis. The sensor is based on (14)N, (17)O, (31)P, and (39)K NMR in a digital NMR instrument equipped with a 1.5 T Halbach magnet for direct detection of ammonium N, total P, and K and indirect evaluation of the organic N content, covering all practical components of NPK in animal slurry. In correlation studies, the obtained NMR measurements show good agreement with reference measurements from commercial laboratories.

Multifractal Analysis for Nutritional Assessment

PubMed Central

Park, Youngja; Lee, Kichun; Ziegler, Thomas R.; Martin, Greg S.; Hebbar, Gautam; Vidakovic, Brani; Jones, Dean P.

2013-01-01

The concept of multifractality is currently used to describe self-similar and complex scaling properties observed in numerous biological signals. Fractals are geometric objects or dynamic variations which exhibit some degree of similarity (irregularity) to the original object in a wide range of scales. This approach determines irregularity of biologic signal as an indicator of adaptability, the capability to respond to unpredictable stress, and health. In the present work, we propose the application of multifractal analysis of wavelet-transformed proton nuclear magnetic resonance (1H NMR) spectra of plasma to determine nutritional insufficiency. For validation of this method on 1H NMR signal of human plasma, standard deviation from classical statistical approach and Hurst exponent (H), left slope and partition function from multifractal analysis were extracted from 1H NMR spectra to test whether multifractal indices could discriminate healthy subjects from unhealthy, intensive care unit patients. After validation, the multifractal approach was applied to spectra of plasma from a modified crossover study of sulfur amino acid insufficiency and tested for associations with blood lipids. The results showed that standard deviation and H, but not left slope, were significantly different for sulfur amino acid sufficiency and insufficiency. Quadratic discriminant analysis of H, left slope and the partition function showed 78% overall classification accuracy according to sulfur amino acid status. Triglycerides and apolipoprotein C3 were significantly correlated with a multifractal model containing H, left slope, and standard deviation, and cholesterol and high-sensitivity C-reactive protein were significantly correlated to H. In conclusion, multifractal analysis of 1H NMR spectra provides a new approach to characterize nutritional status. PMID:23990878

Paramagnetic NMR Investigation of Dendrimer-Based Host-Guest Interactions

PubMed Central

Wang, Fei; Shao, Naimin; Cheng, Yiyun

2013-01-01

In this study, the host-guest behavior of poly(amidoamine) (PAMAM) dendrimers bearing amine, hydroxyl, or carboxylate surface functionalities were investigated by paramagnetic NMR studies. 2,2,6,6-Tetramethylpiperidinyloxy (TEMPO) derivatives were used as paramagnetic guest molecules. The results showed that TEMPO-COOH significantly broaden the 1H NMR peaks of amine- and hydroxyl-terminated PAMAM dendrimers. In comparison, no paramagnetic relaxation enhancement (PRE) was observed between TEMPO-NH2, TEMPO-OH and the three types of PAMAM dendrimers. The PRE phenomenon observed is correlated with the encapsulation of TEMPO-COOH within dendrimer pockets. Protonation of the tertiary amine groups within PAMAM dendrimers plays an important role during this process. Interestingly, the absence of TEMPO-COOH encapsulation within carboxylate-terminated PAMAM dendrimer is observed due to the repulsion of TEMPO-COO- anion and anionic dendrimer surface. The combination of paramagnetic probes and 1H NMR linewidth analysis can be used as a powerful tool in the analysis of dendrimer-based host-guest systems. PMID:23762249

{sup 1}H NMR-based spectroscopy detects metabolic alterations in serum of patients with early-stage ulcerative colitis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Ying; Lin, Lianjie; Xu, Yanbin

2013-04-19

Highlights: •Twenty ulcerative colitis patients and nineteen healthy controls were enrolled. •Increased 3-hydroxybutyrate, glucose, phenylalanine, and decreased lipid were found. •We report early stage diagnosis of ulcerative colitis using NMR-based metabolomics. -- Abstract: Ulcerative colitis (UC) has seriously impaired the health of citizens. Accurate diagnosis of UC at an early stage is crucial to improve the efficiency of treatment and prognosis. In this study, proton nuclear magnetic resonance ({sup 1}H NMR)-based metabolomic analysis was performed on serum samples collected from active UC patients (n = 20) and healthy controls (n = 19), respectively. The obtained spectral profiles were subjected tomore » multivariate data analysis. Our results showed that consistent metabolic alterations were present between the two groups. Compared to healthy controls, UC patients displayed increased 3-hydroxybutyrate, β-glucose, α-glucose, and phenylalanine, but decreased lipid in serum. These findings highlight the possibilities of NMR-based metabolomics as a non-invasive diagnostic tool for UC.« less

Quantifying NMR relaxation correlation and exchange in articular cartilage with time domain analysis

NASA Astrophysics Data System (ADS)

Mailhiot, Sarah E.; Zong, Fangrong; Maneval, James E.; June, Ronald K.; Galvosas, Petrik; Seymour, Joseph D.

2018-02-01

Measured nuclear magnetic resonance (NMR) transverse relaxation data in articular cartilage has been shown to be multi-exponential and correlated to the health of the tissue. The observed relaxation rates are dependent on experimental parameters such as solvent, data acquisition methods, data analysis methods, and alignment to the magnetic field. In this study, we show that diffusive exchange occurs in porcine articular cartilage and impacts the observed relaxation rates in T1-T2 correlation experiments. By using time domain analysis of T2-T2 exchange spectroscopy, the diffusive exchange time can be quantified by measurements that use a single mixing time. Measured characteristic times for exchange are commensurate with T1 in this material and so impacts the observed T1 behavior. The approach used here allows for reliable quantification of NMR relaxation behavior in cartilage in the presence of diffusive fluid exchange between two environments.

NMR-based metabolomic analysis of spatial variation in soft corals.

PubMed

He, Qing; Sun, Ruiqi; Liu, Huijuan; Geng, Zhufeng; Chen, Dawei; Li, Yinping; Han, Jiao; Lin, Wenhan; Du, Shushan; Deng, Zhiwei

2014-03-28

Soft corals are common marine organisms that inhabit tropical and subtropical oceans. They are shown to be rich source of secondary metabolites with biological activities. In this work, soft corals from two geographical locations were investigated using ¹H-NMR spectroscopy coupled with multivariate statistical analysis at the metabolic level. A partial least-squares discriminant analysis showed clear separation among extracts of soft corals grown in Sanya Bay and Weizhou Island. The specific markers that contributed to discrimination between soft corals in two origins belonged to terpenes, sterols and N-containing compounds. The satisfied precision of classification obtained indicates this approach using combined ¹H-NMR and chemometrics is effective to discriminate soft corals collected in different geographical locations. The results revealed that metabolites of soft corals evidently depended on living environmental condition, which would provide valuable information for further relevant coastal marine environment evaluation.

Nuclear magnetic resonance study of the conformation and dynamics of beta-casein at the oil/water interface in emulsions.

PubMed Central

ter Beek, L C; Ketelaars, M; McCain, D C; Smulders, P E; Walstra, P; Hemminga, M A

1996-01-01

A (13)C and (31)P nuclear magnetic resonance (NMR) study has been carried out on beta-casein adsorbed at the interface of a tetradecane/water emulsion. (13)C NMR spectra show signals from the carbonyl, carboxyl, aromatic, and C alpha carbons in beta-casein, well resolved from solvent resonances. Only a small fraction of all carbon atoms in beta-casein contribute to detectable signals; intensity measurements show that the observable spectrum is derived from about 30 to 40 amino acid residues.(31)P NMR spectra show signals from the five phosphoserines on the hydrophilic N-terminal part of the protein. Analysis of T(1) relaxation times of these nuclei, using the model free approach for the spectral density function and the line shape of the alpha-carbon region, indicates that a large part of the protein is in a random coil conformation with restricted motion and a relatively long internal correlation time. The NMR results show that the conformation and dynamics of the N-terminal part of beta-casein are not strongly altered at the oil/water interface, as compared to beta-casein in micelle-like aggregates in aqueous solution. PMID:9172765

Conformational analysis of capsaicin using 13C, 15N MAS NMR, GIAO DFT and GA calculations

NASA Astrophysics Data System (ADS)

Siudem, Paweł; Paradowska, Katarzyna; Bukowicki, Jarosław

2017-10-01

Capsaicin produced by plants from genus Capsicum exerts multiple pharmacological effects and has found applications in food and pharmaceutical industry. The alkaloid was studied by a combined approach: solid-state NMR, GA conformational search and GIAO DFT methods. The 13C CPMAS NMR spectra were recorded using variable contact time and dipolar dephasing experiments. The results of cross-polarization (CP) kinetics, such as TCP values and long T1ρH (100-200 ms), indicated that the capsaicin molecule is fairly mobile, especially at the end of the aliphatic chain. The15N MAS NMR spectrum showed one narrow signal at -255 ppm. Genetic algorithm (GA) search with multi modal optimization was used to find low-energy conformations of capsaicin. Theoretical GIAO DFT calculations were performed using different basis sets to characterize five selected conformations. 13C CPMAS NMR was used as a validation method and the experimental chemical shifts were compared with those calculated for selected stable conformers. Conformational analysis suggests that the side chain can be bent or extended. A comparison of the experimental and the calculated chemical shifts indicates that solid capsaicin does not have the same structure as those established by PWXRD.

Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics

PubMed Central

Rist, Manuela J.; Muhle-Goll, Claudia; Görling, Benjamin; Bub, Achim; Heissler, Stefan; Watzl, Bernhard; Luy, Burkhard

2013-01-01

It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine samples were collected from two healthy volunteers, centrifuged and divided into aliquots. Urine aliquots were frozen either at −20 °C, on dry ice, at −80 °C or in liquid nitrogen and then stored at −20 °C, −80 °C or in liquid nitrogen vapor phase for 1–5 weeks before NMR analysis. Results show spectral changes depending on the freezing procedure, with samples frozen on dry ice showing the largest deviations. The effect was found to be based on pH differences, which were caused by variations in CO2 concentrations introduced by the freezing procedure. Thus, we recommend that urine samples should be frozen at −20 °C and transferred to lower storage temperatures within one week and that freezing procedures should be part of the publication protocol. PMID:24957990

Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics.

PubMed

Rist, Manuela J; Muhle-Goll, Claudia; Görling, Benjamin; Bub, Achim; Heissler, Stefan; Watzl, Bernhard; Luy, Burkhard

2013-04-09

It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine samples were collected from two healthy volunteers, centrifuged and divided into aliquots. Urine aliquots were frozen either at -20 °C, on dry ice, at -80 °C or in liquid nitrogen and then stored at -20 °C, -80 °C or in liquid nitrogen vapor phase for 1-5 weeks before NMR analysis. Results show spectral changes depending on the freezing procedure, with samples frozen on dry ice showing the largest deviations. The effect was found to be based on pH differences, which were caused by variations in CO2 concentrations introduced by the freezing procedure. Thus, we recommend that urine samples should be frozen at -20 °C and transferred to lower storage temperatures within one week and that freezing procedures should be part of the publication protocol.

Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data.

PubMed

Teixeira, João M C; Skinner, Simon P; Arbesú, Miguel; Breeze, Alexander L; Pons, Miquel

2018-05-11

We present Farseer-NMR ( https://git.io/vAueU ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems' responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension.

Effect of autohydrolysis pretreatment on biomass structure and the resulting bio-oil from a pyrolysis process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hao, Naijia; Bezerra, Tais Lacerda; Wu, Qiong

Pyrolysis is a promising method for converting biomass to biofuels. However, some of pyrolysis oil's physiochemical properties still limit its commercial applications. Here, the autohydrolysis pretreatment at 175 ± 3 °C for 40 min was conducted to improve the resulting pine pyrolysis oil’s properties as a fuel. During autohydrolysis, deacetylation and decomposition of hemicellulose was observed by ion-exchange chromatography and Fourier transform infrared spectroscopy (FT-IR). Additionally, the cleavage of lignin ether bonds was clearly determined by 13C cross-polarization/magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR). Phosphitylation followed by 31P NMR analysis of the heavy oils gave detailed structural information ofmore » the hydroxyl groups; the results revealed that autohydrolysis pretreatment led to a reduction of carboxyl acids in the heavy oils generated at all three pyrolysis temperatures (400, 500, and 600 °C). The 31P NMR analysis also revealed that autohydrolysis pretreatment led to a reduction of condensed phenolic hydroxyl groups in the heavy oils produced at 600 °C. 1H- 13C heteronuclear single-quantum correlation (HSQC) NMR analysis showed that at a pyrolysis temperature of 600 °C, the pretreated pine produced lower methoxy group constituents. In both 31P and HSQC NMR results indicated that autohydrolysis pretreatment increased levoglucosan yields in the bio-oils.« less

Effect of autohydrolysis pretreatment on biomass structure and the resulting bio-oil from a pyrolysis process

DOE PAGES

Hao, Naijia; Bezerra, Tais Lacerda; Wu, Qiong; ...

2017-06-29

Pyrolysis is a promising method for converting biomass to biofuels. However, some of pyrolysis oil's physiochemical properties still limit its commercial applications. Here, the autohydrolysis pretreatment at 175 ± 3 °C for 40 min was conducted to improve the resulting pine pyrolysis oil’s properties as a fuel. During autohydrolysis, deacetylation and decomposition of hemicellulose was observed by ion-exchange chromatography and Fourier transform infrared spectroscopy (FT-IR). Additionally, the cleavage of lignin ether bonds was clearly determined by 13C cross-polarization/magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR). Phosphitylation followed by 31P NMR analysis of the heavy oils gave detailed structural information ofmore » the hydroxyl groups; the results revealed that autohydrolysis pretreatment led to a reduction of carboxyl acids in the heavy oils generated at all three pyrolysis temperatures (400, 500, and 600 °C). The 31P NMR analysis also revealed that autohydrolysis pretreatment led to a reduction of condensed phenolic hydroxyl groups in the heavy oils produced at 600 °C. 1H- 13C heteronuclear single-quantum correlation (HSQC) NMR analysis showed that at a pyrolysis temperature of 600 °C, the pretreated pine produced lower methoxy group constituents. In both 31P and HSQC NMR results indicated that autohydrolysis pretreatment increased levoglucosan yields in the bio-oils.« less

Metabolomic profiling of the phytomedicinal constituents of Carica papaya L. leaves and seeds by 1H NMR spectroscopy and multivariate statistical analysis.

PubMed

Gogna, Navdeep; Hamid, Neda; Dorai, Kavita

2015-11-10

Extracts from the Carica papaya L. plant are widely reported to contain metabolites with antibacterial, antioxidant and anticancer activity. This study aims to analyze the metabolic profiles of papaya leaves and seeds in order to gain insights into their phytomedicinal constituents. We performed metabolite fingerprinting using 1D and 2D 1H NMR experiments and used multivariate statistical analysis to identify those plant parts that contain the most concentrations of metabolites of phytomedicinal value. Secondary metabolites such as phenyl propanoids, including flavonoids, were found in greater concentrations in the leaves as compared to the seeds. UPLC-ESI-MS verified the presence of significant metabolites in the papaya extracts suggested by the NMR analysis. Interestingly, the concentration of eleven secondary metabolites namely caffeic, cinnamic, chlorogenic, quinic, coumaric, vanillic, and protocatechuic acids, naringenin, hesperidin, rutin, and kaempferol, were higher in young as compared to old papaya leaves. The results of the NMR analysis were corroborated by estimating the total phenolic and flavonoid content of the extracts. Estimation of antioxidant activity in leaves and seed extracts by DPPH and ABTS in-vitro assays and antioxidant capacity in C2C12 cell line also showed that papaya extracts exhibit high antioxidant activity. Copyright © 2015 Elsevier B.V. All rights reserved.

Differentiation of Organically and Conventionally Grown Tomatoes by Chemometric Analysis of Combined Data from Proton Nuclear Magnetic Resonance and Mid-infrared Spectroscopy and Stable Isotope Analysis.

PubMed

Hohmann, Monika; Monakhova, Yulia; Erich, Sarah; Christoph, Norbert; Wachter, Helmut; Holzgrabe, Ulrike

2015-11-04

Because the basic suitability of proton nuclear magnetic resonance spectroscopy ((1)H NMR) to differentiate organic versus conventional tomatoes was recently proven, the approach to optimize (1)H NMR classification models (comprising overall 205 authentic tomato samples) by including additional data of isotope ratio mass spectrometry (IRMS, δ(13)C, δ(15)N, and δ(18)O) and mid-infrared (MIR) spectroscopy was assessed. Both individual and combined analytical methods ((1)H NMR + MIR, (1)H NMR + IRMS, MIR + IRMS, and (1)H NMR + MIR + IRMS) were examined using principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), linear discriminant analysis (LDA), and common components and specific weight analysis (ComDim). With regard to classification abilities, fused data of (1)H NMR + MIR + IRMS yielded better validation results (ranging between 95.0 and 100.0%) than individual methods ((1)H NMR, 91.3-100%; MIR, 75.6-91.7%), suggesting that the combined examination of analytical profiles enhances authentication of organically produced tomatoes.

Synthesis and characterization of starch-poly(methyl acrylate) graft copolymers using horseradish peroxidase.

PubMed

Wang, Su; Wang, Qiang; Fan, Xuerong; Xu, Jin; Zhang, Ying; Yuan, Jiugang; Jin, Heling; Cavaco-Paulo, Artur

2016-01-20

Horseradish peroxidase (HRP)-mediated graft polymerization in the presence of hydrogen peroxide (H2O2) and acetylacetone (Acac) has been successfully applied to the synthesis of starch-poly(methyl acrylate) (PMA). The graft copolymer was characterized by Fourier transform infrared (FT-IR), elemental analysis, nuclear magnetic resonance ((1)H NMR and (13)C NMR), and differential scanning calorimetry (DSC). FT-IR, elemental analysis and NMR confirmed that methyl acrylate (MA) was grafted onto starch successfully. DSC results showed the graft reaction had changed the crystalline regions of the gelatinized starch. The effects of pH, MA content, HRP dosage, incubation temperature and time on grafting percentage (GP) and grafting efficiency (GE) were also investigated. The GP and GE under optimal conditions reached 30.21% and 45.13%, respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

1H NMR spectroscopic analysis detects metabolic disturbances in rat urine on acute exposure to heavy metal tungsten alloy based metals salt.

PubMed

Tyagi, Ritu; Rana, Poonam; Gupta, Mamta; Bhatnagar, Deepak; Srivastava, Shatakshi; Roy, Raja; Khushu, Subash

2014-03-25

Heavy metal tungsten alloys (HMTAs) have been found to be safer alternatives for making military munitions. Recently, some studies demonstrating the toxic potential of HMTAs have raised concern over the safety issues, and further propose that HMTAs exposure may lead to physiological disturbances as well. To look for the systemic effect of acute toxicity of HMTA based metals salt, (1)H nuclear magnetic resonance ((1)H NMR) spectroscopic profiling of rat urine was carried out. Male Sprague Dawley rats were administered (intraperitoneal) low and high dose of mixture of HMTA based metals salt and NMR spectroscopy was carried out in urine samples collected at 8, 24, 72 and 120 h post dosing (p.d.). Serum biochemical parameters and liver histopathology were also conducted. The (1)H NMR spectra were analysed using multivariate analysis techniques to show the time- and dose-dependent biochemical variations in post HMTA based metals salt exposure. Urine metabolomic analysis showed changes associated with energy metabolism, amino acids, N-methyl nicotinamide, membrane and gut flora metabolites. Multivariate analysis showed maximum variation with best classification of control and treated groups at 24h p.d. At the end of the study, for the low dose group most of the changes at metabolite level reverted to control except for the energy metabolites; whereas, in the high dose group some of the changes still persisted. The observations were well correlated with histopathological and serum biochemical parameters. Further, metabolic pathway analysis clarified that amongst all the metabolic pathways analysed, tricarboxylic acid cycle was most affected at all the time points indicating a switchover in energy metabolism from aerobic to anaerobic. These results suggest that exposure of rats to acute doses of HMTA based metals salt disrupts physiological metabolism with moderate injury to the liver, which might indirectly result from heavy metals induced oxidative stress. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Antibacterial colorants: characterization of prodiginines and their applications on textile materials.

PubMed

Alihosseini, Farzaneh; Ju, Kou-San; Lango, Jozsef; Hammock, Bruce D; Sun, Gang

2008-01-01

A strain of Vibrio sp. isolated from marine sediments produced large quantities of bright red pigments that could be used to dye many fibers including wool, nylon, acrylics, and silk. Characterization of the pigments by electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) revealed three prodiginine-like structures with nonpolar characteristics and low molecular mass. UV-visible spectra of the major constituent in methanol solution showed absorbance at lambda max 530 nm wavelength. The accurate mass result showed that the main isolated product has a molecular mass of m/z 323.1997. Further analysis using mass fragmentation (MS/MS), 1H NMR, COSY, HMQC NMR and DEPT confirmed the detailed structure of the pigment with an elementary composition of C20H25N3O. Fabrics dyed with the microbial prodiginines demonstrated antibacterial activity.

Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA.

PubMed

Kotaka, Masayo; Johnson, Christopher; Lamb, Heather K; Hawkins, Alastair R; Ren, Jingshan; Stammers, David K

2008-08-29

Amongst the most common protein motifs in eukaryotes are zinc fingers (ZFs), which, although largely known as DNA binding modules, also can have additional important regulatory roles in forming protein:protein interactions. AreA is a transcriptional activator central to nitrogen metabolism in Aspergillus nidulans. AreA contains a GATA-type ZF that has a competing dual recognition function, binding either DNA or the negative regulator NmrA. We report the crystal structures of three AreA ZF-NmrA complexes including two with bound NAD(+) or NADP(+). The molecular recognition of AreA ZF-NmrA involves binding of the ZF to NmrA via hydrophobic and hydrogen bonding interactions through helices alpha1, alpha6 and alpha11. Comparison with an earlier NMR solution structure of AreA ZF-DNA complex by overlap of the AreA ZFs shows that parts of helices alpha6 and alpha11 of NmrA are positioned close to the GATA motif of the DNA, mimicking the major groove of DNA. The extensive overlap of DNA with NmrA explains their mutually exclusive binding to the AreA ZF. The presence of bound NAD(+)/NADP(+) in the NmrA-AreaA ZF complex, however, causes minimal structural changes. Thus, any regulatory effects on AreA function mediated by the binding of oxidised nicotinamide dinucleotides to NmrA in the NmrA-AreA ZF complex appear not to be modulated via protein conformational rearrangements.

Principal component directed partial least squares analysis for combining nuclear magnetic resonance and mass spectrometry data in metabolomics: application to the detection of breast cancer.

PubMed

Gu, Haiwei; Pan, Zhengzheng; Xi, Bowei; Asiago, Vincent; Musselman, Brian; Raftery, Daniel

2011-02-07

Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) are the two most commonly used analytical tools in metabolomics, and their complementary nature makes the combination particularly attractive. A combined analytical approach can improve the potential for providing reliable methods to detect metabolic profile alterations in biofluids or tissues caused by disease, toxicity, etc. In this paper, (1)H NMR spectroscopy and direct analysis in real time (DART)-MS were used for the metabolomics analysis of serum samples from breast cancer patients and healthy controls. Principal component analysis (PCA) of the NMR data showed that the first principal component (PC1) scores could be used to separate cancer from normal samples. However, no such obvious clustering could be observed in the PCA score plot of DART-MS data, even though DART-MS can provide a rich and informative metabolic profile. Using a modified multivariate statistical approach, the DART-MS data were then reevaluated by orthogonal signal correction (OSC) pretreated partial least squares (PLS), in which the Y matrix in the regression was set to the PC1 score values from the NMR data analysis. This approach, and a similar one using the first latent variable from PLS-DA of the NMR data resulted in a significant improvement of the separation between the disease samples and normals, and a metabolic profile related to breast cancer could be extracted from DART-MS. The new approach allows the disease classification to be expressed on a continuum as opposed to a binary scale and thus better represents the disease and healthy classifications. An improved metabolic profile obtained by combining MS and NMR by this approach may be useful to achieve more accurate disease detection and gain more insight regarding disease mechanisms and biology. Copyright © 2010 Elsevier B.V. All rights reserved.

High-throughput authentication of edible oils with benchtop Ultrafast 2D NMR.

PubMed

Gouilleux, B; Marchand, J; Charrier, B; Remaud, G S; Giraudeau, P

2018-04-01

We report the use of an Ultrafast 2D NMR approach applied on a benchtop NMR system (43 MHz) for the authentication of edible oils. Our results demonstrate that a profiling strategy based on fast 2D NMR spectra recorded in 2.4 min is more efficient than the standard 1D experiments to classify oils from different botanical origins, since 1D spectra on the same samples suffer from strong peak overlaps. Six edible oils with different botanical origins (olive, hazelnut, sesame, rapeseed, corn and sunflower) have been clearly discriminated by PCA analysis. Furthermore, we show how this approach combined with a PLS model can detect adulteration processes such as the addition of hazelnut oil into olive oil, a common fraud in food industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

Validated ¹H and 13C Nuclear Magnetic Resonance Methods for the Quantitative Determination of Glycerol in Drug Injections.

PubMed

Lu, Jiaxi; Wang, Pengli; Wang, Qiuying; Wang, Yanan; Jiang, Miaomiao

2018-05-15

In the current study, we employed high-resolution proton and carbon nuclear magnetic resonance spectroscopy (¹H and 13 C NMR) for quantitative analysis of glycerol in drug injections without any complex pre-treatment or derivatization on samples. The established methods were validated with good specificity, linearity, accuracy, precision, stability, and repeatability. Our results revealed that the contents of glycerol were convenient to calculate directly via the integration ratios of peak areas with an internal standard in ¹H NMR spectra, while the integration of peak heights were proper for 13 C NMR in combination with an external calibration of glycerol. The developed methods were both successfully applied in drug injections. Quantitative NMR methods showed an extensive prospect for glycerol determination in various liquid samples.

A general algorithm for peak-tracking in multi-dimensional NMR experiments.

PubMed

Ravel, P; Kister, G; Malliavin, T E; Delsuc, M A

2007-04-01

We present an algorithmic method allowing automatic tracking of NMR peaks in a series of spectra. It consists in a two phase analysis. The first phase is a local modeling of the peak displacement between two consecutive experiments using distance matrices. Then, from the coefficients of these matrices, a value graph containing the a priori set of possible paths used by these peaks is generated. On this set, the minimization under constraint of the target function by a heuristic approach provides a solution to the peak-tracking problem. This approach has been named GAPT, standing for General Algorithm for NMR Peak Tracking. It has been validated in numerous simulations resembling those encountered in NMR spectroscopy. We show the robustness and limits of the method for situations with many peak-picking errors, and presenting a high local density of peaks. It is then applied to the case of a temperature study of the NMR spectrum of the Lipid Transfer Protein (LTP).

A novel in situ electrochemical NMR cell with a palisade gold film electrode

NASA Astrophysics Data System (ADS)

Ni, Zu-Rong; Cui, Xiao-Hong; Cao, Shuo-Hui; Chen, Zhong

2017-08-01

In situ electrochemical nuclear magnetic resonance (EC-NMR) has attracted considerable attention because of its ability to directly observe real-time electrochemical processes. Therefore, minimizing the incompatibility between the electrochemical device and NMR detection has become an important challenge. A circular thin metal film deposited on the outer surface of a glass tube with a thickness considerably less than the metal skin depth is considered to be the ideal working electrode. In this study, we demonstrate that such a thin film electrode still has a great influence on the radio frequency field homogeneity in the detective zone of the NMR spectrometer probe and provide theoretical and experimental confirmation of its electromagnetic shielding. Furthermore, we propose a novel palisade gold film device to act as the working electrode. The NMR nutation behavior of protons shows that the uniformity of the radio frequency field is greatly improved, increasing the sensitivity in NMR detection. Another advantage of the proposed device is that an external reference standard adapted to the reaction compound can be inserted as a probe to determine the fluctuation of the physico-chemical environment and achieve high-accuracy quantitative NMR analysis. A three-chamber electrochemical device based on the palisade gold film design was successfully fabricated and the in situ electrochemical NMR performance was validated in a standard 5 mm NMR probe by acquiring voltammograms and high-resolution NMR spectra to characterize the electrochemically generated species. The evolution of in situ EC-NMR spectrum monitoring of the redox transformation between p-benzoquinone and hydroquinone demonstrates the ability of the EC-NMR device to simultaneously quantitatively determine the reactants and elucidate the reaction mechanism at the molecular level.

Syntheses, characterisation and crystal structures of ferrocenyl β-diketones and their Schiff base Nsbnd Nsbnd O ligand derivatives with 2-picolylamine

NASA Astrophysics Data System (ADS)

Artigas, Vania; González, Deborah; Fuentealba, Mauricio

2017-02-01

Ferrocenyl β-diketones compounds β3-4 were synthesised by Claisen condensation reaction between acetylferrocene and ethyl benzoate or 4-bromoethyl benzoate. We also synthesised four new Schiff base ligands L1-4 by condensation reaction between β1-4 and 2-picolylamine. Identities of all these compounds were confirmed by satisfactory elemental analysis, 1H nuclear magnetic resonance (NMR) correlation and infrared (IR) spectroscopy. In addition, all these compounds were authenticated by a single-crystal X-ray diffraction analysis. In solution, 1H NMR spectra of β3 and β4 exhibit a mixture of keto:enol tautomer ratios of 12:88 and 8:92, respectively, calculated by the integration of the free cyclopentadienyl ring. In contrast, the proton NMR spectra of L1-4 showed only the keto-enamine tautomer displacements. In addition, decoupled 13C NMR spectrum clearly confirmed the existence of these tautomers. These results are in accordance with X-ray crystallographic studies, in which the enol and keto-enamine forms were elucidated for β-diketones and Schiff base ligands, respectively.

Exploring high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for metabonomic analysis of apples.

PubMed

Vermathen, Martina; Marzorati, Mattia; Vermathen, Peter

2012-01-01

Classical liquid-state high-resolution (HR) NMR spectroscopy has proved a powerful tool in the metabonomic analysis of liquid food samples like fruit juices. In this paper the application of (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to apple tissue is presented probing its potential for metabonomic studies. The (1)H HR-MAS NMR spectra are discussed in terms of the chemical composition of apple tissue and compared to liquid-state NMR spectra of apple juice. Differences indicate that specific metabolic changes are induced by juice preparation. The feasibility of HR-MAS NMR-based multivariate analysis is demonstrated by a study distinguishing three different apple cultivars by principal component analysis (PCA). Preliminary results are shown from subsequent studies comparing three different cultivation methods by means of PCA and partial least squares discriminant analysis (PLS-DA) of the HR-MAS NMR data. The compounds responsible for discriminating organically grown apples are discussed. Finally, an outlook of our ongoing work is given including a longitudinal study on apples.

Potential effect of diaper and cotton ball contamination on NMR- and LC/MS-based metabonomics studies of urine from newborn babies.

PubMed

Goodpaster, Aaron M; Ramadas, Eshwar H; Kennedy, Michael A

2011-02-01

Nuclear magnetic resonance (NMR) and liquid chromatography/mass spectrometry (LC/MS) based metabonomics screening of urine has great potential for discovery of biomarkers for diseases that afflict newborn and preterm infants. However, urine collection from newborn infants presents a potential confounding problem due to the possibility that contaminants might leach from materials used for urine collection and influence statistical analysis of metabonomics data. In this manuscript, we have analyzed diaper and cotton ball contamination using synthetic urine to assess its potential to influence the outcome of NMR- and LC/MS-based metabonomics studies of human infant urine. Eight diaper brands were examined using the "diaper plus cotton ball" technique. Data were analyzed using conventional principal components analysis, as well as a statistical significance algorithm developed for, and applied to, NMR data. Results showed most diaper brands had distinct contaminant profiles that could potentially influence NMR- and LC/MS-based metabonomics studies. On the basis of this study, it is recommended that diaper and cotton ball brands be characterized using metabonomics methodologies prior to initiating a metabonomics study to ensure that contaminant profiles are minimal or manageable and that the same diaper and cotton ball brands be used throughout a study to minimize variation.

Analysis of commercial proanthocyanidins. Part 4: solid state (13)C NMR as a tool for in situ analysis of proanthocyanidin tannins, in heartwood and bark of quebracho and acacia, and related species.

PubMed

Reid, David G; Bonnet, Susan L; Kemp, Gabre; van der Westhuizen, Jan H

2013-10-01

(13)C NMR is an effective method of characterizing proanthocyanidin (PAC) tannins in quebracho (Schinopsis lorentzii) heartwood and black wattle (Acacia mearnsii) bark, before and after commercial extraction. The B-rings of the constituent flavan-3-ols, catechols (quebracho) or pyrogallols (wattle), are recognized in unprocessed source materials by "marker" signals at ca. 118 or 105ppm, respectively. NMR allows the minimum extraction efficiency to be calculated; ca. 30%, and ca. 80%, for quebracho heartwood and black wattle bark, respectively. NMR can also identify PAC tannin (predominantly robinetinidin), and compare tannin content, in bark from other acacia species; tannin content decreases in the order A. mearnsii, Acacia pycnantha (87% of A. mearnsii), Acacia dealbata and Acacia decurrens (each 74%) and Acacia karroo (30%). Heartwood from an underexploited PAC tannin source, Searsia lancea, taxonomically close to quebracho, shows abundant profisetinidin and catechin PACs. NMR offers the advantage of being applicable to source materials in their native state, and has potential applications in optimizing extraction processes, identification of tannin sources, and characterization of tannin content in cultivar yield improvement programmes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP)

NASA Astrophysics Data System (ADS)

Snyder, David A.; Chantova, Mihaela; Chaudhry, Saadia

2015-06-01

NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase.

Combined chemometric analysis of (1)H NMR, (13)C NMR and stable isotope data to differentiate organic and conventional milk.

PubMed

Erich, Sarah; Schill, Sandra; Annweiler, Eva; Waiblinger, Hans-Ulrich; Kuballa, Thomas; Lachenmeier, Dirk W; Monakhova, Yulia B

2015-12-01

The increased sales of organically produced food create a strong need for analytical methods, which could authenticate organic and conventional products. Combined chemometric analysis of (1)H NMR-, (13)C NMR-spectroscopy data, stable-isotope data (IRMS) and α-linolenic acid content (gas chromatography) was used to differentiate organic and conventional milk. In total 85 raw, pasteurized and ultra-heat treated (UHT) milk samples (52 organic and 33 conventional) were collected between August 2013 and May 2014. The carbon isotope ratios of milk protein and milk fat as well as the α-linolenic acid content of these samples were determined. Additionally, the milk fat was analyzed by (1)H and (13)C NMR spectroscopy. The chemometric analysis of combined data (IRMS, GC, NMR) resulted in more precise authentication of German raw and retail milk with a considerably increased classification rate of 95% compared to 81% for NMR and 90% for IRMS using linear discriminate analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Metabolomic Fingerprinting of Romaneschi Globe Artichokes by NMR Spectroscopy and Multivariate Data Analysis.

PubMed

de Falco, Bruna; Incerti, Guido; Pepe, Rosa; Amato, Mariana; Lanzotti, Virginia

2016-09-01

Globe artichoke (Cynara cardunculus L. var. scolymus L. Fiori) and cardoon (Cynara cardunculus L. var. altilis DC) are sources of nutraceuticals and bioactive compounds. To apply a NMR metabolomic fingerprinting approach to Cynara cardunculus heads to obtain simultaneous identification and quantitation of the major classes of organic compounds. The edible part of 14 Globe artichoke populations, belonging to the Romaneschi varietal group, were extracted to obtain apolar and polar organic extracts. The analysis was also extended to one species of cultivated cardoon for comparison. The (1) H-NMR of the extracts allowed simultaneous identification of the bioactive metabolites whose quantitation have been obtained by spectral integration followed by principal component analysis (PCA). Apolar organic extracts were mainly based on highly unsaturated long chain lipids. Polar organic extracts contained organic acids, amino acids, sugars (mainly inulin), caffeoyl derivatives (mainly cynarin), flavonoids, and terpenes. The level of nutraceuticals was found to be highest in the Italian landraces Bianco di Pertosa zia E and Natalina while cardoon showed the lowest content of all metabolites thus confirming the genetic distance between artichokes and cardoon. Metabolomic approach coupling NMR spectroscopy with multivariate data analysis allowed for a detailed metabolite profile of artichoke and cardoon varieties to be obtained. Relevant differences in the relative content of the metabolites were observed for the species analysed. This work is the first application of (1) H-NMR with multivariate statistics to provide a metabolomic fingerprinting of Cynara scolymus. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Anticancer activity of ferrocenylthiosemicarbazones.

PubMed

Sandra, Cortez-Maya; Elena, Klimova; Marcos, Flores-Alamo; Elena, Martínez-Klimova; Arturo, Ramírez-Ramírez; Teresa, Ramírez Apan; Marcos, Martínez-García

2014-03-01

Aliphatic and aromatic ferrocenylthiosemicarbazones were synthesized. The characterization of the new ferrocenylthiosemicarbazones was done by IR, (1)H-NMR and (13)C-NMR spectroscopy, elemental analysis and X-ray diffraction studies. The biological activity of the obtained compounds was assessed in terms of anticancer activity. Their activity against U251 (human glyoblastoma), PC-3 (human prostatic adenocarcinoma), K562 (human chronic myelogenous leukemia), HCT-15 (human colorectal adenocarcinoma), MCF-7 (human mammary adenocarcinoma) and SKLU-1 (human lung adenocarcinoma) cell lines was studied and compared with cisplatin. All tested compounds showed good activity and the aryl-chloro substituted ferrocenylthiosemicarbazones showed the best anticancer activity.

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

PubMed

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

Metabolic analysis of elicited cell suspension cultures of Cannabis sativa L. by (1)H-NMR spectroscopy.

PubMed

Pec, Jaroslav; Flores-Sanchez, Isvett Josefina; Choi, Young Hae; Verpoorte, Robert

2010-07-01

Cannabis sativa L. plants produce a diverse array of secondary metabolites. Cannabis cell cultures were treated with jasmonic acid (JA) and pectin as elicitors to evaluate their effect on metabolism from two cell lines using NMR spectroscopy and multivariate data analysis. According to principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA), the chloroform extract of the pectin-treated cultures were more different than control and JA-treated cultures; but in the methanol/water extract the metabolome of the JA-treated cells showed clear differences with control and pectin-treated cultures. Tyrosol, an antioxidant metabolite, was detected in cannabis cell cultures. The tyrosol content increased after eliciting with JA.

Theoretical DFT, vibrational and NMR studies of benzimidazole and alkyl derivatives

NASA Astrophysics Data System (ADS)

Infante-Castillo, Ricardo; Rivera-Montalvo, Luis A.; Hernández-Rivera, Samuel P.

2008-04-01

Benzimidazoles are heterocyclic compounds that have awaked great interest during the last few years because of their proven biological activity as antiviral, antimicrobial, and antitumoral agents. For this reason, the development of a systematic FT-IR, FT-Raman and NMR study of 1-substituted compounds in 2-methylbenzimidazole constitutes a significant tool in understanding the molecular dynamics and the structural parameters that govern their behavior. Two new 1-alkyl-2-methylbenzimidazoles compounds were synthesized from reaction of 2-methylbenzimidazole with primary and secondary alkyl halides using a strong base as a catalyst. These compounds were purified and characterized by elemental analysis and different spectroscopic methods. The comparative analysis of vibrational modes of benzimidazole and its alkyl derivatives show that regions of absorption are very similar in all of them. However, changes are produced at low frequencies specifically in the C-H out of plane deformations, ring breathing and ring skeletal vibrations. The ring out-of plane bending modes shift by 10-15 cm -1 in some cases as results of alkyl substitution. The theoretical calculated spectra, using Density Functional Theory (DFT) approximation, and experimental results were consistent with each other. The GIAO method was used to calculate absolute shieldings, which agree consistently with those measured by 1H and 13C NMR. The consistency and efficiency of the GIAO 13C and 1H NMR calculations were thoroughly checked by the analysis of statistical parameters concerning computed and experimental 13C and 1H NMR chemical shift values of the studied compounds.

Optimized "detectors" for dynamics analysis in solid-state NMR

NASA Astrophysics Data System (ADS)

Smith, Albert A.; Ernst, Matthias; Meier, Beat H.

2018-01-01

Relaxation in nuclear magnetic resonance (NMR) results from stochastic motions that modulate anisotropic NMR interactions. Therefore, measurement of relaxation-rate constants can be used to characterize molecular-dynamic processes. The motion is often characterized by Markov processes using an auto-correlation function, which is assumed to be a sum of multiple decaying exponentials. We have recently shown that such a model can lead to severe misrepresentation of the real motion, when the real correlation function is more complex than the model. Furthermore, multiple distributions of motion may yield the same set of dynamics data. Therefore, we introduce optimized dynamics "detectors" to characterize motions which are linear combinations of relaxation-rate constants. A detector estimates the average or total amplitude of motion for a range of motional correlation times. The information obtained through the detectors is less specific than information obtained using an explicit model, but this is necessary because the information contained in the relaxation data is ambiguous, if one does not know the correct motional model. On the other hand, if one has a molecular dynamics trajectory, one may calculate the corresponding detector responses, allowing direct comparison to experimental NMR dynamics analysis. We describe how to construct a set of optimized detectors for a given set of relaxation measurements. We then investigate the properties of detectors for a number of different data sets, thus gaining an insight into the actual information content of the NMR data. Finally, we show an example analysis of ubiquitin dynamics data using detectors, using the DIFRATE software.

PepsNMR for 1H NMR metabolomic data pre-processing.

PubMed

Martin, Manon; Legat, Benoît; Leenders, Justine; Vanwinsberghe, Julien; Rousseau, Réjane; Boulanger, Bruno; Eilers, Paul H C; De Tullio, Pascal; Govaerts, Bernadette

2018-08-17

In the analysis of biological samples, control over experimental design and data acquisition procedures alone cannot ensure well-conditioned 1 H NMR spectra with maximal information recovery for data analysis. A third major element affects the accuracy and robustness of results: the data pre-processing/pre-treatment for which not enough attention is usually devoted, in particular in metabolomic studies. The usual approach is to use proprietary software provided by the analytical instruments' manufacturers to conduct the entire pre-processing strategy. This widespread practice has a number of advantages such as a user-friendly interface with graphical facilities, but it involves non-negligible drawbacks: a lack of methodological information and automation, a dependency of subjective human choices, only standard processing possibilities and an absence of objective quality criteria to evaluate pre-processing quality. This paper introduces PepsNMR to meet these needs, an R package dedicated to the whole processing chain prior to multivariate data analysis, including, among other tools, solvent signal suppression, internal calibration, phase, baseline and misalignment corrections, bucketing and normalisation. Methodological aspects are discussed and the package is compared to the gold standard procedure with two metabolomic case studies. The use of PepsNMR on these data shows better information recovery and predictive power based on objective and quantitative quality criteria. Other key assets of the package are workflow processing speed, reproducibility, reporting and flexibility, graphical outputs and documented routines. Copyright © 2018 Elsevier B.V. All rights reserved.

HPLC, NMR and MALDI-TOF MS analysis of condensed tannins from Lithocarpus glaber leaves with potent free radical scavenging activity.

PubMed

Zhang, Liang Liang; Lin, Yi Ming

2008-12-04

Using acid-catalyzed degradation in the presence of cysteamine, the condensed tannins from Lithocarpus glaber leaves were characterized, following thiolysis, by means of reversed-phase HPLC, 13C-NMR and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analyses. The thiolysis reaction products showed the presence of the procyanidin (PC) and prodelphinidin (PD) structures. The 13C-NMR spectrum revealed that the condensed tannins were comprised of PD (72.4%) and PC (27.6%), and with a greater content of cis configuration rather than the trans configuration of C2-C3. The MALDI-TOF MS analysis proved the presence of PD units, and the maximum degree of polymerization (DP) was an undecamer. The antioxidant activity of condensed tannins from L. glaber leaves was evaluated by using a free radical scavenging activity assay.

Rapid NMR method for the quantification of organic compounds in thin stillage.

PubMed

Ratanapariyanuch, Kornsulee; Shen, Jianheng; Jia, Yunhua; Tyler, Robert T; Shim, Youn Young; Reaney, Martin J T

2011-10-12

Thin stillage contains organic and inorganic compounds, some of which may be valuable fermentation coproducts. This study describes a thorough analysis of the major solutes present in thin stillage as revealed by NMR and HPLC. The concentration of charged and neutral organic compounds in thin stillage was determined by excitation sculpting NMR methods (double pulse field gradient spin echo). Compounds identified by NMR included isopropanol, ethanol, lactic acid, 1,3-propanediol, acetic acid, succinic acid, glycerophosphorylcholine, betaine, glycerol, and 2-phenylethanol. The concentrations of lactic and acetic acid determined with NMR were comparable to those determined using HPLC. HPLC and NMR were complementary, as more compounds were identified using both methods. NMR analysis revealed that stillage contained the nitrogenous organic compounds betaine and glycerophosphorylcholine, which contributed as much as 24% of the nitrogen present in the stillage. These compounds were not observed by HPLC analysis.

PVT Degradation Studies: NMR Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Herman M.; Kouzes, Richard T.

Under certain environmental conditions, polyvinyl toluene (PVT) plastic scintillator has been observed to undergo internal fogging. Nuclear magnetic resonance spectroscopy has been used to elucidate the state of water inside the PVT. The deuterium NMR results show that water absorbed by PVT under warm, humid conditions enters several distinct environments, and when the PVT is transferred from incubation to ambient temperature and humidity the water is lost on a time scale of a few hours from these samples. Most of the deuterium NMR peaks can be assigned to bulk liquid water, but almost 35% of the detected signal intensity ismore » contained in a resonance that resembles spectra of water contained in nanometer-scale pores in mesoporous carbon.« less

Implementation of picoSpin Benchtop NMR Instruments into Organic Chemistry Teaching Laboratories through Spectral Analysis of Fischer Esterification Products

ERIC Educational Resources Information Center

Yearty, Kasey L.; Sharp, Joseph T.; Meehan, Emma K.; Wallace, Doyle R.; Jackson, Douglas M.; Morrison, Richard W.

2017-01-01

[Superscript 1]H NMR analysis is an important analytical technique presented in introductory organic chemistry courses. NMR instrument access is limited for undergraduate organic chemistry students due to the size of the instrument, price of NMR solvents, and the maintenance level required for instrument upkeep. The University of Georgia Chemistry…

Structural analysis of geochemical samples by solid-state nuclear magnetic resonance spectrometry. Role of paramagnetic material

USGS Publications Warehouse

Vassallo, A.M.; Wilson, M.A.; Collin, P.J.; Oades, J.M.; Waters, A.G.; Malcolm, R.L.

1987-01-01

An examination of coals, coal tars, a fulvic acid, and soil fractions by solid-state 13C NMR spectrometry has demonstrated widely differing behavior regarding quantitative representation in the spectrum. Spin counting experiments on coal tars and the fulvic acid show that almost all the sample carbon is observed in both solution and solid-state NMR spectra. Similar experiments on two coals (a lignite and a bituminous coal) show that most (70-97%) of the carbon is observed; however, when the lignite is ion exchanged with 3% (w/w) Fe3+, the fraction of carbon observed drops to below 10%. In additional experiments signal intensity from soil samples is enhanced by a simple dithionite treatment. This is illustrated by 13C, 27Al, and 29Si solid-state NMR experiments on soil fractions. ?? 1987 American Chemical Society.

Theoretical and Experimental Spectroscopic Analysis of Cyano-Substituted Styrylpyridine Compounds

PubMed Central

Castro, Maria Eugenia; Percino, Maria Judith; Chapela, Victor M.; Ceron, Margarita; Soriano-Moro, Guillermo; Lopez-Cruz, Jorge; Melendez, Francisco J.

2013-01-01

A combined theoretical and experimental study on the structure, infrared, UV-Vis and 1H NMR data of trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)] pyridine and trans-4-(m-cyanostyryl)pyridine is presented. The synthesis was carried out with an efficient Knoevenagel condensation using green chemistry conditions. Theoretical geometry optimizations and their IR spectra were carried out using the Density Functional Theory (DFT) in both gas and solution phases. For theoretical UV-Vis and 1H NMR spectra, the Time-Dependent DFT (TD-DFT) and the Gauge-Including Atomic Orbital (GIAO) methods were used, respectively. The theoretical characterization matched the experimental measurements, showing a good correlation. The effect of cyano- and methyl-substituents, as well as of the N-atom position in the pyridine ring on the UV-Vis, IR and NMR spectra, was evaluated. The UV-Vis results showed no significant effect due to electron-withdrawing cyano- and electron-donating methyl-substituents. The N-atom position, however, caused a slight change in the maximum absorption wavelengths. The IR normal modes were assigned for the cyano- and methyl-groups. 1H NMR spectra showed the typical doublet signals due to protons in the trans position of a double bond. The theoretical characterization was visibly useful to assign accurately the signals in IR and 1H NMR spectra, as well as to identify the most probable conformation that could be present in the formation of the styrylpyridine-like compounds. PMID:23429190

Direct detection of ligand binding to Sepharose-immobilised protein using saturation transfer double difference (STDD) NMR spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haselhorst, Thomas; Muenster-Kuehnel, Anja K.; Oschlies, Melanie

2007-08-10

We report an easy and direct application of 'Saturation Transfer Double Difference' (STDD) NMR spectroscopy to identify ligands that bind to a Sepharose-immobilised target protein. The model protein, cytidine 5'-monophosphate sialic acid (CMP-Sia) synthetase, was expressed as a Strep-Tag II fusion protein and immobilised on Strep-Tactin Sepharose. STD NMR experiments of the protein-enriched Sepharose matrix in the presence of a binding ligand (cytidine 5'-triphosphate, CTP) and a non-binding ligand ({alpha}/{beta}-glucose) clearly show that CTP binds to the immobilised enzyme, whereas glucose has no affinity. This approach has three major advantages: (a) only low quantities of protein are required, (b) nomore » specialised NMR technology or the application of additional data analysis by non-routine methods is required, and (c) easy multiple use of the immobilised protein is available.« less

Crocus sativus Petals: Waste or Valuable Resource? The Answer of High-Resolution and High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance.

PubMed

Righi, Valeria; Parenti, Francesca; Tugnoli, Vitaliano; Schenetti, Luisa; Mucci, Adele

2015-09-30

Intact Crocus sativus petals were studied for the first time by high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy, revealing the presence of kinsenoside (2) and goodyeroside A (3), together with 3-hydroxy-γ-butyrolactone (4). These findings were confirmed by HR-NMR analysis of the ethanol extract of fresh petals and showed that, even though carried out rapidly, partial hydrolysis of glucopyranosyloxybutanolides occurs during extraction. On the other hand, kaempferol 3-O-sophoroside (1), which is "NMR-silent" in intact petals, is present in extracts. These results suggest to evaluate the utilization of saffron petals for phytopharmaceutical and nutraceutical purposes to exploit a waste product of massive production of commercial saffron and point to the application of HR-MAS NMR for monitoring bioactive compounds directly on intact petals, avoiding the extraction procedure and the consequent hydrolysis reaction.

Toward nanomolar detection by NMR through SABRE hyperpolarization.

PubMed

Eshuis, Nan; Hermkens, Niels; van Weerdenburg, Bram J A; Feiters, Martin C; Rutjes, Floris P J T; Wijmenga, Sybren S; Tessari, Marco

2014-02-19

SABRE is a nuclear spin hyperpolarization technique based on the reversible association of a substrate molecule and para-hydrogen (p-H2) to a metal complex. During the lifetime of such a complex, generally fractions of a second, the spin order of p-H2 is transferred to the nuclear spins of the substrate molecule via a transient scalar coupling network, resulting in strongly enhanced NMR signals. This technique is generally applied at relatively high concentrations (mM), in large excess of substrate with respect to metal complex. Dilution of substrate ligands below stoichiometry results in progressive decrease of signal enhancement, which precludes the direct application of SABRE to the NMR analysis of low concentration (μM) solutions. Here, we show that the efficiency of SABRE at low substrate concentrations can be restored by addition of a suitable coordinating ligand to the solution. The proposed method allowed NMR detection below 1 μM in a single scan.

Thiol-thione tautomeric analysis, spectroscopic (FT-IR, Laser-Raman, NMR and UV-vis) properties and DFT computations of 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule.

PubMed

Gökce, Halil; Öztürk, Nuri; Ceylan, Ümit; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

2016-06-15

In this study, the 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule (C7H6N4S) molecule has been characterized by using FT-IR, Laser-Raman, NMR and UV-vis spectroscopies. Quantum chemical calculations have been performed to investigate the molecular structure (thione-thiol tautomerism), vibrational wavenumbers, electronic transition absorption wavelengths in DMSO solvent and vacuum, proton and carbon-13 NMR chemical shifts and HOMOs-LUMOs energies at DFT/B3LYP/6-311++G(d,p) level for all five tautomers of the title molecule. The obtained results show that the calculated vibrational wavenumbers, NMR chemical shifts and UV-vis wavelengths are in a good agreement with experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.

Diagnosis of coinfection by schistosomiasis and viral hepatitis B or C using 1H NMR-based metabonomics.

PubMed

Gouveia, Liana Ribeiro; Santos, Joelma Carvalho; Silva, Ronaldo Dionísio; Batista, Andrea Dória; Domingues, Ana Lúcia Coutinho; Lopes, Edmundo Pessoa de Almeida; Silva, Ricardo Oliveira

2017-01-01

Diagnosis of liver involvement due to schistosomiasis in asymptomatic patients from endemic areas previously diagnosed with chronic hepatitis B (HBV) or C (HCV) and periportal fibrosis is challenging. H-1 Nuclear Magnetic Resonance (NMR)-based metabonomics strategy is a powerful tool for providing a profile of endogenous metabolites of low molecular weight in biofluids in a non-invasive way. The aim of this study was to diagnose periportal fibrosis due to schistosomiasis mansoni in patients with chronic HBV or HCV infection through NMR-based metabonomics models. The study included 40 patients divided into two groups: (i) 18 coinfected patients with schistosomiasis mansoni and HBV or HCV; and (ii) 22 HBV or HCV monoinfected patients. The serum samples were analyzed through H-1 NMR spectroscopy and the models were based on Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA). Ultrasonography examination was used to ascertain the diagnosis of periportal fibrosis. Exploratory analysis showed a clear separation between coinfected and monoinfected samples. The supervised model built from PLS-DA showed accuracy, R2 and Q2 values equal to 100%, 98.1% and 97.5%, respectively. According to the variable importance in the projection plot, lactate serum levels were higher in the coinfected group, while the signals attributed to HDL serum cholesterol were more intense in the monoinfected group. The metabonomics models constructed in this study are promising as an alternative tool for diagnosis of periportal fibrosis by schistosomiasis in patients with chronic HBV or HCV infection from endemic areas for Schistosoma mansoni.

LC-UV-solid-phase extraction-NMR-MS combined with a cryogenic flow probe and its application to the identification of compounds present in Greek oregano.

PubMed

Exarchou, Vassiliki; Godejohann, Markus; van Beek, Teris A; Gerothanassis, Ioannis P; Vervoort, Jacques

2003-11-15

Structure elucidation of natural products usually relies on a combination of NMR spectroscopy with mass spectrometry whereby NMR trails MS in terms of the minimum sample amount required. In the present study, the usefulness of on-line solid-phase extraction (SPE) in LC-NMR for peak storage after the LC separation prior to NMR analysis is demonstrated. The SPE unit allows the use of normal protonated solvents for the LC separation and fully deuterated solvents for flushing the trapped compounds to the NMR probe. Thus, solvent suppression is no longer necessary. Multiple trapping of the same analyte from repeated LC injections was utilized to solve the problem of low concentration and to obtain 2D heteronuclear NMR spectra. In addition, a combination of the SPE unit with a recently developed cryoflow NMR probe and an MS was evaluated. This on-line LC-UV-SPE-NMR-MS system was used for the automated analysis of a Greek oregano extract. Combining the data provided by the UV, MS, and NMR spectra, the flavonoids taxifolin, aromadendrin, eriodictyol, naringenin, and apigenin, the phenolic acid rosmarinic acid, and the monoterpene carvacrol were identified. This automated technique is very useful for natural product analysis, and the large sensitivity improvement leads to significantly reduced NMR acquisition times.

NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

PubMed

Bingol, Kerem; Brüschweiler, Rafael

2015-06-05

A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence, and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture, and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously, further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only a few seconds on a computer workstation. NMR/MS Translator synergistically uses the power of NMR and MS, enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases.

Enhancing the resolution of 1H and 13C solid-state NMR spectra by reduction of anisotropic bulk magnetic susceptibility broadening.

PubMed

Hanrahan, Michael P; Venkatesh, Amrit; Carnahan, Scott L; Calahan, Julie L; Lubach, Joseph W; Munson, Eric J; Rossini, Aaron J

2017-10-25

We demonstrate that natural isotopic abundance 2D heteronuclear correlation (HETCOR) solid-state NMR spectra can be used to significantly reduce or eliminate the broadening of 1 H and 13 C solid-state NMR spectra of organic solids due to anisotropic bulk magnetic susceptibility (ABMS). ABMS often manifests in solids with aromatic groups, such as active pharmaceutical ingredients (APIs), and inhomogeneously broadens the NMR peaks of all nuclei in the sample. Inhomogeneous peaks with full widths at half maximum (FWHM) of ∼1 ppm typically result from ABMS broadening and the low spectral resolution impedes the analysis of solid-state NMR spectra. ABMS broadening of solid-state NMR spectra has previously been eliminated using 2D multiple-quantum correlation experiments, or by performing NMR experiments on diluted materials or single crystals. However, these experiments are often infeasible due to their poor sensitivity and/or provide limited gains in resolution. 2D 1 H- 13 C HETCOR experiments have previously been applied to reduce susceptibility broadening in paramagnetic solids and we show that this strategy can significantly reduce ABMS broadening in diamagnetic organic solids. Comparisons of 1D solid-state NMR spectra and 1 H and 13 C solid-state NMR spectra obtained from 2D 1 H- 13 C HETCOR NMR spectra show that the HETCOR spectrum directly increases resolution by a factor of 1.5 to 8. The direct gain in resolution is determined by the ratio of the inhomogeneous 13 C/ 1 H linewidth to the homogeneous 1 H linewidth, with the former depending on the magnitude of the ABMS broadening and the strength of the applied field and the latter on the efficiency of homonuclear decoupling. The direct gains in resolution obtained using the 2D HETCOR experiments are better than that obtained by dilution. For solids with long proton longitudinal relaxation times, dynamic nuclear polarization (DNP) was applied to enhance sensitivity and enable the acquisition of 2D 1 H- 13 C HETCOR NMR spectra. 2D 1 H- 13 C HETCOR experiments were applied to resolve and partially assign the NMR signals of the form I and form II polymorphs of aspirin in a sample containing both forms. These findings have important implications for ultra-high field NMR experiments, optimization of decoupling schemes and assessment of the fundamental limits on the resolution of solid-state NMR spectra.

Solution state nuclear magnetic resonance spectroscopy for biological metabolism and pathway intermediate analysis.

PubMed

Nealon, Gareth L; Howard, Mark J

2016-12-15

Using nuclear magnetic resonance (NMR) spectroscopy in the study of metabolism has been immensely popular in medical- and health-related research but has yet to be widely applied to more fundamental biological problems. This review provides some NMR background relevant to metabolism, describes why 1 H NMR spectra are complex as well as introducing relevant terminology and definitions. The applications and practical considerations of NMR metabolic profiling and 13 C NMR-based flux analyses are discussed together with the elegant 'enzyme trap' approach for identifying novel metabolic pathway intermediates. The importance of sample preparation and data analysis are also described and explained with reference to data precision and multivariate analysis to introduce researchers unfamiliar with NMR and metabolism to consider this technique for their research interests. Finally, a brief glance into the future suggests NMR-based metabolism has room to expand in the 21st century through new isotope labels, and NMR technologies and methodologies. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

NMR-based metabonomic analysis of the hepatotoxicity induced by combined exposure to PCBs and TCDD in rats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu Chunfeng; Department of Pharmacology, Basic Medical College, Jiamusi University, Jiamusi 154007; Wang Yimei

2010-11-01

A metabonomic approach using {sup 1}H NMR spectroscopy was adopted to investigate the metabonomic pattern of rat urine after oral administration of environmental endocrine disruptors (EDs) polychlorinated biphenyls (PCBs) and 2,3,7,8-tetrachlorodibenzo- p-dioxin (TCDD) alone or in combination and to explore the possible hepatotoxic mechanisms of combined exposure to PCBs and TCDD. {sup 1}H NMR spectra of urines collected 24 h before and after exposure were analyzed via pattern recognition by using principal component analysis (PCA). Serum biochemistry and liver histopathology indicated significant hepatotoxicity in the rats of the combined group. The PCA scores plots of urinary {sup 1}H NMR datamore » showed that all the treatment groups could be easily distinguished from the control group, so could the PCBs or TCDD group and the combined group. The loadings plots of the PCA revealed remarkable increases in the levels of lactate, glucose, taurine, creatine, and 2-hydroxy-isovaleric acid and reductions in the levels of 2-oxoglutarate, citrate, succinate, hippurate, and trimethylamine-N-oxide in rat urine after exposure. These changes were more striking in the combined group. The changed metabolites may be considered possible biomarker for the hepatotoxicity. The present study demonstrates that combined exposure to PCBs and TCDD induced significant hepatotoxicity in rats, and mitochondrial dysfunction and fatty acid metabolism perturbations might contribute to the hepatotoxicity. There was good conformity between changes in the urine metabonomic pattern and those in serum biochemistry and liver histopathology. These results showed that the NMR-based metabonomic approach may provide a promising technique for the evaluation of the combined toxicity of EDs.« less

Transformations of the chemical compositions of high molecular weight DOM along a salinity transect: Using two dimensional correlation spectroscopy and principal component analysis approaches

NASA Astrophysics Data System (ADS)

Abdulla, Hussain A. N.; Minor, Elizabeth C.; Dias, Robert F.; Hatcher, Patrick G.

2013-10-01

In a study of chemical transformations of estuarine high-molecular-weight (HMW, >1000 Da) dissolved organic matter (DOM) collected over a period of two years along a transect through the Elizabeth River/Chesapeake Bay system to the coastal Atlantic Ocean off Virginia, USA, δ13C values, N/C ratios, and principal component analysis (PCA) of the solid-state 13C NMR (nuclear magnetic resonance) spectra of HMW-DOM show an abrupt change in both its sources and chemical structural composition occurring around salinity 20. HMW-DOM in the lower salinity region had lighter isotopic values, higher aromatic and lower carbohydrate contents relative to that in the higher salinity region. These changes around a salinity of 20 are possibly due to introduction of a significant amount of new carbon (autotrophic DOM) to the transect. PC-1 loadings plot shows that spatially differing DOM components are similar to previously reported 13C NMR spectra of heteropolysaccharides (HPS) and carboxyl-rich alicyclic molecules (CRAM). Applying two dimensional correlation spectroscopy techniques to 1H NMR spectra from the same samples reveals increases in the contribution of N-acetyl amino sugars, 6-deoxy sugars, and sulfated polysaccharides to HPS components along the salinity transect, which suggests a transition from plant derived carbohydrates to marine produced carbohydrates within the HMW-DOM pool. In contrast to what has been suggested previously, our combined results from 13C NMR, 1H NMR, and FTIR indicate that CRAM consists of at least two different classes of compounds (aliphatic polycarboxyl compounds and lignin-like compounds).

Solid-state {sup 27}Al and {sup 29}Si NMR characterization of hydrates formed in calcium aluminate-silica fume mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pena, P.; Rivas Mercury, J.M.; Aza, A.H. de

2008-08-15

Partially deuterated Ca{sub 3}Al{sub 2}(SiO{sub 4}){sub y}(OH){sub 12-4y}-Al(OH){sub 3} mixtures, prepared by hydration of Ca{sub 3}Al{sub 2}O{sub 6} (C{sub 3}A), Ca{sub 12}Al{sub 14}O{sub 33} (C{sub 12}A{sub 7}) and CaAl{sub 2}O{sub 4} (CA) phases in the presence of silica fume, have been characterized by {sup 29}Si and {sup 27}Al magic-angle spinning-nuclear magnetic resonance (MAS-NMR) spectroscopies. NMR spectroscopy was used to characterize anhydrous and fully hydrated samples. In hydrated compounds, Ca{sub 3}Al{sub 2}(OH){sub 12} and Al(OH){sub 3} phases were detected. From the quantitative analysis of {sup 27}Al NMR signals, the Al(OH){sub 3}/Ca{sub 3}Al{sub 2}(OH){sub 12} ratio was deduced. The incorporation of Simore » into the katoite structure, Ca{sub 3}Al{sub 2}(SiO{sub 4}){sub 3-x}(OH){sub 4x}, was followed by {sup 27}Al and {sup 29}Si NMR spectroscopies. Si/OH ratios were determined from the quantitative analysis of {sup 27}Al MAS-NMR components associated with Al(OH){sub 6} and Al(OSi)(OH){sub 5} environments. The {sup 29}Si NMR spectroscopy was also used to quantify the unreacted silica and amorphous calcium aluminosilicate hydrates formed, C-S-H and C-A-S-H for short. From {sup 29}Si NMR spectra, the amount of Si incorporated into different phases was estimated. Si and Al concentrations, deduced by NMR, transmission electron microscopy, energy dispersive spectrometry, and Rietveld analysis of both X-ray and neutron data, indicate that only a part of available Si is incorporated in katoite structures. - Graphical abstract: Transmission electron micrograph of CaAl{sub 2}O{sub 4}-microsilica mixture hydrated at 90 deg. C for 31 days showing a cubic Ca{sub 3}Al{sub 2.0{+-}}{sub 0.2}(SiO{sub 4}){sub 0.9{+-}}{sub 0.2}(OH){sub 1.8} crystal surrounded by unreacted amorphous silica spheres.« less

Purification and structural characterization of Chinese yam polysaccharide and its activities.

PubMed

Yang, Weifang; Wang, Ying; Li, Xiuping; Yu, Ping

2015-03-06

Purification and structural characterization of Chinese yam polysaccharide were investigated and its activities were analyzed. Results indicated that a single component polysaccharide with a molecular weight of 16,619 Da was obtained after hot water extraction with sequential sevage deproteinization, HSCCC and Sephadex G-100 size-exclusion chromatography. The FTIR analysis showed that it had characteristic absorptive peaks and contained uronic acid. The methylation and GC-MS analysis showed that it comprised of glucose and galactose with a molar ratio of 1.52:1, and that it mainly contained 1,3-linked-glc, 1-linked-gal and 1,6-linked-gal glycosidic bonds. (1)H NMR and (13)C NMR spectra analysis showed that there were two α-configurations and one β-configuration, and that β-1,3-glucose, α-1-galactose, α-1,6-galactose might exist in the structure of the purified polysaccharide. The determination of the antioxidative activity showed that it could scavenge hydroxyl and superoxide radicals. The purified polysaccharide displayed a certain inhibitory activity against Escherichia coli, with a MIC of 2.5 mg/mL. Copyright © 2014 Elsevier Ltd. All rights reserved.

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.

PubMed

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M; Montelione, Gaetano T

2013-08-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

PDBStat: A Universal Restraint Converter and Restraint Analysis Software Package for Protein NMR

PubMed Central

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M.; Montelione, Gaetano T

2013-01-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data. PMID:23897031

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Dynamics and cluster formation in charged and uncharged Ficoll70 solutions

NASA Astrophysics Data System (ADS)

Palit, Swomitra; Yethiraj, Anand

2017-08-01

We apply pulsed-field-gradient NMR (PFG NMR) technique to measure the translational diffusion for both uncharged and charged polysaccharide (Ficoll70) in water. Analysis of the data indicates that the NMR signal attenuation above a certain packing fraction can be adequately fitted with a bi-exponential function. The self-diffusion measurements also show that the Ficoll70, an often-used compact, spherical polysucrose molecule, is itself nonideal, exhibiting signs of both softness and attractive interactions in the form of a stable suspension consisting of monomers and clusters. Further, we can quantify the fraction of monomers and clusters. This work strengthens the picture of the existence of a bound water layer within and around a porous Ficoll70 particle.

Analysis of monoglycerides, diglycerides, sterols, and free fatty acids in coconut (Cocos nucifera L.) oil by 31P NMR spectroscopy.

PubMed

Dayrit, Fabian M; Buenafe, Olivia Erin M; Chainani, Edward T; de Vera, Ian Mitchelle S

2008-07-23

Phosphorus-31 nuclear magnetic resonance spectroscopy ( (31)P NMR) was used to differentiate virgin coconut oil (VCO) from refined, bleached, deodorized coconut oil (RCO). Monoglycerides (MGs), diglycerides (DGs), sterols, and free fatty acids (FFAs) in VCO and RCO were converted into dioxaphospholane derivatives and analyzed by (31)P NMR. On the average, 1-MG was found to be higher in VCO (0.027%) than RCO (0.019%). 2-MG was not detected in any of the samples down to a detection limit of 0.014%. On the average, total DGs were lower in VCO (1.55%) than RCO (4.10%). When plotted in terms of the ratio [1,2-DG/total DGs] versus total DGs, VCO and RCO samples grouped separately. Total sterols were higher in VCO (0.096%) compared with RCO (0.032%), and the FFA content was 8 times higher in VCO than RCO (0.127% vs 0.015%). FFA determination by (31)P NMR and titration gave comparable results. Principal components analysis shows that the 1,2-DG, 1,3-DG, and FFAs are the most important parameters for differentiating VCO from RCO.

NMR Metabolic profiling of green tea (Camellia sinensis L.) leaves grown at Kemuning, Indonesia

NASA Astrophysics Data System (ADS)

Wahyuni, D. S. C.; Kristanti, M. W.; Putri, R. K.; Rinanto, Y.

2017-01-01

Green tea (Camellia sinensis L.) has been famous as a beverage and natural medicine. It contains a broad range of primary and secondary metabolites i.e. polyphenols. Nuclear Magnetic Resonance (NMR) has been widely used for metabolic profiling in medicinal plants. It provides a very fast and detailed analysis of the biomolecular composition of crude extracts. Moreover, an NMR spectrum is a physical characteristic of a compound and thus highly reproducible. Therefore, this study aims to profile metabolites of three different varieties of green tea C. Sinensis grown in Kemuning, Middle Java. Three varieties of green tea collected on Kemuning (TR1 2025, Gambung 4/5, and Chiaruan 143) were used in this study. 1H-NMR spectra were recorded at 230C on a 400 MHz Agilent WB (Widebore). The analysis was performed on dried green tea leaves and analyzed by 1H-NMR, 2D-J-resolved and 1H-1H correlated spectroscopy (COSY). MestRenova version 11.0.0 applied to identify metabolites in samples. A 1H-NMR spectrum of tea showed amino acids and organic acids signal at the area δ 0.8-4.0. These were theanine, alanine, threonine, succinic acid, aspartic acid, lactic acid. Anomeric protons of carbohydrate were shown by the region of β-glucose, α-glucose, fructose and sucrose. The phenolic region was depicted at area δ 5.5-8.5. Epigallocatechin derivates and caffeine were detected in the tea leaves. The detail compound identification was observed and discussed in the text.

Classification of edible oils by employing 31P and 1H NMR spectroscopy in combination with multivariate statistical analysis. A proposal for the detection of seed oil adulteration in virgin olive oils.

PubMed

Vigli, Georgia; Philippidis, Angelos; Spyros, Apostolos; Dais, Photis

2003-09-10

A combination of (1)H NMR and (31)P NMR spectroscopy and multivariate statistical analysis was used to classify 192 samples from 13 types of vegetable oils, namely, hazelnut, sunflower, corn, soybean, sesame, walnut, rapeseed, almond, palm, groundnut, safflower, coconut, and virgin olive oils from various regions of Greece. 1,2-Diglycerides, 1,3-diglycerides, the ratio of 1,2-diglycerides to total diglycerides, acidity, iodine value, and fatty acid composition determined upon analysis of the respective (1)H NMR and (31)P NMR spectra were selected as variables to establish a classification/prediction model by employing discriminant analysis. This model, obtained from the training set of 128 samples, resulted in a significant discrimination among the different classes of oils, whereas 100% of correct validated assignments for 64 samples were obtained. Different artificial mixtures of olive-hazelnut, olive-corn, olive-sunflower, and olive-soybean oils were prepared and analyzed by (1)H NMR and (31)P NMR spectroscopy. Subsequent discriminant analysis of the data allowed detection of adulteration as low as 5% w/w, provided that fresh virgin olive oil samples were used, as reflected by their high 1,2-diglycerides to total diglycerides ratio (D > or = 0.90).

Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP).

PubMed

Snyder, David A; Chantova, Mihaela; Chaudhry, Saadia

2015-06-01

NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase. Copyright © 2015 Elsevier Inc. All rights reserved.

The NMR contribution to protein-protein networking in Fe-S protein maturation.

PubMed

Banci, Lucia; Camponeschi, Francesca; Ciofi-Baffoni, Simone; Piccioli, Mario

2018-03-22

Iron-sulfur proteins were among the first class of metalloproteins that were actively studied using NMR spectroscopy tailored to paramagnetic systems. The hyperfine shifts, their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues are an efficient fingerprint of the nature and the oxidation state of the Fe-S cluster. NMR significantly contributed to the analysis of the magnetic coupling patterns and to the understanding of the electronic structure occurring in [2Fe-2S], [3Fe-4S] and [4Fe-4S] clusters bound to proteins. After the first NMR structure of a paramagnetic protein was obtained for the reduced E. halophila HiPIP I, many NMR structures were determined for several Fe-S proteins in different oxidation states. It was found that differences in chemical shifts, in patterns of unobserved residues, in internal mobility and in thermodynamic stability are suitable data to map subtle changes between the two different oxidation states of the protein. Recently, the interaction networks responsible for maturing human mitochondrial and cytosolic Fe-S proteins have been largely characterized by combining solution NMR standard experiments with those tailored to paramagnetic systems. We show here the contribution of solution NMR in providing a detailed molecular view of "Fe-S interactomics". This contribution was particularly effective when protein-protein interactions are weak and transient, and thus difficult to be characterized at high resolution with other methodologies.

Automated Microflow NMR: Routine Analysis of Five-Microliter Samples

PubMed Central

Jansma, Ariane; Chuan, Tiffany; Geierstanger, Bernhard H.; Albrecht, Robert W.; Olson, Dean L.; Peck, Timothy L.

2006-01-01

A microflow CapNMR probe double-tuned for 1H and 13C was installed on a 400-MHz NMR spectrometer and interfaced to an automated liquid handler. Individual samples dissolved in DMSO-d6 are submitted for NMR analysis in vials containing as little as 10 μL of sample. Sets of samples are submitted in a low-volume 384-well plate. Of the 10 μL of sample per well, as with vials, 5 μL is injected into the microflow NMR probe for analysis. For quality control of chemical libraries, 1D NMR spectra are acquired under full automation from 384-well plates on as many as 130 compounds within 24 h using 128 scans per spectrum and a sample-to-sample cycle time of ∼11 min. Because of the low volume requirements and high mass sensitivity of the microflow NMR system, 30 nmol of a typical small molecule is sufficient to obtain high-quality, well-resolved, 1D proton or 2D COSY NMR spectra in ∼6 or 20 min of data acquisition time per experiment, respectively. Implementation of pulse programs with automated solvent peak identification and suppression allow for reliable data collection, even for samples submitted in fully protonated DMSO. The automated microflow NMR system is controlled and monitored using web-based software. PMID:16194121

¹H NMR spectroscopy reveals the effect of genotype and growth conditions on composition of sea buckthorn (Hippophaë rhamnoides L.) berries.

PubMed

Kortesniemi, Maaria; Sinkkonen, Jari; Yang, Baoru; Kallio, Heikki

2014-03-15

¹H NMR spectroscopy and multivariate data analysis were applied to the metabolic profiling and discrimination of wild sea buckthorn (Hippophaë rhamnoides L.) berries from different locations in Finland (subspecies (ssp.) rhamnoides) and China (ssp. sinensis). Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) showed discrimination of the two subspecies and different growth sites. The discrimination of ssp. rhamnoides was mainly associated with typically higher temperature, radiation and humidity and lower precipitation in the south, yielding higher levels of O-ethyl β-d-glucopyranoside and d-glucose, and lower levels of malic, quinic and ascorbic acids. Significant metabolic differences (p<0.05) in genetically identical berries were observed between latitudes 60° and 67° north in Finland. High altitudes (> 2,000 m) correlated with greater levels of malic and ascorbic acids in ssp. sinensis. The NMR metabolomics approach applied here is effective for identification of metabolites, geographical origin and subspecies of sea buckthorn berries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Characterization of oils and fats by 1H NMR and GC/MS fingerprinting: classification, prediction and detection of adulteration.

PubMed

Fang, Guihua; Goh, Jing Yeen; Tay, Manjun; Lau, Hiu Fung; Li, Sam Fong Yau

2013-06-01

The correct identification of oils and fats is important to consumers from both commercial and health perspectives. Proton nuclear magnetic resonance ((1)H NMR) spectroscopy, gas chromatography-mass spectrometry (GC/MS) fingerprinting and chemometrics were employed successfully for the quality control of oils and fats. Principal component analysis (PCA) of both techniques showed group clustering of 14 types of oils and fats. Partial least squares discriminant analysis (PLS-DA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) using GC/MS data had excellent classification sensitivity and specificity compared to models using NMR data. Depending on the availability of the instruments, data from either technique can effectively be applied for the establishment of an oils and fats database to identify unknown samples. Partial least squares (PLS) models were successfully established for the detection of as low as 5% of lard and beef tallow spiked into canola oil, thus illustrating possible applications in Islamic and Jewish countries. Copyright © 2012 Elsevier Ltd. All rights reserved.

NMR analysis of cleaved Escherichia coli thioredoxin (1-73/74-108) and its P76A variant: cis/trans peptide isomerization.

PubMed Central

Yu, W. F.; Tung, C. S.; Wang, H.; Tasayco, M. L.

2000-01-01

Inspection of high resolution three-dimensional (3D) structures from the protein database reveals an increasing number of cis-Xaa-Pro and cis-Xaa-Yaa peptide bonds. However, we are still far from being able to predict whether these bonds will remain cis upon single-site substitution of Pro or Yaa and/or cleavage of a peptide bond close to it in the sequence. We have chosen oxidized Escherichia coli thioredoxin (Trx), a member of the Trx superfamily with a single alpha/beta domain and cis P76 to determine the effect of single-site substitution and/or cleavage on this isomer. Standard two-dimensional (2D) NMR analysis were performed on cleaved Trx (1-73/74-108) and its P76A variant. Analysis of the NOE connectivities indicates remarkable similarity between the secondary and supersecondary structure of the noncovalent complexes and Trx. Analysis of the 2D version of the HCCH-TOCSY and HMQC-NOESY-HMQC and 13C-filtered HMQC-NOESY spectra of cleaved Trx with uniformly 13C-labeled 175 and P76 shows surprising conservation of both cis P76 and packing of 175 against W31. A similar NMR analysis of its P76A variant provides no evidence for cis A76 and shows only subtle local changes in both the packing of 175 and the interstrand connectivities between its most protected hydrophobic strands (beta2 and beta4). Indeed, a molecular simulation model for the trans P76A variant of Trx shows only subtle local changes around the substitution site. In conclusion, cleavage of R73 is insufficient to provoke cis/trans isomerization of P76, but cleavage and single-site substitution (P76A) favors the trans isomer. PMID:10739243

Rapid acquisition of data dense solid-state CPMG NMR spectral sets using multi-dimensional statistical analysis

DOE PAGES

Mason, H. E.; Uribe, E. C.; Shusterman, J. A.

2018-01-01

Tensor-rank decomposition methods have been applied to variable contact time 29 Si{ 1 H} CP/CPMG NMR data sets to extract NMR dynamics information and dramatically decrease conventional NMR acquisition times.

Rapid acquisition of data dense solid-state CPMG NMR spectral sets using multi-dimensional statistical analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mason, H. E.; Uribe, E. C.; Shusterman, J. A.

Tensor-rank decomposition methods have been applied to variable contact time 29 Si{ 1 H} CP/CPMG NMR data sets to extract NMR dynamics information and dramatically decrease conventional NMR acquisition times.

A sulfur amino acid-free meal increases plasma lipids in humans.

PubMed

Park, Youngja; Le, Ngoc-Anh; Yu, Tianwei; Strobel, Fred; Gletsu-Miller, Nana; Accardi, Carolyn J; Lee, Kichun S; Wu, Shaoxiong; Ziegler, Thomas R; Jones, Dean P

2011-08-01

The content of sulfur amino acid (SAA) in a meal affects postprandial plasma cysteine concentrations and the redox potential of cysteine/cystine. Because such changes can affect enzyme, transporter, and receptor activities, meal content of SAA could have unrecognized effects on metabolism during the postprandial period. This pilot study used proton NMR ((1)H-NMR) spectroscopy of human plasma to test the hypothesis that dietary SAA content changes macronutrient metabolism. Healthy participants (18-36 y, 5 males and 3 females) were equilibrated for 3 d to adequate SAA, fed chemically defined meals without SAA for 5 d (depletion), and then fed isoenergetic, isonitrogenous meals containing 56 mg·kg(-1)·d(-1) SAA for 4.5 d (repletion). On the first and last day of consuming the chemically defined meals, a morning meal containing 60% of the daily food intake was given and plasma samples were collected over an 8-h postprandial time course for characterization of metabolic changes by (1)H-NMR spectroscopy. SAA-free food increased peak intensity in the plasma (1)H-NMR spectra in the postprandial period. Orthogonal signal correction/partial least squares-discriminant analysis showed changes in signals associated with lipids, some amino acids, and lactate, with notable increases in plasma lipid signals (TG, unsaturated lipid, cholesterol). Conventional lipid analyses confirmed higher plasma TG and showed an increase in plasma concentration of the lipoprotein lipase inhibitor, apoC-III. The results show that plasma (1)H-NMR spectra can provide useful macronutrient profiling following a meal challenge protocol and that a single meal with imbalanced SAA content alters postprandial lipid metabolism.

Synthesis of metal complexes involving Schiff base ligand with methylenedioxy moiety: spectral, thermal, XRD and antimicrobial studies.

PubMed

Sundararajan, M L; Jeyakumar, T; Anandakumaran, J; Karpanai Selvan, B

2014-10-15

Metal complexes of Zn(II), Cd(II), Ni(II), Cu(II), Fe(III), Co(II), Mn(II) Hg(II), and Ag(I) have been synthesized from Schiff base ligand, prepared by the condensation of 3,4-(methylenedioxy)aniline and 5-bromo salicylaldehyde. All the compounds have been characterized by using elemental analysis, molar conductance, FT-IR, UV-Vis, (1)H NMR, (13)C NMR, mass spectra, powder XRD and thermal analysis (TG/DTA) technique. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). The FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectral data suggest that the ligand coordinate to the metal atom by imino nitrogen and phenolic oxygen as bidentate manner. Mass spectral data further support the molecular mass of the compounds and their structure. Powder XRD indicates the crystalline state and morphology of the ligand and its metal complexes. The thermal behaviors of the complexes prove the presence of lattice as well as coordinated water molecules in the complexes. Melting point supports the thermal stability of all the compounds. The in vitro antimicrobial effects of the synthesized compounds were tested against five bacterial and three fungal species by well diffusion method. Antioxidant activities have also been performed for all the compounds. Metal complexes show more biological activity than the Schiff base. Copyright © 2014 Elsevier B.V. All rights reserved.

Prediction of recrystallization behavior of troglitazone/polyvinylpyrrolidone solid dispersion by solid-state NMR.

PubMed

Ito, Atsutoshi; Watanabe, Tomoyuki; Yada, Shuichi; Hamaura, Takeshi; Nakagami, Hiroaki; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2010-01-04

The purpose of this study was to elaborate the relationship between the (13)C CP/MAS NMR spectra and the recrystallization behavior during the storage of troglitazone solid dispersions. The solid dispersions were prepared by either the solvent method or by co-grinding. The recrystallization behavior under storage conditions at 40 degrees C/94% RH was evaluated by the Kolmogorov-Johnson-Mehl-Avrami (KJMA) equation. Solid dispersions prepared by the solvent method or by prolonged grinding brought about inhibition of the nucleation and the nuclei growth at the same time. No differences in the PXRD profiles were found in the samples prepared by the co-grinding and solvent methods, however, (13)C CP/MAS NMR showed significant differences in the spectra. The correlation coefficients using partial least square regression analysis between the PXRD profiles and the apparent nuclei-growth constant or induction period to nucleation were 0.1305 or 0.6350, respectively. In contrast, those between the (13)C CP/MAS NMR spectra and the constant or the period were 0.9916 or 0.9838, respectively. The (13)C CP/MAS NMR spectra had good correlation with the recrystallization kinetic parameters evaluated by the KJMA equation. Consequently, solid-state NMR was judged to be a useful tool for the prediction of the recrystallization behavior of solid dispersions.

Fingerprinting analysis of Saposhnikovia divaricata using 1H nuclear magnetic resonance spectroscopy and high performance liquid chromatography.

PubMed

Xin, Yue-Yang; Deng, An-Jun; Du, Guan-Hua; Zhang, Jin-Lan; Qin, Hai-Lin

2010-09-01

The (1)H nuclear magnetic resonance ((1)H NMR) fingerprints of fractionated non-polar and polar extracts (control substance for plant drug [CSPD] A and B) from the roots of 12 specimens of Saposhnikovia divaricata (Turcz.) Schischk were achieved with Fourier Transform (FT)-NMR spectrometer and assigned by comparison to each other and to the (1)H NMR spectra of the isolated individual compounds. These fingerprints were found to be uniform in terms of the specificity for the implication of all 12 specimens being systematically of the same origin. The uniformity was further affirmed by high performance liquid chromatography (HPLC), which also revealed exactly identical specificity for the identified S. divaricata species with the (1)H NMR appearances of corresponding CSPD on the part of the composition of characteristic constituents when comparing to corresponding individual compounds. This investigation unambiguously shows that the specific signals from the chemotaxonomically significant compounds of chromones and coumarins in S. divaricata are exhibited distinctively in the composite features of both (1)H NMR fingerprints and HPLC profiles. The (1)H NMR and HPLC profiles established can successfully be used as reference for the authentication of the origin of S. divaricata species as well as for chemotaxonomic studies.

The use of IRMS, (1)H NMR and chemical analysis to characterise Italian and imported Tunisian olive oils.

PubMed

Camin, Federica; Pavone, Anita; Bontempo, Luana; Wehrens, Ron; Paolini, Mauro; Faberi, Angelo; Marianella, Rosa Maria; Capitani, Donatella; Vista, Silvia; Mannina, Luisa

2016-04-01

Isotope Ratio Mass Spectrometry (IRMS), (1)H Nuclear Magnetic Resonance ((1)H NMR), conventional chemical analysis and chemometric elaboration were used to assess quality and to define and confirm the geographical origin of 177 Italian PDO (Protected Denomination of Origin) olive oils and 86 samples imported from Tunisia. Italian olive oils were richer in squalene and unsaturated fatty acids, whereas Tunisian olive oils showed higher δ(18)O, δ(2)H, linoleic acid, saturated fatty acids β-sitosterol, sn-1 and 3 diglyceride values. Furthermore, all the Tunisian samples imported were of poor quality, with a K232 and/or acidity values above the limits established for extra virgin olive oils. By combining isotopic composition with (1)H NMR data using a multivariate statistical approach, a statistical model able to discriminate olive oil from Italy and those imported from Tunisia was obtained, with an optimal differentiation ability arriving at around 98%. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conformational distribution of baclofen analogues by 1H and 13C NMR analysis and ab initio HF MO STO-3G or STO-3G* calculations

NASA Astrophysics Data System (ADS)

Vaccher, Claude; Berthelot, Pascal; Debaert, Michel; Vermeersch, Gaston; Guyon, René; Pirard, Bernard; Vercauteren, Daniel P.; Dory, Magdalena; Evrard, Guy; Durant, François

1993-12-01

The conformations of 3-(substituted furan-2-yl) and 3-(substituted thien-2-yl)-γ-aminobutyric acid 1-9 in solution (D 2O) are estimated from high-resolution (300 MHz) 1H NMR coupling data. Conformations and populations of conformers are calculated by means of a modified Karplus-like relationship for the vicinal coupling constants. The results are compared with X-ray crystallographic investigations (torsion angles) and ab initio HF MO ST-3G or STO-3G* calculations. 1H NMR spectral analysis shows how 1-9 in solution retain the preferred g- conformation around the C3C4 bond, as found in the solid state, while a partial rotation is set up around the C2C3 bond: the conformations about C2C3 are all highly populated in solution. The 13C spin-lattice relaxation times are also discussed.

Experimental and DFT studies of (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline: electronic and vibrational properties.

PubMed

Sun, Wenqi; Yuan, Guozan; Liu, Jingxin; Ma, Li; Liu, Chengbu

2013-04-01

The title molecule (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline (DPEQ) was synthesized and characterized by FT-IR, UV-vis, NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results indicate that the theoretical vibrational frequencies, 1H and 13C NMR chemical shift values show good agreement with experimental data. The electronic properties like UV-vis spectral analysis and HOMO-LUMO analysis of DPEQ have been reported and compared with experimental data. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP). Copyright © 2013 Elsevier B.V. All rights reserved.

Experimental and DFT studies of (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline: Electronic and vibrational properties

NASA Astrophysics Data System (ADS)

Sun, Wenqi; Yuan, Guozan; Liu, Jingxin; Ma, Li; Liu, Chengbu

2013-04-01

The title molecule (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline (DPEQ) was synthesized and characterized by FT-IR, UV-vis, NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results indicate that the theoretical vibrational frequencies, 1H and 13C NMR chemical shift values show good agreement with experimental data. The electronic properties like UV-vis spectral analysis and HOMO-LUMO analysis of DPEQ have been reported and compared with experimental data. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP).

Application of chemometrics in quality control of Turmeric (Curcuma longa) based on Ultra-violet, Fourier transform-infrared and 1H NMR spectroscopy.

PubMed

Gad, Haidy A; Bouzabata, Amel

2017-12-15

Turmeric (Curcuma longa L.) belongs to the family Zingiberaceae that is widely used as a spice in food preparations in addition to its biological activities. UV, FT-IR, 1 H NMR in addition to HPLC were applied to construct a metabolic fingerprint for Turmeric in an attempt to assess its quality. 30 samples were analyzed, and then principal component analysis (PCA) and hierarchical clustering analysis (HCA) were utilized to assess the differences and similarities between collected samples. PCA score plot based on both HPLC and UV spectroscopy showed the same discriminatory pattern, where the samples were segregated into four main groups depending on their total curcuminoids content. The results revealed that UV could be utilized as a simple and rapid alternative for HPLC. However, FT-IR failed to discriminate between the same species. By applying 1 H NMR, the metabolic variability between samples was more evident in the essential oils/fatty acid region. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid approach to identify the presence of Arabica and Robusta species in coffee using 1H NMR spectroscopy.

PubMed

Monakhova, Yulia B; Ruge, Winfried; Kuballa, Thomas; Ilse, Maren; Winkelmann, Ole; Diehl, Bernd; Thomas, Freddy; Lachenmeier, Dirk W

2015-09-01

NMR spectroscopy was used to verify the presence of Arabica and Robusta species in coffee. Lipophilic extracts of authentic roasted and green coffees showed the presence of established markers for Robusta (16-O-methylcafestol (16-OMC)) and for Arabica (kahweol). The integration of the 16-OMC signal (δ 3.165 ppm) was used to estimate the amount of Robusta in coffee blends with an approximate limit of detection of 1-3%. The method was successfully applied for the analysis of 77 commercial coffee samples (coffee pods, coffee capsules, and coffee beans). Furthermore, principal component analysis (PCA) was applied to the spectra of lipophilic and aqueous extracts of 20 monovarietal authentic samples. Clusters of the two species were observed. NMR spectroscopy can be used as a rapid prescreening tool to discriminate Arabica and Robusta coffee species before the confirmation applying the official method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Monitoring of pistachio (Pistacia Vera) ripening by high field nuclear magnetic resonance spectroscopy.

PubMed

Sciubba, Fabio; Avanzato, Damiano; Vaccaro, Angela; Capuani, Giorgio; Spagnoli, Mariangela; Di Cocco, Maria Enrica; Tzareva, Irina Nikolova; Delfini, Maurizio

2017-04-01

The metabolic profiling of pistachio (Pistacia vera) aqueous extracts from two different cultivars, namely 'Bianca' and 'Gloria', was monitored over the months from May to September employing high field NMR spectroscopy. A large number of water-soluble metabolites were assigned by means of 1D and 2D NMR experiments. The change in the metabolic profiles monitored over time allowed the pistachio development to be investigated. Specific temporal trends of amino acids, sugars, organic acids and other metabolites were observed and analysed by multivariate Partial Least Squares (PLS) analysis. Statistical analysis showed that while in the period from May to September there were few differences between the two cultivars, the ripening rate was different.

Sulfonamide-containing PTP 1B inhibitors: Docking studies, synthesis and model validation

NASA Astrophysics Data System (ADS)

Niu, Enli; Gan, Qiang; Chen, Xi; Feng, Changgen

2017-01-01

PTP 1B plays an important role in regulating insulin signaling pathway and is regarded as a valid target for curing diabetes and obesity. In this paper, two novel sulfonamide-containing PTP 1B inhibitors were designed, synthesized in mild condition, and characterized by FT-IR, 1H NMR, 13C NMR and elemental analysis. The single crystal of compounds 7 and 8 were obtained and their structures were determined by X-ray single crystal diffraction analysis. In addition, their inhibitory activity were predicted by genetic algorithm, and carried on in vitro enzyme activity test. Of which compound 8 showed good inhibitory activity, in consistent with docking studies.

Collaborative development for setup, execution, sharing and analytics of complex NMR experiments.

PubMed

Irvine, Alistair G; Slynko, Vadim; Nikolaev, Yaroslav; Senthamarai, Russell R P; Pervushin, Konstantin

2014-02-01

Factory settings of NMR pulse sequences are rarely ideal for every scenario in which they are utilised. The optimisation of NMR experiments has for many years been performed locally, with implementations often specific to an individual spectrometer. Furthermore, these optimised experiments are normally retained solely for the use of an individual laboratory, spectrometer or even single user. Here we introduce a web-based service that provides a database for the deposition, annotation and optimisation of NMR experiments. The application uses a Wiki environment to enable the collaborative development of pulse sequences. It also provides a flexible mechanism to automatically generate NMR experiments from deposited sequences. Multidimensional NMR experiments of proteins and other macromolecules consume significant resources, in terms of both spectrometer time and effort required to analyse the results. Systematic analysis of simulated experiments can enable optimal allocation of NMR resources for structural analysis of proteins. Our web-based application (http://nmrplus.org) provides all the necessary information, includes the auxiliaries (waveforms, decoupling sequences etc.), for analysis of experiments by accurate numerical simulation of multidimensional NMR experiments. The online database of the NMR experiments, together with a systematic evaluation of their sensitivity, provides a framework for selection of the most efficient pulse sequences. The development of such a framework provides a basis for the collaborative optimisation of pulse sequences by the NMR community, with the benefits of this collective effort being available to the whole community. Copyright © 2013 Elsevier Inc. All rights reserved.

1H-NMR METABONOMICS ANALYSIS OF SERA DIFFERENTIATES BETWEEN MAMMARY TUMOR-BEARING MICE AND HEALTHY CONTROLS

EPA Science Inventory

Global analysis of 1H-NMR spectra of serum is an appealing approach for the rapid detection of cancer. To evaluate the usefulness of this method in distinguishing between mammary tumor-bearing mice and healthy controls, we conducted 1H-NMR metabonomic analyses on serum samples ob...

Online low-field NMR spectroscopy for process control of an industrial lithiation reaction-automated data analysis.

PubMed

Kern, Simon; Meyer, Klas; Guhl, Svetlana; Gräßer, Patrick; Paul, Andrea; King, Rudibert; Maiwald, Michael

2018-05-01

Monitoring specific chemical properties is the key to chemical process control. Today, mainly optical online methods are applied, which require time- and cost-intensive calibration effort. NMR spectroscopy, with its advantage being a direct comparison method without need for calibration, has a high potential for enabling closed-loop process control while exhibiting short set-up times. Compact NMR instruments make NMR spectroscopy accessible in industrial and rough environments for process monitoring and advanced process control strategies. We present a fully automated data analysis approach which is completely based on physically motivated spectral models as first principles information (indirect hard modeling-IHM) and applied it to a given pharmaceutical lithiation reaction in the framework of the European Union's Horizon 2020 project CONSENS. Online low-field NMR (LF NMR) data was analyzed by IHM with low calibration effort, compared to a multivariate PLS-R (partial least squares regression) approach, and both validated using online high-field NMR (HF NMR) spectroscopy. Graphical abstract NMR sensor module for monitoring of the aromatic coupling of 1-fluoro-2-nitrobenzene (FNB) with aniline to 2-nitrodiphenylamine (NDPA) using lithium-bis(trimethylsilyl) amide (Li-HMDS) in continuous operation. Online 43.5 MHz low-field NMR (LF) was compared to 500 MHz high-field NMR spectroscopy (HF) as reference method.

New milbemycin metabolites from the genetically engineered strain Streptomyces bingchenggensis BCJ60.

PubMed

Li, Jian-Song; Du, Min-Na; Zhang, Hui; Zhang, Ji; Zhang, Shao-Yong; Wang, Hai-Yan; Chen, An-Liang; Wang, Ji-Dong; Xiang, Wen-Sheng

2017-04-01

Two new milbemycin derivatives, 27-methoxylmilbemycin α 31 (1) and 27-oxomilbemycin α 31 (2), were isolated from the genetically engineered strain Streptomyces bingchenggensis BCJ60. Their structures were determined by 1D NMR, 2D NMR and HR-ESI-MS spectral analysis, and comparison with previous reports. The acaricidal and nematocidal capacities of compounds 1 and 2 were evaluated against Tetranychus cinnabarinus and Bursaphelenchus xylophilus, respectively. The results showed that the two new macrocyclic lactones 1 and 2 possessed potent acaricidal and nematocidal activities.

A sink for methane on Mars? The answer is blowing in the wind

NASA Astrophysics Data System (ADS)

Knak Jensen, Svend J.; Skibsted, Jørgen; Jakobsen, Hans J.; ten Kate, Inge L.; Gunnlaugsson, Haraldur P.; Merrison, Jonathan P.; Finster, Kai; Bak, Ebbe; Iversen, Jens J.; Kondrup, Jens C.; Nørnberg, Per

2014-07-01

Tumbling experiments that mimic the wind erosion of quartz grains in an atmosphere of 13C-enriched methane are reported. The eroded grains are analyzed by 13C and 29Si solid-state NMR techniques after several months of tumbling. The analysis shows that methane has reacted with the eroded surface to form covalent Si-CH3 bonds, which stay intact for temperatures up to at least 250 °C. The NMR findings offer an explanation for the fast disappearance of methane on Mars.

Quantitative (13)C Solid-State NMR Spectra by Multiple-Contact Cross-polarization for Drug Delivery: From Active Principles to Excipients and Drug Carriers.

PubMed

Saïdi, Fadila; Taulelle, Francis; Martineau, Charlotte

2016-08-01

In this contribution, we present an analysis of the main parameters influencing the efficiency of the (1)H → (13)C multiple-contact cross-polarization nuclear magnetic resonance (NMR) experiment in the context of solid pharmaceutical materials. Using the optimum experimental conditions, quantitative (13)C NMR spectra are then obtained for porous metal-organic frameworks (potential drug carriers) and for components present in drug formulations (active principle ingredient and excipients, amorphous or crystalline). Finally, we show that mixtures of components can also be quantified with this method and, hence, that it represents an ideal tool for quantification of pharmaceutical formulations by (13)C cross-polarization under magic-angle spinning NMR in the industry as it is robust and easy to set up, much faster than direct (13)C polarization and is efficient for samples at natural abundance. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

A self optimizing synthetic organic reactor system using real-time in-line NMR spectroscopy† †Electronic supplementary information (ESI) available: Details about the methodology, LabView scripts, experimental set-ups, additional spectra and self-optimization can be found in the SI. See DOI: 10.1039/c4sc03075c Click here for additional data file.

PubMed Central

Sans, Victor; Porwol, Luzian; Dragone, Vincenza

2015-01-01

A configurable platform for synthetic chemistry incorporating an in-line benchtop NMR that is capable of monitoring and controlling organic reactions in real-time is presented. The platform is controlled via a modular LabView software control system for the hardware, NMR, data analysis and feedback optimization. Using this platform we report the real-time advanced structural characterization of reaction mixtures, including 19F, 13C, DEPT, 2D NMR spectroscopy (COSY, HSQC and 19F-COSY) for the first time. Finally, the potential of this technique is demonstrated through the optimization of a catalytic organic reaction in real-time, showing its applicability to self-optimizing systems using criteria such as stereoselectivity, multi-nuclear measurements or 2D correlations. PMID:29560211

Protein analysis by 31p NMR spectroscopy in ionic liquid: quantitative determination of enzymatically created cross-links.

PubMed

Monogioudi, Evanthia; Permi, Perttu; Filpponen, Ilari; Lienemann, Michael; Li, Bin; Argyropoulos, Dimitris; Buchert, Johanna; Mattinen, Maija-Liisa

2011-02-23

Cross-linking of β-casein by Trichoderma reesei tyrosinase (TrTyr) and Streptoverticillium mobaraense transglutaminase (Tgase) was analyzed by (31)P nuclear magnetic resonance (NMR) spectroscopy in ionic liquid (IL). According to (31)P NMR, 91% of the tyrosine side chains were cross-linked by TrTyr at high dosages. When Tgase was used, no changes were observed because a different cross-linking mechanism was operational. However, this verified the success of the phosphitylation of phenolics within the protein matrix in the IL. Atomic force microscopy (AFM) in solid state showed that disk-shaped nanoparticles were formed in the reactions with average diameters of 80 and 20 nm for TrTyr and Tgase, respectively. These data further advance the current understanding of the action of tyrosinases on proteins on molecular and chemical bond levels. Quantitative (31)P NMR in IL was shown to be a simple and efficient method for the study of protein modification.

Detergent/Nanodisc Screening for High-Resolution NMR Studies of an Integral Membrane Protein Containing a Cytoplasmic Domain

PubMed Central

Maslennikov, Innokentiy; Choe, Senyon; Riek, Roland

2013-01-01

Because membrane proteins need to be extracted from their natural environment and reconstituted in artificial milieus for the 3D structure determination by X-ray crystallography or NMR, the search for membrane mimetic that conserve the native structure and functional activities remains challenging. We demonstrate here a detergent/nanodisc screening study by NMR of the bacterial α-helical membrane protein YgaP containing a cytoplasmic rhodanese domain. The analysis of 2D [15N,1H]-TROSY spectra shows that only a careful usage of low amounts of mixed detergents did not perturb the cytoplasmic domain while solubilizing in parallel the transmembrane segments with good spectral quality. In contrast, the incorporation of YgaP into nanodiscs appeared to be straightforward and yielded a surprisingly high quality [15N,1H]-TROSY spectrum opening an avenue for the structural studies of a helical membrane protein in a bilayer system by solution state NMR. PMID:23349867

Authentication of animal origin of heparin and low molecular weight heparin including ovine, porcine and bovine species using 1D NMR spectroscopy and chemometric tools.

PubMed

Monakhova, Yulia B; Diehl, Bernd W K; Fareed, Jawed

2018-02-05

High resolution (600MHz) nuclear magnetic resonance (NMR) spectroscopy is used to distinguish heparin and low-molecular weight heparins (LMWHs) produced from porcine, bovine and ovine mucosal tissues as well as their blends. For multivariate analysis several statistical methods such as principal component analysis (PCA), factor discriminant analysis (FDA), partial least squares - discriminant analysis (PLS-DA), linear discriminant analysis (LDA) were utilized for the modeling of NMR data of more than 100 authentic samples. Heparin and LMWH samples from the independent test set (n=15) were 100% correctly classified according to its animal origin. Moreover, by using 1 H NMR coupled with chemometrics and several batches of bovine heparins from two producers were differentiated. Thus, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of animal origin and process based manufacturing difference in heparin products. Copyright © 2017 Elsevier B.V. All rights reserved.

Study of acute biochemical effects of thallium toxicity in mouse urine by NMR spectroscopy.

PubMed

Tyagi, Ritu; Rana, Poonam; Khan, Ahmad Raza; Bhatnagar, Deepak; Devi, M Memita; Chaturvedi, Shubhra; Tripathi, Rajendra P; Khushu, Subash

2011-10-01

Thallium (Tl) is a toxic heavy metal and its exposure to the human body causes physiological and biochemical changes due to its interference with potassium-dependent biological reactions. A high-resolution (1)H NMR spectroscopy based metabonomic approach has been applied for investigating acute biochemical effects caused by thallium sulfate (Tl(2)SO(4)). Male strain A mice were divided in three groups and received three doses of Tl(2)SO(4) (5, 10 and 20 mg kg(-1) b.w., i.p.). Urine samples collected at 3, 24, 72 and 96 h post-dose time points were analyzed by (1)H NMR spectroscopy. NMR spectral data were processed and analyzed using principal components analysis to represent biochemical variations induced by Tl(2)SO(4). Results showed Tl-exposed mice urine to have distinct metabonomic phenotypes and revealed dose- and time-dependent clustering of treated groups. The metabolic signature of urine analysis from Tl(2)SO(4)-treated animals exhibited an increase in the levels of creatinine, taurine, hippurate and β-hydroxybutyrate along with a decrease in energy metabolites trimethylamine and choline. These findings revealed Tl-induced disturbed gut flora, membrane metabolite, energy and protein metabolism, representing physiological dysfunction of vital organs. The present study indicates the great potential of NMR-based metabonomics in mapping metabolic response for toxicology, which could ultimately lead to identification of potential markers for Tl toxicity. Copyright © 2011 John Wiley & Sons, Ltd.

Utility of magnetic resonance imaging and nuclear magnetic resonance-based metabolomics for quantification of inflammatory lung injury

PubMed Central

Serkova, Natalie J.; Van Rheen, Zachary; Tobias, Meghan; Pitzer, Joshua E.; Wilkinson, J. Erby; Stringer, Kathleen A.

2008-01-01

Magnetic resonance imaging (MRI) and metabolic nuclear magnetic resonance (NMR) spectroscopy are clinically available but have had little application in the quantification of experimental lung injury. There is a growing and unfulfilled need for predictive animal models that can improve our understanding of disease pathogenesis and therapeutic intervention. Integration of MRI and NMR could extend the application of experimental data into the clinical setting. This study investigated the ability of MRI and metabolic NMR to detect and quantify inflammation-mediated lung injury. Pulmonary inflammation was induced in male B6C3F1 mice by intratracheal administration of IL-1β and TNF-α under isoflurane anesthesia. Mice underwent MRI at 2, 4, 6, and 24 h after dosing. At 6 and 24 h lungs were harvested for metabolic NMR analysis. Data acquired from IL-1β+TNF-α-treated animals were compared with saline-treated control mice. The hyperintense-to-total lung volume (HTLV) ratio derived from MRI was higher in IL-1β+TNF-α-treated mice compared with control at 2, 4, and 6 h but returned to control levels by 24 h. The ability of MRI to detect pulmonary inflammation was confirmed by the association between HTLV ratio and histological and pathological end points. Principal component analysis of NMR-detectable metabolites also showed a temporal pattern for which energy metabolism-based biomarkers were identified. These data demonstrate that both MRI and metabolic NMR have utility in the detection and quantification of inflammation-mediated lung injury. Integration of these clinically available techniques into experimental models of lung injury could improve the translation of basic science knowledge and information to the clinic. PMID:18441091

Profiling Redox and Energy Coenzymes in Whole Blood, Tissue and Cells Using NMR Spectroscopy.

PubMed

Gowda, G A Nagana

2018-05-14

Coenzymes of cellular redox reactions and cellular energy, as well as antioxidants mediate biochemical reactions fundamental to the functioning of all living cells. Conventional analysis methods lack the opportunity to evaluate these important redox and energy coenzymes and antioxidants in a single step. Major coenzymes include redox coenzymes: NAD⁺ (oxidized nicotinamide adenine dinucleotide), NADH (reduced nicotinamide adenine dinucleotide), NADP⁺ (oxidized nicotinamide adenine dinucleotide phosphate) and NADPH (reduced nicotinamide adenine dinucleotide phosphate); energy coenzymes: ATP (adenosine triphosphate), ADP (adenosine diphosphate) and AMP (adenosine monophosphate); and antioxidants: GSSG (oxidized glutathione) and GSH (reduced glutathione). We show here that a simple ¹H NMR experiment can measure these coenzymes and antioxidants in tissue and whole blood apart from a vast pool of other metabolites. In addition, focused on the goal of identification of coenzymes in subcellular fractions, we demonstrate analysis of coenzymes in the cytoplasm using breast cancer cells. Owing to their unstable nature, or low concentrations, most of the coenzymes either evade detection or lose their integrity when established sample preparation and analysis methods are used. To overcome this challenge, here we describe the development of new methods to detect these molecules without affecting the integrity of other metabolites. We used an array of 1D and 2D NMR methods, chemical shift databases, pH measurements and spiking with authentic compounds to establish the identity of peaks for the coenzymes and antioxidants in NMR spectra. Interestingly, while none of the coenzymes and antioxidants were detected in plasma, they were abundant in whole blood. Considering that the coenzymes and antioxidants represent a sensitive measure of human health and risk for numerous diseases, the presented NMR methods to measure them in one step potentially open new opportunities in the metabolomics field.

A solid-phase extraction procedure coupled to 1H NMR, with chemometric analysis, to seek reliable markers of the botanical origin of honey.

PubMed

Beretta, Giangiacomo; Caneva, Enrico; Regazzoni, Luca; Bakhtyari, Nazanin Golbamaki; Maffei Facino, Roberto

2008-07-14

The aim of this work was to establish an analytical method for identifying the botanical origin of honey, as an alternative to conventional melissopalynological, organoleptic and instrumental methods (gas-chromatography coupled to mass spectrometry (GC-MS), high-performance liquid chromatography HPLC). The procedure is based on the (1)H nuclear magnetic resonance (NMR) profile coupled, when necessary, with electrospray ionisation-mass spectrometry (ESI-MS) and two-dimensional NMR analyses of solid-phase extraction (SPE)-purified honey samples, followed by chemometric analyses. Extracts of 44 commercial Italian honeys from 20 different botanical sources were analyzed. Honeydew, chestnut and linden honeys showed constant, specific, well-resolved resonances, suitable for use as markers of origin. Honeydew honey contained the typical resonances of an aliphatic component, very likely deriving from the plant phloem sap or excreted into it by sap-sucking aphids. Chestnut honey contained the typical signals of kynurenic acid and some structurally related metabolite. In linden honey the (1)H NMR profile gave strong signals attributable to the mono-terpene derivative cyclohexa-1,3-diene-1-carboxylic acid (CDCA) and to its 1-O-beta-gentiobiosyl ester (CDCA-GBE). These markers were not detectable in the other honeys, except for the less common nectar honey from rosa mosqueta. We compared and analyzed the data by multivariate techniques. Principal component analysis found different clusters of honeys based on the presence of these specific markers. The results, although obviously only preliminary, suggest that the (1)H NMR profile (with HPLC-MS analysis when necessary) can be used as a reference framework for identifying the botanical origin of honey.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Coordination Polymer: Synthesis, Spectral Characterization and Thermal Behaviour of Starch-Urea Based Biodegradable Polymer and Its Polymer Metal Complexes

PubMed Central

Malik, Ashraf; Parveen, Shadma; Ahamad, Tansir; Alshehri, Saad M.; Singh, Prabal Kumar; Nishat, Nahid

2010-01-01

A starch-urea-based biodegradable coordination polymer modified by transition metal Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) was prepared by polycondensation of starch and urea. All the synthesized polymeric compounds were characterized by Fourier transform-infrared spectroscopy (FT-IR), 1H-NMR spectroscopy, 13C-NMR spectroscopy, UV-visible spectra, magnetic moment measurements, differential scanning calorimeter (DSC), and thermogravimetric analysis (TGA). The results of electronic spectra and magnetic moment measurements indicate that Mn(II), Co(II), and Ni(II) complexes show octahedral geometry, while Cu(II) and Zn(II) complexes show square planar and tetrahedral geometry, respectively. The thermogravimetric analysis revealed that all the polymeric metal complexes are more thermally stable than the parental ligand. In addition, biodegradable studies of all the polymeric compounds were also carried out through ASTM standards of biodegradable polymers by CO2 evolution method. PMID:20414461

Fractionation and physicochemical characterization of lignin from waste jute bags: Effect of process parameters on yield and thermal degradation.

PubMed

Ahuja, Dheeraj; Kaushik, Anupama; Chauhan, Ghanshyam S

2017-04-01

In this work lignin was extracted from waste jute bags using soda cooking method and effect of varying alkali concentration and pH on yield, purity, structure and thermal degradation of lignin were studied. The Lignin yield, chemical composition and purity were assessed using TAPPI method and UV-vis spectroscopy. Yield and purity of lignin ranged from 27 to 58% and 50-94%, respectively for all the samples and was maximum for 8% alkali concentration and at pH 2 giving higher thermal stability. Chemical structure, thermal stability and elementary analysis of lignin were studied using FTIR, H NMR, thermo gravimetric analysis (TGA) and Elemental analyzer. FTIR and H NMR results showed that core structure of lignin starts breaking beyond 10% alkali concentration. S/G ratio shows the dominance of Syringyl unit over guaiacyl unit. Copyright © 2017 Elsevier B.V. All rights reserved.

NMR analysis of biodiesel

USDA-ARS?s Scientific Manuscript database

Biodiesel is usually analyzed by the various methods called for in standards such as ASTM D6751 and EN 14214. Nuclear magnetic resonance (NMR) is not one of these methods. However, NMR, with 1H-NMR commonly applied, can be useful in a variety of applications related to biodiesel. These include monit...

NMR investigations of molecular dynamics

NASA Astrophysics Data System (ADS)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

A novel method for the investigation of liquid/liquid distribution coefficients and interface permeabilities applied to the water-octanol-drug system.

PubMed

Stein, Paul C; di Cagno, Massimiliano; Bauer-Brandl, Annette

2011-09-01

In this work a new, accurate and convenient technique for the measurement of distribution coefficients and membrane permeabilities based on nuclear magnetic resonance (NMR) is described. This method is a novel implementation of localized NMR spectroscopy and enables the simultaneous analysis of the drug content in the octanol and in the water phase without separation. For validation of the method, the distribution coefficients at pH = 7.4 of four active pharmaceutical ingredients (APIs), namely ibuprofen, ketoprofen, nadolol, and paracetamol (acetaminophen), were determined using a classical approach. These results were compared to the NMR experiments which are described in this work. For all substances, the respective distribution coefficients found with the two techniques coincided very well. Furthermore, the NMR experiments make it possible to follow the distribution of the drug between the phases as a function of position and time. Our results show that the technique, which is available on any modern NMR spectrometer, is well suited to the measurement of distribution coefficients. The experiments present also new insight into the dynamics of the water-octanol interface itself and permit measurement of the interface permeability.

qHNMR Analysis of Purity of Common Organic Solvents--An Undergraduate Quantitative Analysis Laboratory Experiment

ERIC Educational Resources Information Center

Bell, Peter T.; Whaley, W. Lance; Tochterman, Alyssa D.; Mueller, Karl S.; Schultz, Linda D.

2017-01-01

NMR spectroscopy is currently a premier technique for structural elucidation of organic molecules. Quantitative NMR (qNMR) methodology has developed more slowly but is now widely accepted, especially in the areas of natural product and medicinal chemistry. However, many undergraduate students are not routinely exposed to this important concept.…

Lignin Composition and Structure in Young versus Adult Eucalyptus globulus Plants1

PubMed Central

Rencoret, Jorge; Gutiérrez, Ana; Nieto, Lidia; Jiménez-Barbero, J.; Faulds, Craig B.; Kim, Hoon; Ralph, John; Martínez, Ángel T.; del Río, José C.

2011-01-01

Lignin changes during plant growth were investigated in a selected Eucalyptus globulus clone. The lignin composition and structure were studied in situ by a new procedure enabling the acquisition of two-dimensional nuclear magnetic resonance (2D-NMR) spectra on wood gels formed in the NMR tube as well as by analytical pyrolysis-gas chromatography-mass spectrometry. In addition, milled-wood lignins were isolated and analyzed by 2D-NMR, pyrolysis-gas chromatography-mass spectrometry, and thioacidolysis. The data indicated that p-hydroxyphenyl and guaiacyl units are deposited at the earlier stages, whereas the woods are enriched in syringyl (S) lignin during late lignification. Wood 2D-NMR showed that β-O-4′ and resinol linkages were predominant in the eucalypt lignin, whereas other substructures were present in much lower amounts. Interestingly, open β-1′ structures could be detected in the isolated lignins. Phenylcoumarans and cinnamyl end groups were depleted with age, spirodienone abundance increased, and the main substructures (β-O-4′ and resinols) were scarcely modified. Thioacidolysis revealed a higher predominance of S units in the ether-linked lignin than in the total lignin and, in agreement with NMR, also indicated that resinols are the most important nonether linkages. Dimer analysis showed that most of the resinol-type structures comprised two S units (syringaresinol), the crossed guaiacyl-S resinol appearing as a minor substructure and pinoresinol being totally absent. Changes in hemicelluloses were also shown by the 2D-NMR spectra of the wood gels without polysaccharide isolation. These include decreases of methyl galacturonosyl, arabinosyl, and galactosyl (anomeric) signals, assigned to pectin and related neutral polysaccharides, and increases of xylosyl (which are approximately 50% acetylated) and 4-O-methylglucuronosyl signals. PMID:21098672

Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

PubMed Central

Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

2018-01-01

Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

NMR metabolomics of esca disease-affected Vitis vinifera cv. Alvarinho leaves.

PubMed

Lima, Marta R M; Felgueiras, Mafalda L; Graça, Gonçalo; Rodrigues, João E A; Barros, António; Gil, Ana M; Dias, Alberto C P

2010-09-01

Esca is a destructive disease that affects vineyards leading to important losses in wine production. Information about the response of Vitis vinifera plants to this disease is scarce, particularly concerning changes in plant metabolism. In order to study the metabolic changes in Vitis plants affected by esca, leaves from both infected and non-affected cordons of V. vinifera cv. Alvarinho (collected in the Vinho Verde region, Portugal) were analysed. The metabolite composition of leaves from infected cordons with visible symptoms [diseased leaves (dl)] and from asymptomatic cordons [healthy leaves (hl)] was evaluated by 1D and 2D (1)H-nuclear magnetic resonance (NMR) spectroscopy. Principal component analysis (PCA) of the NMR spectra showed a clear separation between dl and hl leaves, indicating differential compound production due to the esca disease. NMR/PCA analysis allowed the identification of specific compounds characterizing each group, and the corresponding metabolic pathways are discussed. Altogether, the study revealed a significant increase of phenolic compounds in dl, compared with hl, accompanied by a decrease in carbohydrates, suggesting that dl are rerouting carbon and energy from primary to secondary metabolism. Other metabolic alterations detected comprised increased levels of methanol, alanine, and gamma-aminobutyric acid in dl, which might be the result of the activation of other defence mechanisms.

Quantitative analysis of NMR spectra with chemometrics

NASA Astrophysics Data System (ADS)

Winning, H.; Larsen, F. H.; Bro, R.; Engelsen, S. B.

2008-01-01

The number of applications of chemometrics to series of NMR spectra is rapidly increasing due to an emerging interest for quantitative NMR spectroscopy e.g. in the pharmaceutical and food industries. This paper gives an analysis of advantages and limitations of applying the two most common chemometric procedures, Principal Component Analysis (PCA) and Multivariate Curve Resolution (MCR), to a designed set of 231 simple alcohol mixture (propanol, butanol and pentanol) 1H 400 MHz spectra. The study clearly demonstrates that the major advantage of chemometrics is the visualisation of larger data structures which adds a new exploratory dimension to NMR research. While robustness and powerful data visualisation and exploration are the main qualities of the PCA method, the study demonstrates that the bilinear MCR method is an even more powerful method for resolving pure component NMR spectra from mixtures when certain conditions are met.

A Sulfur Amino Acid–Free Meal Increases Plasma Lipids in Humans123

PubMed Central

Park, Youngja; Le, Ngoc-Anh; Yu, Tianwei; Strobel, Fred; Gletsu-Miller, Nana; Accardi, Carolyn J.; Lee, Kichun S.; Wu, Shaoxiong; Ziegler, Thomas R.; Jones, Dean P.

2011-01-01

The content of sulfur amino acid (SAA) in a meal affects postprandial plasma cysteine concentrations and the redox potential of cysteine/cystine. Because such changes can affect enzyme, transporter, and receptor activities, meal content of SAA could have unrecognized effects on metabolism during the postprandial period. This pilot study used proton NMR (1H-NMR) spectroscopy of human plasma to test the hypothesis that dietary SAA content changes macronutrient metabolism. Healthy participants (18–36 y, 5 males and 3 females) were equilibrated for 3 d to adequate SAA, fed chemically defined meals without SAA for 5 d (depletion), and then fed isoenergetic, isonitrogenous meals containing 56 mg·kg−1·d−1 SAA for 4.5 d (repletion). On the first and last day of consuming the chemically defined meals, a morning meal containing 60% of the daily food intake was given and plasma samples were collected over an 8-h postprandial time course for characterization of metabolic changes by 1H-NMR spectroscopy. SAA-free food increased peak intensity in the plasma 1H-NMR spectra in the postprandial period. Orthogonal signal correction/partial least squares-discriminant analysis showed changes in signals associated with lipids, some amino acids, and lactate, with notable increases in plasma lipid signals (TG, unsaturated lipid, cholesterol). Conventional lipid analyses confirmed higher plasma TG and showed an increase in plasma concentration of the lipoprotein lipase inhibitor, apoC-III. The results show that plasma 1H-NMR spectra can provide useful macronutrient profiling following a meal challenge protocol and that a single meal with imbalanced SAA content alters postprandial lipid metabolism. PMID:21677075

NMR-based automated protein structure determination.

PubMed

Würz, Julia M; Kazemi, Sina; Schmidt, Elena; Bagaria, Anurag; Güntert, Peter

2017-08-15

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures. Copyright © 2017 Elsevier Inc. All rights reserved.

Separation and analysis of trace degradants in a pharmaceutical formulation using on-line capillary isotachophoresis-NMR.

PubMed

Eldridge, Stacie L; Almeida, Valentino K; Korir, Albert K; Larive, Cynthia K

2007-11-15

NMR spectroscopy is widely used in the pharmaceutical industry for the structure elucidation of pharmaceutical impurities, especially when coupled to a separation method, such as HPLC. However, NMR has relatively poor sensitivity compared with other techniques such as mass spectrometry, limiting its applicability in impurity analyses. This limitation is addressed here through the on-line coupling of microcoil NMR with capillary isotachophoresis (cITP), a separation method that can concentrate dilute components by 2-3 orders of magnitude. With this approach, 1H NMR spectra can be acquired for microgram (nanomole) quantities of trace impurities in a complex sample matrix. cITP-NMR was used in this work to isolate and detect 4-aminophenol (PAP) in an acetaminophen sample spiked at the 0.1% level, with no interference from the parent compound. Analysis of an acetaminophen thermal degradation sample revealed resonances of several degradation products in addition to PAP, confirming the effectiveness of on-line cITP-NMR for trace analyses of pharmaceutical formulations. Subsequent LC-MS/MS analysis provided complementary information for the structure elucidation of the unknown degradation products, which were dimers formed during the degradation process.

Effects of Histidine Supplementation on Global Serum and Urine 1H NMR-based Metabolomics and Serum Amino Acid Profiles in Obese Women from a Randomized Controlled Study.

PubMed

Du, Shanshan; Sun, Shuhong; Liu, Liyan; Zhang, Qiao; Guo, Fuchuan; Li, Chunlong; Feng, Rennan; Sun, Changhao

2017-06-02

The aim of current study was to investigate the metabolic changes associated with histidine supplementation in serum and urine metabolic signatures and serum amino acid (AA) profiles. Serum and urine 1 H NMR-based metabolomics and serum AA profiles were employed in 32 and 37 obese women with metabolic syndrome (MetS) intervened with placebo or histidine for 12 weeks. Multivariable statistical analysis were conducted to define characteristic metabolites. In serum 1 H NMR metabolic profiles, increases in histidine, glutamine, aspartate, glycine, choline, and trimethylamine-N-oxide (TMAO) were observed; meanwhile, decreases in cholesterol, triglycerides, fatty acids and unsaturated lipids, acetone, and α/β-glucose were exhibited after histidine supplement. In urine 1 H NMR metabolic profiles, citrate, creatinine/creatine, methylguanidine, and betaine + TMAO were higher, while hippurate was lower in histidine supplement group. In serum AA profiles, 10 AAs changed after histidine supplementation, including increased histidine, glycine, alanine, lysine, asparagine, and tyrosine and decreased leucine, isoleucine, ornithine, and citrulline. The study showed a systemic metabolic response in serum and urine metabolomics and AA profiles to histidine supplementation, showing significantly changed metabolism in AAs, lipid, and glucose in obese women with MetS.

Mathematical Development and Computational Analysis of Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) Based on Bloch Nuclear Magnetic Resonance (NMR) Diffusion Model for Myocardial Motion.

PubMed

Dada, Michael O; Jayeoba, Babatunde; Awojoyogbe, Bamidele O; Uno, Uno E; Awe, Oluseyi E

2017-09-13

Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) is a tagged image analysis method that can measure myocardial motion and strain in near real-time and is considered a potential candidate to make magnetic resonance tagging clinically viable. However, analytical expressions of radially tagged transverse magnetization in polar coordinates (which is required to appropriately describe the shape of the heart) have not been explored because the physics required to directly connect myocardial deformation of tagged Nuclear Magnetic Resonance (NMR) transverse magnetization in polar geometry and the appropriate harmonic phase parameters are not yet available. The analytical solution of Bloch NMR diffusion equation in spherical geometry with appropriate spherical wave tagging function is important for proper analysis and monitoring of heart systolic and diastolic deformation with relevant boundary conditions. In this study, we applied Harmonic Phase MRI method to compute the difference between tagged and untagged NMR transverse magnetization based on the Bloch NMR diffusion equation and obtained radial wave tagging function for analysis of myocardial motion. The analytical solution of the Bloch NMR equations and the computational simulation of myocardial motion as developed in this study are intended to significantly improve healthcare for accurate diagnosis, prognosis and treatment of cardiovascular related deceases at the lowest cost because MRI scan is still one of the most expensive anywhere. The analysis is fundamental and significant because all Magnetic Resonance Imaging techniques are based on the Bloch NMR flow equations.

CONNJUR R: An annotation strategy for fostering reproducibility in bio-NMR: protein spectral assignment

PubMed Central

Fenwick, Matthew; Hoch, Jeffrey C.; Ulrich, Eldon; Gryk, Michael R.

2015-01-01

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata. PMID:26253947

Selection of Annonaceae Species for the Control of Spodoptera frugiperda (Lepidoptera: Noctuidae) and Metabolic Profiling of Duguetia lanceolata Using Nuclear Magnetic Resonance Spectroscopy.

PubMed

Alves, D S; Machado, A R T; Campos, V A C; Oliveira, D F; Carvalho, G A

2016-04-01

This study was performed to investigate the activity of 19 dichloromethane-soluble fractions obtained from the methanolic extracts of 10 Annonaceae species against the fall armyworm, Spodoptera frugiperda (J. E. Smith). The stem bark of Duguetia lanceolata A. St.-Hil. showed the highest insecticidal activity, with a median lethal time (LT50) of 61.4 h and a median lethal concentration (LC50) of 946.5 µg/ml of diet. The dichloromethane-soluble fractions from six D. lanceolata specimens were subjected to evaluation of their activities against S. frugiperda and metabolomic analysis using hydrogen (1H) nuclear magnetic resonance (NMR) spectroscopy. Although all of the samples affected S. frugiperda mortality, their insecticidal activities varied according to the sample used in the experiments. Using partial least squares regression of the results, the D. lanceolata specimens were grouped according to their metabolite profile and insecticidal activity. A detailed analysis via uni- and bidimensional NMR spectroscopy showed that the peaks in the 1H NMR spectra associated with increased insecticidal activity could be attributed to 2,4,5-trimethoxystyrene, which suggests that this substance is involved in the insecticidal activity of the stem bark fraction of D. lanceolata.

Sensitivity enhancement by chromatographic peak concentration with ultra-high performance liquid chromatography-nuclear magnetic resonance spectroscopy for minor impurity analysis.

PubMed

Tokunaga, Takashi; Akagi, Ken-Ichi; Okamoto, Masahiko

2017-07-28

High performance liquid chromatography can be coupled with nuclear magnetic resonance (NMR) spectroscopy to give a powerful analytical method known as liquid chromatography-nuclear magnetic resonance (LC-NMR) spectroscopy, which can be used to determine the chemical structures of the components of complex mixtures. However, intrinsic limitations in the sensitivity of NMR spectroscopy have restricted the scope of this procedure, and resolving these limitations remains a critical problem for analysis. In this study, we coupled ultra-high performance liquid chromatography (UHPLC) with NMR to give a simple and versatile analytical method with higher sensitivity than conventional LC-NMR. UHPLC separation enabled the concentration of individual peaks to give a volume similar to that of the NMR flow cell, thereby maximizing the sensitivity to the theoretical upper limit. The UHPLC concentration of compound peaks present at typical impurity levels (5.0-13.1 nmol) in a mixture led to at most three-fold increase in the signal-to-noise ratio compared with LC-NMR. Furthermore, we demonstrated the use of UHPLC-NMR for obtaining structural information of a minor impurity in a reaction mixture in actual laboratory-scale development of a synthetic process. Using UHPLC-NMR, the experimental run times for chromatography and NMR were greatly reduced compared with LC-NMR. UHPLC-NMR successfully overcomes the difficulties associated with analyses of minor components in a complex mixture by LC-NMR, which are problematic even when an ultra-high field magnet and cryogenic probe are used. Copyright © 2017 Elsevier B.V. All rights reserved.

Real time neutron diffraction and NMR of the Empress II glass-ceramic system.

PubMed

O'Donnell, M D; Hill, R G; Karpukhina, N; Law, R V

2011-10-01

This study reports real time neutron diffraction on the Empress II glass-ceramic system. The commercial glass-ceramics was characterized by real time neutron diffraction, ³¹P and ²⁹Si solid-state MAS-NMR, DSC and XRD. On heating, the as-received glass ceramic contained lithium disilicate (Li₂Si₂O₅), which melted with increasing temperature. This was revealed by neutron diffraction which showed the Bragg peaks for this phase had disappeared by 958°C in agreement with thermal analysis. On cooling lithium metasilicate (Li₂SiO₃) started to form at around 916°C and a minor phase of cristobalite at around 852°C. The unit cell volume of both Li-silicate phases increased linearly with temperature at a rate of +17×10⁻³ ų.°C⁻¹. Room temperature powder X-ray diffraction (XRD) of the material after cooling confirms presence of the lithium metasilicate and cristobalite as the main phases and shows, in addition, small amount of lithium disilicate and orthophosphate. ³¹P MAS-NMR reveals presence of the lithiorthophosphate (Li₃PO₄) before and after heat treatment. The melting of lithium disilicate on heating and crystallisation of lithium metasilicate on cooling agree with endothermic and exotermic features respectively observed by DSC. ²⁹Si MAS-NMR shows presence of lithium disilicate phase in the as-received glass-ceramic, though not in the major proportion, and lithium metasilicate in the material after heat treatment. Both phases have significantly long T₁ relaxation time, especially the lithium metasilicate, therefore, a quantitative analysis of the ²⁹Si MAS-NMR spectra was not attempted. Significance. The findings of the present work demonstrate importance of the commercially designed processing parameters in order to preserve desired characteristics of the material. Processing the Empress II at a rate slower than recommended 60°C min⁻¹ or long isothermal hold at the maximal processing temperature 920°C can cause crystallization of lithium metasilicate and cristobalite instead of lithium disilicate as major phase. Copyright © 2011 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Quantitative analysis of sitagliptin using the (19)F-NMR method: a universal technique for fluorinated compound detection.

PubMed

Zhang, Fen-Fen; Jiang, Meng-Hong; Sun, Lin-Lin; Zheng, Feng; Dong, Lei; Shah, Vishva; Shen, Wen-Bin; Ding, Ya

2015-01-07

To expand the application scope of nuclear magnetic resonance (NMR) technology in quantitative analysis of pharmaceutical ingredients, (19)F nuclear magnetic resonance ((19)F-NMR) spectroscopy has been employed as a simple, rapid, and reproducible approach for the detection of a fluorine-containing model drug, sitagliptin phosphate monohydrate (STG). ciprofloxacin (Cipro) has been used as the internal standard (IS). Influential factors, including the relaxation delay time (d1) and pulse angle, impacting the accuracy and precision of spectral data are systematically optimized. Method validation has been carried out in terms of precision and intermediate precision, linearity, limit of detection (LOD) and limit of quantification (LOQ), robustness, and stability. To validate the reliability and feasibility of the (19)F-NMR technology in quantitative analysis of pharmaceutical analytes, the assay result has been compared with that of (1)H-NMR. The statistical F-test and student t-test at 95% confidence level indicate that there is no significant difference between these two methods. Due to the advantages of (19)F-NMR, such as higher resolution and suitability for biological samples, it can be used as a universal technology for the quantitative analysis of other fluorine-containing pharmaceuticals and analytes.

Comparison of the substituent effects on the (13) C NMR with the (1) H NMR chemical shifts of CH=N in substituted benzylideneanilines.

PubMed

Wang, Linyan; Cao, Chaotun; Cao, Chenzhong

2015-07-01

Fifty-two samples of substituted benzylideneanilines XPhCH=NPhYs (XBAYs) were synthesized, and their NMR spectra were determined in this paper. Together with the NMR data of other 77 samples of XBAYs quoted from literatures, the (1) H NMR chemical shifts (δH (CH=N)) and (13) C NMR chemical shifts (δC (CH=N)) of the CH=N bridging group were investigated for total of 129 samples of XBAYs. The result shows that the δH (CH=N) and δC (CH=N) have no distinctive linear relationship, which is contrary to the theoretical thought that declared the δH (CH=N) values would increase as the δC (CH=N) values increase. With the in-depth analysis, we found that the effects of σF and σR of X/Y group on the δH (CH=N) and the δC (CH=N) are opposite; the effects of the substituent specific cross-interaction effect between X and Y (Δσ(2) ) on the δH (CH=N) and the δC (CH=N) are different; the contributions of parameters in the regression equations of the δH (CH=N) and the δC (CH=N) [Eqns and 7), respectively] also have an obvious difference. Copyright © 2015 John Wiley & Sons, Ltd.

The structure of the acidic exopolysaccharide produced by Pseudomonas "gingeri" strain Pf9.

PubMed

Cescutti, P; Osman, S F; Fett, W F; Weisleder, D

1995-10-02

The structure of the acidic exopolysaccharide produced by the mushroom pathogen Pseudomonas "gingeri" strain Pf9, a bacterium which causes ginger blotch, was investigated by chemical analysis, mass spectrometry and 1D and 2D NMR spectroscopy. The polysaccharide consists of the linear trisaccharide repeating unit [formula: see text] where the cyclic pyruvic acetal groups at O-4 and O-6 of the mannopyranosyl residues have the S-configuration. Methylation analysis under neutral conditions and NMR data showed that the mannose residues are acetylated at O-2. This exopolysaccharide has the same structure as the E. coli K55 capsular polysaccharide and differs from the Klebsiella K5 capsular polysaccharide only in the position of acetylation (C-2 of the glucopyranose residue).

Vibrational analysis, NBO analysis, NMR, UV-VIS, hyperpolarizability analysis of Trimethadione by density functional theory

NASA Astrophysics Data System (ADS)

Vijayachamundeeswari, S. P.; Yagna Narayana, B.; Jone Pradeepa, S.; Sundaraganesan, N.

2015-11-01

Trimethadione (TMD) is an anticonvulsant drug widely used against absences seizures. We have characterised the TMD by various spectra including UV-VIS, IR, Raman, GC-MS and NMR. In this work, we made use of Density Functional Theory (DFT) B3LYP method with 6-31G (d, p) basis set, to calculate the molecular structure of TMD, and predicted its infrared, Raman and ultraviolet spectra for the first time. FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm-1 and 3500-50 cm-1, respectively. The vibrational frequencies were calculated and scaled values were compared with the experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes. The optimized geometry parameters were calculated. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The predicted first hyperpolarizibility also shows that the molecule might have convincingly good nonlinear optical (NLO) activities. The calculated HOMO-LUMO energy gap discloses that charge transfer occurs within the molecule.

LC-NMR Technique in the Analysis of Phytosterols in Natural Extracts

PubMed Central

Horník, Štěpán; Sajfrtová, Marie; Sýkora, Jan; Březinová, Anna; Wimmer, Zdeněk

2013-01-01

The ability of LC-NMR to detect simultaneously free and conjugated phytosterols in natural extracts was tested. The advantages and disadvantages of a gradient HPLC-NMR method were compared to the fast composition screening using SEC-NMR method. Fractions of free and conjugated phytosterols were isolated and analyzed by isocratic HPLC-NMR methods. The results of qualitative and quantitative analyses were in a good agreement with the literature data. PMID:24455424

Structures of glycans bound to receptors from saturation transfer difference (STD) NMR spectroscopy: quantitative analysis by using CORCEMA-ST.

PubMed

Enríquez-Navas, Pedro M; Guzzi, Cinzia; Muñoz-García, Juan C; Nieto, Pedro M; Angulo, Jesús

2015-01-01

Glycan-receptor interactions are of fundamental relevance for a large number of biological processes, and their kinetics properties (medium/weak binding affinities) make them appropriated to be studied by ligand observed NMR techniques, among which saturation transfer difference (STD) NMR spectroscopy has been shown to be a very robust and powerful approach. The quantitative analysis of the results from a STD NMR study of a glycan-receptor interaction is essential to be able to translate the resulting spectral intensities into a 3D molecular model of the complex. This chapter describes how to carry out such a quantitative analysis by means of the Complete Relaxation and Conformational Exchange Matrix Approach for STD NMR (CORCEMA-ST), in general terms, and an example of a previous work on an antibody-glycan interaction is also shown.

Substituent effect study on experimental ¹³C NMR chemical shifts of (3-(substituted phenyl)-cis-4,5-dihydroisoxazole-4,5-diyl)bis(methylene)diacetate derivatives.

PubMed

Kara, Yesim S

2015-12-05

Eleven novel (3-(substituted phenyl)-cis-4,5-dihydroisoxazole-4,5-diyl)bis(methylene) diacetate derivatives were synthesized in the present study. These dihydroisoxazole derivatives were characterized by IR, (1)H NMR, (13)C NMR and elemental analyses. Their (13)C NMR spectra were measured in Deuterochloroform (CDCl3). The correlation analysis for the substituent-induced chemical shift (SCS) with Hammett substituent constant (σ), inductive substituent constant (σI), different of resonance substituent constants (σR, σR(o)) and Swain-Lupton substituent parameters (F, R) were performed using SSP (single substituent parameter), and DSP (dual substituent parameter) methods, as well as single and multiple regression analysis. From the result of regression analysis, the effect of substituent on the (13)C NMR chemical shifts was explained. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigation of the dynamic stereochemistry of dimesityl-2,4,6-trimethoxyphenylmethane by complete lineshape analysis and 2D EXSY NMR spectroscopy.

PubMed

Denkova, Pavletta; Vassilev, Nikolay; Van Lokeren, Luk; Willem, Rudolph

2008-04-01

The static and dynamic stereochemistry of dimesityl-2,4,6-trimethoxyphenylmethane in solution was investigated by lineshape analysis of 1D NMR spectra and cross-peak amplitude processing in 2D EXSY spectra, recorded at variable temperatures. Previous studies on this propeller-shaped chiral compound show that the stereomer threshold interconversion is associated with helicity reversal and occurs through [1,2]- and [1,3]-two ring flips of one mesityl and the 2,4,6-trimethoxyphenyl rings. In the present study, the experimental rate constants of the [1,2]- and [1,3]-two ring flips, which are identical, were determined at various temperatures by combining quantitative 2D EXSY spectra processing and complete lineshape analysis (CLSA) of 1D NMR spectra. The latter were subjected to reference deconvolution and linear prediction in order to eliminate the lineshape distortions due to magnetic field inhomogeneity. The activation parameters of these ring flips were determined by an Eyring equation analysis of the temperature dependence of the rate constant. The experimentally determined activation enthalpy and entropy for the two-ring flips, and those obtained from theoretical ab initio calculations at different levels of theory and basis sets, were found to be in good agreement. Copyright (c) 2008 John Wiley & Sons, Ltd.

Sepsis does not alter red blood cell glucose metabolism or Na+ concentration: A 2H-, 23Na-NMR study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hotchkiss, R.S.; Song, S.K.; Ling, C.S.

The effects of sepsis on intracellular Na+ concentration ((Na+)i) and glucose metabolism were examined in rat red blood cells (RBCs) by using 23Na- and 2H-nuclear magnetic resonance (NMR) spectroscopy. Sepsis was induced in 15 halothane-anesthetized female Sprague-Dawley rats by using the cecal ligation and perforation technique; 14 control rats underwent cecal manipulation without ligation. The animals were fasted for 36 h, but allowed free access to water. At 36 h postsurgery, RBCs were examined by 23Na-NMR by using dysprosium tripolyphosphate as a chemical shift reagent. Human RBCs from 17 critically ill nonseptic patients and from 7 patients who were diagnosedmore » as septic were also examined for (Na+)i. Five rat RBC specimens had (Na+)i determined by both 23Na-NMR and inductively coupled plasma-atomic emission spectroscopy (ICP-AES). For glucose metabolism studies, RBCs from septic and control rats were suspended in modified Krebs-Henseleit buffer containing (6,6-2H2)glucose and examined by 2H-NMR. No significant differences in (Na+)i or glucose utilization were found in RBCs from control or septic rats. There were no differences in (Na+)i in the two groups of patients. The (Na+)i determined by NMR spectroscopy agreed closely with measurements using ICP-AES and establish that 100% of the (Na+)i of the RBC is visible by NMR. Glucose measurements determined by 2H-NMR correlated closely (correlation coefficient = 0.93) with enzymatic analysis. These studies showed no evidence that sepsis disturbed RBC membrane function or metabolism.« less

Combining 27Al Solid-State NMR and First-Principles Simulations To Explore Crystal Structure in Disordered Aluminum Oxynitride.

PubMed

Tu, Bingtian; Liu, Xin; Wang, Hao; Wang, Weimin; Zhai, Pengcheng; Fu, Zhengyi

2016-12-19

The nuclear magnetic resonance (NMR) technique gives insight into the local information in a crystal structure, while Rietveld refinement of powder X-ray diffraction (PXRD) sketches out the framework of a crystal lattice. In this work, first-principles calculations were combined with the solid-state NMR technique and Rietveld refinement to explore the crystal structure of a disordered aluminum oxynitride (γ-alon). The theoretical NMR parameters (chemical shift, δ iso , quadrupolar coupling constants, C Q , and asymmetry parameter, η) of Al 22.5 O 28.5 N 3.5 , predicted by the gauge-including projector augmented wave (GIPAW) algorithm, were used to facilitate the analytical investigation of the 27 Al magic-angle spinning (MAS) NMR spectra of the as-prepared sample, whose formula was confirmed to be Al 2.811 O 3.565 N 0.435 by quantitative analysis. The experimental δ iso , C Q , and η of 27 Al showed a small discrepancy compared with theoretical models. The ratio of aluminum located at the 8a to 16d sites was calculated to be 0.531 from the relative integration of peaks in the 27 Al NMR spectra. The occupancies of aluminum at the 8a and 16d positions were determined through NMR investigations to be 0.9755 and 0.9178, respectively, and were used in the Rietveld refinement to obtain the lattice parameter and anion parameter of Al 2.811 O 3.565 N 0.435 . The results from 27 Al NMR investigations and PXRD structural refinement complemented each other. This work provides a powerful and accessible strategy to precisely understand the crystal structure of novel oxynitride materials with multiple disorder.

MAS-NMR investigations of the crystallization behaviour of lithium aluminum silicate (LAS) glasses containing P 2O 5 and TiO 2 nucleants

NASA Astrophysics Data System (ADS)

Ananthanarayanan, A.; Kothiyal, G. P.; Montagne, L.; Revel, B.

2010-06-01

Lithium aluminum silicate (LAS) glass of composition (mol%) 20.4Li 2O-4.0Al 2O 3-68.6SiO 2-3.0K 2O-2.6B 2O 3-0.5P 2O 5-0.9TiO 2 was prepared by melt quenching. The glass was then nucleated and crystallized based on differential thermal analysis (DTA) data and was characterized by 29Si, 31P, 11B and 27Al MAS-NMR. XRD and 29Si NMR showed that lithium metasilicate (Li 2SiO 3) is the first phase to c form followed by cristobalite (SiO 2) and lithium disilicate (Li 2Si 2O 5). 29Si MAS-NMR revealed a change in the network structure already for the glasses nucleated at 550 °C. Since crystalline Li 3PO 4, as observed by 31P MAS-NMR, forms concurrently with the silicate phases, we conclude that crystalline Li 3PO 4 does not act as a nucleating agent for lithium silicate phases. Moreover, 31P NMR indicates the formation of M-PO 4 ( M=B, Al or Ti) complexes. The presence of BO 3 and BO 4 structural units in all the glass/glass-ceramic samples is revealed through 11B MAS-NMR. B remains in the residual glass and the crystallization of silicate phases causes a reduction in the number of alkali ions available for charge compensation. As a result, the number of trigonally coordinated B (BO 3) increases at the expense of tetrahedrally coordinated B (BO 4). The 27Al MAS-NMR spectra indicate the presence of tetrahedrally coordinated Al species, which are only slightly perturbed by the crystallization.

Quantitative analysis of amygdalin and prunasin in Prunus serotina Ehrh. using (1) H-NMR spectroscopy.

PubMed

Santos Pimenta, Lúcia P; Schilthuizen, Menno; Verpoorte, Robert; Choi, Young Hae

2014-01-01

Prunus serotina is native to North America but has been invasively introduced in Europe since the seventeenth century. This plant contains cyanogenic glycosides that are believed to be related to its success as an invasive plant. For these compounds, chromatographic- or spectrometric-based (targeting on HCN hydrolysis) methods of analysis have been employed so far. However, the conventional methods require tedious preparation steps and a long measuring time. To develop a fast and simple method to quantify the cyanogenic glycosides, amygdalin and prunasin in dried Prunus serotina leaves without any pre-purification steps using (1) H-NMR spectroscopy. Extracts of Prunus serotina leaves using CH3 OH-d4 and KH2 PO4 buffer in D2 O (1:1) were quantitatively analysed for amygdalin and prunasin using (1) H-NMR spectroscopy. Different internal standards were evaluated for accuracy and stability. The purity of quantitated (1) H-NMR signals was evaluated using several two-dimensional NMR experiments. Trimethylsilylpropionic acid sodium salt-d4 proved most suitable as the internal standard for quantitative (1) H-NMR analysis. Two-dimensional J-resolved NMR was shown to be a useful tool to confirm the structures and to check for possible signal overlapping with the target signals for the quantitation. Twenty-two samples of P. serotina were subsequently quantitatively analysed for the cyanogenic glycosides prunasin and amygdalin. The NMR method offers a fast, high-throughput analysis of cyanogenic glycosides in dried leaves permitting simultaneous quantification and identification of prunasin and amygdalin in Prunus serotina. Copyright © 2013 John Wiley & Sons, Ltd.

Preparation, Characterization, and Antimicrobial Activities of Bimetallic Complexes of Sarcosine with Zn(II) and Sn(IV)

PubMed Central

Arafat, Yasir; Ali, Saqib; Shahzadi, Saira; Shahid, Muhammad

2013-01-01

Heterobimetallic complexes of Zn(II) and Sn(IV) with sarcosine have been synthesized at room temperature under stirring conditions by the reaction of sarcosine and zinc acetate in 2 : 1 molar ratio followed by the stepwise addition of CS2 and organotin(IV) halides, where R = Me, n-Bu, and Ph. The complexes were characterized by elemental analysis, FT-IR and NMR (1H, 13C) spectroscopy. IR data showed that the ligand acts in a bidentate manner. NMR data revealed the four coordinate geometry in solution state. In vitro antimicrobial activities data showed that complexes (3) and (4) were effective against bacterial and fungal strains with few exceptions. PMID:24235910

A flavone derivative from Sesbania sesban leaves and its cytotoxicity against murine leukemia P-388 cells

NASA Astrophysics Data System (ADS)

Dianhar, Hanhan; Syah, Yana Maolana; Mujahidin, Didin; Hakim, Euis Holisotan; Juliawaty, Lia Dewi

2014-03-01

Sesbania sesban, locally named as Jayanti, is one of Indonesia plants belonging to Fabaceae family. This species is traditionally used by Indonesian people to cure digestive disorders, fever, or headache. Jayanti can grow well in tropical to subtropical region, such as in Asia and Africa. Based on literature, qualitative analysis of the methanol extract of leaves of S. sesban showed that it contained flavonoids, alkaloids, saponins and glycosides. In addition, the activity assay of extracts of different tissues of this species showed antitumor, antimalarial, and antidiabetic activityies (leaves and seed extracts), antioxidants (flower extract), and analgesic (wood extract). Though the extracts of S. sesban parts showed interesting activities, chemical study of those extracts have not been widely reported. Therefore, the objective of this research was to isolate the secondary metabolites from methanol extract of leaves of S. sesban and to determine their cytotoxicity against murine leukemia P-388 cells. One compound has been obtained and identified as 3-hydroxy-4',7-dimethoxyflavone (1), a new isolated compound from nature. This compound was obtained through separation of methanol extract using various chromatographic techniques, such as vacuum liquid chromatography and radial chromatography. The structure elucidation of isolated compound was based on 1D NMR (1H-NMR and 13C-NMR) and 2D NMR (HMBC). The cytotoxicity of methanol extract and compound 1 against murine leukemia P-388 cells examined through MTT assay showed IC50 value of 60.04 μg/mL and 5.40 μg/mL, respectively.

Hyperthyroidism results in increased glycolytic capacity in the rat heart. A 31P-NMR study.

PubMed

Seymour, A M; Eldar, H; Radda, G K

1990-11-12

We have investigated the metabolic adaptations that occur in the thyroxine-treated rat heart. Rats were made hyperthyroid by daily intra-peritoneal injections of thyroxine (35 micrograms/100 g body weight) over seven days. 31P-NMR investigations of isolated glucose-perfused isometric hearts showed that thyroxine treatment caused an increase in Pi (from 4.9 mumols.(g dry wt.)-1 in control hearts to 11.7 mumols.(g dry wt.)-1 in hyperthyroid hearts), a decrease in phosphocreatine (from 36.5 mumols.(g dry wt.)-1 to 21.8 mumols.(g dry wt.)-1) with no change in ATP or ADP concentrations under the same conditions of cardiac work. The unidirectional exchange flux Pi----ATP was measured by saturation transfer NMR in hyperthyroid rat hearts. This exchange (which has been shown to contain a significant glycolytic component) increased by 2.2-fold in thyroxine-treated hearts in comparison to control hearts (to 3.6 mumols.(g dry wt.)-1.s-1, from 1.6 mumols.(g dry wt.)-1.s-1). In parallel experiments, NMR analysis of extracts from hyperthyroid rat hearts showed significantly elevated levels of glucose 6-phosphate, and fructose 6-phosphate. Measurements of enzyme activities isolated from hyperthyroid and control tissue showed a 40% increase in phosphofructokinase activity. These data together with the increased concentration of Pi show that both glycolytic and glycogenolytic fluxes are increased in the hyperthyroid rat heart. This metabolic adaptation may be necessary to cope with the increased number and activity of Na+/K(+)-ATPase pumps that occur in response to thyroxine treatment.

A flavone derivative from Sesbania sesban leaves and its cytotoxicity against murine leukemia P-388 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dianhar, Hanhan, E-mail: liadewi@chem.itb.ac.id; Syah, Yana Maolana, E-mail: liadewi@chem.itb.ac.id; Mujahidin, Didin, E-mail: liadewi@chem.itb.ac.id

2014-03-24

Sesbania sesban, locally named as Jayanti, is one of Indonesia plants belonging to Fabaceae family. This species is traditionally used by Indonesian people to cure digestive disorders, fever, or headache. Jayanti can grow well in tropical to subtropical region, such as in Asia and Africa. Based on literature, qualitative analysis of the methanol extract of leaves of S. sesban showed that it contained flavonoids, alkaloids, saponins and glycosides. In addition, the activity assay of extracts of different tissues of this species showed antitumor, antimalarial, and antidiabetic activityies (leaves and seed extracts), antioxidants (flower extract), and analgesic (wood extract). Though themore » extracts of S. sesban parts showed interesting activities, chemical study of those extracts have not been widely reported. Therefore, the objective of this research was to isolate the secondary metabolites from methanol extract of leaves of S. sesban and to determine their cytotoxicity against murine leukemia P-388 cells. One compound has been obtained and identified as 3-hydroxy-4',7-dimethoxyflavone (1), a new isolated compound from nature. This compound was obtained through separation of methanol extract using various chromatographic techniques, such as vacuum liquid chromatography and radial chromatography. The structure elucidation of isolated compound was based on 1D NMR ({sup 1}H-NMR and {sup 13}C-NMR) and 2D NMR (HMBC). The cytotoxicity of methanol extract and compound 1 against murine leukemia P-388 cells examined through MTT assay showed IC{sub 50} value of 60.04 μg/mL and 5.40 μg/mL, respectively.« less

13C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall.

PubMed

Foston, Marcus; Samuel, Reichel; Ragauskas, Arthur J

2012-09-07

The ability to accurately and rapidly measure plant cell wall composition, relative monolignol content and lignin-hemicellulose inter-unit linkage distributions has become essential to efforts centered on reducing the recalcitrance of biomass by genetic engineering. Growing (13)C enriched transgenic plants is a viable route to achieve the high-throughput, detailed chemical analysis of whole plant cell wall before and after pretreatment and microbial or enzymatic utilization by (13)C nuclear magnetic resonance (NMR) in a perdeuterated ionic liquid solvent system not requiring component isolation. 1D (13)C whole cell wall ionic liquid NMR of natural abundant and (13)C enriched corn stover stem samples suggest that a high level of uniform labeling (>97%) can significantly reduce the total NMR experiment times up to ~220 times. Similarly, significant reduction in total NMR experiment time (~39 times) of the (13)C enriched corn stover stem samples for 2D (13)C-(1)H heteronuclear single quantum coherence NMR was found.

Analysis of fluorinated proteins by mass spectrometry.

PubMed

Luck, Linda A

2014-01-01

(19)F NMR has been used as a probe for investigating bioorganic and biological systems for three decades. Recent reviews have touted this nucleus for its unique characteristics that allow probing in vivo biological systems without endogenous signals. (19)F nucleus is exceptionally sensitive to molecular and microenvironmental changes and thus can be exploited to explore structure, dynamics, and changes in a protein or molecule in the cellular environment. We show how mass spectrometry can be used to assess and characterize the incorporation of fluorine into proteins. This methodology can be applied to a number of systems where (19)F NMR is used.

Synthesis of Novel Compounds as New Potent Tyrosinase Inhibitors

PubMed Central

Hamidian, Hooshang

2013-01-01

In the present paper, we report the synthesis and pharmacological evaluation of a new series of azo compounds with different groups (1-naphthol, 2-naphthol, and N,N-dimethylaniline) and trifluoromethoxy and fluoro substituents in the scaffold. All synthesized compounds (5a–5f) showed the most potent mushroom tyrosinase inhibition (IC50 values in the range of 4.39 ± 0.76–1.71 ± 0.49 µM), comparable to the kojic acid, as reference standard inhibitor. All the novel compounds were characterized by FT-IR, 1H NMR, 13C NMR, and elemental analysis. PMID:24260737

Multispectral Analysis of NMR Imagery

NASA Technical Reports Server (NTRS)

Butterfield, R. L.; Vannier, M. W. And Associates; Jordan, D.

1985-01-01

Conference paper discusses initial efforts to adapt multispectral satellite-image analysis to nuclear magnetic resonance (NMR) scans of human body. Flexibility of these techniques makes it possible to present NMR data in variety of formats, including pseudocolor composite images of pathological internal features. Techniques do not have to be greatly modified from form in which used to produce satellite maps of such Earth features as water, rock, or foliage.

78 FR 22151 - Fees for Official Inspection and Official Weighing Services Under the United States Grain...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-15

... kit) \\5\\ 17.50 (v) NIR or NMR Analysis (protein, oil, starch, etc.) 2.40 (vi) Waxy corn (per test) 2...) (d) All other Mycotoxins (rapid test kit 38.50 method-applicant provides kit) \\3\\ (e) NIR or NMR... kit) \\3\\ (e) NIR or NMR Analysis (protein, oil, starch, 18.60 etc.) (f) Sunflower oil (per test) 18.60...

Reliability of ^1^H NMR analysis for assessment of lipid oxidation at frying temperatures

USDA-ARS?s Scientific Manuscript database

The reliability of a method using ^1^H NMR analysis for assessment of oil oxidation at a frying temperature was examined. During heating and frying at 180 °C, changes of soybean oil signals in the ^1^H NMR spectrum including olefinic (5.16-5.30 ppm), bisallylic (2.70-2.88 ppm), and allylic (1.94-2.1...

Classification of Ilex species based on metabolomic fingerprinting using nuclear magnetic resonance and multivariate data analysis.

PubMed

Choi, Young Hae; Sertic, Sarah; Kim, Hye Kyong; Wilson, Erica G; Michopoulos, Filippos; Lefeber, Alfons W M; Erkelens, Cornelis; Prat Kricun, Sergio D; Verpoorte, Robert

2005-02-23

The metabolomic analysis of 11 Ilex species, I. argentina, I. brasiliensis, I. brevicuspis, I. dumosavar. dumosa, I. dumosa var. guaranina, I. integerrima, I. microdonta, I. paraguariensis var. paraguariensis, I. pseudobuxus, I. taubertiana, and I. theezans, was carried out by NMR spectroscopy and multivariate data analysis. The analysis using principal component analysis and classification of the (1)H NMR spectra showed a clear discrimination of those samples based on the metabolites present in the organic and aqueous fractions. The major metabolites that contribute to the discrimination are arbutin, caffeine, phenylpropanoids, and theobromine. Among those metabolites, arbutin, which has not been reported yet as a constituent of Ilex species, was found to be a biomarker for I. argentina,I. brasiliensis, I. brevicuspis, I. integerrima, I. microdonta, I. pseudobuxus, I. taubertiana, and I. theezans. This reliable method based on the determination of a large number of metabolites makes the chemotaxonomical analysis of Ilex species possible.

Understanding the NMR properties and conformational behavior of indole vs. azaindole group in protoberberines: NICS and NCS analysis

NASA Astrophysics Data System (ADS)

Kadam, Shivaji S.; Toušek, Jaromír; Maier, Lukáš; Pipíška, Matej; Sklenář, Vladimír; Marek, Radek

2012-11-01

We report here the preparation and the structural investigation into a series of 8-(indol-1-yl)-7,8-dihydroprotoberberine derivatives derived from berberine, palmatine, and coptisine. Structures of these new compounds were characterized mainly by 2D NMR spectroscopy and the conformational behavior was investigated by using methods of density-functional theory (DFT). PBE0/6-311+G** calculated NMR chemical shifts for selected derivatives correlate excellently with the experimental NMR data and support the structural conclusions drawn from the NMR experiments. An interesting role of the nitrogen atom in position N7' of the indole moiety in 8-(7-azaindol-1-yl)-7,8-dihydroprotoberberines as compared to other 8-indolyl derivatives is investigated in detail. The experimentally observed trends in NMR chemical shifts are rationalized by DFT calculations and analysis based on the nucleus-independent chemical shifts (NICS) and natural localized molecular orbitals (NLMOs).

A comparative uncertainty study of the calibration of macrolide antibiotic reference standards using quantitative nuclear magnetic resonance and mass balance methods.

PubMed

Liu, Shu-Yu; Hu, Chang-Qin

2007-10-17

This study introduces the general method of quantitative nuclear magnetic resonance (qNMR) for the calibration of reference standards of macrolide antibiotics. Several qNMR experimental conditions were optimized including delay, which is an important parameter of quantification. Three kinds of macrolide antibiotics were used to validate the accuracy of the qNMR method by comparison with the results obtained by the high performance liquid chromatography (HPLC) method. The purities of five common reference standards of macrolide antibiotics were measured by the 1H qNMR method and the mass balance method, respectively. The analysis results of the two methods were compared. The qNMR is quick and simple to use. In a new medicine research and development process, qNMR provides a new and reliable method for purity analysis of the reference standard.

Isolation and characterization of a bactericidal withanolide from Physalis virginiana.

PubMed

Gibson, Kathleen A; Reese, R Neil; Halaweish, Fathi T; Ren, Yulin

2012-01-01

Physalis virginiana (Virginia Groundcherry) is a member of the family Solenaceae. Several species of the Physalis genus have been used traditionally by American Indians as medicinal treatments. This study investigated the antibacterial activity of chemicals extracted from P. virginiana through antibacterial disc and cytotoxicity assays. Isolation and purification of an antimicrobial compound was achieved through flash chromatography and preparative HPLC. Finally, identification of chemical structure was determined from (1)H and (13)C NMR and MS. Disc assays showed that crude ethanol extracts were effective antibacterial agents against one gram-negative and seven gram-positive bacterial strains. Cytotoxicity assays indicated that it is less toxic than gentamicin controls. Isolation of the active component showed it to be a relatively polar compound. (1)H and (13)C NMR chemical shifts together with HRMS indicated a similar structure to withanolides previously identified from Physalis angulata. HRMS analysis showed a molecular mass of 472.2857 which corresponds to a molecular formula C(28)H(40)O(6). An antibacterial withanolide was isolated from P. virginiana using flash chromatography and HPLC separations. The chemical structure was determined by NMR and MS to be the withanolide physagulin V.

Isolation and characterization of a bactericidal withanolide from Physalis virginiana

PubMed Central

Gibson, Kathleen A.; Reese, R. Neil; Halaweish, Fathi T.; Ren, Yulin

2012-01-01

Background: Physalis virginiana (Virginia Groundcherry) is a member of the family Solenaceae. Several species of the Physalis genus have been used traditionally by American Indians as medicinal treatments. Materials and Methods: This study investigated the antibacterial activity of chemicals extracted from P. virginiana through antibacterial disc and cytotoxicity assays. Isolation and purification of an antimicrobial compound was achieved through flash chromatography and preparative HPLC. Finally, identification of chemical structure was determined from 1H and 13C NMR and MS. Results: Disc assays showed that crude ethanol extracts were effective antibacterial agents against one gram-negative and seven gram-positive bacterial strains. Cytotoxicity assays indicated that it is less toxic than gentamicin controls. Isolation of the active component showed it to be a relatively polar compound. 1H and 13C NMR chemical shifts together with HRMS indicated a similar structure to withanolides previously identified from Physalis angulata. HRMS analysis showed a molecular mass of 472.2857 which corresponds to a molecular formula C28H40O6. Conclusion: An antibacterial withanolide was isolated from P. virginiana using flash chromatography and HPLC separations. The chemical structure was determined by NMR and MS to be the withanolide physagulin V. PMID:22438659

Sonochemical synthesis and DFT studies of nano novel Schiff base cadmium complexes: Green, efficient, recyclable catalysts and precursors of Cd NPs

NASA Astrophysics Data System (ADS)

Parsaee, Zohreh

2017-10-01

Novel asymmetric (N4) Schiff bases (Ln, n = 1-3) and their nanosized cadmium complexes derived of 4,4'-(pentylazanediyl) dibenzaldehyde and aminobenzaldehyde are synthesized by sonochemical method and characterized based on physicochemical analysis including 1H NMR, 13C NMR, SEM, TGA, Mass, FT-IR, UV-Vis spectroscopy, elemental analysis, magnetic moment and molar conductance measurements. According to the analytic results of the NMR, UV-Vis and magnetic moment studies, it is found that the geometrical structures of these complexes [CdII2LnCl4], (L = C45H40N5X, X = CH3, Cl, OH) are square planer. The synthesized complexes were so effective as nanocatalyst on the oxidation of primary and secondary alcohols. The oxidation reactions were carried out in ethyl-methyl-imidazolium ionic liquid in presence of NaOCl. In addition Cd NPs were synthesized through the thermal decomposition of mentioned complexes and characterized by using FT-IR, SEM, TEM, EDX and XRD methods, which indicated close accordance to the standard pattern of CdO nanoparticles and an acceptable size at the nanorange (22-27 nm). Furthermore geometrical optimization of the Cd2LnCl4 calculated using DFT/B3LYP with LanL2DZ/6-311+G (d,p) level. The electronic parameter including HOMO-LUMO orbitals, bond gap, chemical hardness-softness, electronegativity, electrophilicity, NMR chemical shifts and IR frequencies were calculated. The calculated NMR shifts and vibrational frequencies showed excellent agreement with experimental data.

QM/MM methodology, docking and spectroscopic (FT-IR/FT-Raman, NMR, UV) and Fukui function analysis on adrenergic agonist

NASA Astrophysics Data System (ADS)

Uma Maheswari, J.; Muthu, S.; Sundius, Tom

2015-02-01

The Fourier transform infrared, FT-Raman, UV and NMR spectra of Ternelin have been recorded and analyzed. Harmonic vibrational frequencies have been investigated with the help of HF with 6-31G (d,p) and B3LYP with 6-31G (d,p) and LANL2DZ basis sets. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. The polarizability (α) and the first hyperpolarizability (β) values of the investigated molecule have been computed using DFT quantum mechanical calculations. Stability of the molecule arising from hyper conjugative interactions, and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in Ternelin. Finally the calculated results were compared to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. Molecular docking studies have been carried out in the active site of Ternelin and reactivity with ONIOM was also investigated.

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Vibrational, NMR spectrum and orbital analysis of 3,3',5,5'-tetrabromobisphenol A: a combined experimental and computational study.

PubMed

Qiu, Shanshan; Wei, Jin; Pan, Feng; Liu, Jingping; Zhang, Aiqian

2013-03-15

In the present work, the experimental and theoretical studies on the structure, vibrations, NMR and HOMO-LUMO analysis of 3,3',5,5'-tetrabromobisphenol A (TBBPA) are presented. The FT-IR (400-4000 cm(-1)) and FT-Raman (100-4000 cm(-1)) spectra of TBBPA were recorded. The molecular geometry, vibrational frequencies were calculated by using density functional theory (DFT) method with the 6-31G(d) basis set. The optimized geometric properties, scaled vibrational wavenumbers, IR intensities, Raman activities show good agreement with the experimental data. The assigned vibrational modes of the IR and Raman spectra were compared with the corresponding properties of the polybrominated diphenyl ethers (PBDEs). Comparative analysis indicated that the red shift of C-Br vibration could probably be ascribed to the further electronic density equalization due to the p-π conjugation between O atom and the benzene. The natural bonding orbital (NBO) analysis demonstrated that the intermolecular hyperconjugative interactions are mainly formed by the orbital overlap between σ (O-H), σ(*) (C-C), π (C-C), π(*) (C-C) bond orbitals. Compared to the higher E((2)) value (33.65-34.82 kcal/mol) originated from LP(2)O to π(*) (C-C), the one (E((2)): 8.23-9.73 kcal/mol) from LP(3)Br and π(*) (C-C) contributes to the preferential tendency of C-Br breakage to the C-O breakage in the transformation. The calculated NMR results obtained on the 6-31G(d) level proves good agreement with the experimental data (r(2)=0.999). Analysis of isosurface of the related orbital shows that all the main excitation exhibit π-π(*) character localized on the benzene rings. Copyright © 2012 Elsevier B.V. All rights reserved.

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide.

PubMed

Oktaviani, Nur Alia; Risør, Michael W; Lee, Young-Ho; Megens, Rik P; de Jong, Djurre H; Otten, Renee; Scheek, Ruud M; Enghild, Jan J; Nielsen, Niels Chr; Ikegami, Takahisa; Mulder, Frans A A

2015-06-01

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

Synthesis, characterization and anti-microbial activity of phenylurea-formaldehyde resin (PUF) and its polymer metal complexes (PUF-Mn(II)

NASA Astrophysics Data System (ADS)

Ahamad, Tansir; Alshehri, Saad M.

2012-10-01

Phenylurea-formaldehyde polymer (PUF) was synthesized via polycondensation of phenylurea and formaldehyde in basic medium, its polymer-metal complexes [PUF-M(II)] were prepared with Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) ions. PUF and PUF-M(II) were characterized with magnetic moment measurements, elemental and spectral (UV-visible, FTIR, 1H-NMR, 13C-NMR and ESR) analysis. The thermal behaviors of all the synthesized polymers were carried out using thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The thermal data revealed that all of the PUF-M(II) showed higher thermal stabilities than the PUF and also ascribed that the PUF-Cu(II) showed better thermal stability than the other PUF-M(II). The kinetic parameters such as activation energy, pre-exponential factor etc., were evaluated for these polymer metal complexes using Coats-Redfern equation. In addition, the antimicrobial activity of the synthesized polymers was tested against several microorganisms using agar well diffusion methods. Among all of the PUF-M(II), the antimicrobial activity of the PUF-Cu(II) showed the highest zone of inhibition because of its higher stability constant and may be used in biomedical applications.

Recommendations of the wwPDB NMR Validation Task Force

PubMed Central

Montelione, Gaetano T.; Nilges, Michael; Bax, Ad; Güntert, Peter; Herrmann, Torsten; Richardson, Jane S.; Schwieters, Charles; Vranken, Wim F.; Vuister, Geerten W.; Wishart, David S.; Berman, Helen M.; Kleywegt, Gerard J.; Markley, John L.

2013-01-01

As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with the wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment. PMID:24010715

Physical and molecular changes during the storage of gluten-free rice and oat bread.

PubMed

Hager, Anna-Sophie; Bosmans, Geertrui M; Delcour, Jan A

2014-06-18

Gluten-free bread crumb generally firms more rapidly than regular wheat bread crumb. We here combined differential scanning calorimetry (DSC), texture analysis, and time-domain proton nuclear magnetic resonance (TD (1)H NMR) to investigate the mechanisms underlying firming of gluten-free rice and oat bread. The molecular mobility of water and biopolymers in flour/water model systems and changes thereof after heating and subsequent cooling to room temperature were investigated as a basis for underpinning the interpretation of TD (1)H NMR profiles of fresh crumb. The proton distributions of wheat and rice flour/water model systems were comparable, while that of oat flour/water samples showed less resolved peaks and an additional population at higher T2 relaxation times representing lipid protons. No significant crumb moisture loss during storage was observed for the gluten-free bread loaves. Crumb firming was mainly caused by amylopectin retrogradation and water redistribution within bread crumb. DSC, texture, and TD (1)H NMR data correlated well and showed that starch retrogradation and crumb firming are much more pronounced in rice flour bread than in oat flour bread.

New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xue, Junfeng; Isern, Nancy G.; Ewing, R James

An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequencymore » of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.« less

Classification of Coffee Beans by GC-C-IRMS, GC-MS, and (1)H-NMR.

PubMed

Arana, Victoria Andrea; Medina, Jessica; Esseiva, Pierre; Pazos, Diego; Wist, Julien

2016-01-01

In a previous work using (1)H-NMR we reported encouraging steps towards the construction of a robust expert system for the discrimination of coffees from Colombia versus nearby countries (Brazil and Peru), to assist the recent protected geographical indication granted to Colombian coffee in 2007. This system relies on fingerprints acquired on a 400 MHz magnet and is thus well suited for small scale random screening of samples obtained at resellers or coffee shops. However, this approach cannot easily be implemented at harbour's installations, due to the elevated operational costs of cryogenic magnets. This limitation implies shipping the samples to the NMR laboratory, making the overall approach slower and thereby more expensive and less attractive for large scale screening at harbours. In this work, we report on our attempt to obtain comparable classification results using alternative techniques that have been reported promising as an alternative to NMR: GC-MS and GC-C-IRMS. Although statistically significant information could be obtained by all three methods, the results show that the quality of the classifiers depends mainly on the number of variables included in the analysis; hence NMR provides an advantage since more molecules are detected to obtain a model with better predictions.

Classification of Coffee Beans by GC-C-IRMS, GC-MS, and 1H-NMR

PubMed Central

Arana, Victoria Andrea; Esseiva, Pierre; Pazos, Diego

2016-01-01

In a previous work using 1H-NMR we reported encouraging steps towards the construction of a robust expert system for the discrimination of coffees from Colombia versus nearby countries (Brazil and Peru), to assist the recent protected geographical indication granted to Colombian coffee in 2007. This system relies on fingerprints acquired on a 400 MHz magnet and is thus well suited for small scale random screening of samples obtained at resellers or coffee shops. However, this approach cannot easily be implemented at harbour's installations, due to the elevated operational costs of cryogenic magnets. This limitation implies shipping the samples to the NMR laboratory, making the overall approach slower and thereby more expensive and less attractive for large scale screening at harbours. In this work, we report on our attempt to obtain comparable classification results using alternative techniques that have been reported promising as an alternative to NMR: GC-MS and GC-C-IRMS. Although statistically significant information could be obtained by all three methods, the results show that the quality of the classifiers depends mainly on the number of variables included in the analysis; hence NMR provides an advantage since more molecules are detected to obtain a model with better predictions. PMID:27516919

Comparison of IRMS and NMR spectrometry for the determination of intramolecular 13C isotope composition: application to ethanol.

PubMed

Gilbert, Alexis; Hattori, Ryota; Silvestre, Virginie; Wasano, Nariaki; Akoka, Serge; Hirano, Satoshi; Yamada, Keita; Yoshida, Naohiro; Remaud, Gérald S

2012-09-15

Isotopic (13)C NMR is a relatively recent technique which allows the determination of intramolecular (13)C isotope composition at natural abundance. It has been used in various scientific fields such as authentication, counterfeiting or plant metabolism. Although its precision has already been evaluated, the determination of its trueness remains still challenging. To deal with that issue, a comparison with another normalized technique must be achieved. In this work, we compare the intramolecular (13)C isotope distribution of ethanol from different origins obtained using both Isotope Ratio Mass Spectrometry (IRMS) and Nuclear Magnetic Resonance (NMR) spectrometry techniques. The IRMS approach consists of the oxidation of ethanol to acetic acid followed by the degradation of the latter for the analysis of each fragments formed. We show here that the oxidation of ethanol to acetic acid does not bring any significant error on the determination of the site-specific δ(13)C (δ(13)C(i)) of ethanol using the IRMS approach. The difference between the data obtained for 16 samples from different origins using IRMS and NMR approaches is not statistically significant and remains below 0.3‰. These results are encouraging for the future studies using isotopic NMR, especially in combination with the IRMS approach. Copyright © 2012. Published by Elsevier B.V.

High-throughput microcoil NMR of compound libraries using zero-dispersion segmented flow analysis.

PubMed

Kautz, Roger A; Goetzinger, Wolfgang K; Karger, Barry L

2005-01-01

An automated system for loading samples into a microcoil NMR probe has been developed using segmented flow analysis. This approach enhanced 2-fold the throughput of the published direct injection and flow injection methods, improved sample utilization 3-fold, and was applicable to high-field NMR facilities with long transfer lines between the sample handler and NMR magnet. Sample volumes of 2 microL (10-30 mM, approximately 10 microg) were drawn from a 96-well microtiter plate by a sample handler, then pumped to a 0.5-microL microcoil NMR probe as a queue of closely spaced "plugs" separated by an immiscible fluorocarbon fluid. Individual sample plugs were detected by their NMR signal and automatically positioned for stopped-flow data acquisition. The sample in the NMR coil could be changed within 35 s by advancing the queue. The fluorocarbon liquid wetted the wall of the Teflon transfer line, preventing the DMSO samples from contacting the capillary wall and thus reducing sample losses to below 5% after passage through the 3-m transfer line. With a wash plug of solvent between samples, sample-to-sample carryover was <1%. Significantly, the samples did not disperse into the carrier liquid during loading or during acquisitions of several days for trace analysis. For automated high-throughput analysis using a 16-second acquisition time, spectra were recorded at a rate of 1.5 min/sample and total deuterated solvent consumption was <0.5 mL (1 US dollar) per 96-well plate.

Probing porous media with gas diffusion NMR

NASA Technical Reports Server (NTRS)

Mair, R. W.; Wong, G. P.; Hoffmann, D.; Hurlimann, M. D.; Patz, S.; Schwartz, L. M.; Walsworth, R. L.

1999-01-01

We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks.

Is Low-field NMR a Complementary Tool to GC-MS in Quality Control of Essential Oils? A Case Study: Patchouli Essential Oil.

PubMed

Krause, Andre; Wu, Yu; Tian, Runtao; van Beek, Teris A

2018-04-24

High-field NMR is an expensive and important quality control technique. In recent years, cheaper and simpler low-field NMR has become available as a new quality control technique. In this study, 60 MHz 1 H-NMR was compared with GC-MS and refractometry for the detection of adulteration of essential oils, taking patchouli essential oil as a test case. Patchouli essential oil is frequently adulterated, even today. In total, 75 genuine patchouli essential oils, 10 commercial patchouli essential oils, 10 other essential oils, 17 adulterants, and 1 patchouli essential oil, spiked at 20% with those adulterants, were measured. Visual inspection of the NMR spectra allowed for easy detection of 14 adulterants, while gurjun and copaiba balsams proved difficult and one adulterant could not be detected. NMR spectra of 10 random essential oils differed not only strongly from patchouli essential oil but also from one another, suggesting that fingerprinting by low-field NMR is not limited to patchouli essential oil. Automated chemometric evaluation of NMR spectra was possible by similarity analysis (Mahalanobis distance) based on the integration from 0.1 - 8.1 ppm in 0.01 ppm increments. Good quality patchouli essential oils were recognised as well as 15 of 17 deliberate adulterations. Visual qualitative inspection by GC-MS allowed for the detection of all volatile adulterants. Nonvolatile adulterants, and all but one volatile adulterant, could be detected by semiquantitation. Different chemometric approaches showed satisfactory results. Similarity analyses were difficult with nonvolatile adulterants. Refractive index measurements could detect only 8 of 17 adulterants. Due to advantages such as simplicity, rapidity, reproducibility, and ability to detect nonvolatile adulterants, 60 MHz 1 H-NMR is complimentary to GC-MS for quality control of essential oils. Georg Thieme Verlag KG Stuttgart · New York.

Development and Validation of 2D Difference Intensity Analysis for Chemical Library Screening by Protein-Detected NMR Spectroscopy.

PubMed

Egner, John M; Jensen, Davin R; Olp, Michael D; Kennedy, Nolan W; Volkman, Brian F; Peterson, Francis C; Smith, Brian C; Hill, R Blake

2018-03-02

An academic chemical screening approach was developed by using 2D protein-detected NMR, and a 352-chemical fragment library was screened against three different protein targets. The approach was optimized against two protein targets with known ligands: CXCL12 and BRD4. Principal component analysis reliably identified compounds that induced nonspecific NMR crosspeak broadening but did not unambiguously identify ligands with specific affinity (hits). For improved hit detection, a novel scoring metric-difference intensity analysis (DIA)-was devised that sums all positive and negative intensities from 2D difference spectra. Applying DIA quickly discriminated potential ligands from compounds inducing nonspecific NMR crosspeak broadening and other nonspecific effects. Subsequent NMR titrations validated chemotypes important for binding to CXCL12 and BRD4. A novel target, mitochondrial fission protein Fis1, was screened, and six hits were identified by using DIA. Screening these diverse protein targets identified quinones and catechols that induced nonspecific NMR crosspeak broadening, hampering NMR analyses, but are currently not computationally identified as pan-assay interference compounds. The results established a streamlined screening workflow that can easily be scaled and adapted as part of a larger screening pipeline to identify fragment hits and assess relative binding affinities in the range of 0.3-1.6 mm. DIA could prove useful in library screening and other applications in which NMR chemical shift perturbations are measured. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and spectral characterization of Zn(II) microsphere series for antimicrobial application

NASA Astrophysics Data System (ADS)

Singh, Ajay K.; Pandey, Sarvesh K.; Pandey, O. P.; Sengupta, S. K.

2014-09-01

Microsphere series have been synthesized by reacting zinc(II) acetate dihydrate with Schiff bases derived from 2-hydrazino-5-[substituted phenyl]-1,3,4-thiadiazole/oxadiazole/triazole with salicylaldehyde. Elemental analysis suggests that the complexes have 1:2 and 1:1 stoichiometry of the type [Zn(L)2(H2O)2] and [Zn(L‧)(H2O)2]; LH = Schiff bases derived from 2-hydrazino-5-[substituted phenyl]-1,3,4-thia/oxadiazole with salicylaldehyde; L‧H2 = Schiff bases derived from 3-(substituted phenyl)-4-amino-5-hydrazino-1,2,4-triazole and salicylaldehyde and were characterized by elemental analyses, IR, 1H NMR and 13C NMR spectral data. Scanning electron microscopy (SEM) showed that synthesized materials have microsphere like structure and there EDX analysis comparably matches with elemental analysis. For the antimicrobial application Schiff bases and their zinc(II) complexes were screened for four bacteria e.g. Bacillus subtilis, Pseudomonas aeruginosa, Salmonella typhi, Streptococcus pyogenes and four fungi e.g. Cyrtomium falcatum, Aspergillus niger, Fusarium oxysporium and Curvularia pallescence by the reported method. Schiff base and Zn(II) compounds showed significant antimicrobial activities. However, activities increase upon chelation. Thermal analysis (TGA) data of compound (10) showed its stability up to 300 °C.

Quality assurance in the pre-analytical phase of human urine samples by (1)H NMR spectroscopy.

PubMed

Budde, Kathrin; Gök, Ömer-Necmi; Pietzner, Maik; Meisinger, Christine; Leitzmann, Michael; Nauck, Matthias; Köttgen, Anna; Friedrich, Nele

2016-01-01

Metabolomic approaches investigate changes in metabolite profiles, which may reflect changes in metabolic pathways and provide information correlated with a specific biological process or pathophysiology. High-resolution (1)H NMR spectroscopy is used to identify metabolites in biofluids and tissue samples qualitatively and quantitatively. This pre-analytical study evaluated the effects of storage time and temperature on (1)H NMR spectra from human urine in two settings. Firstly, to evaluate short time effects probably due to acute delay in sample handling and secondly, the effect of prolonged storage up to one month to find markers of sample miss-handling. A number of statistical procedures were used to assess the differences between samples stored under different conditions, including Projection to Latent Structure Discriminant Analysis (PLS-DA), non-parametric testing as well as mixed effect linear regression analysis. The results indicate that human urine samples can be stored at 10 °C for 24 h or at -80 °C for 1 month, as no relevant changes in (1)H NMR fingerprints were observed during these time periods and temperature conditions. However, some metabolites most likely of microbial origin showed alterations during prolonged storage but without facilitating classification. In conclusion, the presented protocol for urine sample handling and semi-automatic metabolite quantification is suitable for large-scale epidemiological studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Modifications of the 1H NMR metabolite profile of processed mullet (Mugil cephalus) roes under different storage conditions.

PubMed

Scano, Paola; Rosa, Antonella; Locci, Emanuela; Manzo, Giorgia; Dessì, M Assunta

2012-06-01

(1)H NMR spectroscopy was employed to study the modifications over time of the water-soluble low molecular weight metabolites extracted from samples of salted and dried mullet (Mugil cephalus) roes (mullet bottarga) stored at different conditions. Samples of grated mullet bottarga were stored for 7 months at -20 °C, at 3 °C, and at room temperature in the presence and in the absence of light and then timely extracted and analyzed by NMR. Principal component multivariate data analysis applied to the spectral data indicated that samples stored at -20 °C maintained similar features over time whereas, along PC1, samples stored at room temperature in the presence and in the absence of light showed, over time, marked metabolite modifications. The comparative analysis of the integrated areas of the selected regions of the (1)H NMR spectra indicated that the major compositional changes due to storage conditions were (i) the increase of the derivatives of the breakdown of phosphatidylcholine (choline, phosphorylcholine, and glycerol), (ii) the breakdown of nucleosides, (iii) the decrease of methionine, tryptophan, and tyrosine, and (iv) the cyclization of creatine. These changes were observed at different storage conditions, with more pronounced trends in the samples stored at room temperature. The role of metabolites in food aging is discussed. Copyright © 2012 John Wiley & Sons, Ltd.

Multivariate analysis relating oil shale geochemical properties to NMR relaxometry

USGS Publications Warehouse

Birdwell, Justin E.; Washburn, Kathryn E.

2015-01-01

Low-field nuclear magnetic resonance (NMR) relaxometry has been used to provide insight into shale composition by separating relaxation responses from the various hydrogen-bearing phases present in shales in a noninvasive way. Previous low-field NMR work using solid-echo methods provided qualitative information on organic constituents associated with raw and pyrolyzed oil shale samples, but uncertainty in the interpretation of longitudinal-transverse (T1–T2) relaxometry correlation results indicated further study was required. Qualitative confirmation of peaks attributed to kerogen in oil shale was achieved by comparing T1–T2 correlation measurements made on oil shale samples to measurements made on kerogen isolated from those shales. Quantitative relationships between T1–T2 correlation data and organic geochemical properties of raw and pyrolyzed oil shales were determined using partial least-squares regression (PLSR). Relaxometry results were also compared to infrared spectra, and the results not only provided further confidence in the organic matter peak interpretations but also confirmed attribution of T1–T2 peaks to clay hydroxyls. In addition, PLSR analysis was applied to correlate relaxometry data to trace element concentrations with good success. The results of this work show that NMR relaxometry measurements using the solid-echo approach produce T1–T2 peak distributions that correlate well with geochemical properties of raw and pyrolyzed oil shales.

Effects of salt and nanoparticles on the segmental motion of poly(ethylene oxide) in its crystalline and amorphous phases: 2H and 7Li NMR studies.

PubMed

Vogel, M; Herbers, C; Koch, B

2008-09-11

We use (2)H NMR to investigate the segmental motion of poly(ethylene oxide) (PEO) in neat and nanocomposite materials that do and do not contain salt. Specifically, in addition to a neat low-molecular-weight PEO, we study mixtures of this polymer with TiO 2 nanoparticles and LiClO 4. To characterize the polymer dynamics over a wide range of time scales, we combine (2)H NMR spin-lattice relaxation, line-shape, and stimulated-echo analyses. The results consistently show that the presence of nanoparticles hardly affects the behavior of the polymer, while addition of salt leads to substantial changes; e.g., it reduces the crystallinity. For neat PEO and a PEO-TiO 2 mixture, stimulated-echo spectroscopy enables measurement of rotational correlation functions for the crystalline phase. Analysis of the decays allows us to determine correlation times, to demonstrate the existence of a nonexponential relaxation, which implies a high complexity of the polymer dynamics in the crystal, and to show that the reorientation can be described as a large-angle jump. For a PEO-TiO 2-LiClO 4 mixture, we use (2)H and (7)Li NMR to study the polymer and the lithium dynamics, respectively. Analysis of the (7)Li spin-lattice relaxation reveals a high lithium ionic mobility in this nanocomposite polymer electrolyte. The (7)Li stimulated-echo decay is well described by a stretched exponential extending over about 6 orders of magnitude, indicating that a broad and continuous distribution of correlation times characterizes the fluctuations of the local lithium ionic environments.

Nuclear magnetic resonance (NMR)-based metabolomics for cancer research.

PubMed

Ranjan, Renuka; Sinha, Neeraj

2018-05-07

Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research. Copyright © 2018 John Wiley & Sons, Ltd.

Metabolomic Analysis Reveals Extended Metabolic Consequences of Marginal Vitamin B-6 Deficiency in Healthy Human Subjects

PubMed Central

Lamers, Yvonne; Bandyopadhyay, Nirmalya; Chi, Yueh-Yun; Lee, Kichen; Kim, Steven; da Silva, Vanessa; Hove, Nikolas; Ranka, Sanjay; Kahveci, Tamer; Muller, Keith E.; Stevens, Robert D.; Newgard, Christopher B.; Stacpoole, Peter W.; Jones, Dean P.

2013-01-01

Marginal deficiency of vitamin B-6 is common among segments of the population worldwide. Because pyridoxal 5′-phosphate (PLP) serves as a coenzyme in the metabolism of amino acids, carbohydrates, organic acids, and neurotransmitters, as well as in aspects of one-carbon metabolism, vitamin B-6 deficiency could have many effects. Healthy men and women (age: 20-40 y; n = 23) were fed a 2-day controlled, nutritionally adequate diet followed by a 28-day low-vitamin B-6 diet (<0.5 mg/d) to induce marginal deficiency, as reflected by a decline of plasma PLP from 52.6±14.1 (mean ± SD) to 21.5±4.6 nmol/L (P<0.0001) and increased cystathionine from 131±65 to 199±56 nmol/L (P<0.001). Fasting plasma samples obtained before and after vitamin B6 restriction were analyzed by 1H-NMR with and without filtration and by targeted quantitative analysis by mass spectrometry (MS). Multilevel partial least squares-discriminant analysis and S-plots of NMR spectra showed that NMR is effective in classifying samples according to vitamin B-6 status and identified discriminating features. NMR spectral features of selected metabolites indicated that vitamin B-6 restriction significantly increased the ratios of glutamine/glutamate and 2-oxoglutarate/glutamate (P<0.001) and tended to increase concentrations of acetate, pyruvate, and trimethylamine-N-oxide (adjusted P<0.05). Tandem MS showed significantly greater plasma proline after vitamin B-6 restriction (adjusted P<0.05), but there were no effects on the profile of 14 other amino acids and 45 acylcarnitines. These findings demonstrate that marginal vitamin B-6 deficiency has widespread metabolic perturbations and illustrate the utility of metabolomics in evaluating complex effects of altered vitamin B-6 intake. PMID:23776431

Synthesis, spectroscopic characterization, crystal structure, DNA interaction study and invitro biological screenings of 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid

NASA Astrophysics Data System (ADS)

Sirajuddin, Muhammad; Nooruddin; Ali, Saqib; McKee, Vickie; Khan, Shahan Zeb; Malook, Khan

2015-01-01

The titled compound, 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid was synthesized and characterized by various techniques like elemental analyses, FT-IR, NMR (1H, and 13C) and single crystal X-ray structural analysis. The appearance of the OH peak of the carboxylic acid in the FT-IR and NMR spectra conform the formation of the compound. A good agreement was found between the calculated values of C, H, N and found values in elemental analysis that show the purity of the compound. Protons H2 and H3 are in cis conformation with each other as conformed both from 1H NMR as well as from single crystal X-ray analysis. The molecular structure of the title compound, C10H10NO3Cl, is stabilized by short intramolecular Osbnd H- - -O hydrogen bonds within the molecule. In the crystal structure, intermolecular Nsbnd H- - -O hydrogen bonds link molecules into zigzag chains resulting in a dendrimer like structure. The title compound was screened for biological activities like interaction with DNA, cytotoxicity, antitumor and antioxidant activities. DNA interaction study reveals that the binding mode of interaction of the compound with SS-DNA is intercalative as it results in hypochromism along with significant red shift of 5 nm. It was also found to be effective antioxidant of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and show almost comparable antioxidant activity to that of the standard and known antioxidant, ascorbic acid, at higher concentration. The antitumor activity data of the compound shows that it can be used as potent antitumor agent.

Comprehensive analysis of commercial willow bark extracts by new technology platform: combined use of metabolomics, high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy and high-resolution radical scavenging assay.

PubMed

Agnolet, Sara; Wiese, Stefanie; Verpoorte, Robert; Staerk, Dan

2012-11-02

Here, proof-of-concept of a new analytical platform used for the comprehensive analysis of a small set of commercial willow bark products is presented, and compared with a traditional standardization solely based on analysis of salicin and salicin derivatives. The platform combines principal component analysis (PCA) of two chemical fingerprints, i.e., HPLC and (1)H NMR data, and a pharmacological fingerprint, i.e., high-resolution 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS(+)) reduction profile, with targeted identification of constituents of interest by hyphenated HPLC-solid-phase extraction-tube transfer NMR, i.e., HPLC-SPE-ttNMR. Score plots from PCA of HPLC and (1)H NMR fingerprints showed the same distinct grouping of preparations formulated as capsules of Salix alba bark and separation of S. alba cortex. Loading plots revealed this to be due to high amount of salicin in capsules and ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba cortex, respectively. PCA of high-resolution radical scavenging profiles revealed clear separation of preparations along principal component 1 due to the major radical scavengers (+)-catechin and ampelopsin. The new analytical platform allowed identification of 16 compounds in commercial willow bark extracts, and identification of ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba bark extract is reported for the first time. The detection of the novel compound, ethyl 1-hydroxy-6-oxocyclohex-2-enecarboxylate, is also described. Copyright © 2012 Elsevier B.V. All rights reserved.

The influence of a sports drink on the postexercise metabolism of elite athletes as investigated by NMR-based metabolomics.

PubMed

Miccheli, Alfredo; Marini, Federico; Capuani, Giorgio; Miccheli, Alberta Tomassini; Delfini, Maurizio; Di Cocco, Maria Enrica; Puccetti, Caterina; Paci, Maurizio; Rizzo, Marta; Spataro, Antonio

2009-10-01

The aim of this study is to evaluate the systemic effects of an isotonic sports drink on the metabolic status of athletes of the Italian Olympic rowing team during recovery after strenuous and prolonged physical exercise by means of nuclear magnetic resonance (NMR)-based metabolomics analysis on plasma and urine. Forty-four male athletes of the Italian Olympic rowing team were enrolled in a double-blind crossover study. All subjects underwent 2 evaluations at 1-week intervals. The evaluation was performed on a rowing ergometer after strenuous physical exercise to produce a state of dehydration. Afterward, the athletes were rehydrated either with a green tea-based carbohydrate-hydroelectrolyte drink or with oligomineral water. Three blood samples were drawn for each subject: at rest, after the exercise, and following rehydratation, while 2 urine samples were collected: at rest and after the rehydratation period. Biofluid samples were analyzed by high-resolution (1)H NMR metabolic profiling combined with multilevel simultaneous data-analysis (MSCA) and partial-least squares-discriminant analysis (PLS-DA). The between-subject variations, as evaluated by MSCA, reflected the variations of lactate levels induced by the physical exercise. Analysis of the within-individual variance using multilevel PLS-DA models of plasma and urine metabolic profiles showed an effect of the green tea-based sports drink on glucose, citrate, and lactate levels in plasma and on acetone, 3-OH-butyrate, and lactate levels in urine. The increase of caffeine and hippuric acid levels in urine indicated the absorption of green tea extract components. NMR-based metabolomics allowed the complex effects of a green tea extract-based carbohydrate/hydroelectrolyte beverage on the energy metabolism of athletes during recovery by postexercise rehydration to be evaluated.

Synthesis, spectroscopic, and molecular structure characterizations of some azo derivatives of 2-hydroxyacetophenone

NASA Astrophysics Data System (ADS)

Albayrak, Çiğdem; Gümrükçüoğlu, İsmail E.; Odabaşoğlu, Mustafa; İskeleli, Nazan Ocak; Ağar, Erbil

2009-08-01

Some novel azo compounds were prepared by the reaction of 2-hydroxyacetophenone with aniline and its substituted derivatives. The structures of synthesized azo compounds were determined by IR, UV-Vis, 1H NMR and 13C NMR spectroscopic techniques and the structures of some of these compounds were also determined by X-ray diffraction studies. Structural analysis using IR in solid state shows that the azo form is favoured in the azo compounds whereas UV-Vis analysis of the azo compounds in solution has shown that there is a azo and ionic form. The azo compounds in the basic solvents dimethylformamide (DMF) and dimethylsulfoxide (DMSO) are both azo and ionic form while these compounds in ethyl alcohol (EtOH) and chloroform (CHCl 3) are only azo form.

27 Al MAS NMR Studies of HBEA Zeolite at Low to High Magnetic Fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian Zhi; Wan, Chuan; Vjunov, Aleksei

27Al single pulse (SP) MAS NMR spectra of HBEA zeolites with high Si/Al ratios of 71 and 75 were obtained at three magnetic field strengths of 7.05, 11.75 and 19.97 T. High field 27Al MAS NMR spectra acquired at 19.97 T show significantly improved spectral resolution, resulting in at least two well-resolved tetrahedral-Al NMR peaks. Based on the results obtained from 27Al MAS and MQMAS NMR acquired at 19.97 T, four different quadrupole peaks are used to deconvolute the 27Al SP MAS spectra acquired at vari-ous fields by using the same set of quadrupole coupling constants, asymmetric parameters and relativemore » integrated peak intensities for the tetrahedral Al peaks. The line shapes of individual peaks change from typical quadrupole line shape at low field to essentially symmetrical line shapes at high field. We demonstrate that for fully hydrated HBEA zeolites the effect of second order quadrupole interaction can be ignored and quantitative spectral analysis can be performed by directly fitting the high field spectra using mixed Gaussian/Lorentzian line shapes. Also, the analytical steps described in our work allow direct assignment of spectral intensity to individual Al tetrahedral sites (T-sites) of zeolite HBEA. Finally, the proposed concept is suggested generally applicable to other zeo-lite framework types, thus, allowing a direct probing of Al distributions by NMR spectroscopic methods in zeolites with high confi-dence.« less

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

Automatic 1H-NMR Screening of Fatty Acid Composition in Edible Oils

PubMed Central

Castejón, David; Fricke, Pascal; Cambero, María Isabel; Herrera, Antonio

2016-01-01

In this work, we introduce an NMR-based screening method for the fatty acid composition analysis of edible oils. We describe the evaluation and optimization needed for the automated analysis of vegetable oils by low-field NMR to obtain the fatty acid composition (FAC). To achieve this, two scripts, which automatically analyze and interpret the spectral data, were developed. The objective of this work was to drive forward the automated analysis of the FAC by NMR. Due to the fact that this protocol can be carried out at low field and that the complete process from sample preparation to printing the report only takes about 3 min, this approach is promising to become a fundamental technique for high-throughput screening. To demonstrate the applicability of this method, the fatty acid composition of extra virgin olive oils from various Spanish olive varieties (arbequina, cornicabra, hojiblanca, manzanilla, and picual) was determined by 1H-NMR spectroscopy according to this protocol. PMID:26891323

Is organic matter found in glaciers similar to soil organic matter? A detailed molecular-level investigation of organic matter found in cryoconite holes on the Athabasca Glacier

NASA Astrophysics Data System (ADS)

Simpson, M. J.; Xu, Y.; Eyles, N.; Simpson, A. J.; Baer, A.

2009-04-01

Cryoconite is a dark-coloured, dust-like material found on the surfaces of glaciers. Cryoconite has received much interest recently because cryoconite holes, which are produced by accelerated ice melt, act as habitats for microbes on glacier surfaces and accelerate ice melt. To the best of our knowledge, cyroconite organic matter (COM) has not yet been chemically characterized at the molecular level. In this study, organic matter biomarkers and a host of Nuclear Magnetic Resonance (NMR) techniques were used to characterize COM from the Athabasca Glacier in the Canadian Rocky Mountains. The research questions that were targeted by this study include: 1) what are the sources of COM on the Athabasca Glacier; 2) are there any biomarker and/or NMR evidence for microbial community activity in the cryoconite holes; and 3) is the COM structurally similar to terrestrial OM? Solvent extracts contained large quantities of fatty acids, n-alkanols, n-alkanes, wax esters and sterols. A large contribution of C23, C25 and C27 relative to C29 and C31 n-alkanes suggests that allochthonous COM is mainly from lower order plants (mosses, lichens). This is confirmed by the absence of lignin phenols (after copper (II) oxidation) in extracts and NMR analyses of COM. Solution-state 1H NMR reveals prominent signals from microbial components, while solid-state 13C Cross Polarization Magic Angle Spinning NMR analysis shows an atypically high alkyl/O-alkyl ratio, suggesting that COM is unique compared to organic matter found in nearby soils. The NMR results suggest that COM is dominated by microbial-derived compounds which were confirmed by phospholipid fatty acid analysis, which showed a significant microbial contribution, primarily from bacteria and minor microeukaryotes. Both biomarker and NMR data suggest that COM likely supports active microbial communities on the Athabasca Glacier and that COM composition is uniquely different than that found in terrestrial environments. Our data indicate that windblown or meltwater fluvial OM rich materials from adjacent peatlands or mosses and lichens developed on tundra soils can be trapped and preserved in cryoconite holes in glaciers and may be an important mechanism for promoting active bacterial colonies in glacial environments both modern and ancient. Given that such material is incorporated within the glacier in the accumulation zone or flushed by meltwaters into subglacial environments, reworked COM may provide nutrient sources for active microbial communities found within and under glaciers.

Prognosis Biomarkers of Severe Sepsis and Septic Shock by 1H NMR Urine Metabolomics in the Intensive Care Unit

PubMed Central

Modesto-Alapont, Vicente; Gonzalez-Marrachelli, Vannina; Vento-Rehues, Rosa; Jorda-Miñana, Angela; Blanquer-Olivas, Jose; Monleon, Daniel

2015-01-01

Early diagnosis and patient stratification may improve sepsis outcome by a timely start of the proper specific treatment. We aimed to identify metabolomic biomarkers of sepsis in urine by 1H-NMR spectroscopy to assess the severity and to predict outcomes. Urine samples were collected from 64 patients with severe sepsis or septic shock in the ICU for a 1H NMR spectra acquisition. A supervised analysis was performed on the processed spectra, and a predictive model for prognosis (30-days mortality/survival) of sepsis was constructed using partial least-squares discriminant analysis (PLS-DA). In addition, we compared the prediction power of metabolomics data respect the Sequential Organ Failure Assessment (SOFA) score. Supervised multivariate analysis afforded a good predictive model to distinguish the patient groups and detect specific metabolic patterns. Negative prognosis patients presented higher values of ethanol, glucose and hippurate, and on the contrary, lower levels of methionine, glutamine, arginine and phenylalanine. These metabolites could be part of a composite biopattern of the human metabolic response to sepsis shock and its mortality in ICU patients. The internal cross-validation showed robustness of the metabolic predictive model obtained and a better predictive ability in comparison with SOFA values. Our results indicate that NMR metabolic profiling might be helpful for determining the metabolomic phenotype of worst-prognosis septic patients in an early stage. A predictive model for the evolution of septic patients using these metabolites was able to classify cases with more sensitivity and specificity than the well-established organ dysfunction score SOFA. PMID:26565633

Challenges in analysis of high-molar mass dextrans: comparison of HPSEC, AsFlFFF and DOSY NMR spectroscopy.

PubMed

Maina, Ndegwa Henry; Pitkänen, Leena; Heikkinen, Sami; Tuomainen, Päivi; Virkki, Liisa; Tenkanen, Maija

2014-01-01

Dilute solutions of various dextran standards, a high-molar mass (HMM) commercial dextran from Leuconostoc spp., and HMM dextrans isolated from Weissella confusa and Leuconostoc citreum were analyzed with high-performance size-exclusion chromatography (HPSEC), asymmetric flow field-flow fractionation (AsFlFFF), and diffusion-ordered NMR spectroscopy (DOSY). HPSEC analyses were performed in aqueous and dimethyl sulfoxide (DMSO) solutions, while only aqueous solutions were utilized in AsFlFFF and DOSY. The study showed that all methods were applicable to dextran analysis, but differences between the aqueous and DMSO-based solutions were obtained for HMM samples. These differences were attributed to the presence of aggregates in aqueous solution that were less prevalent in DMSO. The study showed that DOSY provides an estimate of the size of HMM dextrans, though calibration standards may be required for each experimental set-up. To our knowledge, this is the first study utilizing these three methods in analyzing HMM dextrans. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

PubMed Central

Ferro, Monica; Pastori, Nadia; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco

2017-01-01

Two different formulations of cyclodextrin nanosponges (CDNS), obtained by polycondensation of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn), were treated with aqueous solutions of ibuprofen sodium salt (IbuNa) affording hydrogels that, after lyophilisation, gave two solid CDNS-drug formulations. 1H fast MAS NMR and 13C CP-MAS NMR spectra showed that IbuNa was converted in situ into its acidic and dimeric form (IbuH) after freeze-drying. 13C CP-MAS NMR spectra also indicated that the structure of the nanosponge did not undergo changes upon drug loading compared to the unloaded system. However, the 13C NMR spectra collected under variable contact time cross-polarization (VCT-CP) conditions showed that the polymeric scaffold CDNS changed significantly its dynamic regime on passing from the empty CDNS to the drug-loaded CDNS, thus showing that the drug encapsulation can be seen as the formation of a real supramolecular aggregate rather than a conglomerate of two solid components. Finally, the structural features obtained from the different solid-state NMR approaches reported matched the information from powder X-ray diffraction profiles. PMID:28228859

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy.

PubMed

Ferro, Monica; Castiglione, Franca; Pastori, Nadia; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco; Mele, Andrea

2017-01-01

Two different formulations of cyclodextrin nanosponges (CDNS), obtained by polycondensation of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn), were treated with aqueous solutions of ibuprofen sodium salt (IbuNa) affording hydrogels that, after lyophilisation, gave two solid CDNS-drug formulations. 1 H fast MAS NMR and 13 C CP-MAS NMR spectra showed that IbuNa was converted in situ into its acidic and dimeric form (IbuH) after freeze-drying. 13 C CP-MAS NMR spectra also indicated that the structure of the nanosponge did not undergo changes upon drug loading compared to the unloaded system. However, the 13 C NMR spectra collected under variable contact time cross-polarization (VCT-CP) conditions showed that the polymeric scaffold CDNS changed significantly its dynamic regime on passing from the empty CDNS to the drug-loaded CDNS, thus showing that the drug encapsulation can be seen as the formation of a real supramolecular aggregate rather than a conglomerate of two solid components. Finally, the structural features obtained from the different solid-state NMR approaches reported matched the information from powder X-ray diffraction profiles.

Determination of Diethyl Phthalate and Polyhexamethylene Guanidine in Surrogate Alcohol from Russia

PubMed Central

Monakhova, Yulia B.; Kuballa, Thomas; Leitz, Jenny; Lachenmeier, Dirk W.

2011-01-01

Analytical methods based on spectroscopic techniques were developed and validated for the determination of diethyl phthalate (DEP) and polyhexamethylene guanidine (PHMG), which may occur in unrecorded alcohol. Analysis for PHMG was based on UV-VIS spectrophotometry after derivatization with Eosin Y and 1H NMR spectroscopy of the DMSO extract. Analysis of DEP was performed with direct UV-VIS and 1H NMR methods. Multivariate curve resolution and spectra computation methods were used to confirm the presence of PHMG and DEP in the investigated beverages. Of 22 analysed alcohol samples, two contained DEP or PHMG. 1H NMR analysis also revealed the presence of signals of hawthorn extract in three medicinal alcohols used as surrogate alcohol. The simple and cheap UV-VIS methods can be used for rapid screening of surrogate alcohol samples for impurities, while 1H NMR is recommended for specific confirmatory analysis if required. PMID:21647285

Determination of diethyl phthalate and polyhexamethylene guanidine in surrogate alcohol from Russia.

PubMed

Monakhova, Yulia B; Kuballa, Thomas; Leitz, Jenny; Lachenmeier, Dirk W

2011-01-01

Analytical methods based on spectroscopic techniques were developed and validated for the determination of diethyl phthalate (DEP) and polyhexamethylene guanidine (PHMG), which may occur in unrecorded alcohol. Analysis for PHMG was based on UV-VIS spectrophotometry after derivatization with Eosin Y and (1)H NMR spectroscopy of the DMSO extract. Analysis of DEP was performed with direct UV-VIS and (1)H NMR methods. Multivariate curve resolution and spectra computation methods were used to confirm the presence of PHMG and DEP in the investigated beverages. Of 22 analysed alcohol samples, two contained DEP or PHMG. (1)H NMR analysis also revealed the presence of signals of hawthorn extract in three medicinal alcohols used as surrogate alcohol. The simple and cheap UV-VIS methods can be used for rapid screening of surrogate alcohol samples for impurities, while (1)H NMR is recommended for specific confirmatory analysis if required.

Structural characterization and anticancer activity (MCF7 and MDA-MB-231) of polysaccharides fractionated from brown seaweed Sargassum wightii.

PubMed

Vaikundamoorthy, Ramalingam; Krishnamoorthy, Varunkumar; Vilwanathan, Ravikumar; Rajendran, Rajaram

2018-05-01

The purpose of this study was to investigate the anticancer activity of polysaccharides from brown seaweed Sargassum wightii (SWP) on human breast cancer cells. Initially, two polysaccharide fractions (SWP1 and SWP2) were isolated and purified from the crude polysaccharides using DEAE-52 cellulose and Sephadex G-100 column chromatography. As a result, SWP1 was obtained with the yield of 21.48% was characterized using chemical analysis, GC-MS, 1 H NMR and 13 C NMR. The chemical composition of the extracted polysaccharide contains a neutral polysaccharide with a high total sugar content and low protein, phenol and flavonoid content. GC-MS analysis revealed the presence of galactofuranose and arabinose and NMR spectra shows the presence of β-galactose signals. Anticancer activity shows that the polysaccharides significantly reduce the proliferation of breast cancer cells (MCF7 and MDA-MB-231) in a dose-dependent manner. Further, polysaccharides induced the apoptosis in the breast cancer cells by increasing ROS generation, cleaving mitochondrial membrane and nuclei damage. Finally, polysaccharides increased the activity of caspase 3/9, thus leads to apoptosis of breast cancer. Together, polysaccharides from S. wightii could be a new source of natural anticancer agent against breast cancer with potential value in the manufacturing supplements and drugs. Copyright © 2018 Elsevier B.V. All rights reserved.

In vitro mutagenicity, NMR metabolite characterization of azo and triphenylmethanes dyes by adherents bacteria and the role of the "cna" adhesion gene in activated sludge.

PubMed

Ayed, Lamia; Bakir, Karima; Ben Mansour, Hedi; Hammami, Saousen; Cheref, Abdelkrim; Bakhrouf, Amina

2017-02-01

Staphylococcus aureus, showing the greatest decolorization ability, was further investigated for Methyl Red (MR) Congo Red (CR), Crystal Violet (CV) and Malachite Green (MG) decolorization using response surface methodology (RSM). The chemometric methods use, based on statistical design of experiments (DOEs) such as RSM is becoming increasingly widespread in several sciences such as analytical chemistry, engineering and environmental chemistry. Stapphylococcus aureus ATCC 25923, Stapphylococcus aureus (S1) and Stapphylococcus aureus (S2), were isolated from textile wastewater plant located in KsarHellal, Tunisia and were tested for their decolorization capacity. PCR technique was utilized to identify the 3 bacterial strains and to detect the adhesin gene "cna". Biodegradation of MR, CR, CV and MG (750 ppm), were investigated under shaking condition in Mineral Salt Medium (MSM) solution at pH 7.5 and temperature 30 °C, using a 3.7 × 10 5  CFU/ml as inoculum size. Our results showed that Staphylococcus aureus had a high decolorization capacity. Nuclear magnetic resonance (NMR) spectroscopy analysis confirmed the biodegradation of dyes. The four dyes mutagenicity with the S9 metabolizing system decreased significantly after biodegradation and totally disappeared. Nuclear magnetic resonance (NMR) spectroscopy analysis confirmed the biodegradation of dyes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Citrinamides, new potentiators of antifungal miconazole activity, produced by Penicillium sp. FKI-1938.

PubMed

Fukuda, Takashi; Hasegawa, Yoko; Sakabe, Yasunari; Tomoda, Hiroshi; Omura, Satoshi

2008-09-01

Two new aromatic alkaloids, designated citrinamides A and B, were isolated from the culture broth of Penicillium sp. FKI-1938 by solvent extraction, silica gel column chromatography and HPLC. Their structures were elucidated by spectroscopic analysis, including NMR and amino acid analysis. Citrinamides A and B showed moderate potentiation of miconazole activity against Candida albicans.

1H NMR spectra dataset and solid-state NMR data of cowpea (Vigna unguiculata).

PubMed

Alves Filho, Elenilson G; Silva, Lorena M A; Teofilo, Elizita M; Larsen, Flemming H; de Brito, Edy S

2017-04-01

In this article the NMR data from chemical shifts, coupling constants, and structures of all the characterized compounds were provided, beyond a complementary PCA evaluation for the corresponding manuscript (E.G. Alves Filho, L.M.A. Silva, E.M. Teofilo, F.H. Larsen, E.S. de Brito, 2017) [3]. In addition, a complementary assessment from solid-state NMR data was provided. For further chemometric analysis, numerical matrices from the raw 1 H NMR data were made available in Microsoft Excel workbook format (.xls).

Novel dimeric metabolites from Alternaria tagetica.

PubMed

Gamboa-Angulo, M M; Alejos-González, F; Escalante-Erosa, F; García-Sosa, K; Delgado-Lamas, G; Peña-Rodríguez, L M

2000-08-01

Two novel polyketides, bis-7-O-8' '.8-O-7' '- and bis-7-O-7' '. 8-O-8' '-zinniol (2 and 3, respectively) were isolated from the organic crude extract of culture filtrates from Alternaria tagetica. Both structures were determined on the basis of their spectroscopic data (IR, MS, (1)H NMR, (13)C NMR, and 2D NMR experiments) and confirmed by chemical synthesis. Zinniol (1) was isolated as a major component, and its (13)C NMR data was correctly assigned after careful analysis of data from its 2D NMR experiments (HMQC and HMBC).

Thalassosamide, a Siderophore Discovered from the Marine-Derived Bacterium Thalassospira profundimaris.

PubMed

Zhang, Fan; Barns, Kenneth; Hoffmann, F Michael; Braun, Doug R; Andes, David R; Bugni, Tim S

2017-09-22

Here we describe the rapid identification and prioritization of novel active marine natural products using an improved dereplication strategy. During the course of our screening of marine natural product libraries, a new cyclic trihydroxamate compound, thalassosamide, was discovered from the α-proteobacterium Thalassospira profundimaris. Its structure was determined by 2D NMR and MS/MS experiments, and the absolute configuration of the lysine-derived units was established by Marfey's analysis, whereas that of C-9, 9', and 9″ was determined via the circular dichroism data of the [Rh 2 (OCOCF 3 ) 4 ] complex and DFT NMR calculations. Thalassosamide showed moderate in vivo efficacy against Pseudomonas aeruginosa.

Long-range anisotropic effects in a V-shaped Tröger's base diformanilide: Conformational study by NMR assignment and DFT calculations

NASA Astrophysics Data System (ADS)

Trupp, Leandro; Laurella, Sergio L.; Tettamanzi, M. Cristina; Barja, Beatriz C.; Bruttomesso, Andrea C.

2018-04-01

Herein we describe the synthesis and conformational analysis of a Tröger's base diformanilide whose distinctive NMR spectra was fully assigned via DFT calculations. The complexity of the spectra originated by the presence of three conformers in equilibrium shows that the nuclei in each side of the molecule are sensitive to the configuration not only of the closest formamide moiety but also of the farthest one, due to long-range anisotropic effects. The temperature and the solvent polarity influence were analyzed to determine the different conformer populations and the corresponding rotational activation parameters.

Multiple biological activities and molecular docking studies of newly synthesized 3-(pyridin-4-yl)-1H-pyrazole-5-carboxamide chalcone hybrids.

PubMed

Sribalan, Rajendran; Banuppriya, Govindharasu; Kirubavathi, Maruthan; Jayachitra, A; Padmini, Vediappen

2016-12-01

A series of fifteen new chemical entities, 3-(pyridin-4-yl)-1H-pyrazole-5-carboxamide chalcones (6a-o), were synthesized as new hybrids with enriched biological activities compared to their parent molecules. The compounds were characterized by 1 H NMR, 13 C NMR, Mass and IR spectral studies. Their antibacterial, anti-inflammatory and antioxidant activities have been evaluated. These compounds showed moderate to good antibacterial, anti-inflammatory and antioxidant activities. The molecular docking analysis was performed with cyclooxygenase enzyme to ascertain the probable binding model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Contribution of first-principles calculations to multinuclear NMR analysis of borosilicate glasses.

PubMed

Soleilhavoup, Anne; Delaye, Jean-Marc; Angeli, Frédéric; Caurant, Daniel; Charpentier, Thibault

2010-12-01

Boron-11 and silicon-29 NMR spectra of xSiO(2)-(1-x)B(2)O(3) glasses (x=0.40, 0.80 and 0.83) have been calculated using a combination of molecular dynamics (MD) simulations with density functional theory (DFT) calculations of NMR parameters. Structure models of 200 atoms have been generated using classical force fields and subsequently relaxed at the PBE-GGAlevel of DFT theory. The gauge including projector augmented wave (GIPAW) method is then employed for computing the shielding and electric field gradient tensors for each silicon and boron atom. Silicon-29 MAS and boron-11 MQMAS NMR spectra of two glasses (x=0.40 and 0.80) have been acquired and theoretical spectra are found to well agree with the experimental data. For boron-11, the NMR parameter distributions have been analysed using a Kernel density estimation (KDE) approach which is shown to highlight its main features. Accordingly, a new analytical model that incorporates the observed correlations between the NMR parameters is introduced. It significantly improves the fit of the (11)B MQMAS spectra and yields, therefore, more reliable NMR parameter distributions. A new analytical model for a quantitative description of the dependence of the silicon-29 and boron-11 isotropic chemical shift upon the bond angles is proposed, which incorporates possibly the effect of SiO(2)-B(2)O(3) intermixing. Combining all the above procedures, we show how distributions of Si-O-T and B-O-T (T=Si, B) bond angles can be estimated from the distribution of isotropic chemical shift of silicon-29 and boron-11, respectively. Copyright © 2010 John Wiley & Sons, Ltd.

Probing the calcium and sodium local environment in bones and teeth using multinuclear solid state NMR and X-ray absorption spectroscopy.

PubMed

Laurencin, Danielle; Wong, Alan; Chrzanowski, Wojciech; Knowles, Jonathan C; Qiu, Dong; Pickup, David M; Newport, Robert J; Gan, Zhehong; Duer, Melinda J; Smith, Mark E

2010-02-07

Despite the numerous studies of bone mineral, there are still many questions regarding the exact structure and composition of the mineral phase, and how the mineral crystals become organised with respect to each other and the collagen matrix. Bone mineral is commonly formulated as hydroxyapatite, albeit with numerous substitutions, and has previously been studied by (31)P and (1)H NMR, which has given considerable insight into the complexity of the mineral structure. However, to date, there has been no report of an NMR investigation of the other major component of bone mineral, calcium, nor of common minority cations like sodium. Here, direct analysis of the local environment of calcium in two biological apatites, equine bone (HB) and bovine tooth (CT), was carried out using both (43)Ca solid state NMR and Ca K-edge X-ray absorption spectroscopy, revealing important structural information about the calcium coordination shell. The (43)Ca delta(iso) in HB and CT is found to correlate with the average Ca-O bond distance measured by Ca K-edge EXAFS, and the (43)Ca NMR linewidths show that there is a greater distribution in chemical bonding around calcium in HB and CT, compared to synthetic apatites. In the case of sodium, (23)Na MAS NMR, high resolution 3Q-MAS NMR, as well as (23)Na{(31)P} REDOR and (1)H{(23)Na} R(3)-HMQC correlation experiments give the first direct evidence that some sodium is located inside the apatite phase in HB and CT, but with a greater distribution of environments compared to a synthetic sodium substituted apatite (Na-HA).

Correlation of porous and functional properties of food materials by NMR relaxometry and multivariate analysis.

PubMed

Haiduc, Adrian Marius; van Duynhoven, John

2005-02-01

The porous properties of food materials are known to determine important macroscopic parameters such as water-holding capacity and texture. In conventional approaches, understanding is built from a long process of establishing macrostructure-property relations in a rational manner. Only recently, multivariate approaches were introduced for the same purpose. The model systems used here are oil-in-water emulsions, stabilised by protein, and form complex structures, consisting of fat droplets dispersed in a porous protein phase. NMR time-domain decay curves were recorded for emulsions with varied levels of fat, protein and water. Hardness, dry matter content and water drainage were determined by classical means and analysed for correlation with the NMR data with multivariate techniques. Partial least squares can calibrate and predict these properties directly from the continuous NMR exponential decays and yields regression coefficients higher than 82%. However, the calibration coefficients themselves belong to the continuous exponential domain and do little to explain the connection between NMR data and emulsion properties. Transformation of the NMR decays into a discreet domain with non-negative least squares permits the use of multilinear regression (MLR) on the resulting amplitudes as predictors and hardness or water drainage as responses. The MLR coefficients show that hardness is highly correlated with the components that have T2 distributions of about 20 and 200 ms whereas water drainage is correlated with components that have T2 distributions around 400 and 1800 ms. These T2 distributions very likely correlate with water populations present in pores with different sizes and/or wall mobility. The results for the emulsions studied demonstrate that NMR time-domain decays can be employed to predict properties and to provide insight in the underlying microstructural features.

Cation Ordering in Li[NixMnxCo(1-2x)]O2-Layered Cathode Materials: A Nuclear Magnetic Resonance (NMR), Pair Distribution Function, X-ray Absorption Spectroscopy, and Electrochemical Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng,D.; Cabana, J.; Breger, J.

2007-01-01

Several members of the compositional series Li[NixMnxCo(1-2x)]O2 (0.01 = x = 1/3) were synthesized and characterized. X-ray diffraction results confirm the presence of the layered a-NaFeO2-type structure, while X-ray absorption near-edge spectroscopy experiments verify the presence of Ni2+, Mn4+, and Co3+. Their local environment and short-range ordering were investigated by using a combination of 6Li magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy and neutron pair distribution function (PDF) analysis, associated with reverse Monte Carlo (RMC) calculations. The 6Li MAS NMR spectra of compounds with low Ni/Mn contents (x = 0.10) show several well-resolved resonances, which start to mergemore » when the amount of Ni and Mn increases, finally forming a broad resonance at high Ni/Mn contents. Analysis of the 6Li MAS NMR 6Li[Ni0.02Mn0.02Co0.96]O2 spectrum, is consistent with the formation of Ni2+ and Mn4+ clusters within the transition-metal layers, even at these low-doping levels. The oxidation state of Ni in this high Co content sample strongly depends upon the Li/transition metal ratio of the starting materials. Neutron PDF analysis of the highest Ni/Mn content sample Li[Ni1/3Mn1/3Co1/3]O2 shows a tendency for Ni cations to be close to Mn cations in the first coordination shell; however, the Co3+ ions are randomly distributed. Analysis of the intensity of the 'LiCoO2' resonance, arising from Li surrounded by Co3+ in its first two cation coordination shells, for the whole series provides further evidence for a nonrandom distribution of the transition-metal cations. The presence of the insulator-to-metal transition seen in the electrochemical profiles of these materials upon charging correlates strongly with the concentration of the 'LiCoO2' resonance.« less

A discrete three-layer stack aggregate of a linear porphyrin tetramer: solution-phase structure elucidation by NMR and X-ray scattering.

PubMed

Hutin, Marie; Sprafke, Johannes K; Odell, Barbara; Anderson, Harry L; Claridge, Tim D W

2013-08-28

Formation of stacked aggregates can dramatically alter the properties of aromatic π-systems, yet the solution-phase structure elucidation of these aggregates is often impossible because broad distributions of species are formed, giving uninformative spectroscopic data. Here, we show that a butadiyne-linked zinc porphyrin tetramer forms a remarkably well-defined aggregate, consisting of exactly three molecules, in a parallel stacked arrangement (in chloroform at room temperature; concentration 1 mM-0.1 μM). The aggregate has a mass of 14.7 kDa. Unlike most previously reported aggregates, it gives sharp NMR resonances and aggregation is in slow exchange on the NMR time scale. The structure was elucidated using a range of NMR techniques, including diffusion-editing, (1)H-(29)Si HMBC, (1)H-(1)H COSY, TOCSY and NOESY, and (1)H-(13)C edited HSQC spectroscopy. Surprisingly, the (1)H-(1)H COSY spectrum revealed many long-range residual dipolar couplings (RDCs), and detailed analysis of magnetic field-induced (1)H-(13)C RDCs provided further evidence for the structural model. The size and shape of the aggregate is supported by small-angle X-ray scattering (SAXS) data. It adopts a geometry that maximizes van der Waals contact between the porphyrins, while avoiding clashes between side chains. The need for interdigitation of the side chains prevents formation of stacks consisting of more than three layers. Although a detailed analysis has only been carried out for one compound (the tetramer), comparison with the NMR spectra of other oligomers indicates that they form similar three-layer stacks. In all cases, aggregation can be prevented by addition of pyridine, although at low pyridine concentrations, disaggregation takes many hours to reach equilibrium.

A sulfated alpha-L-fucan from sea cucumber.

PubMed

Ribeiro, A C; Vieira, R P; Mourão, P A; Mulloy, B

1994-03-04

A purified sulfated alpha-L-fucan from the sea cucumber body wall was studied, before and after almost complete desulfation, using methylation analysis and NMR spectroscopy. NMR analysis indicates that 2,4-di-O-sulfo-L-fucopyranose and unsubstituted fucopyranose are present in equal proportions, and that 2-O-sulfo-L-fucopyranose is present in twice that proportion. There is some NMR evidence that a regular repeating sequence of four residues comprises most or all of the polysaccharide chain.

Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qu, Yi; Feng, Ju; Deng, Shuang

2014-11-19

Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis ofmore » the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.« less

Lithological controls on gas hydrate saturation: Insights from signal classification of NMR downhole data

NASA Astrophysics Data System (ADS)

Bauer, Klaus; Kulenkampff, Johannes; Henninges, Jan; Spangenberg, Erik

2016-04-01

Nuclear magnetic resonance (NMR) downhole data are analyzed with a new strategy to study gas hydrate-bearing sediments in the Mackenzie Delta (NW Canada). NMR logging is a powerful tool to study geological reservoir formations. The measurements are based on interactions between the magnetic moments of protons in geological formation water and an external magnetic field. Inversion of the measured raw data provides so-called transverse relaxation time (T2) distribution curves or spectra. Different parts of the T2 curve are related with distinct pore radii and corresponding fluid components. A common practice in the analysis of T2 distribution curves is to extract single-valued parameters such as apparent total porosity. Moreover, the derived total NMR apparent porosity and the gamma-gamma density log apparent porosity can be combined to estimate gas hydrate saturation in hydrate-bearing sediments. To avoid potential loss of information, in our new approach we analyze the entire T2 distribution curves as quasi-continuous signals to characterize the rock formation. The approach is applied to NMR data measured in gas hydrate research well Mallik 5L-38. We use self-organizing maps, a neural network clustering technique, to subdivide the data set of NMR T2 distribution curves into classes with a similar and distinctive signal shape. The method includes (1) preparation of data vectors, (2) unsupervised learning, (3) cluster definition, and (4) classification and depth mapping of all NMR signals. Each signal class thus represents a specific pore size distribution which can be interpreted in terms of distinct lithologies and reservoir types. A key step in the interpretation strategy is to reconcile the NMR classes with other log data not considered in the clustering analysis, such as gamma ray, photo-electric factor, hydrate saturation, and other logs. Our results defined six main lithologies within the target zone. Gas hydrate layers were recognized by their low signal amplitudes for all relaxation times. Highly concentrated methane hydrates occur in sand and shaly sand. Most importantly, two subtypes of hydrate-bearing sands and shaly sands were identified. They show distinct NMR signals and differ in hydrate saturation and gamma ray values. An inverse linear relationship between hydrate saturation and clay content was concluded. Finally, we infer that the gas hydrate is not grain coating, but rather, pore filling with matrix support is the preferred growth habit model for the studied formation.

A new Schiff base compound N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone): synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, 1H NMR and 13C NMR spectra.

PubMed

Saheb, Vahid; Sheikhshoaie, Iran

2011-10-15

The Schiff base compound, N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone) (NDHA) is synthesized through the condensation of 2-hydroxylacetophenone and 2,2-dimethyl 1,3-amino propane in methanol at ambient temperature. The yellow crystalline precipitate is used for X-ray single-crystal determination and measuring Fourier transform infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP, PBEPBE and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the FTIR, (1)H NMR and (13)C NMR spectra of the compound. Time-dependent density functional theory (TDDFT) method is used to calculate the UV-visible spectrum of NDHA. Vibrational frequencies are determined experimentally and compared with those obtained theoretically. Vibrational assignments and analysis of the fundamental modes of the compound are also performed. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR and (13)C NMR chemical shifts calculated by all DFT methods are consistent with the experimental data. However, the NMR shielding tensors computed at the B3LYP/6-31+G(d,p) level of theory are in better agreement with experimental (1)H NMR and (13)C NMR spectra. The electronic absorption spectrum calculated at the B3LYP/6-31+G(d,p) level by using TD-DFT method is in accordance with the observed UV-visible spectrum of NDHA. In addition, some quantum descriptors of the molecule are calculated and conformational analysis is performed and the results were compared with the crystallographic data. Copyright © 2011 Elsevier B.V. All rights reserved.

NMR relaxation studies in doped poly-3-methylthiophene

NASA Astrophysics Data System (ADS)

Singh, K. Jugeshwar; Clark, W. G.; Gaidos, G.; Reyes, A. P.; Kuhns, P.; Thompson, J. D.; Menon, R.; Ramesh, K. P.

2015-05-01

NMR relaxation rates (1 /T1 ), magnetic susceptibility, and electrical conductivity studies in doped poly-3-methylthiophene are reported in this paper. The magnetic susceptibility data show the contributions from both Pauli and Curie spins, with the size of the Pauli term depending strongly on the doping level. Proton and fluorine NMR relaxation rates have been studied as a function of temperature (3-300 K) and field (for protons at 0.9, 9.0, 16.4, and 23.4 T, and for fluorine at 9.0 T). The temperature dependence of T1 is classified into three regimes: (a) For T <(g μBB /2 kB ) , the relaxation mechanism follows a modified Korringa relation due to electron-electron interactions and disorder. 1H - T1 is due to the electron-nuclear dipolar interaction in addition to the contact term. (b) For the intermediate temperature range (g μBB /2 kB )

Naked mole-rat cortical neurons are resistant to acid-induced cell death.

PubMed

Husson, Zoé; Smith, Ewan St John

2018-05-09

Regulation of brain pH is a critical homeostatic process and changes in brain pH modulate various ion channels and receptors and thus neuronal excitability. Tissue acidosis, resulting from hypoxia or hypercapnia, can activate various proteins and ion channels, among which acid-sensing ion channels (ASICs) a family of primarily Na + permeable ion channels, which alongside classical excitotoxicity causes neuronal death. Naked mole-rats (NMRs, Heterocephalus glaber) are long-lived, fossorial, eusocial rodents that display remarkable behavioral/cellular hypoxia and hypercapnia resistance. In the central nervous system, ASIC subunit expression is similar between mouse and NMR with the exception of much lower expression of ASIC4 throughout the NMR brain. However, ASIC function and neuronal sensitivity to sustained acidosis has not been examined in the NMR brain. Here, we show with whole-cell patch-clamp electrophysiology of cultured NMR and mouse cortical and hippocampal neurons that NMR neurons have smaller voltage-gated Na + channel currents and more hyperpolarized resting membrane potentials. We further demonstrate that acid-mediated currents in NMR neurons are of smaller magnitude than in mouse, and that all currents in both species are reversibly blocked by the ASIC antagonist benzamil. We further demonstrate that NMR neurons show greater resistance to acid-induced cell death than mouse neurons. In summary, NMR neurons show significant cellular resistance to acidotoxicity compared to mouse neurons, contributing factors likely to be smaller ASIC-mediated currents and reduced NaV activity.

NMR-based metabonomic study of the sub-acute toxicity of titanium dioxide nanoparticles in rats after oral administration

NASA Astrophysics Data System (ADS)

Bu, Qian; Yan, Guangyan; Deng, Pengchi; Peng, Feng; Lin, Hongjun; Xu, Youzhi; Cao, Zhixing; Zhou, Tian; Xue, Aiqin; Wang, Yanli; Cen, Xiaobo; Zhao, Ying-Lan

2010-03-01

As titanium dioxide nanoparticles (TiO2 NPs) are widely used commercially, their potential toxicity on human health has attracted particular attention. In the present study, the oral toxicological effects of TiO2 NPs (dosed at 0.16, 0.4 and 1 g kg - 1, respectively) were investigated using conventional approaches and metabonomic analysis in Wistar rats. Serum chemistry, hematology and histopathology examinations were performed. The urine and serum were investigated by 1H nuclear magnetic resonance (NMR) using principal components and partial least squares discriminant analysis. The metabolic signature of urinalysis in TiO2 NP-treated rats showed increases in the levels of taurine, citrate, hippurate, histidine, trimethylamine-N-oxide (TMAO), citrulline, α-ketoglutarate, phenylacetylglycine (PAG) and acetate; moreover, decreases in the levels of lactate, betaine, methionine, threonine, pyruvate, 3-D-hydroxybutyrate (3-D-HB), choline and leucine were observed. The metabonomics analysis of serum showed increases in TMAO, choline, creatine, phosphocholine and 3-D-HB as well as decreases in glutamine, pyruvate, glutamate, acetoacetate, glutathione and methionine after TiO2 NP treatment. Aspartate aminotransferase (AST), creatine kinase (CK) and lactate dehydrogenase (LDH) were elevated and mitochondrial swelling in heart tissue was observed in TiO2 NP-treated rats. These findings indicate that disturbances in energy and amino acid metabolism and the gut microflora environment may be attributable to the slight injury to the liver and heart caused by TiO2 NPs. Moreover, the NMR-based metabolomic approach is a reliable and sensitive method to study the biochemical effects of nanomaterials.

Didanosine polymorphism in a supercritical antisolvent process.

PubMed

Bettini, R; Menabeni, R; Tozzi, R; Pranzo, M B; Pasquali, I; Chierotti, M R; Gobetto, R; Pellegrino, L

2010-04-01

Solid-state properties of active ingredients are crucial in pharmaceutical development owing to their significant clinical and economical implications. In the present work we investigated the solid-state properties and the solubility in water of didanosine, DDI, re-crystallized from a dimethylsulfoxide solution using supercritical CO(2) as an antisolvent (SAS process) for comparison with the commercially available drug product. We also applied modern solid-state NMR (SS NMR) techniques, namely 2D (1)H DQ CRAMPS (Combined Rotation And Multiple Pulse Spectroscopy) and (1)H-(13)C on- and off-resonance CP (cross polarization) FSLG-HETCOR experiments, known for providing reliable information about (1)H-(1)H and (1)H-(13)C intra- and intermolecular proximities, in order to address polymorphism issues arising from the crystallization of a new form in the supercritical process. A new polymorph of didanosine was obtained from the supercritical antisolvent process and characterized by means of 1D and 2D multinuclear ((1)H, (13)C, (15)N) SS NMR. The particle size of the new crystal phase was reduced by varying the antisolvent density through a pressure increase. The structural differences between the commercial product and the SAS re-crystallized DDI are highlighted by X-ray diffractometry and well described by solid-state NMR. The carbon C6 (13)C chemical shift suggests that both commercial and re-crystallized didanosine samples are in the enol form. The analysis of homo- and heteronuclear proximities obtained by means of 2D NMR experiments shows that commercial and SAS re-crystallized DDI possess very similar molecular conformation and hydrogen bond network, but different packing. The new polymorph proved to be a metastable form at ambient conditions, showing higher solubility in water and lower stability to mechanical stress. 2009 Wiley-Liss, Inc. and the American Pharmacists Association

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE PAGES

Foston, Marcus B.; Samuel, Reichel; He, Jian; ...

2016-01-19

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foston, Marcus B.; Samuel, Reichel; He, Jian

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A Multidisciplinary Approach to High Throughput Nuclear Magnetic Resonance Spectroscopy

PubMed Central

Pourmodheji, Hossein; Ghafar-Zadeh, Ebrahim; Magierowski, Sebastian

2016-01-01

Nuclear Magnetic Resonance (NMR) is a non-contact, powerful structure-elucidation technique for biochemical analysis. NMR spectroscopy is used extensively in a variety of life science applications including drug discovery. However, existing NMR technology is limited in that it cannot run a large number of experiments simultaneously in one unit. Recent advances in micro-fabrication technologies have attracted the attention of researchers to overcome these limitations and significantly accelerate the drug discovery process by developing the next generation of high-throughput NMR spectrometers using Complementary Metal Oxide Semiconductor (CMOS). In this paper, we examine this paradigm shift and explore new design strategies for the development of the next generation of high-throughput NMR spectrometers using CMOS technology. A CMOS NMR system consists of an array of high sensitivity micro-coils integrated with interfacing radio-frequency circuits on the same chip. Herein, we first discuss the key challenges and recent advances in the field of CMOS NMR technology, and then a new design strategy is put forward for the design and implementation of highly sensitive and high-throughput CMOS NMR spectrometers. We thereafter discuss the functionality and applicability of the proposed techniques by demonstrating the results. For microelectronic researchers starting to work in the field of CMOS NMR technology, this paper serves as a tutorial with comprehensive review of state-of-the-art technologies and their performance levels. Based on these levels, the CMOS NMR approach offers unique advantages for high resolution, time-sensitive and high-throughput bimolecular analysis required in a variety of life science applications including drug discovery. PMID:27294925

NMR ANALYSIS OF MALE FATHEAD MINNOW URINARY METABOLITES: A POTENTIAL APPROACH FOR STUDYING IMPACTS OF CHEMICAL EXPOSURES

EPA Science Inventory

The potential for profiling endogenous metabolites in urine from male fathead minnows (Pimephales promelas) to assess chemical exposures was explored using nuclear magnetic resonance (NMR) spectroscopy. Both one dimensional (1D) and two dimensional (2D) NMR spectroscopy w...

Push-through direct injection NMR: an optimized automation method applied to metabolomics

EPA Science Inventory

There is a pressing need to increase the throughput of NMR analysis in fields such as metabolomics and drug discovery. Direct injection (DI) NMR automation is recognized to have the potential to meet this need due to its suitability for integration with the 96-well plate format. ...

An Integrated Laboratory Project in NMR Spectroscopy.

ERIC Educational Resources Information Center

Hudson, Reggie L.; Pendley, Bradford D.

1988-01-01

Describes an advanced NMR project that can be done with a 60-MHz continuous-wave proton spectrometer. Points out the main purposes are to give students experience in second-order NMR analysis, the simplification of spectra by raising the frequency, and the effect of non-hydrogen nuclei on proton resonances. (MVL)

¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations Part II: CP kinetics and relaxation analysis.

PubMed

Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Szeleszczuk, Łukasz; Wawer, Iwona

2016-04-15

Excipients used in the solid drug formulations differ in their NMR relaxation and (13)C cross-polarization (CP) kinetics parameters. Therefore, experimental parameters like contact time of cross-polarization and repetition time have a major impact on the registered solid state NMR spectra and in consequence on the results of the NMR analysis. In this work the CP kinetics and relaxation of the most common pharmaceutical excipients: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. The studied excipients differ significantly in their optimum repetition time (from 5 s to 1200 s) and T(1ρ)(I) parameters (from 2 ms to 73 ms). The practical use of those differences in the excipients composition analysis was demonstrated on the example of commercially available tablets containing indapamide as an API. The information presented in this article will help to choose the correct acquisition parameters and also will save the time and effort needed for their optimization in the NMR analysis of the solid drug formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

PubMed Central

Lankadurai, Brian P.; Furdui, Vasile I.; Reiner, Eric J.; Simpson, André J.; Simpson, Myrna J.

2013-01-01

1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined. PMID:24958147

Non-invasive NMR stratigraphy of a multi-layered artefact: an ancient detached mural painting.

PubMed

Di Tullio, Valeria; Capitani, Donatella; Presciutti, Federica; Gentile, Gennaro; Brunetti, Brunetto Giovanni; Proietti, Noemi

2013-10-01

NMR stratigraphy was used to investigate in situ, non-destructively and non-invasively, the stratigraphy of hydrogen-rich layers of an ancient Nubian detached mural painting. Because of the detachment procedure, a complex multi-layered artefact was obtained, where, besides layers of the original mural painting, also the materials used during the procedure all became constitutive parts of the artefact. NMR measurements in situ enabled monitoring of the state of conservation of the artefact and planning of minimum representative sampling to validate results obtained in situ by solid-state NMR analysis of the samples. This analysis enabled chemical characterization of all organic materials. Use of reference compounds and prepared specimens assisted data interpretation.

NMR analysis and chemical shift calculations of poly(lactic acid) dimer model compounds with different tacticities

USDA-ARS?s Scientific Manuscript database

In this work, PLA dimer model compounds with different tacticities were synthesized and studied in detail by 1H and 13C NMR in three solvents, CDCl3/CCl4 (20/80 v/v), CDCl3 and DMSO-d6. All the peaks in the 1H and 13C NMR spectra were assigned with the help of two-dimensional NMR. Although the solve...

Complete structure of the cell surface polysaccharide of Streptococcus oralis ATCC 10557: A receptor for lectin-mediated interbacterial adherence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1991-07-02

Lectin-carbohydrate binding is known to play an important role in a number of different cell-cell interactions including those between certain species of oral streptococci and actinomyces that colonize teeth. The cell wall polysaccharides of Streptococcus oralis ATCC 10557, S. oralis 34, and Streptococcus mitis J22, although not identical antigenically, each function as a receptor molecule for the galactose and N-acetylgalactosamine reactive fimbrial lectins of Actinomyces viscosus and Actinomyces naeslundii. Carbohydrate analysis of the receptor polysaccharide isolated from S. oralis ATCC 10557 shows galactose (3 mol), glucose (1 mol), GalNAc (1 mol), and rhamnose (1 mol). {sup 1}H NMR spectra ofmore » the polysaccharide show that is partially O-acetylated. Analysis of the {sup 1}H NMR spectrum of the de-O-acetylated polysaccharide shows that it is composed of repeating subunits containing six monosaccharides and that the subunits are joined by a phosphodiester linkage. The {sup 1}H and {sup 13}C NMR spectra were completely assigned by two-dimensional homonuclear correlation methods and by {sup 1}H-detected heteronuclear multiple-quantum correlation ({sup 1}H({sup 13}C)HMQC). The complete {sup 1}H and {sup 13}C assignment of the native polysaccharide was carried out by the same techniques augmented by a {sup 13}C-coupled hybrid HMQC-COSY method, which is shown to be especially useful for carbohydrates in which strong coupling and overlapping peaks in the {sup 1}H spectrum pose difficulties.« less

Teaching NMR spectra analysis with nmr.cheminfo.org.

PubMed

Patiny, Luc; Bolaños, Alejandro; Castillo, Andrés M; Bernal, Andrés; Wist, Julien

2018-06-01

Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of exercises and tools to help solving them. Only a small number of exercises are currently available, but contributors are invited to submit new ones and suggest new types of problems. Copyright © 2018 John Wiley & Sons, Ltd.

Integrated NMR Core and Log Investigations With Respect to ODP LEG 204

NASA Astrophysics Data System (ADS)

Arnold, J.; Pechnig, R.; Clauser, C.; Anferova, S.; Blümich, B.

2005-12-01

NMR techniques are widely used in the oil industry and are one of the most suitable methods to evaluate in-situ formation porosity and permeability. Recently, efforts are directed towards adapting NMR methods also to the Ocean Drilling Program (ODP) and the upcoming Integrated Ocean Drilling Program (IODP). We apply a newly developed light-weight, mobile NMR core scanner as a non-destructive instrument to determine routinely rock porosity and to estimate the pore size distribution. The NMR core scanner is used for transverse relaxation measurements on water-saturated core sections using a CPMG sequence with a short echo time. A regularized Laplace-transform analysis yields the distribution of transverse relaxation times T2. In homogeneous magnetic fields, T2 is proportional to the pore diameter of rocks. Hence, the T2 signal maps the pore-size distribution of the studied rock samples. For fully saturated samples the integral of the distribution curve and the CPMG echo amplitude extrapolated to zero echo time are proportional to porosity. Preliminary results show that the NMR core scanner is a suitable tool to determine rock porosity and to estimate pore size distribution of limestones and sandstones. Presently our investigations focus on Leg 204, where NMR Logging-While-Drilling (LWD) was performed for the first time in ODP. Leg 204 was drilled into Hydrate Ridge on the Cascadia accretionary margin, offshore Oregon. All drilling and logging operations were highly successful, providing excellent core, wireline, and LWD data from adjacent boreholes. Cores recovered during Leg 204 consist mainly of clay and claystone. As the NMR core scanner operates at frequencies higher than that of the well-logging sensor it has a shorter dead time. This advantage makes the NMR core scanner sensitive to signals with T2 values down to 0.1 ms as compared to 3 ms in NMR logging. Hence, we can study even rocks with small pores, such as the mudcores recovered during Leg 204. We present a comparison of data from core scanning and NMR logging. Future integration of conventional wireline data and electrical borehole wall images (RAB/FMS) will provide a detailed characterization of the sediments in terms of lithology, petrophysics and, fluid flow properties.

Statistical total correlation spectroscopy scaling for enhancement of metabolic information recovery in biological NMR spectra.

PubMed

Maher, Anthony D; Fonville, Judith M; Coen, Muireann; Lindon, John C; Rae, Caroline D; Nicholson, Jeremy K

2012-01-17

The high level of complexity in nuclear magnetic resonance (NMR) metabolic spectroscopic data sets has fueled the development of experimental and mathematical techniques that enhance latent biomarker recovery and improve model interpretability. We previously showed that statistical total correlation spectroscopy (STOCSY) can be used to edit NMR spectra to remove drug metabolite signatures that obscure metabolic variation of diagnostic interest. Here, we extend this "STOCSY editing" concept to a generalized scaling procedure for NMR data that enhances recovery of latent biochemical information and improves biological classification and interpretation. We call this new procedure STOCSY-scaling (STOCSY(S)). STOCSY(S) exploits the fixed proportionality in a set of NMR spectra between resonances from the same molecule to suppress or enhance features correlated with a resonance of interest. We demonstrate this new approach using two exemplar data sets: (a) a streptozotocin rat model (n = 30) of type 1 diabetes and (b) a human epidemiological study utilizing plasma NMR spectra of patients with metabolic syndrome (n = 67). In both cases significant biomarker discovery improvement was observed by using STOCSY(S): the approach successfully suppressed interfering NMR signals from glucose and lactate that otherwise dominate the variation in the streptozotocin study, which then allowed recovery of biomarkers such as glycine, which were otherwise obscured. In the metabolic syndrome study, we used STOCSY(S) to enhance variation from the high-density lipoprotein cholesterol peak, improving the prediction of individuals with metabolic syndrome from controls in orthogonal projections to latent structures discriminant analysis models and facilitating the biological interpretation of the results. Thus, STOCSY(S) is a versatile technique that is applicable in any situation in which variation, either biological or otherwise, dominates a data set at the expense of more interesting or important features. This approach is generally appropriate for many types of NMR-based complex mixture analyses and hence for wider applications in bioanalytical science.

Experimental research of gas shale electrical properties by NMR and the combination of imbibition and drainage

NASA Astrophysics Data System (ADS)

Dong, Xu; Sun, Jianmeng; Li, Jun; Gao, Hui; Liu, Xuefeng; Wang, Jinjie

2015-08-01

Gas shale has shown considerable force in gas production worldwide, but little attention has been paid to its electrical properties, which are essential for reservoir evaluation and differentiating absorbed gas and free gas. In this study, experiments are designed to research water saturation establishment methods and electrical properties of gas shale. Nuclear magnetic resonance (NMR) with short echo space (TE) is used to identify water saturation and distribution of saturated pores which contribute to the conductivity. The experimental results indicate that NMR with shorter TE can estimate porosity and fluid distribution better than NMR with longer TE. A full range of water saturation is established by the combination of new-type spontaneous imbibition and semi-permeable plate drainage techniques. Spontaneous imbibition gains water saturation from 0% to near irreducible water saturation, and, semi-permeable plate drainage desaturates from 100% to irreducible water saturation. The RI-Sw curve shows a nonlinear relationship, and can be divided into three parts with different behaviors. The comparative analysis of transverse relaxation time (T2) distribution and RI-Sw curves, indicates that free water, and water trapped by capillarity in the non-clay matrix, differ in terms of electrical conductivity from water absorbed in clay. The new experiments prove the applicability of imbibition, drainage and NMR in investigating electrical properties of gas shale and differentiating fluid distribution which makes contribution to conductivity.

Enantiodiscrimination of flexible cyclic solutes using NMR spectroscopy in polypeptide chiral mesophases: investigation of cis-decalin and THF.

PubMed

Aroulanda, Christie; Lafon, Olivier; Lesot, Philippe

2009-08-06

The conformational dynamics and orientational behavior of two model cyclic molecules, cis-decalin (cis-dec) and tetrahydrofurane (THF), dissolved in weakly ordering, polypeptidic chiral liquid crystals (CLCs) are theoretically discussed and experimentally investigated using deuterium and carbon-13 NMR spectroscopies. The analysis of enantiomeric and enantiotopic discriminations in these compounds is shown to depend on the rate of conformational exchange regime, slow or fast. The slow exchange regime is illustrated through the case of cis-dec at low temperature (243 K). We show that the deuterium NMR spectra in this regime can be qualitatively and quantitatively interpreted by restricting the conformational pathway of cis-dec to two enantiomeric conformers of C(2)-symmetry. The orientational order parameters of these interconverting enantiomers are calculated by matching the (2)H quadrupolar splittings with calculated conformer structures. The fast exchange regime is investigated through the examples of cis-dec at high temperature (356 K) and THF at room temperature (300 K). The (2)H NMR spectra above the coalescence temperature are analyzed by introducing the concept of "average molecular structure". This fictitious structure allows easily identifying NMR equivalences of solutes dissolved in CLC. However, it cannot be applied to determine consistent orientational order parameters. This study emphasizes that enantiotopic discriminations observed for flexible molecules in the fast exchange regime can be quantitatively interpreted only by considering the orientational order of each conformer.

Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human.

PubMed

MacRae, Sheila L; Zhang, Quanwei; Lemetre, Christophe; Seim, Inge; Calder, Robert B; Hoeijmakers, Jan; Suh, Yousin; Gladyshev, Vadim N; Seluanov, Andrei; Gorbunova, Vera; Vijg, Jan; Zhang, Zhengdong D

2015-04-01

Genome maintenance (GM) is an essential defense system against aging and cancer, as both are characterized by increased genome instability. Here, we compared the copy number variation and mutation rate of 518 GM-associated genes in the naked mole rat (NMR), mouse, and human genomes. GM genes appeared to be strongly conserved, with copy number variation in only four genes. Interestingly, we found NMR to have a higher copy number of CEBPG, a regulator of DNA repair, and TINF2, a protector of telomere integrity. NMR, as well as human, was also found to have a lower rate of germline nucleotide substitution than the mouse. Together, the data suggest that the long-lived NMR, as well as human, has more robust GM than mouse and identifies new targets for the analysis of the exceptional longevity of the NMR. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

¹H NMR and multivariate data analysis of the relationship between the age and quality of duck meat.

PubMed

Liu, Chunli; Pan, Daodong; Ye, Yangfang; Cao, Jinxuan

2013-11-15

To contribute to a better understanding of the factors affecting meat quality, we investigated the influence of age on the chemical composition of duck meat. Aging probably affects the quality of meat through changes in metabolism. Therefore, we studied the metabolic composition of duck meat using (1)H nuclear magnetic resonance (NMR) spectroscopy. Comprehensive multivariate data analysis showed significant differences between extracts from ducks that had been aged for four different time periods. Although lactate and anserine increased with age, fumarate, betaine, taurine, inosine and alkyl-substituted free amino acids decreased. These results contribute to a better understanding of changes in duck meat metabolism as meat ages, which could be used to help assess the quality of duck meat as a food. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthesis and antibacterial activity of bis-[2-hydroxy-3-(1,7,8,9,10-pentamethyl-3,5-dioxo-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-en-4-yloxy)-propyl]-dimethyl-ammonium chloride.

PubMed

Struga, Marta; Kossakowski, Jerzy; Stefańska, Joanna; Zimniak, Andrzej; Koziol, Anna E

2008-06-01

A new quaternary ammonium compound, bis-[2-hydroxy-3-(1,7,8,9,10-pentamethyl-3,5-dioxo-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-en-4-yloxy)-propyl]-dimethyl-ammonium chloride (4), was synthesized. The compound was investigated for antibacterial activity, including Gram-positive cocci and Gram-negative rods, and antifungal activity. Compound 4 showed significant inhibition against Staphylococcus aureus. Research was carried out over 4 standard strains and 40 hospital strains. Elementary analysis and/or MS, (1)H NMR and (13)C NMR spectra confirmed the identity of the products. The molecular structure of 3 was determined by an X-ray analysis.

ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

NASA Astrophysics Data System (ADS)

Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

Application of quantitative 1H NMR for the calibration of protoberberine alkaloid reference standards.

PubMed

Wu, Yan; He, Yi; He, Wenyi; Zhang, Yumei; Lu, Jing; Dai, Zhong; Ma, Shuangcheng; Lin, Ruichao

2014-03-01

Quantitative nuclear magnetic resonance spectroscopy (qNMR) has been developed into an important tool in the drug analysis, biomacromolecule detection, and metabolism study. Compared with mass balance method, qNMR method bears some advantages in the calibration of reference standard (RS): it determines the absolute amount of a sample; other chemical compound and its certified reference material (CRM) can be used as internal standard (IS) to obtain the purity of the sample. Protoberberine alkaloids have many biological activities and have been used as reference standards for the control of many herbal drugs. In present study, the qNMR methods were developed for the calibration of berberine hydrochloride, palmatine hydrochloride, tetrahydropalmatine, and phellodendrine hydrochloride with potassium hydrogen phthalate as IS. Method validation was carried out according to the guidelines for the method validation of Chinese Pharmacopoeia. The results of qNMR were compared with those of mass balance method and the differences between the results of two methods were acceptable based on the analysis of estimated measurement uncertainties. Therefore, qNMR is an effective and reliable analysis method for the calibration of RS and can be used as a good complementarity to the mass balance method. Copyright © 2013 Elsevier B.V. All rights reserved.

3D TOCSY-HSQC NMR for metabolic flux analysis using non-uniform sampling

DOE PAGES

Reardon, Patrick N.; Marean-Reardon, Carrie L.; Bukovec, Melanie A.; ...

2016-02-05

13C-Metabolic Flux Analysis ( 13C-MFA) is rapidly being recognized as the authoritative method for determining fluxes through metabolic networks. Site-specific 13C enrichment information obtained using NMR spectroscopy is a valuable input for 13C-MFA experiments. Chemical shift overlaps in the 1D or 2D NMR experiments typically used for 13C-MFA frequently hinder assignment and quantitation of site-specific 13C enrichment. Here we propose the use of a 3D TOCSY-HSQC experiment for 13C-MFA. We employ Non-Uniform Sampling (NUS) to reduce the acquisition time of the experiment to a few hours, making it practical for use in 13C-MFA experiments. Our data show that the NUSmore » experiment is linear and quantitative. Identification of metabolites in complex mixtures, such as a biomass hydrolysate, is simplified by virtue of the 13C chemical shift obtained in the experiment. In addition, the experiment reports 13C-labeling information that reveals the position specific labeling of subsets of isotopomers. As a result, the information provided by this technique will enable more accurate estimation of metabolic fluxes in larger metabolic networks.« less

Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.

PubMed

Chen, Jia-Liang; Zhao, Yu; Gong, Yan-Jun; Pan, Bin-Bin; Wang, Xiao; Su, Xun-Cheng

2018-02-01

Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.

Structures in solutions from joint experimental-computational analysis: applications to cyclic molecules and studies of noncovalent interactions.

PubMed

Aliev, Abil E; Mia, Zakirin A; Khaneja, Harmeet S; King, Frank D

2012-01-26

The potential of an approach combining nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations for full structural characterizations in solution is assessed using cyclic organic compounds, namely, benzazocinone derivatives 1-3 with fused five- and eight-membered aliphatic rings, camphoric anhydride 4, and bullvalene 5. Various MD simulations were considered, using force field and semiempirical QM treatments, implicit and explicit solvation, and high-temperature MD calculations for selecting plausible molecular geometries for subsequent QM geometry optimizations using mainly B3LYP, M062X, and MP2 methods. The QM-predicted values of NMR parameters were compared to their experimental values for verification of the final structures derived from the MD/QM analysis. From these comparisons, initial estimates of quality thresholds (calculated as rms deviations) were 0.7-0.9 Hz for (3)J(HH) couplings, 0.07-0.11 Å for interproton distances, 0.05-0.08 ppm for (1)H chemical shifts, and 1.0-2.1 ppm for (13)C chemical shifts. The obtained results suggest that the accuracy of the MD analysis in predicting geometries and relative conformational energies is not critical and that the final geometry refinements of the structures selected from the MD simulations using QM methods are sufficient for correcting for the expected inaccuracy of the MD analysis. A unique example of C(sp(3))-H···N(sp(3)) intramolecular noncovalent interaction is also identified using the NMR/MD/QM and the natural bond orbital analyses. As the NMR/MD/QM approach relies on the final QM geometry optimization, comparisons of geometric characteristics predicted by different QM methods and those from X-ray and neutron diffraction measurements were undertaken using rigid and flexible cyclic systems. The joint analysis shows that intermolecular noncovalent interactions present in the solid state alter molecular geometries significantly compared to the geometries of isolated molecules from QM calculations.

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

PubMed Central

Sharp, Kim A.; O’Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua

2015-01-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. PMID:25739366

“Invisible” Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations

PubMed Central

Fizil, Ádám; Gáspári, Zoltán; Barna, Terézia; Marx, Florentine; Batta, Gyula

2015-01-01

Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20–40 % at 298 K in a disulfide-rich protein. In addition, sensitive 15N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR “dark matter”. Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction. PMID:25676351

Synthesis of palm oil fatty acid and trimethylolpropane based ester for biolubricant base stocks

NASA Astrophysics Data System (ADS)

Nor, Nurazira Mohd; Derawi, Darfizzi; Salimon, Jumat

2018-04-01

RBD palm oil become one of the interesting renewable resources in biolubricant application. However, palm oil cannot be used directly as lubricant due to some performance limitations such as thermal and oxidative stability. This drawback can be overcome by chemical modification through esterification with polyhydric alcohol such as trimethylolpropane (TMP). The synthesis of ester was carried out via esterification of palm oil fatty acid (POFA) with TMP in the presence of 2% sulphuric acid as catalyst at 150 °C for 5 hours. Gas Chromatography equipped with a Flame Ionization Detector (GC-FID) was used to determine the percentage composition of POTMP ester. The structure confirmation of POTMP ester was proven by Fourier Transformation Infra-Red (FTIR), proton and carbon Nuclear Magnetic Resonance (1H-NMR and 13C-NMR) spectroscopy analysis. The result showed that POTMP ester has successfully synthesized with 97.7% composition of triesters (TE), proved by GC chromatogram. Presence of ester group also evidenced by 1H NMR at 2.27-2.30 ppm and 13C NMR at 173.52-173.54 ppm. The percentage yield of POTMP ester produced was 82% and exist in liquid form at room temperature.

Electronic properties of GeTe and Ag- or Sb-substituted GeTe studied by low-temperature Te 125 NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, J.; Levin, E. M.; Lee, Y.

We have carried out 125Te nuclear magnetic resonance (NMR) in a wide temperature range of 1.5–300 K to investigate the electronic properties of Ge 50 Te 50, Ag 2 Ge 48Te 50 , and Sb 2 Ge 48 Te 50 from a microscopic point of view. From the temperature dependence of the NMR shift (K) and nuclear spin lattice relaxation rate (1/T 1), we found that two bands contribute to the physical properties of the materials. One band overlaps the Fermi level providing the metallic state where no strong electron correlations are revealed by Korringa analysis. The other band ismore » separated from the Fermi level by an energy gap of E g/k B ~67 K, which gives rise to semiconductorlike properties. First-principles calculation reveals that the metallic band originates from the Ge vacancy while the semiconductorlike band is related to the fine structure of the density of states near the Fermi level. We find low-temperature Te125 NMR data for the materials studied here clearly show that Ag substitution increases hole concentration while Sb substitution decreases it.« less

Electronic properties of GeTe and Ag- or Sb-substituted GeTe studied by low-temperature Te 125 NMR

DOE PAGES

Cui, J.; Levin, E. M.; Lee, Y.; ...

2016-08-18

We have carried out 125Te nuclear magnetic resonance (NMR) in a wide temperature range of 1.5–300 K to investigate the electronic properties of Ge 50 Te 50, Ag 2 Ge 48Te 50 , and Sb 2 Ge 48 Te 50 from a microscopic point of view. From the temperature dependence of the NMR shift (K) and nuclear spin lattice relaxation rate (1/T 1), we found that two bands contribute to the physical properties of the materials. One band overlaps the Fermi level providing the metallic state where no strong electron correlations are revealed by Korringa analysis. The other band ismore » separated from the Fermi level by an energy gap of E g/k B ~67 K, which gives rise to semiconductorlike properties. First-principles calculation reveals that the metallic band originates from the Ge vacancy while the semiconductorlike band is related to the fine structure of the density of states near the Fermi level. We find low-temperature Te125 NMR data for the materials studied here clearly show that Ag substitution increases hole concentration while Sb substitution decreases it.« less

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

PubMed

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR

NASA Astrophysics Data System (ADS)

Lange, Adam; Giller, Karin; Hornig, Sönke; Martin-Eauclaire, Marie-France; Pongs, Olaf; Becker, Stefan; Baldus, Marc

2006-04-01

The active site of potassium (K+) channels catalyses the transport of K+ ions across the plasma membrane-similar to the catalytic function of the active site of an enzyme-and is inhibited by toxins from scorpion venom. On the basis of the conserved structures of K+ pore regions and scorpion toxins, detailed structures for the K+ channel-scorpion toxin binding interface have been proposed. In these models and in previous solution-state nuclear magnetic resonance (NMR) studies using detergent-solubilized membrane proteins, scorpion toxins were docked to the extracellular entrance of the K+ channel pore assuming rigid, preformed binding sites. Using high-resolution solid-state NMR spectroscopy, here we show that high-affinity binding of the scorpion toxin kaliotoxin to a chimaeric K+ channel (KcsA-Kv1.3) is associated with significant structural rearrangements in both molecules. Our approach involves a combined analysis of chemical shifts and proton-proton distances and demonstrates that solid-state NMR is a sensitive method for analysing the structure of a membrane protein-inhibitor complex. We propose that structural flexibility of the K+ channel and the toxin represents an important determinant for the high specificity of toxin-K+ channel interactions.

MULTIVARIATE CURVE RESOLUTION OF NMR SPECTROSCOPY METABONOMIC DATA

EPA Science Inventory

Sandia National Laboratories is working with the EPA to evaluate and develop mathematical tools for analysis of the collected NMR spectroscopy data. Initially, we have focused on the use of Multivariate Curve Resolution (MCR) also known as molecular factor analysis (MFA), a tech...

Structure of pectic polysaccharides from sunflower salts-soluble fraction

USDA-ARS?s Scientific Manuscript database

The manuscript discusses the structural features of pectin polysaccharides extracted from seedless sunflower head residues. The analysis using 1H, 13C and two-dimensional gHSQC NMR showed various numbers of methyl and hydroxyl groups attached to the anomeric carbons in the pectin backbone at differe...

Application of comprehensive NMR-based analysis strategy in annotation, isolation and structure elucidation of low molecular weight metabolites of Ricinus communis seeds.

PubMed

Vučković, Ivan; Rapinoja, Marja-Leena; Vaismaa, Matti; Vanninen, Paula; Koskela, Harri

2016-01-01

Powder-like extract of Ricinus communis seeds contain a toxic protein, ricin, which has a history of military, criminal and terroristic use. As the detection of ricin in this "terrorist powder" is difficult and time-consuming, related low mass metabolites have been suggested to be useful for screening as biomarkers of ricin. To apply a comprehensive NMR-based analysis strategy for annotation, isolation and structure elucidation of low molecular weight plant metabolites of Ricinus communis seeds. The seed extract was prepared with a well-known acetone extraction approach. The common metabolites were annotated from seed extract dissolved in acidic solution using (1)H NMR spectroscopy with spectrum library comparison and standard addition, whereas unconfirmed metabolites were identified using multi-step off-line HPLC-DAD-NMR approach. In addition to the common plant metabolites, two previously unreported compounds, 1,3-digalactoinositol and ricinyl-alanine, were identified with support of MS analyses. The applied comprehensive NMR-based analysis strategy provided identification of the prominent low molecular weight metabolites with high confidence. Copyright © 2015 John Wiley & Sons, Ltd.

Quantitative analysis of Earth's field NMR spectra of strongly-coupled heteronuclear systems.

PubMed

Halse, Meghan E; Callaghan, Paul T; Feland, Brett C; Wasylishen, Roderick E

2009-09-01

In the Earth's magnetic field, it is possible to observe spin systems consisting of unlike spins that exhibit strongly coupled second-order NMR spectra. Such spectra result when the J-coupling between two unlike spins is of the same order of magnitude as the difference in their Larmor precession frequencies. Although the analysis of second-order spectra involving only spin-(1/2) nuclei has been discussed since the early days of NMR spectroscopy, NMR spectra involving spin-(1/2) nuclei and quadrupolar (I>(1/2)) nuclei have rarely been treated. Two examples are presented here, the tetrahydroborate anion, BH4-, and the ammonium cation, NH4+. For the tetrahydroborate anion, (1)J((11)B,(1)H)=80.9Hz, and in an Earth's field of 53.3microT, nu((1)H)=2269Hz and nu((11)B)=728Hz. The (1)H NMR spectra exhibit features that both first- and second-order perturbation theory are unable to reproduce. On the other hand, second-order perturbation theory adequately describes (1)H NMR spectra of the ammonium anion, (14)NH4+, where (1)J((14)N,(1)H)=52.75Hz when nu((1)H)=2269Hz and nu((14)N)=164Hz. Contrary to an early report, we find that the (1)H NMR spectra are independent of the sign of (1)J((14)N,(1)H). Exact analysis of two-spin systems consisting of quadrupolar nuclei and spin-(1/2) nuclei are also discussed.

Simultaneous 19F-1H medium resolution NMR spectroscopy for online reaction monitoring

NASA Astrophysics Data System (ADS)

Zientek, Nicolai; Laurain, Clément; Meyer, Klas; Kraume, Matthias; Guthausen, Gisela; Maiwald, Michael

2014-12-01

Medium resolution nuclear magnetic resonance (MR-NMR) spectroscopy is currently a fast developing field, which has an enormous potential to become an important analytical tool for reaction monitoring, in hyphenated techniques, and for systematic investigations of complex mixtures. The recent developments of innovative MR-NMR spectrometers are therefore remarkable due to their possible applications in quality control, education, and process monitoring. MR-NMR spectroscopy can beneficially be applied for fast, non-invasive, and volume integrating analyses under rough environmental conditions. Within this study, a simple 1/16″ fluorinated ethylene propylene (FEP) tube with an ID of 0.04″ (1.02 mm) was used as a flow cell in combination with a 5 mm glass Dewar tube inserted into a benchtop MR-NMR spectrometer with a 1H Larmor frequency of 43.32 MHz and 40.68 MHz for 19F. For the first time, quasi-simultaneous proton and fluorine NMR spectra were recorded with a series of alternating 19F and 1H single scan spectra along the reaction time coordinate of a homogeneously catalysed esterification model reaction containing fluorinated compounds. The results were compared to quantitative NMR spectra from a hyphenated 500 MHz online NMR instrument for validation. Automation of handling, pre-processing, and analysis of NMR data becomes increasingly important for process monitoring applications of online NMR spectroscopy and for its technical and practical acceptance. Thus, NMR spectra were automatically baseline corrected and phased using the minimum entropy method. Data analysis schemes were designed such that they are based on simple direct integration or first principle line fitting, with the aim that the analysis directly revealed molar concentrations from the spectra. Finally, the performance of 1/16″ FEP tube set-up with an ID of 1.02 mm was characterised regarding the limit of detection (LOQ (1H) = 0.335 mol L-1 and LOQ (19F) = 0.130 mol L-1 for trifluoroethanol in D2O (single scan)) and maximum quantitative flow rates up to 0.3 mL min-1. Thus, a series of single scan 19F and 1H NMR spectra acquired with this simple set-up already presents a valuable basis for quantitative reaction monitoring.

High-field 95 Mo and 183 W static and MAS NMR study of polyoxometalates.

PubMed

Haouas, Mohamed; Trébosc, Julien; Roch-Marchal, Catherine; Cadot, Emmanuel; Taulelle, Francis; Martineau-Corcos, Charlotte

2017-10-01

The potential of high-field NMR to measure solid-state 95 Mo and 183 W NMR in polyoxometalates (POMs) is explored using some archetypical structures like Lindqvist, Keggin and Dawson as model compounds that are well characterized in solution. NMR spectra in static and under magic angle spinning (MAS) were obtained, and their analysis allowed extraction of the NMR parameters, including chemical shift anisotropy and quadrupolar coupling parameters. Despite the inherent difficulties of measurement in solid state of these low-gamma NMR nuclei, due mainly to the low spectral resolution and poor signal-to-noise ratio, the observed global trends compare well with the solution-state NMR data. This would open an avenue for application of solid-state NMR to POMs, especially when liquid-state NMR is not possible, e.g., for poorly soluble or unstable compounds in solution, and for giant molecules with slow tumbling motion. This is the case of Keplerate where we provide here the first NMR characterization of this class of POMs in the solid state. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Obtaining aluminas from the thermal decomposition of their different precursors: An {sup 27}Al MAS NMR and X-ray powder diffraction studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chagas, L.H.; De Carvalho, G.S.G.; San Gil, R.A.S.

2014-01-01

Graphical abstract: - Highlights: • We synthesized three precursors of alumina from different methods. • The calcination of the precursors generated several alumina polymorphs. • XRD and NMR were used for structural investigation of the polymorphs. • The synthesis route determines the structural and textural properties of the solids. - Abstract: A commercial sample of Boehmite was used as precursor of alumina polymorphs. For comparison, three other precursors were synthesized from different methods. Particularly, the use of excess of urea promoted a very crystalline form of basic aluminum carbonate. The characteristics of the four precursors were investigated by thermal, vibrationalmore » and X-ray powder diffraction (XRD) analysis. Additionally, the nuclear magnetic resonance, with magic angle spinning ({sup 27}Al MAS NMR), was used to verify the coordination of aluminum cations. Each precursor was calcined at various temperatures generating alumina polymorphs, which were structurally analyzed by XRD and {sup 27}Al MAS NMR. Due to interest in catalysis supports, special attention was given to the γ-Al{sub 2}O{sub 3} phase, which in addition to structural investigation was subjected to textural analysis. The results showed that, from different synthesis procedures and common route of calcination, one can obtain materials with the same composition but with different structural and textural properties, which in turn can significantly influence the performance of a supported catalyst.« less

A rapid NMR-based method for discrimination of strain-specific cell wall teichoic acid structures reveals a third backbone type in Lactobacillus plantarum.

PubMed

Tomita, Satoru; Tanaka, Naoto; Okada, Sanae

2017-03-01

The lactic acid bacterium Lactobacillus plantarum is capable of producing strain-specific structures of cell wall teichoic acid (WTA), an anionic polysaccharide found in the Gram-positive bacterial cell wall. In this study, we established a rapid, NMR-based procedure to discriminate WTA structures in this species, and applied it to 94 strains of L. plantarum. Six previously reported glycerol- and ribitol-containing WTA subtypes were successfully identified from 78 strains, suggesting that these were the dominant structures. However, the level of structural variety differed markedly among bacterial sources, possibly reflecting differences in strain-level microbial diversity. WTAs from eight strains were not identified based on NMR spectra and were classified into three groups. Structural analysis of a partial degradation product of an unidentified WTA produced by strain TUA 1496L revealed that the WTA was 1-O-β-d-glucosylglycerol. Two-dimensional NMR analysis of the polymer structure showed phosphodiester bonds between C-3 and C-6 of the glycerol and glucose residues, suggesting a polymer structure of 3,6΄-linked poly(1-O-β-d-glucosyl-sn-glycerol phosphate). This is the third WTA backbone structure in L. plantarum, following 3,6΄-linked poly(1-O-α-d-glucosyl-sn-glycerol phosphate) and 1,5-linked poly(ribitol phosphate). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Synthesis, characterization and anti-microbial activity of phenylurea-formaldehyde resin (PUF) and its polymer metal complexes (PUF-Mn(II).

PubMed

Ahamad, Tansir; Alshehri, Saad M

2012-10-01

Phenylurea-formaldehyde polymer (PUF) was synthesized via polycondensation of phenylurea and formaldehyde in basic medium, its polymer-metal complexes [PUF-M(II)] were prepared with Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) ions. PUF and PUF-M(II) were characterized with magnetic moment measurements, elemental and spectral (UV-visible, FTIR, 1H-NMR, 13C-NMR and ESR) analysis. The thermal behaviors of all the synthesized polymers were carried out using thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The thermal data revealed that all of the PUF-M(II) showed higher thermal stabilities than the PUF and also ascribed that the PUF-Cu(II) showed better thermal stability than the other PUF-M(II). The kinetic parameters such as activation energy, pre-exponential factor etc., were evaluated for these polymer metal complexes using Coats-Redfern equation. In addition, the antimicrobial activity of the synthesized polymers was tested against several microorganisms using agar well diffusion methods. Among all of the PUF-M(II), the antimicrobial activity of the PUF-Cu(II) showed the highest zone of inhibition because of its higher stability constant and may be used in biomedical applications. Copyright © 2012 Elsevier B.V. All rights reserved.

Toward Reliable Lipoprotein Particle Predictions from NMR Spectra of Human Blood: An Interlaboratory Ring Test.

PubMed

Monsonis Centelles, Sandra; Hoefsloot, Huub C J; Khakimov, Bekzod; Ebrahimi, Parvaneh; Lind, Mads V; Kristensen, Mette; de Roo, Niels; Jacobs, Doris M; van Duynhoven, John; Cannet, Claire; Fang, Fang; Humpfer, Eberhard; Schäfer, Hartmut; Spraul, Manfred; Engelsen, Søren B; Smilde, Age K

2017-08-01

Lipoprotein profiling of human blood by 1 H nuclear magnetic resonance (NMR) spectroscopy is a rapid and promising approach to monitor health and disease states in medicine and nutrition. However, lack of standardization of measurement protocols has prevented the use of NMR-based lipoprotein profiling in metastudies. In this study, a standardized NMR measurement protocol was applied in a ring test performed across three different laboratories in Europe on plasma and serum samples from 28 individuals. Data was evaluated in terms of (i) spectral differences, (ii) differences in LPD predictions obtained using an existing prediction model, and (iii) agreement of predictions with cholesterol concentrations in high- and low-density lipoproteins (HDL and LDL) particles measured by standardized clinical assays. ANOVA-simultaneous component analysis (ASCA) of the ring test spectral ensemble that contains methylene and methyl peaks (1.4-0.6 ppm) showed that 97.99% of the variance in the data is related to subject, 1.62% to sample type (serum or plasma), and 0.39% to laboratory. This interlaboratory variation is in fact smaller than the maximum acceptable intralaboratory variation on quality control samples. It is also shown that the reproducibility between laboratories is good enough for the LPD predictions to be exchangeable when the standardized NMR measurement protocol is followed. With the successful implementation of this protocol, which results in reproducible prediction of lipoprotein distributions across laboratories, a step is taken toward bringing NMR more into scope of prognostic and diagnostic biomarkers, reducing the need for less efficient methods such as ultracentrifugation or high-performance liquid chromatography (HPLC).

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

PubMed

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterization of Two Distinct Amorphous Forms of Valsartan by Solid-State NMR.

PubMed

Skotnicki, Marcin; Apperley, David C; Aguilar, Juan A; Milanowski, Bartłomiej; Pyda, Marek; Hodgkinson, Paul

2016-01-04

Valsartan (VAL) is an antihypertensive drug marketed in an amorphous form. Amorphous materials can have different physicochemical properties depending on preparation method, thermal history, etc., but the nature of such materials is difficult to study by diffraction techniques. This study characterizes two different amorphous forms of valsartan (AR and AM) using solid-state NMR (SSNMR) as a primary investigation tool, supported by solution-state NMR, FT-IR, TMDSC, and dissolution tests. The two forms are found to be clearly distinct, with a significantly higher level of structural arrangement in the AR form, as observed in (13)C, (15)N, and (1)H SSNMR. (13)C and (15)N NMR indicates that the fully amorphous material (AM) contains an approximately equal ratio of cis-trans conformers about the amide bond, whereas the AR form exists mainly as one conformer, with minor conformational "defects". (1)H ultrafast MAS NMR shows significant differences in the hydrogen bonding involving the tetrazole and acid hydrogens between the two materials, while (15)N NMR shows that both forms exist as a 1,2,3,4-tetrazole tautomer. NMR relaxation times show subtle differences in local and bulk molecular mobility, which can be connected with the glass transition, the stability of the glassy material, and its response to aging. Counterintuitively the fully amorphous material is found to have a significantly lower dissolution rate than the apparently more ordered AR material.

Certified Reference Material for Use in 1H, 31P, and 19F Quantitative NMR, Ensuring Traceability to the International System of Units.

PubMed

Rigger, Romana; Rück, Alexander; Hellriegel, Christine; Sauermoser, Robert; Morf, Fabienne; Breitruck, KathrinBreitruck; Obkircher, Markus

2017-09-01

In recent years, quantitative NMR (qNMR) spectroscopy has become one of the most important tools for content determination of organic substances and quantitative evaluation of impurities. Using Certified Reference Materials (CRMs) as internal or external standards, the extensively used qNMR method can be applied for purity determination, including unbroken traceability to the International System of Units (SI). The implementation of qNMR toward new application fields, e.g., metabolomics, environmental analysis, and physiological pathway studies, brings along more complex molecules and systems, thus making use of 1H qNMR challenging. A smart workaround is possible by the use of other NMR active nuclei, namely 31P and 19F. This article presents the development of three classes of qNMR CRMs based on different NMR active nuclei (1H, 31P, and 19F), and the corresponding approaches to establish traceability to the SI through primary CRMs from the National Institute of Standards and Technology and the National Metrology Institute of Japan. These TraceCERT® qNMR CRMs are produced under ISO/IEC 17025 and ISO Guide 34 using high-performance qNMR.

Synthesis and characterization of 3-acetoxy-2-methyl-N-(phenyl)benzamide and 3-acetoxy-2-methyl-N-(4- methylphenyl)benzamide

NASA Astrophysics Data System (ADS)

Kırca, Başak Koşar; Çakmak, Şükriye; Kütük, Halil; Odabaşoğlu, Mustafa; Büyükgüngör, Orhan

2018-01-01

This study treats about two successfully synthesized secondary amide compounds 3-Acetoxy-2-methyl-N-(phenyl)benzamide, I and 3-Acetoxy-2-methyl-N-(4-methylphenyl)benzamide, II. Compounds were characterized by FTIR, 1H NMR, 13C NMR and X-ray single crystal diffraction analysis techniques. Single crystal X-ray diffraction analyses show that while I crystallized in the orthorhombic system with space group Pbca, II crystallized in the triclinic system with space group P-1 and the asymmetric unit of II consists of two crystallographically independent molecules. Lattice constants are a = 7.9713 (3) Å, b = 9.5059 (3) Å, c = 37.1762 (2) Å, Z = 8 for I and a = 7.5579 (8) Å, b = 8.8601 (8) Å, c = 23.363 (3) Å, α = 97.011 (9) °, β = 96.932 (9)°, γ = 90.051 (8)°, Z = 4 for II. Crystallographic studies also show that the supramolecular structures were stabilized by intramolecular, intermolecular hydrogen bonds and Csbnd H … π interactions for both compounds. Characteristic amide bonds were observed in IR and NMR spectra.

Transient α-helices in the disordered RPEL motifs of the serum response factor coactivator MKL1

NASA Astrophysics Data System (ADS)

Mizuguchi, Mineyuki; Fuju, Takahiro; Obita, Takayuki; Ishikawa, Mitsuru; Tsuda, Masaaki; Tabuchi, Akiko

2014-06-01

The megakaryoblastic leukemia 1 (MKL1) protein functions as a transcriptional coactivator of the serum response factor. MKL1 has three RPEL motifs (RPEL1, RPEL2, and RPEL3) in its N-terminal region. MKL1 binds to monomeric G-actin through RPEL motifs, and the dissociation of MKL1 from G-actin promotes the translocation of MKL1 to the nucleus. Although structural data are available for RPEL motifs of MKL1 in complex with G-actin, the structural characteristics of RPEL motifs in the free state have been poorly defined. Here we characterized the structures of free RPEL motifs using NMR and CD spectroscopy. NMR and CD measurements showed that free RPEL motifs are largely unstructured in solution. However, NMR analysis identified transient α-helices in the regions where helices α1 and α2 are induced upon binding to G-actin. Proline mutagenesis showed that the transient α-helices are locally formed without helix-helix interactions. The helix content is higher in the order of RPEL1, RPEL2, and RPEL3. The amount of preformed structure may correlate with the binding affinity between the intrinsically disordered protein and its target molecule.

Coal liquefaction process streams characterization and evaluation: Analysis of Black Thunder coal and liquefaction products from HRI Bench Unit Run CC-15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pugmire, R.J.; Solum, M.S.

This study was designed to apply {sup 13}C-nuclear magnetic resonance (NMR) spectrometry to the analysis of direct coal liquefaction process-stream materials. {sup 13}C-NMR was shown to have a high potential for application to direct coal liquefaction-derived samples in Phase II of this program. In this Phase III project, {sup 13}C-NMR was applied to a set of samples derived from the HRI Inc. bench-scale liquefaction Run CC-15. The samples include the feed coal, net products and intermediate streams from three operating periods of the run. High-resolution {sup 13}C-NMR data were obtained for the liquid samples and solid-state CP/MAS {sup 13}C-NMR datamore » were obtained for the coal and filter-cake samples. The {sup 1}C-NMR technique is used to derive a set of twelve carbon structural parameters for each sample (CONSOL Table A). Average molecular structural descriptors can then be derived from these parameters (CONSOL Table B).« less

Dynamic aggregation of the mid-sized gadolinium complex {Ph4[Gd(DTTA)(H2O)2](-)3}.

PubMed

Jaccard, Hugues; Miéville, Pascal; Cannizzo, Caroline; Mayer, Cédric R; Helm, Lothar

2014-02-01

A compound binding three Gd(3+) ions, {Ph4[Gd(DTTA)(H2O)2](-) 3} (where H5DTTA is diethylenetriaminetetraacetic acid), has been synthesized around a hydrophobic center made up of four phenyl rings. In aqueous solution the molecules start to self-aggregate at concentrations well below 1 mM as shown by the increase of rotational correlation times and by the decrease of the translational self-diffusion constant. NMR spectra recorded in aqueous solution of the diamagnetic analogue {Ph4[Y(DTTA)(H2O)2](-)3} show that the aggregation is dynamic and due to intermolecular π-stacking interactions between the hydrophobic aromatic centers. From estimations of effective radii, it can be concluded that the aggregates are composed of two to three monomers. The paramagnetic {Ph4[Gd(DTTA)(H2O)2](-)3} exhibits concentration-dependent (1)H NMR relaxivities with high values of approximately 50 mM(-1) s(-1) (30 MHz, 25 °C) at gadolinium concentrations above 20 mM. A combined analysis of (1)H NMR dispersion profiles measured at different concentrations of the compound and (17)O NMR data measured at various temperatures was performed using different theoretical approaches. The fitted parameters showed that the increase in relaxivity with increasing concentration of the compound is due to slower global rotational motion and an increase of the Lipari-Szabo order parameter S(2).

Application of INEPT nitrogen-15 and silicon-29 nuclear magnetic resonance spectrometry to derivatized fulvic acids

USGS Publications Warehouse

Thorn, K.A.; Folan, D.W.; Arterburn, J.B.; Mikita, M.A.; MacCarthy, P.

1989-01-01

Use of the INEPT experiment has been examined in two derivatization studies of the Suwannee River fulvic acid. In the first study, the fulvic acid was derivatized with 15N enriched hydroxylamine. The quantitative 15N NMR spectrum, acquired with a 45° pulse angle, 2.0 second pulse delay and inverse gated decoupling, showed that oximes (390-340 ppm) were the major derivatives, followed by nitriles (270-240 ppm), hydroxamic acids (170-160 ppm), secondary amides (150-115 ppm), and lactams (115-90 ppm). The INEPT 15N NMR spectrum was acquired using refocussing delays and polarization transfer times optimized for signal enhancement of singly protonated nitrogens. INEPT greatly enhanced the amide and lactam resonances, and showed that resonances downfield of 180 ppm in the quantitative spectrum represented nonprotonated nitrogens. In the second study, the fulvic acid was first methylated with diazomethane and then silylated with hexamethyldisilazane. The 29Si NMR spectra exhibited two major peaks, from approximately 33 to 22 ppm, representing silyl esters of carboxylic acids, and from 22 to 13 ppm, representing silyl ethers of alcohols and phenols. The INEPT 29Si NMR spectrum was virtually identical to the quantitative 29Si spectrum, acquired with a 90° pulse angle, 5.0 second pulse delay, inverse gated decoupling, and relaxation reagent. INEPT therefore can be used for quantitative analysis of trimethylsilyl derivatives of the fulvic acid, saving spectrometer time and eliminating the need for relaxation reagents.

Regioselective Hydration of an Alkene and Analysis of the Alcohol Product by Remote Access NMR: A Classroom Demonstration

ERIC Educational Resources Information Center

Smith, Maureen E.; Johnson, Sara L.; Masterson, Douglas S.

2013-01-01

A two-part demonstration was conducted in our first-semester organic chemistry course designed to introduce students to the formation of alcohols, regioselective reactions, and analysis of organic products by NMR analysis. This demonstration utilized the oxymercuration-demercuration sequence to prepare an alcohol from an alkene in a Markovnikov…

A novel tridentate Schiff base dioxo-molybdenum(VI) complex: synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, ¹H NMR and ¹³C NMR spectra.

PubMed

Saheb, Vahid; Sheikhshoaie, Iran; Stoeckli-Evans, Helen

2012-09-01

A new dioxo-molybdenum(VI) complex [MoO(2)(L)(H(2)O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H(2)L) and MoO(2)(acac)(2). The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the UV-visible, FTIR, (1)H NMR and (13)C NMR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TDDFT) method is used to calculate the electronic transitions of the complex. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental (1)H NMR spectra. However, the (13)C NMR shielding tensors computed at the B3LYP level, employing a combined basis set of DGDZVP for Mo and 6-31+G(2df,p) for other atoms, are in better agreement with experimental (13)C NMR spectra. The electronic transitions calculated at the B3LYP/DGDZVP level by using TD-DFT method is in accordance with the observed UV-visible spectrum of the compound. Copyright © 2012 Elsevier B.V. All rights reserved.

High-performance liquid chromatography with nuclear magnetic resonance detection applied to organosilicon polymers. Part 2. Comparison with other methods.

PubMed

Blechta, Vratislav; Kurfürst, Milan; Sýkora, Jan; Schraml, Jan

2007-03-23

LC-NMR utilizing (1)H and (29)Si NMR spectroscopy is ideally suited for the analysis of silicones. It is shown that reversed phase gradient LC-NMR surpasses standard gel permeation chromatography (GPC) and diffusion ordered spectroscopy (DOSY) in the analysis of model hydride terminated polydimethylsiloxane. (1)H and (29)Si NMR in the stopped-flow arrangement leads to full identification of the components. Concentration gradient introduces a dependence of the (29)Si shifts on solvent composition, this dependence can be substantially reduced by a proposed method of referencing. It is shown that the ADEQUATE version of powerful but insensitive 2D INADEQUATE experiment can be used for complete line assignment.

Hepatic lipid profiling of deer mice fed ethanol using {sup 1}H and {sup 31}P NMR spectroscopy: A dose-dependent subchronic study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernando, Harshica; Bhopale, Kamlesh K.; Boor, Paul J.

2012-11-01

Chronic alcohol abuse is a 2nd major cause of liver disease resulting in significant morbidity and mortality. Alcoholic liver disease (ALD) is characterized by a wide spectrum of pathologies starting from fat accumulation (steatosis) in early reversible stage to inflammation with or without fibrosis and cirrhosis in later irreversible stages. Previously, we reported significant steatosis in the livers of hepatic alcohol dehydrogenase (ADH)-deficient (ADH{sup −}) vs. hepatic ADH-normal (ADH{sup +}) deer mice fed 4% ethanol daily for 2 months [Bhopale et al., 2006, Alcohol 39, 179–188]. However, ADH{sup −} deer mice fed 4% ethanol also showed a significant mortality. Therefore,more » a dose-dependent study was conducted to understand the mechanism and identify lipid(s) involved in the development of ethanol-induced fatty liver. ADH{sup −} and ADH{sup +} deer mice fed 1, 2 or 3.5% ethanol daily for 2 months and fatty infiltration in the livers were evaluated by histology and by measuring dry weights of extracted lipids. Lipid metabolomic changes in extracted lipids were determined by proton ({sup 1}H) and {sup 31}phosphorus ({sup 31}P) nuclear magnetic resonance (NMR) spectroscopy. The NMR data was analyzed by hierarchical clustering (HC) and principle component analysis (PCA) for pattern recognition. Extensive vacuolization by histology and significantly increased dry weights of total lipids found only in the livers of ADH{sup −} deer mice fed 3.5% ethanol vs. pair-fed controls suggest a dose-dependent formation of fatty liver in ADH{sup −} deer mouse model. Analysis of NMR data of ADH{sup −} deer mice fed 3.5% ethanol vs. pair-fed controls shows increases for total cholesterol, esterified cholesterol, fatty acid methyl esters (FAMEs), triacylglycerides and unsaturation, and decreases for free cholesterol, phospholipids and allylic and diallylic protons. Certain classes of neutral lipids (cholesterol esters, fatty acyl chain (-COCH{sub 2}-) and FAMEs) were also mildly increased in ADH{sup −} deer mice fed 1 or 2% ethanol. Only small increases were observed for allylic and diallylic protons, FAMEs and unsaturations in ADH{sup +} deer mice fed 3.5% ethanol vs. pair-fed controls. PCA of NMR data showed increased clustering by gradual separation of ethanol-fed ADH{sup −} deer mice groups from their respective pair-fed control groups and corresponding ethanol-fed ADH{sup +} deer mice groups. Our data indicate that dose of ethanol and hepatic ADH deficiency are two key factors involved in initiation and progression of alcoholic fatty liver disease. Further studies on characterization of individual lipid entities and associated metabolic pathways altered in our deer mouse model after different durations of ethanol feeding could be important to delineate mechanism(s) and identify potential biomarker candidate(s) of early stage ALD. -- Highlights: ► Dose-dependent ethanol-induced fatty liver was studied in deer mouse model. ► A NMR-based lipidomic approach with histology and dry lipid weights was used. ► We used principal component analysis (PCA) to analyze the NMR lipidomic data. ► Dose-dependent clustering patterns by PCA were compared among the groups.« less

An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV-Vis, MEP diagrams, NBO, NLO, FMO) of the 1,5-methanoazocino[4,3-b]indole core structure

NASA Astrophysics Data System (ADS)

Uludağ, Nesimi; Serdaroğlu, Goncagül

2018-03-01

This study examines the synthesis of azocino[4,3-b]indole structure, which constitutes the tetracyclic framework of uleine, dasycarpidoneand tubifolidineas well as ABDE substructure of the strychnosalkaloid family. It has been synthesized by Fischer indolization of 2 and through the cylization of 4 by 2,3-dichlor-5-6-dicyanobenzoquinone (DDQ). 1H and 1C NMR chemical shifts have been predicted with GIAO approach and the calculated chemical shifts show very good agreement with observed shifts. FT-IR spectroscopy is important for the analysis of functional groups of synthesized compounds and we also supported FT-IR vibrational analysis with computational IR analysis. The vibrational spectral analysis was performed at B3LYP level of the theory in both the gas and the water phases and it was compared with the observed IR values for the important functional groups. The DFT calculations have been conducted to determine the most stable structure of the 1,2,3,4,5,6,7-Hexahydro-1,5-methanoazocino [4,3-b] indole (5). The Frontier Molecular Orbital Analysis, quantum chemical parameters, physicochemical properties have been predicted by using the same theory of level in both gas phase and the water phase, at 631 + g** and 6311++g** basis sets. TD- DFT calculations have been performed to predict the UV- Vis spectral analysis for this synthesized molecule. The Natural Bond Orbital (NBO) analysis have been performed at B3LYP level of theory to elucidate the intra-molecular interactions such as electron delocalization and conjugative interactions. NLO calculations were conducted to obtain the electric dipole moment and polarizability of the title compound.

Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma

PubMed Central

2013-01-01

Nuclear magnetic resonance spectroscopy (NMR) provides robust readouts of many metabolic parameters in one experiment. However, identification of clinically relevant markers in 1H NMR spectra is a major challenge. Association of NMR-derived quantities with genetic variants can uncover biologically relevant metabolic traits. Using NMR data of plasma samples from 1,757 individuals from the KORA study together with 655,658 genetic variants, we show that ratios between NMR intensities at two chemical shift positions can provide informative and robust biomarkers. We report seven loci of genetic association with NMR-derived traits (APOA1, CETP, CPS1, GCKR, FADS1, LIPC, PYROXD2) and characterize these traits biochemically using mass spectrometry. These ratios may now be used in clinical studies. PMID:23414815

Investigation of structure, vibrational and NMR spectra of oxycodone and naltrexone: A combined experimental and theoretical study

NASA Astrophysics Data System (ADS)

Tavakol, Hossein; Esfandyari, Maryam; Taheri, Salman; Heydari, Akbar

2011-08-01

In this work, two important opioid antagonists, naltrexone and oxycodone, were prepared from thebaine and were characterized by IR, 1H NMR and 13C NMR spectroscopy. Moreover, computational NMR and IR parameters were obtained using density functional theory (DFT) at B3LYP/6-311++G** level of theory. Complete NMR and vibrational assignment were carried out using the observed and calculated spectra. The IR frequencies and NMR chemical shifts, determined experimentally, were compared with those obtained theoretically from DFT calculations, showed good agreements. The RMS errors observed between experimental and calculated data for the IR absorptions are 85 and 105 cm -1, for the 1H NMR peaks are 0.87 and 0.17 ppm and for those of 13C NMR are 5.6 and 5.3 ppm, respectively for naltrexone and oxycodone.

Establishment and optimization of NMR-based cell metabonomics study protocols for neonatal Sprague-Dawley rat cardiomyocytes.

PubMed

Zhang, Ming; Sun, Bo; Zhang, Qi; Gao, Rong; Liu, Qiao; Dong, Fangting; Fang, Haiqin; Peng, Shuangqing; Li, Famei; Yan, Xianzhong

2017-01-15

A quenching, harvesting, and extraction protocol was optimized for cardiomyocytes NMR metabonomics analysis in this study. Trypsin treatment and direct scraping cells in acetonitrile were compared for sample harvesting. The results showed trypsin treatment cause normalized concentration increasing of phosphocholine and metabolites leakage, since the trypsin-induced membrane broken and long term harvesting procedures. Then the intracellular metabolite extraction efficiency of methanol and acetonitrile were compared. As a result, washing twice with phosphate buffer, direct scraping cells and extracting with acetonitrile were chosen to prepare cardiomyocytes extracts samples for metabonomics studies. This optimized protocol is rapid, effective, and exhibits greater metabolite retention. Copyright © 2016 Elsevier Inc. All rights reserved.

Non-Linear Signal Detection Improvement by Radiation Damping in Single-Pulse NMR Spectra

PubMed Central

Schlagnitweit, Judith; Morgan, Steven W; Nausner, Martin; Müller, Norbert; Desvaux, Hervé

2012-01-01

When NMR lines overlap and at least one of them is affected by radiation damping, the resonance line shapes of all lines are no longer Lorentzian. We report the appearance of narrow signal distortions, which resemble hole-burnt spectra. This new experimental phenomenon facilitates the detection of tiny signals hidden below the main resonance. Theoretical analysis based on modified Maxwell–Bloch equations shows that the presence of strong transverse magnetization creates a feedback through the coil, which influences the magnetization of all spins with overlapping resonance lines. In the time domain this leads to cross-precession terms between magnetization densities, which ultimately cause non-linear behavior. Numerical simulations corroborate this interpretation. PMID:22266720

Structural assignment of poecillastrins B and C, macrolide lactams from the deep-water Caribbean sponge Poecillastra species.

PubMed

Takada, Kentaro; Choi, Byoung W; Rashid, Mohammad A; Gamble, William R; Cardellina, John H; Van, Que N; Lloyd, John R; McMahon, James B; Gustafson, Kirk R

2007-03-01

Two new chondropsin-type macrolide lactams, poecillastrins B (1) and C (2), were isolated from aqueous extracts of the marine sponge Poecillastra sp. These trace metabolites were isolated in low yield (400-600 microg), and their structures were determined primarily by analysis of NMR data acquired using a cyrogenically cooled probe. High-quality 1D and 2D NMR data sets allowed complete assignment of the spectroscopic data and defined the new structures as 35-membered ring analogues of poecillastrin A (3). Compounds 1 and 2 showed potent cytotoxic activity against a human melanoma tumor cell line (LOX) with an IC50 value of less than 1 microg/mL.

Synthesis and anti-proliferative activity of fluoro-substituted chalcones.

PubMed

Burmaoglu, Serdar; Algul, Oztekin; Anıl, Derya Aktas; Gobek, Arzu; Duran, Gulay Gulbol; Ersan, Ronak Haj; Duran, Nizami

2016-07-01

A series of novel fluoro-substituted chalcone derivatives have been synthesized. All synthesized compounds were characterized by (1)H nuclear magnetic resonance (NMR), (13)C NMR, and elemental analysis. Their anti-proliferative activities were evaluated against five cancer cells lines, namely, A549, A498, HeLa, A375, and HepG2 using the MTT method. Most of the compounds showed moderate to high activity with IC50 values in the range of 0.029-0.729μM. Of all the synthesized compounds, 10 and 19 exhibited the most potent anti-proliferative activities against cancer cells, and 10 was identified as the most promising compound. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural and Biological Behaviour of Co(II), Cu(II) and Ni(II) Metal Complexes of Some Amino Acid Derived Schiff-Bases

PubMed Central

Chohan, Zahid H.; Praveen, M.; Ghaffar, A.

1997-01-01

Biologically active tridentate amino acid (Alanine, Glycine & Tyrosine) derived Schiff-bases and their Co(II), Cu(II) & Ni(II) complexes have been synthesised and characterised on the basis of their conductance and magnetic measurements, elemental analysis and 13C-NMR, 1H-NMR, IR and electronic spectral data. These Schiff-bases and their complexes have been evaluated for their antibacterial activity against bacterial species such as Staphylococcus aureus, Escherichia coli, Klebsiella pneumonae, Proteus vulgarus and Pseudomonas aeruginosa and this activity data show the metal complexes to be more antibacterial than the Schiff-bases against one or more bacterial species. PMID:18475798

Synthesis, Characterization, Crystal Structure, and Biological Studies of a Cadmium(II) Complex with a Tridentate Ligand 4′-Chloro-2,2′:6′,2′′-Terpyridine

PubMed Central

Saghatforoush, L. A.; Valencia, L.; Chalabian, F.; Ghammamy, Sh.

2011-01-01

A new Cd(II) complex with the ligand 4′-chloro-2,2′6′,2′′-terpyridine (Cltpy), [Cd(Cltpy)(I)2], has been synthesized and characterized by CHN elemental analysis, 1H-NMR, 13C-NMR, and IR spectroscopy and structurally analyzed by X-ray single-crystal diffraction. The single-crystal X-ray analyses show that the coordination number in complex is five with three terpyridine (Cltpy) N-donor atoms and two iodine atoms. The antibacterial activities of Cltpy and its Cd(II) complex are tested against different bacteria. PMID:21738495

A facile approach towards synthesis, characterization, single crystal structure, and DFT study of 5-bromosalicylalcohol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rastogi, Rupali, E-mail: rastogirupali@ymail.com; Tarannum, Nazia; Butcher, R. J.

2016-03-15

5-Bromosalicylalcohol was prepared by the interaction of NaBH{sub 4} and 5-bromosalicylaldehyde. The use of sodium borohydride makes the reaction easy, facile, economic and does not require any toxic catalyst. The compound is characterized by FTIR, {sup 1}H NMR, {sup 13}C NMR, TEM and ESI-mass spectra. Crystal structure is determined by single crystal X-ray analysis. Quantum mechanical calculations of geometries, energies and thermodynamic parameters are carried out using density functional theory (DFT/B3LYP) method with 6-311G(d,p) basis set. The optimized geometrical parameters obtained by B3LYP method show good agreement with experimental data.

NMR reaction monitoring in flow synthesis

PubMed Central

Gomez, M Victoria

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed. PMID:28326137

Beyond Fourier

NASA Astrophysics Data System (ADS)

Hoch, Jeffrey C.

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development.

NMR reaction monitoring in flow synthesis.

PubMed

Gomez, M Victoria; de la Hoz, Antonio

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

Micro-structural characterization of the hydration products of bauxite-calcination-method red mud-coal gangue based cementitious materials.

PubMed

Liu, Xiaoming; Zhang, Na; Yao, Yuan; Sun, Henghu; Feng, Huan

2013-11-15

In this research, the micro-structural characterization of the hydration products of red mud-coal gangue based cementitious materials has been investigated through SEM-EDS, (27)Al MAS NMR and (29)Si MAS NMR techniques, in which the used red mud was derived from the bauxite calcination method. The results show that the red mud-coal gangue based cementitious materials mainly form fibrous C-A-S-H gel, needle-shaped/rod-like AFt in the early hydration period. With increasing of the hydration period, densification of the pastes were promoted resulting in the development of strength. EDS analysis shows that with the Ca/Si of red mud-coal gangue based cementitious materials increases, the average Ca/Si and Ca/(Si+Al) atomic ratio of C-A-S-H gel increases, while the average Al/Si atomic ratio of C-A-S-H gel decreases. MAS NMR analysis reveals that Al in the hydration products of red mud-coal gangue based cementitious materials exists in the forms of Al(IV) and Al(VI), but mainly in the form of Al(VI). Increasing the Ca/Si ratio of raw material promotes the conversion of [AlO4] to [AlO6] and inhibits the combination between [AlO4] and [SiO4] to form C-A-S-H gel. Meanwhile, the polymerization degree of [SiO4] in the hydration products declines. Published by Elsevier B.V.

Using nuclear magnetic resonance and transient electromagnetics to characterise water distribution beneath an ice covered volcanic crater: the case of Sherman Crater Mt. Baker Washington.

USGS Publications Warehouse

Irons, Trevor P.; Martin, Kathryn; Finn, Carol A.; Bloss, Benjamin; Horton, Robert J.

2014-01-01

Surface and laboratory Nuclear Magnetic Resonance (NMR) measurements combined with transient electromagnetic (TEM) data are powerful tools for subsurface water detection. Surface NMR (sNMR) and TEM soundings, laboratory NMR, complex resistivity, and X-Ray Diffraction (XRD) analysis were all conducted to characterise the distribution of water within Sherman Crater on Mt. Baker, WA. Clay rich rocks, particularly if water saturated, can weaken volcanoes, thereby increasing the potential for catastrophic sector collapses that can lead to far-travelled, destructive debris flows. Detecting the presence and volume of shallow groundwater is critical for evaluating these landslide hazards. The TEM data identified a low resistivity layer (<10 ohm-m), under 60 m of glacial ice related to water saturated clays. The TEM struggles to resolve the presence or absence of a plausible thin layer of bulk liquid water on top of the clay. The sNMR measurements did not produce any observable signal, indicating the lack of substantial accumulated bulk water below the ice. Laboratory analysis on a sample from the crater wall that likely represented the clays beneath the ice confirmed that the controlling factor for the lack of sNMR signal was the fine-grained nature of the media. The laboratory measurements further indicated that small pores in clays detected by the XRD contain as much as 50% water, establishing an upper bound on the water content in the clay layer. Forward modelling of geologic scenarios revealed that bulk water layers as thin as ½ m between the ice and clay layer would have been detectable using sNMR. The instrumentation conditions which would allow for sNMR detection of the clay layer are investigated. Using current instrumentation the combined analysis of the TEM and sNMR data allow for valuable characterisation of the groundwater system in the crater. The sNMR is able to reduce the uncertainty of the TEM in regards to the presence of a bulk water layer, a valuable piece of information in hazard assessment.

Spectral, optical, thermal, Hirshfeld, antimicrobial studies and computational calculations of a new organic crystal, 1H-benzo[d]imidazol-3-ium-3,5-dinitrobenzoate

NASA Astrophysics Data System (ADS)

Sathya, K.; Dhamodharan, P.; Dhandapani, M.

2017-06-01

Single crystals of 1H-benzo[d]imidazol-3-ium-3,5-dinitrobenzoate (BDNB) were grown by reacting 3,5-dinitrobenzoic acid and benzimidazole by slow evaporation method. UV-Vis-NIR spectral studies of the BDNB show that the crystal is excellently transparent in entire visible region. Chemically and magnetically equivalent protons in BDNB were identified by 1H NMR technique. The carbon frame work of the molecule was established by 13C NMR spectroscopy. Proton transfer mechanism was confirmed by the presence of N+H group in BDNB by FT-IR spectroscopic technique. TG/DTA analyses confirmed that the crystal is stable up to172 °C. Single crystal XRD analysis was carried out to ascertain the molecular structure and the crystal belongs to monoclinic system with space group P21/c. Computational studies that include optimization of molecular geometry, natural bond analysis, Mulliken population analysis and HOMO-LUMO analysis were performed using B3LYP method at 6-31 g level. The low HOMO-LUMO energy gap of BDNB confirms high reactivity of BDNB. Hirshfeld analysis expose that O⋯H/H⋯O interactions are the prominent interactions. Theoretical calculations indicate that first order hyperpolarizability is 16 times greater than urea. The results show that the BDNB may be used for opto-electronic applications. The antimicrobial and antioxidant analyses shows concentration of the compound increases inhibition activity also increases.

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

CP/MAS ¹³C NMR study of pulp hornification using nanocrystalline cellulose as a model system.

PubMed

Idström, Alexander; Brelid, Harald; Nydén, Magnus; Nordstierna, Lars

2013-01-30

The hornification process of paper pulp was investigated using solid-state (13)C NMR spectroscopy. Nanocrystalline cellulose was used to serve as a model system of the crystalline parts of the fibrils in pulp fibers. Characterization of the nanocrystalline cellulose dimensions was carried out using scanning electron microscopy. The samples were treated by drying and wetting cycles prior to NMR analysis where the hornification phenomenon was recorded by spectral changes of the cellulose C-4 carbon signals. An increase of the crystalline signal and a decrease of the signals corresponding to the accessible amorphous domains were found for both paper pulp and nanocrystalline cellulose. These spectral changes grew stronger with repeating drying and wetting cycles. The results show that cellulose co-crystallization contribute to hornification. Another conclusion is that the surfaces of higher hydrophobicity in cellulose fibrils have an increased preference for aggregation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae-A 2D NMR Metabolomics Study.

PubMed

Vergara, Fredd; Shino, Amiu; Kikuchi, Jun

2016-09-02

Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of ¹H-(13)C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae.

Biochemical consequences of alginate encapsulation: a NMR study of insulin-secreting cells.

PubMed

Simpson, Nicholas E; Grant, Samuel C; Gustavsson, Lenita; Peltonen, Vilje-Mia; Blackband, Stephen J; Constantinidis, Ioannis

2006-04-01

In this study we explore the biochemical consequences of alginate encapsulation on betaTC3 cells. (13)C NMR spectroscopy and isotopomer analysis were used to investigate the effects of encapsulation on several enzymatic processes associated with the TCA cycle. Our data show statistically significant differences in various enzymatic fluxes related to the TCA cycle and insulin secretion between monolayer and alginate-encapsulated cultures. The principal cause for these effects was the process of trypsinization. Embedding the trypsinized cells in alginate beads did not have a compounded effect on the enzymatic fluxes of entrapped cells. However, an additional small but statistically significant decrease in insulin secretion was measured in encapsulated cells. Finally, differences in either enzymatic fluxes or glucose consumption as a function of bead diameter were not observed. However, differences in T(2), assessed by (1)H NMR microimaging, were observed as a function of bead diameter, suggesting that smaller beads became more organized with time in culture, while larger beads displayed a looser organization.

NMR-based metabolic study of fruits of Physalis peruviana L. grown in eight different Peruvian ecosystems.

PubMed

Maruenda, Helena; Cabrera, Rodrigo; Cañari-Chumpitaz, Cristhian; Lopez, Juan M; Toubiana, David

2018-10-01

The berry of Physalis peruviana L. (Solanaceae) represents an important socio-economical commodity for Latin America. The absence of a clear phenotype renders it difficult to trace its place of origin. In this study, Cape gooseberries from eight different regions within the Peruvian Andes were profiled for their metabolism implementing a NMR platform. Twenty-four compounds could be unequivocally identified and sixteen quantified. One-way ANOVA and post-hoc Tukey test revealed that all of the quantified metabolites changed significantly among regions: Bambamarca I showed the most accumulated significant differences. The coefficient of variation demonstrated high phenotypic plasticity for amino acids, while sugars displayed low phenotypic plasticity. Correlation analysis highlighted the closely coordinated behavior of the amino acid profile. Finally, PLS-DA revealed a clear separation among the regions based on their metabolic profiles, accentuating the discriminatory capacity of NMR in establishing significant phytochemical differences between producing regions of the fruit of P. peruviana L. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structural characterization of lignin isolated from coconut (Cocos nucifera) coir fibers.

PubMed

Rencoret, Jorge; Ralph, John; Marques, Gisela; Gutiérrez, Ana; Martínez, Ángel T; del Río, José C

2013-03-13

The structure of the isolated milled "wood" lignin from coconut coir has been characterized using different analytical methods, including Py-GC/MS, 2D NMR, DFRC, and thioacidolysis. The analyses demonstrated that it is a p-hydroxyphenyl-guaiacyl-syringyl (H-G-S) lignin, with a predominance of G units (S/G ratio 0.23) and considerable amounts of associated p-hydroxybenzoates. Two-dimensional NMR indicated that the main substructures present in this lignin include β-O-4' alkyl aryl ethers followed by phenylcoumarans and resinols. Two-dimensional NMR spectra also indicated that coir lignin is partially acylated at the γ-carbon of the side chain with p-hydroxybenzoates and acetates. DFRC analysis showed that acetates preferentially acylate the γ-OH in S rather than in G units. Despite coir lignin's being highly enriched in G-units, thioacidolysis indicated that β-β' resinol structures are mostly derived from sinapyl alcohol. Finally, we find evidence that the flavone tricin is incorporated into the coconut coir lignin, as has been recently noted for various grasses.

Two-dimensional NMR spectroscopy of 13C methanol at less than 5 μT

NASA Astrophysics Data System (ADS)

Shim, Jeong Hyun; Lee, Seong-Joo; Hwang, Seong-min; Yu, Kwon-Kyu; Kim, Kiwoong

2014-09-01

Two-dimensional (2D) spectroscopy is one of the most significant applications of nuclear magnetic resonance (NMR). Here, we demonstrate that the 2D NMR can be performed even at a low magnetic field of less than 5 μT, which is ten times less than the Earth’s magnetic field. The pulses used in the experiment were composed of circularly polarized fields for coherent as well as wideband excitations. Since the excitation band covers the entire spectral range, the simplest two-pulse sequence delivered the full 2D spectrum. At 5 μT, methanol with 13C enriched up to 99% belongs to a strongly coupled regime, and thus its 2D spectrum exhibits complicated spectral correlations, which can be exploited as a fingerprint in chemical analysis. In addition, we show that, with compressive sensing, the acquisition of the 2D spectrum can be accelerated to take only 45% of the overall duration.

DOSY Analysis of Micromolar Analytes: Resolving Dilute Mixtures by SABRE Hyperpolarization.

PubMed

Reile, Indrek; Aspers, Ruud L E G; Tyburn, Jean-Max; Kempf, James G; Feiters, Martin C; Rutjes, Floris P J T; Tessari, Marco

2017-07-24

DOSY is an NMR spectroscopy technique that resolves resonances according to the analytes' diffusion coefficients. It has found use in correlating NMR signals and estimating the number of components in mixtures. Applications of DOSY in dilute mixtures are, however, held back by excessively long measurement times. We demonstrate herein, how the enhanced NMR sensitivity provided by SABRE hyperpolarization allows DOSY analysis of low-micromolar mixtures, thus reducing the concentration requirements by at least 100-fold. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isolation and structure elucidation of the nucleoside antibiotic strepturidin from Streptomyces albus DSM 40763.

PubMed

Pesic, Alexander; Steinhaus, Britta; Kemper, Sebastian; Nachtigall, Jonny; Kutzner, Hans Jürgen; Höfle, Gerhard; Süssmuth, Roderich D

2014-06-01

The antibiotic strepturidin (1) was isolated from the microorganism Streptomyces albus DSM 40763, and its structure elucidated by spectroscopic methods and chemical degradation studies. The determination of the relative and absolute stereocenters was partially achieved using chiral GC/EI-MS analysis and microderivatization by acetal ring formation and subsequent 2D-NMR analysis of key (1)H,(1)H-NOESY NMR correlations and extraction of (1)H,(13)C coupling constants from (1)H,(13)C-HMBC NMR spectra. Based on these results, a biosynthesis model was proposed.

1H, 13C, 15N NMR analysis of sildenafil base and citrate (Viagra) in solution, solid state and pharmaceutical dosage forms.

PubMed

Wawer, Iwona; Pisklak, Maciej; Chilmonczyk, Zdzisław

2005-08-10

Sildenafil citrate (SC) (Viagra) and sildenafil base in pure form are easily and unequivocally characterized by multinuclear NMR spectroscopy. Analysis of chemical shifts indicates that: (i) N6-H forms intramolecular hydrogen bonds, (ii) N25 is protonated in the salt and (iii) intermolecular OH...N hydrogen bonds involving N2 and N4 are present in the solid sildenafil citrate. 13C CPMAS NMR method has been proposed for the identification and quantitation of Viagra in its pharmaceutical formulations.

In Vivo Use of 1D and 2D 1H NMR to Examine the Glycosylation of Scopoletin in Duboisia myoporoides Cell Suspensions.

PubMed

Fliniaux, Ophélie; Roscher, Albrecht; Cailleu, Dominique; Mesnard, François

2018-06-14

Cell suspensions initiated from Duboisia myoporoides -a shrub belonging to the Solanaceae family and being a rich source of tropane alkaloids-previously showed their ability to glycosylate scopoletin into scopolin, which represent coumarins showing health benefits. To investigate the time course of this glycosylation reaction, an in vivo NMR approach was developed using a perfusion system in an 8-mm NMR tube and 1 H NMR with 1D and 2D (TOCSY and NOESY) experiments. The time course of metabolic changes could therefore be followed without any labeling. Georg Thieme Verlag KG Stuttgart · New York.

Characterization and elimination of undesirable protein residues in plant cell walls for enhancing lignin analysis by solution-state 2D gel-NMR methods

USDA-ARS?s Scientific Manuscript database

Proteins exist in every plant cell wall. Certain protein residues interfere with lignin characterization and quantification. The current solution-state 2D-NMR technique (gel-NMR) for whole plant cell wall structural profiling provides detailed information regarding cell walls and proteins. However, ...

Why Is It so? The [superscript 1]H-NMR CH[subscript 2] Splitting in Substituted Propanes

ERIC Educational Resources Information Center

Lim, Kieran F.; Dereani, Marino

2010-01-01

Nuclear magnetic resonance (NMR) spectroscopy is an important tool in the structural analysis of both organic and inorganic molecules. Proton NMR spectra can yield information about the chemical or bonding environment surrounding various protons, the number of protons in those environments, and the number of neighbouring protons around each…

Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

ERIC Educational Resources Information Center

Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

2015-01-01

A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

ImatraNMR: novel software for batch integration and analysis of quantitative NMR spectra.

PubMed

Mäkelä, A V; Heikkilä, O; Kilpeläinen, I; Heikkinen, S

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. Copyright © 2011 Elsevier Inc. All rights reserved.

Identification of Imitation Cheese and Imitation Ice Cream Based on Vegetable Fat Using NMR Spectroscopy and Chemometrics

PubMed Central

Monakhova, Yulia B.; Godelmann, Rolf; Andlauer, Claudia; Kuballa, Thomas; Lachenmeier, Dirk W.

2013-01-01

Vegetable oils and fats may be used as cheap substitutes for milk fat to manufacture imitation cheese or imitation ice cream. In this study, 400 MHz nuclear magnetic resonance (NMR) spectroscopy of the fat fraction of the products was used in the context of food surveillance to validate the labeling of milk-based products. For sample preparation, the fat was extracted using an automated Weibull-Stoldt methodology. Using principal component analysis (PCA), imitation products can be easily detected. In both cheese and ice cream, a differentiation according to the type of raw material (milk fat and vegetable fat) was possible. The loadings plot shows that imitation products were distinguishable by differences in their fatty acid ratios. Furthermore, a differentiation of several types of cheese (Edamer, Gouda, Emmentaler, and Feta) was possible. Quantitative data regarding the composition of the investigated products can also be predicted from the same spectra using partial least squares (PLS) regression. The models obtained for 13 compounds in cheese (R 2 0.75–0.95) and 17 compounds in ice cream (R 2 0.83–0.99) (e.g., fatty acids and esters) were suitable for a screening analysis. NMR spectroscopy was judged as suitable for the routine analysis of dairy products based on milk or on vegetable fat substitutes. PMID:26904597

In vivo observation of tree drought response with low-field NMR and neutron imaging

DOE PAGES

Malone, Michael W.; Yoder, Jacob; Hunter, James F.; ...

2016-05-06

Using a simple low-field NMR system, we monitored water content in a living tree in a greenhouse over 2 months. By continuously running the system, we observed changes in tree water content on a scale of half an hour. The data showed a diurnal change in water content consistent both with previous NMR and biological observations. Neutron imaging experiments show that our NMR signal is primarily due to water being rapidly transported through the plant, and not to other sources of hydrogen, such as water in cytoplasm, or water in cell walls. After accounting for the role of temperature inmore » the observed NMR signal, we demonstrate a change in the diurnal signal behavior due to simulated drought conditions for the tree. Lastly, these results illustrate the utility of our system to perform noninvasive measurements of tree water content outside of a temperature controlled environment.« less

NMR spectroscopy of Group 13 metal ions: biologically relevant aspects.

PubMed

André, J P; Mäcke, H R

2003-12-01

In spite of the fact that Group 13 metal ions (Al(3+), Ga(3+), In(3+) and Tl(+/3+)) show no main biological role, they are NMR-active nuclides which can be used in magnetic resonance spectroscopy of biologically relevant systems. The fact that these metal ions are quadrupolar (with the exception of thallium) means that they are particularly sensitive to ligand type and coordination geometry. The line width of the NMR signals of their complexes shows a strong dependence on the symmetry of coordination, which constitutes an effective tool in the elucidation of structures. Here we report published NMR studies of this family of elements, applied to systems of biological importance. Special emphasis is given to binding studies of these cations to biological molecules, such as proteins, and to chelating agents of radiopharmaceutical interest. The possibility of in vivo NMR studies is also stressed, with extension to (27)Al-based MRI (magnetic resonance imaging) experiments.

In vivo observation of tree drought response with low-field NMR and neutron imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malone, Michael W.; Yoder, Jacob; Hunter, James F.

Using a simple low-field NMR system, we monitored water content in a living tree in a greenhouse over 2 months. By continuously running the system, we observed changes in tree water content on a scale of half an hour. The data showed a diurnal change in water content consistent both with previous NMR and biological observations. Neutron imaging experiments show that our NMR signal is primarily due to water being rapidly transported through the plant, and not to other sources of hydrogen, such as water in cytoplasm, or water in cell walls. After accounting for the role of temperature inmore » the observed NMR signal, we demonstrate a change in the diurnal signal behavior due to simulated drought conditions for the tree. Lastly, these results illustrate the utility of our system to perform noninvasive measurements of tree water content outside of a temperature controlled environment.« less

Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

PubMed

Wang, Cheng; He, Lidong; Li, Da-Wei; Bruschweiler-Li, Lei; Marshall, Alan G; Brüschweiler, Rafael

2017-10-06

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more 1 H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.

Compositional differences among Chinese soy sauce types studied by (13)C NMR spectroscopy coupled with multivariate statistical analysis.

PubMed

Kamal, Ghulam Mustafa; Wang, Xiaohua; Bin Yuan; Wang, Jie; Sun, Peng; Zhang, Xu; Liu, Maili

2016-09-01

Soy sauce a well known seasoning all over the world, especially in Asia, is available in global market in a wide range of types based on its purpose and the processing methods. Its composition varies with respect to the fermentation processes and addition of additives, preservatives and flavor enhancers. A comprehensive (1)H NMR based study regarding the metabonomic variations of soy sauce to differentiate among different types of soy sauce available on the global market has been limited due to the complexity of the mixture. In present study, (13)C NMR spectroscopy coupled with multivariate statistical data analysis like principle component analysis (PCA), and orthogonal partial least square-discriminant analysis (OPLS-DA) was applied to investigate metabonomic variations among different types of soy sauce, namely super light, super dark, red cooking and mushroom soy sauce. The main additives in soy sauce like glutamate, sucrose and glucose were easily distinguished and quantified using (13)C NMR spectroscopy which were otherwise difficult to be assigned and quantified due to serious signal overlaps in (1)H NMR spectra. The significantly higher concentration of sucrose in dark, red cooking and mushroom flavored soy sauce can directly be linked to the addition of caramel in soy sauce. Similarly, significantly higher level of glutamate in super light as compared to super dark and mushroom flavored soy sauce may come from the addition of monosodium glutamate. The study highlights the potentiality of (13)C NMR based metabonomics coupled with multivariate statistical data analysis in differentiating between the types of soy sauce on the basis of level of additives, raw materials and fermentation procedures. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat

PubMed Central

2013-01-01

Background The naked mole rats (NMRs) are small-sized underground rodents with plenty of unusual traits. Their life expectancy can be up to thirty years, more than seven times longer than laboratory rat. Furthermore, they are resistant to both congenital and experimentally induced cancer genesis. These peculiar physiological and pathological characteristics allow them to become a suitable model for cancer and aging research. Results In this paper, we carried out a genome-wide comparative analysis of rat and NMR using the recently published genome sequence of NMR. First, we identified all the rat-NMR orthologous genes and specific genes within each of them. The expanded and contracted numbers of protein families in NMR were also analyzed when compared to rat. Seven cancer-related protein families appeared to be significantly expanded, whereas several receptor families were found to be contracted in NMR. We then chose those rat genes that were inexistent in NMR and adopted KEGG pathway database to investigate the metabolic processes in which their proteins may be involved. These genes were significantly enriched in two rat cancer pathways, "Pathway in cancer" and "Bladder cancer". In the rat "Pathway in cancer", 9 out of 14 paths leading to evading apoptosis appeared to be affected in NMR. In addition, a significant number of other NMR-missing genes enriched in several cancer-related pathways have been known to be related to a variety of cancers, implying that many of them may be also related to tumorigenesis in mammals. Finally, investigation of sequence variations among orthologous proteins between rat and NMR revealed that significant fragment insertions/deletions within important functional domains were present in some NMR proteins, which might lead to expressional and/or functional changes of these genes in different species. Conclusions Overall, this study provides insights into understanding the possible anti-cancer mechanisms of NMR as well as searching for new cancer-related candidate genes. PMID:24565050

Extraction and [superscript 1]H NMR Analysis of Fats from Convenience Foods: A Laboratory Experiment for Organic Chemistry

ERIC Educational Resources Information Center

Hartel, Aaron M.; Moore, Amy C.

2014-01-01

The extraction and analysis of fats from convenience foods (crackers, cookies, chips, candies) has been developed as an experiment for a second-year undergraduate organic chemistry laboratory course. Students gravimetrically determine the fat content per serving and then perform a [superscript 1]H NMR analysis of the recovered fat to determine the…

NMR-based conformational analysis of perezone and analogues.

PubMed

Zepeda, L Gerardo; Burgueño-Tapia, Eleuterio; Pérez-Hernández, Nury; Cuevas, Gabriel; Joseph-Nathan, Pedro

2013-04-01

Complete assignment of the (1)H NMR chemical shift and coupling constant values of perezone (1), O-methylperezone (2) and 6-hydroxyperezone (3) was carried out by total-line-shape-fitting calculations using the PERCH iterative spectra analysis software (PERCH Solutions Ltd., Kuopio, Finland). The resulting simulated spectra for the three compounds showed strong similarity to their corresponding experimental spectra. Particularly, all vicinal, allylic and homoallylic coupling constant values for the side chain of the three compounds were very similar, thus revealing that the conformation of these three molecules in solution is indeed almost identical. This fact is in agreement with extended side chain conformations over folded chain conformations because 1, 2 and 3 undergo completely different intramolecular cycloaddition reactions. In addition, results of double pulsed field gradient spin echo NOESY 1D experiments performed on perezone (1) were unable to provide evidence for folded conformers. Copyright © 2013 John Wiley & Sons, Ltd.

Highly Accurate Quantitative Analysis Of Enantiomeric Mixtures from Spatially Frequency Encoded 1H NMR Spectra.

PubMed

Plainchont, Bertrand; Pitoux, Daisy; Cyrille, Mathieu; Giraud, Nicolas

2018-02-06

We propose an original concept to measure accurately enantiomeric excesses on proton NMR spectra, which combines high-resolution techniques based on a spatial encoding of the sample, with the use of optically active weakly orienting solvents. We show that it is possible to simulate accurately dipolar edited spectra of enantiomers dissolved in a chiral liquid crystalline phase, and to use these simulations to calibrate integrations that can be measured on experimental data, in order to perform a quantitative chiral analysis. This approach is demonstrated on a chemical intermediate for which optical purity is an essential criterion. We find that there is a very good correlation between the experimental and calculated integration ratios extracted from G-SERF spectra, which paves the way to a general method of determination of enantiomeric excesses based on the observation of 1 H nuclei.

Structural analysis and biomedical applications of dextran produced by a new isolate Pediococcus pentosaceus screened from biodiversity hot spot Assam.

PubMed

Patel, Seema; Kasoju, Naresh; Bora, Utpal; Goyal, Arun

2010-09-01

Dextran produced by a natural isolate of Pediococcus pentosaceus, screened from Assam, in the Northeastern region of India, was estimated, purified, structure characterised and functionality analysed. The dextran concentration in the cell free supernatant of the isolate P. pentosaceus was 10.2mg/ml. FT-IR analysis revealed the hydroxyl and carboxyl functional groups present in the dextran. (1)H NMR and (13)C NMR spectral data revealed that the dextran has a linear backbone of alpha-(1-->6) linked D-glucose residues. The decrease in viscosity of dextran solution with the increase in shear rate, threw light on its typical non-Newtonian pseudoplastic behaviour. The cytotoxicity tests on human cervical cancer (HeLa) cell line was studied which showed the dextran is non-toxic and biocompatible, rendering it safe for drug delivery, tissue engineering and various other biomedical applications. (c) 2010 Elsevier Ltd. All rights reserved.

Untargeted NMR Spectroscopic Analysis of the Metabolic Variety of New Apple Cultivars

PubMed Central

Eisenmann, Philipp; Ehlers, Mona; Weinert, Christoph H.; Tzvetkova, Pavleta; Silber, Mara; Rist, Manuela J.; Luy, Burkhard; Muhle-Goll, Claudia

2016-01-01

Metabolome analyses by NMR spectroscopy can be used in quality control by generating unique fingerprints of different species. Hundreds of components and their variation between different samples can be analyzed in a few minutes/hours with high accuracy and low cost of sample preparation. Here, apple peel and pulp extracts of a variety of apple cultivars were studied to assess their suitability to discriminate between the different varieties. The cultivars comprised mainly newly bred varieties or ones that were brought onto the market in recent years. Multivariate analyses of peel and pulp extracts were able to unambiguously identify all cultivars, with peel extracts showing a higher discriminative power. The latter was increased if the highly concentrated sugar metabolites were omitted from the analysis. Whereas sugar concentrations lay within a narrow range, polyphenols, discussed as potential health promoting substances, and acids varied remarkably between the cultivars. PMID:27657148

Untargeted NMR Spectroscopic Analysis of the Metabolic Variety of New Apple Cultivars.

PubMed

Eisenmann, Philipp; Ehlers, Mona; Weinert, Christoph H; Tzvetkova, Pavleta; Silber, Mara; Rist, Manuela J; Luy, Burkhard; Muhle-Goll, Claudia

2016-09-19

Metabolome analyses by NMR spectroscopy can be used in quality control by generating unique fingerprints of different species. Hundreds of components and their variation between different samples can be analyzed in a few minutes/hours with high accuracy and low cost of sample preparation. Here, apple peel and pulp extracts of a variety of apple cultivars were studied to assess their suitability to discriminate between the different varieties. The cultivars comprised mainly newly bred varieties or ones that were brought onto the market in recent years. Multivariate analyses of peel and pulp extracts were able to unambiguously identify all cultivars, with peel extracts showing a higher discriminative power. The latter was increased if the highly concentrated sugar metabolites were omitted from the analysis. Whereas sugar concentrations lay within a narrow range, polyphenols, discussed as potential health promoting substances, and acids varied remarkably between the cultivars.

Molecular structure, vibrational spectra and DFT molecular orbital calculations (TD-DFT and NMR) of the antiproliferative drug Methotrexate

NASA Astrophysics Data System (ADS)

Ayyappan, S.; Sundaraganesan, N.; Aroulmoji, V.; Murano, E.; Sebastian, S.

2010-09-01

The FT-IR and FT-Raman spectral studies of the Methotrexate (MTX) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of MTX have been investigated with the help of B3LYP density functional theory (DFT) using 6-31G(d) as basis set. Detailed analysis of the vibrational spectra has been made with the aid of theoretically predicted vibrational frequencies. The vibrational analysis confirms the differently acting ring modes, steric repulsion, conjugation and back-donation. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complement with the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Good correlations between the experimental 1H and 13C NMR chemical shifts in DMSO solution and calculated GIAO shielding tensors were found.

Time-Domain Nuclear Magnetic Resonance Investigation of Water Dynamics in Different Ginger Cultivars.

PubMed

Huang, Chongyang; Zhou, Qi; Gao, Shan; Bao, Qingjia; Chen, Fang; Liu, Chaoyang

2016-01-20

Different ginger cultivars may contain different nutritional and medicinal values. In this study, a time-domain nuclear magnetic resonance method was employed to study water dynamics in different ginger cultivars. Significant differences in transverse relaxation time T2 values assigned to the distribution of water in different parts of the plant were observed between Henan ginger and four other ginger cultivars. Ion concentration and metabolic analysis showed similar differences in Mn ion concentrations and organic solutes among the different ginger cultivars, respectively. On the basis of Pearson's correlation analysis, many organic solutes and 6-gingerol, the main active substance of ginger, exhibited significant correlations with water distribution as determined by NMR T2 relaxation, suggesting that the organic solute differences may impact water distribution. Our work demonstrates that low-field NMR relaxometry provides useful information about water dynamics in different ginger cultivars as affected by the presence of different organic solutes.

Targeted Molecular Imaging of Cancer Cells Using MS2-Based 129 Xe NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeong, Keunhong; Netirojjanakul, Chawita; Munch, Henrik K.

Targeted, selective, and highly sensitive 129Xe NMR nanoscale biosensors have been synthesized using a spherical MS2 viral capsid, Cryptophane A molecules, and DNA aptamers. The biosensors showed strong binding specificity toward targeted lymphoma cells (Ramos line). Hyperpolarized 129Xe NMR signal contrast and hyper-CEST 129Xe MRI image contrast indicated its promise as highly sensitive hyperpolarized 129Xe NMR nanoscale biosensor for future applications in cancer detection in vivo.

Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

PubMed

Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

2017-06-28

Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.

PubMed

Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

2013-04-01

We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. Copyright © 2013 Wiley Periodicals, Inc.

Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR) Methodology

PubMed Central

Wen, Jia-Long; Sun, Shao-Long; Xue, Bai-Liang; Sun, Run-Cang

2013-01-01

The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA), nitrobenzene oxidation (NBO), and derivatization followed by reductive cleavage (DFRC). Recent advances in nuclear magnetic resonance (NMR) technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ), as well as their applications are reviewed. PMID:28809313

Structural and Nutritional Properties of Pasta from Triticum monococcum and Triticum durum Species. A Combined ¹H NMR, MRI, and Digestibility Study.

PubMed

Pasini, Gabriella; Greco, Fulvia; Cremonini, Mauro A; Brandolini, Andrea; Consonni, Roberto; Gussoni, Maristella

2015-05-27

The aim of the present study was to characterize the structure of two different types of pasta, namely Triticum turgidum ssp. durum (cv. Saragolla) and Triticum monococcum ssp. monococcum (cv. Monlis), under different processing conditions. MRI analysis and NMR spectroscopy (i.e., T1 and T2 NMR relaxation times and diffusion parameters) were conducted on pasta, and (1)H NMR spectroscopic analysis of the chemical compounds released by pasta samples during the cooking process was performed. In addition, starch digestibility (enzimatically determined) was also investigated. The NMR results indicated that Saragolla pasta has a more compact structure, ascribed to pasta network and in particular to different technological gluten properties, that mainly determine the lower ability of Monlis pasta in binding water. These results correlate well with the lower rate of starch hydrolysis measured for Monlis pasta compared to Saragolla when both are dried at high temperature.

Study on 1H-NMR fingerprinting of Rhodiolae Crenulatae Radix et Rhizoma.

PubMed

Wen, Shi-yuan; Zhou, Jiang-tao; Chen, Yan-yan; Ding, Li-qin; Jiang, Miao-miao

2015-07-01

Nuclear magnetic resonance (1H-NMR) fingerprint of Rhodiola rosea medicinal materials was established, and used to distinguish the quality of raw materials from different sources. Pulse sequence for water peak inhibition was employed to acquire 1H-NMR spectra with the temperature at 298 K and spectrometer frequency of 400.13 MHz. Through subsection integral method, the obtained NMR data was subjected to similarity analysis and principal component analysis (PCA). 10 batches raw materials of Rhodiola rosea from different origins were successfully distinguished by PCA. The statistical results indicated that rhodiola glucoside, butyl alcohol, maleic acid and alanine were the main differential ingredients. This method provides an auxiliary method of Chinese quality approach to evaluate the quality of Rhodiola crenulata without using natural reference substances.

Biological Investigations of Adaptive Networks: Neuronal Control of Conditioned Responses

DTIC Science & Technology

1989-07-01

The program also controls A/D sampling of voltage trace from NMR transducer and disk files for NMR, neural spikes, and synchronization. * HSAD . Basic...format which ANALYZE (by John Desmond) can read. e FIG.HIRES Reads C-64 HSAD files and EVENT NMR files and generates oscilloscope-like figures showing

Structure and magnetic properties of SiO{sub 2}/PCL novel sol–gel organic–inorganic hybrid materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Catauro, Michelina, E-mail: michelina.catauro@unina2.it; Bollino, Flavia; Cristina Mozzati, Maria

2013-07-15

Organic–inorganic nanocomposite materials have been synthesized via sol–gel. They consist of an inorganic SiO{sub 2} matrix, in which different percentages of poly(ε-caprolactone) (PCL) have been incorporated. The formation of H-bonds among the carbonyl groups of the polymer chains and Si–OH group of the inorganic matrix has been proved by means of Fourier transform infrared spectroscopy (FT-IR) analysis and has been confirmed by solid-state nuclear magnetic resonance (NMR). X-Ray diffraction (XRD) analysis highlighted the amorphous nature of the synthesized materials. Scanning electron microscope (SEM) micrograph and atomic force microscope (AFM) topography showed their homogeneous morphology and nanostructure nature. Considering the opportunitymore » to synthesize these hybrid materials under microgravity conditions by means of magnetic levitation, superconducting quantum interference device (SQUID) magnetometry has been used to quantify their magnetic susceptibility. This measure has shown that the SiO{sub 2}/PCL hybrid materials are diamagnetic and that their diamagnetic susceptibility is independent of temperature and increases with the PCL amount. - Graphical abstract: Characterization and magnetic properties of SiO{sub 2}/PCL organic–inorganic hybrid materials synthesized via sol–gel. FT-IR, Fourier transform infrared spectroscopy; solid-state NMR: solid-state nuclear magnetic resonance; SQUID: superconducting quantum interference device. - Highlights: • Sol–gel synthesis of SiO{sub 2}/PCL amorphous class I organic–inorganic hybrid materials. • FT-IR and NMR analyses show the hydrogen bonds formation between SiO{sub 2} and PCL. • AFM and SEM analyses confirm that the SiO{sub 2}/PCL are homogenous hybrid materials. • The SQUID measures show that the simples are diamagnetic. • Diamagnetic susceptibility of SiO{sub 2}/PCL materials increases with the PCL amount.« less

Solid state structural investigations of the bis(chalcone) compound with single crystal X-ray crystallography, DFT, gamma-ray spectroscopy and chemical spectroscopy methods

NASA Astrophysics Data System (ADS)

Yakalı, Gül; Biçer, Abdullah; Eke, Canel; Cin, Günseli Turgut

2018-04-01

A bis(chalcone), (2E,6E)-2,6-bis((E)-3phenylallidene)cyclohexanone, was characterized by 1H NMR, 13C NMR, FTIR, UV-Vis spectroscopy, gamma-ray spectroscopy and single crystal X- ray structural analysis. The optimized molecular structure of the compound is calculated using DFT/B3LYP with 6-31G (d,p) level. The calculated geometrical parameters are in good agreement with the experimental data obtained from our reported X-ray structure. The powder and single crystal compounds were gama-irradiated using clinical electron linear accelerator and 60Co gamma-ray source, respectively. Spectral studies (1H NMR, 13C NMR, FTIR and UV-Vis) of powder chalcone compound were also investigated before and after irradiation. Depending on the irradiation notable changes were observed in spectral features powder sample. Single crystal X-ray diffraction investigation shows that both unirradiated and irradiated single crystal samples crystallizes in a orthorhombic crystal system in the centrosymmetric space group Pbcn and exhibits an C-H..O intramolecular and intermolecular hydrogen bonds. The crystal packing is stabilised by strong intermolecular bifurcate C-H..O hydrogen bonds and π…π stacking interactions. The asymmetric unit of the title compound contains one-half of a molecule. The other half of the molecule is generated with (1-x,y,-3/2-z) symmetry operator. The molecule is almost planar due to having π conjugated system of chalcones. However, irradiated single crystal compound showed significant changes lattice parameters, crystal volume and density. According to results of gamma-ray spectroscopy, radioactive elements of powder compound which are 123Sb(n,g),124Sb,57Fe(g,p),56Mn, 55Mn(g,n), and 54Mn were determined using photoactivation analysis. However, the most intensive gamma-ray energy signals are 124Sb.

Metabonomics by proton nuclear magnetic resonance in human pleural effusions: A route to discriminate between benign and malignant pleural effusions and to target small molecules as potential cancer biomarkers.

PubMed

Zennaro, Lucio; Vanzani, Paola; Nicolè, Lorenzo; Cappellesso, Rocco; Fassina, Ambrogio

2017-05-01

Cytopathology is a noninvasive and cost-effective method for detecting cancer cells in pleural effusions (PEs), although in many cases, the diagnostic performance is hindered by the paucity of significant cells or the lack of clear morphological criteria. This study presents the results of an omics approach to improving the diagnostic performance of PE cytology. Metabolic profiling with proton nuclear magnetic resonance ( 1 H-NMR) was performed for 92 PEs (44 malignant cases of 8 different cancers and 48 benign cases of 7 nonneoplastic conditions). Light's criteria were used to further classify PEs as transudates or exudates, and 1 H-NMR spectroscopy was used to differentiate malignant pleural effusions (mPEs) from benign pleural effusions (bPEs). 1 H-NMR metabolic analysis showed clearly different spectra for mPEs and bPEs in the regions of the signals due to lipids, branched amino acids, and lactate, which were increased in mPEs. Transudates and exudates in bPEs were differentiated as well on the basis of the 1 H-NMR signals from lipids and lipoproteins, which were increased in exudates. Subject to validation in further larger studies, 1 H-NMR metabonomics could be an effective and reliable ancillary tool for PE investigations and diagnoses. Cancer Cytopathol 2017;125:341-348. © 2017 American Cancer Society. © 2017 American Cancer Society.

NMR crystallography to probe the breathing effect of the MIL-53(Al) metal-organic framework using solid-state NMR measurements of 13C-27Al distances.

PubMed

Giovine, Raynald; Volkringer, Christophe; Trébosc, Julien; Amoureux, Jean Paul; Loiseau, Thierry; Lafon, Olivier; Pourpoint, Frédérique

2017-03-01

The metal-organic framework MIL-53(Al) (aluminium terephthalate) exhibits a structural transition between two porous structures with large pore (lp) or narrow pore (np) configurations. This transition, called the breathing effect, is observed upon changes in temperature or external pressure, as well as with the adsorption of guest molecules, such as H 2 O, within the pores. We show here how these different pore openings can be detected by observing the dephasing of 13 C magnetization under 13 C- 27 Al dipolar couplings using Rotational-Echo Saturation-Pulse Double-Resonance (RESPDOR) solid-state NMR experiments with Simultaneous Frequency and Amplitude Modulation (SFAM) recoupling. These double-resonance NMR experiments between 13 C and 27 Al nuclei, which have close Larmor frequencies, are feasible thanks to the use of a frequency splitter. The experimental SFAM-RESPDOR signal fractions agree well with those simulated from the MIL-53(Al)-lp and -np crystal structures obtained from powder X-ray diffraction analysis. Hence, these 13 C- 27 Al solid-state NMR experiments validate these structures and confirm their rigidity. A similar agreement is reported for the framework ligands in the as-synthesized (as) MIL-53(Al), in which the pores contain free ligands. Furthermore, in this case, 13 C-{ 27 Al} SFAM-RESPDOR experiments allow an estimation of the average distance between the free ligands and the 27 Al nuclei of the framework.

A Solid-State NMR Experiment: Analysis of Local Structural Environments in Phosphate Glasses

ERIC Educational Resources Information Center

Anderson, Stanley E.; Saiki, David; Eckert, Hellmut; Meise-Gresch, Karin

2004-01-01

An experiment that can be used to directly study the local chemical environments of phosphorus in solid amorphous materials is demonstrated. The experiment aims at familiarizing the students of chemistry with the principles of solid-state NMR, by having them synthesize a simple phosphate glass, and making them observe the (super 31)P NMR spectrum,…

Characterization of a polyhydroxyalkanoate obtained from pineapple peel waste using Ralsthonia eutropha.

PubMed

Vega-Castro, Oscar; Contreras-Calderon, Jose; León, Emilson; Segura, Almir; Arias, Mario; Pérez, León; Sobral, Paulo J A

2016-08-10

Agro-industrial waste can be the production source of biopolymers such as polyhydroxyalkanoates. The aim of this study was to produce and characterize Polyhydroxyalkanoates produced from pineapple peel waste fermentation processes. The methodology includes different pineapple peel waste fermentation conditions. The produced biopolymer was characterized using FTIR, GC-MS and NMR. The best fermentation condition for biopolymer production was obtained using pH 9, Carbon/Nitrogen 11, carbon/phosphorus 6 and fermentation time of 60h. FTIR analyzes showed PHB group characteristics, such as OH, CH and CO. In addition, GC-MS showed two monomers with 4 and 8 carbons, referred to PHB and PHBHV. H(1) NMR analysis showed 0.88-0.97 and 5.27ppm signals, corresponding to CH3 and CH, respectively. In conclusion, polyhydroxyalkanoate production from pineapple peels waste is an alternative for the treatment of waste generated in Colombia's fruit industry. Copyright © 2016 Elsevier B.V. All rights reserved.

Unconventional Tight Reservoirs Characterization with Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Santiago, C. J. S.; Solatpour, R.; Kantzas, A.

2017-12-01

The increase in tight reservoir exploitation projects causes producing many papers each year on new, modern, and modified methods and techniques on estimating characteristics of these reservoirs. The most ambiguous of all basic reservoir property estimations deals with permeability. One of the logging methods that is advertised to predict permeability but is always met by skepticism is Nuclear Magnetic Resonance (NMR). The ability of NMR to differentiate between bound and movable fluids and providing porosity increased the capability of NMR as a permeability prediction technique. This leads to a multitude of publications and the motivation of a review paper on this subject by Babadagli et al. (2002). The first part of this presentation is dedicated to an extensive review of the existing correlation models for NMR based estimates of tight reservoir permeability to update this topic. On the second part, the collected literature information is used to analyze new experimental data. The data are collected from tight reservoirs from Canada, the Middle East, and China. A case study is created to apply NMR measurement in the prediction of reservoir characterization parameters such as porosity, permeability, cut-offs, irreducible saturations etc. Moreover, permeability correlations are utilized to predict permeability. NMR experiments were conducted on water saturated cores. NMR T2 relaxation times were measured. NMR porosity, the geometric mean relaxation time (T2gm), Irreducible Bulk Volume (BVI), and Movable Bulk Volume (BVM) were calculated. The correlation coefficients were computed based on multiple regression analysis. Results are cross plots of NMR permeability versus the independently measured Klinkenberg corrected permeability. More complicated equations are discussed. Error analysis of models is presented and compared. This presentation is beneficial in understanding existing tight reservoir permeability models. The results can be used as a guide for choosing the best permeability estimation model for tight reservoirs data.

Beyond Fourier.

PubMed

Hoch, Jeffrey C

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development. Copyright © 2017 Elsevier Inc. All rights reserved.

Evidence for altered metabolic pathways during environmental stress: (1)H-NMR spectroscopy based metabolomics and clinical studies on subjects of sea-voyage and Antarctic-stay.

PubMed

Yadav, Anand Prakash; Chaturvedi, Shubhra; Mishra, Kamla Prasad; Pal, Sunil; Ganju, Lilly; Singh, Shashi Bala

2014-08-01

The Antarctic context is an analogue of space travel, with close similarity in ambience of extreme climate, isolation, constrained living spaces, disrupted sleep cycles, and environmental stress. The present study examined the impact of the harsh habitat of Antarctica on human physiology and its metabolic pathways, by analyzing human serum samples, using (1)H-NMR spectroscopy for identification of metabolites; and quantifying other physiological and clinical parameters for correlation between expression data and metabolite data. Sera from seven adult males (of median age 36years) who participated in this study, from the 28th Indian Expeditionary group to the Antarctica station Maitri, were collected in chronological sequence. These included: i) baseline control; ii) during ship journey; iii) at Antarctica, in the months of March, May, August and November; to enable study of temporal evolution of monitored physiological states. 29 metabolites in serum were identified from the 400MHz (1)H-NMR spectra. Out of these, 19 metabolites showed significant variations in levels, during the ship journey and the stay at Maitri, compared to the base-line levels. Further biochemical analysis also supported these results, indicating that the ship journey, and the long-term Antarctic exposure, affected kidney and liver functioning. Our metabolite data highlights for the first time the effect of environmental stress on the patho-physiology of the human system. Multivariate analysis tools were employed for this metabonomics study, using (1)H-NMR spectroscopy. Copyright © 2014. Published by Elsevier Inc.

High-resolution NMR study of light and heavy crude oils: “structure-property” analysis

NASA Astrophysics Data System (ADS)

Rakhmatullin, I.; Efimov, S.; Varfolomeev, M.; Klochkov, V.

2018-05-01

Measurements of three light and one heavy crude oil samples were carried out by high-resolution nuclear magnetic resonance (NMR) spectroscopy methods. Quantitative fractions of aromatic molecules and functional groups constituting oil hydrocarbons were determined, and comparative analysis of the oil samples of different viscosity and origin was done.

Intercalation complex of proflavine with DNA: Structure and dynamics by solid-state NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Pei; Juang, Chilong; Harbison, G.S.

1990-07-06

The structure of the complex formed between the intercalating agent proflavine and fibrous native DNA was studied by one- and two-dimensional high-resolution solid-state nuclear magnetic resonance (NMR). Carbon-13-labeled proflavine was used to show that the drug is stacked with the aromatic ring plane perpendicular to the fiber axis and that it is essentially immobile. Natural abundance carbon-13 NMR of the DNA itself shows that proflavine binding does not change the puckering of the deoxyribose ring. However, phosphorus-31 NMR spectra show profound changes in the orientation of the phosphodiester grouping on proflavine binding, with some of the phosphodiesters tilting almost parallelmore » to the helix axis, and a second set almost perpendicular. The first group to the phosphodiesters probably spans the intercalation sites, whereas the tilting of the second set likely compensates for the unwinding of the DNA by the intercalator.« less

NMR in the SPINE Structural Proteomics project.

PubMed

Ab, E; Atkinson, A R; Banci, L; Bertini, I; Ciofi-Baffoni, S; Brunner, K; Diercks, T; Dötsch, V; Engelke, F; Folkers, G E; Griesinger, C; Gronwald, W; Günther, U; Habeck, M; de Jong, R N; Kalbitzer, H R; Kieffer, B; Leeflang, B R; Loss, S; Luchinat, C; Marquardsen, T; Moskau, D; Neidig, K P; Nilges, M; Piccioli, M; Pierattelli, R; Rieping, W; Schippmann, T; Schwalbe, H; Travé, G; Trenner, J; Wöhnert, J; Zweckstetter, M; Kaptein, R

2006-10-01

This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

Investigation of Local Structures in Cation-ordered Microwave Dielectric A Solid-state NMR and First Principle Calculation Study

NASA Astrophysics Data System (ADS)

Kalfarisi, Rony G.

Solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy has proven to be a powerful method to probe the local structure and dynamics of a system. In powdered solids, the nuclear spins experience various anisotropic interactions which depend on the molecular orientation. These anisotropic interactions make ssNMR very useful as they give a specific appearance to the resonance lines of the spectra. The position and shape of these resonance lines can be related to local structure and dynamics of the system under study. My research interest has focused around studying local structures and dynamics of quadrupolar nuclei in materials using ssNMR spectroscopy. 7Li and 93Nb ssNMR magic angle spinning (MAS) spectra, acquired at 17.6 and 7.06 T, have been used to evaluate the structural and dynamical properties of cation-ordered microwave dielectric materials. Microwave dielectric materials are essential in the application of wireless telecommunication, biomedical engineering, and other scientific and industrial implementations that use radio and microwave signals. The study of the local environment with respect to average structure, such as X-ray diffraction study, is essential for the better understanding of the correlations between structures and properties of these materials. The investigation for short and medium range can be performed with the use of ssNMR techniques. Even though XRD results show cationic ordering at the B-site (third coordination sphere), NMR spectra show a presence of disorder materials. This was indicated by the observation of a distribution in NMR parameters derived from experimental . {93}Nb NMR spectraand supported by theoretical calculations.

The transcription repressor NmrA is subject to proteolysis by three Aspergillus nidulans proteases

PubMed Central

Zhao, Xiao; Hume, Samantha L; Johnson, Christopher; Thompson, Paul; Huang, Junyong; Gray, Joe; Lamb, Heather K; Hawkins, Alastair R

2010-01-01

The role of specific cleavage of transcription repressor proteins by proteases and how this may be related to the emerging theme of dinucleotides as cellular signaling molecules is poorly characterized. The transcription repressor NmrA of Aspergillus nidulans discriminates between oxidized and reduced dinucleotides, however, dinucleotide binding has no effect on its interaction with the zinc finger in the transcription activator AreA. Protease activity in A. nidulans was assayed using NmrA as the substrate, and was absent in mycelium grown under nitrogen sufficient conditions but abundant in mycelium starved of nitrogen. One of the proteases was purified and identified as the protein Q5BAR4 encoded by the gene AN2366.2. Fluorescence confocal microscopy showed that the nuclear levels of NmrA were reduced approximately 38% when mycelium was grown on nitrate compared to ammonium and absent when starved of nitrogen. Proteolysis of NmrA occurred in an ordered manner by preferential digestion within a C-terminal surface exposed loop and subsequent digestion at other sites. NmrA digested at the C-terminal site was unable to bind to the AreA zinc finger. These data reveal a potential new layer of control of nitrogen metabolite repression by the ordered proteolytic cleavage of NmrA. NmrA digested at the C-terminal site retained the ability to bind NAD+ and showed a resistance to further digestion that was enhanced by the presence of NAD+. This is the first time that an effect of dinucleotide binding to NmrA has been demonstrated. PMID:20506376

Molecular Characterization of Cryoconite Organic Matter from the Athabasca Glacier, Canadian Rocky Mountains

NASA Astrophysics Data System (ADS)

Xu, Y.; Simpson, M. J.; Eyles, N.; Simpson, A.; Baer, A. J.

2009-05-01

Cryoconite is a dark-colored, dust-like material found on the surfaces of glaciers. Cryoconite holes, which are produced by accelerated ice melt due to more solar radiation absorption by cryoconite than bare ice, act as habitats for microbial life and biologically mediated chemical reactions on otherwise relatively inert glacier surfaces. Cryoconite holes may behave as bacterial shelters during "Snowball Earth" events postulated for the Neoproterozoic Earth. In this study organic matter (OM) biomarkers and a host of one- and two-dimensional NMR techniques were used to characterize cryoconite organic matter (COM) collected from the Athabasca Glacier in the Canadian Rocky Mountains. Solvent extracts contain large quantities of fatty acids, n-alkanols, n- alkanes, wax esters and sterols. A large contribution of C23 and C25 relative to C29 and C31 n-alkanes ([C23/(C23+C29)] = 0.51) suggests that allochthonous COM is derived mainly from lower order plants such as mosses and lichens. This is confirmed by the absence of lignin-derived phenols, a biomarker of terrestrial vascular plants, after copper (II) oxidation in extracts and NMR analyses of COM. Solution-state 1H NMR reveals prominent peptide/protein structures which are characteristic of microbial inputs, while solid-state 13C CP/MAS NMR analysis shows a very high alkyl/O-alkyl ratio (2.16), suggesting that COM is unique compared to organic matter found in nearby soils which have alkyl/O-alkyl ratio of ~0.39. Our NMR results suggest that COM is dominated by microbial-derived compounds, which is also confirmed by phospholipid fatty acid results (6,950µg/gOC) which show significant microbial contributions to COM primarily from bacteria and minor microeukaryotes. Both biomarker and NMR data suggest that COM likely supports active microbial communities on the Athabasca Glacier. Given that such material is incorporated within the glacier in the accumulation zone or flushed by meltwaters into subglacial environments, reworked COM may provide nutrient sources for active microbial communities found within and under glaciers.

The relationship between crystal structure and methyl and t-butyl group dynamics in van der Waals organic solids

NASA Astrophysics Data System (ADS)

Beckmann, Peter A.; Paty, Carol; Allocco, Elizabeth; Herd, Maria; Kuranz, Carolyn; Rheingold, Arnold L.

2004-03-01

We report x-ray diffractometry in a single crystal of 2-t-butyl-4-methylphenol (TMP) and low-frequency solid state nuclear magnetic resonance (NMR) proton relaxometry in a polycrystalline sample of TMP. The x-ray data show TMP to have a monoclinic, P21/c, structure with eight molecules per unit cell and two crystallographically inequivalent t-butyl group (C(CH3)3) sites. The proton spin-lattice relaxation rates were measured between 90 and 310 K at NMR frequencies of 8.50, 22.5, and 53.0 MHz. The relaxometry data is fitted with two models characterizing the dynamics of the t-butyl groups and their constituent methyl groups, both of which are consistent with the determined x-ray structure. In addition to presenting results for TMP, we review previously reported x-ray diffractometry and low-frequency NMR relaxometry in two other van der Waals solids which have a simpler structure. In both cases, a unique model for the reorientational dynamics was found. Finally, we review a similar previously reported analysis in a van der Waals solid with a very complex structure in which case fitting the NMR relaxometry requires very many parameters and serves mainly as a flag for a careful x-ray diffraction study.

NMR Chemical Exchange as a Probe for Ligand-Binding Kinetics in a Theophylline-Binding RNA Aptamer

PubMed Central

Latham, Michael P.; Zimmermann, Grant R.; Pardi, Arthur

2009-01-01

The apparent on- and off-rate constants for theophylline binding to its RNA aptamer in the absence of Mg2+ were determined here by 2D 1H-1H NMR ZZ-exchange spectroscopy. Analysis of the build-up rate of the exchange cross peaks for several base-paired imino protons in the RNA yielded an apparent kon of 600 M-1 s-1. This small apparent kon results from the free RNA existing as a dynamic equilibrium of inactive states rapidly interconverting with a low population of active species. The data here indicate that the RNA aptamer employs a conformational selection mechanism for binding theophylline in the absence of Mg2+. The kinetic data here also explain a very unusual property of this RNA-theophylline system, slow exchange on the NMR chemical shift timescale for a weak-binding complex. To our knowledge, it is unprecedented to have such a weak binding complex (Kd ≈ 3.0 mM at 15 °C) show slow exchange on the NMR chemical shift timescale, but the results clearly demonstrate that slow exchange and weak binding are readily rationalized by a small kon. Comparisons with other ligand-receptor interactions are presented. PMID:19317486

Evidence of a DHA Signature in the Lipidome and Metabolome of Human Hepatocytes.

PubMed

Ghini, Veronica; Di Nunzio, Mattia; Tenori, Leonardo; Valli, Veronica; Danesi, Francesca; Capozzi, Francesco; Luchinat, Claudio; Bordoni, Alessandra

2017-02-08

Cell supplementation with bioactive molecules often causes a perturbation in the whole intracellular environment. Omics techniques can be applied for the assessment of this perturbation. In this study, the overall effect of docosahexaenoic acid (DHA) supplementation on cultured human hepatocyte lipidome and metabolome has been investigated using nuclear magnetic resonance (NMR) in combination with traditional techniques. The effect of two additional bioactives sharing with DHA the lipid-lowering effect-propionic acid (PRO) and protocatechuic acid (PCA)-has also been evaluated in the context of possible synergism. NMR analysis of the cell lipid extracts showed that DHA supplementation, alone or in combination with PCA or PRO, strongly altered the cell lipid profile. The perfect discrimination between cells receiving DHA (alone or in combination) and the other cells reinforced the idea of a global rearrangement of the lipid environment induced by DHA. Notably, gas chromatography and fluorimetric analyses confirmed the strong discrimination obtained by NMR. The DHA signature was evidenced not only in the cell lipidome, but also in the metabolome. Results reported herein indicate that NMR, combined with other techniques, represents a fundamental approach to studying the effect of bioactive supplementation, particularly in the case of molecules with a broad spectrum of mechanisms of action.

Physicochemical characterization and structural evaluation of a specific 2:1 cocrystal of naproxen-nicotinamide.

PubMed

Ando, Shigeru; Kikuchi, Junko; Fujimura, Yuko; Ida, Yasuo; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2012-09-01

Physicochemical characterization and structural evaluation of a 2:1 naproxen-nicotinamide cocrystal were performed. The 2:1 cocrystal showed rapid naproxen dissolution and less water vapor adsorption, indicating better pharmaceutical properties of naproxen. The unique 2:1 cocrystal formation was evaluated by solid-state nuclear magnetic resonance (NMR). The assignments of all H and (13) C peaks for naproxen and the cocrystal were performed using dipolar-insensitive nuclei enhanced by polarization transfer and (1) H-(13) C cross-polarization (CP)-heteronuclear correlation (HETCOR) NMR measurements. The (13) C chemical shift revealed that two naproxen molecules and one nicotinamide molecule existed in the asymmetric unit of the cocrystal. The (1) H chemical shifts indicated that the carboxylic group of the naproxen in the cocrystal was nonionized, and the CH-π interaction between naproxens was very strong. From the (1) H-(13) C CP-HETCOR NMR spectrum with contact time of 5 ms, two different synthons, carboxylic acid-amide and carboxylic acid-pyridine ring, were found between naproxen and nicotinamide. Single-crystal X-ray analysis, which supported the solid-state NMR results, clarified the geometry and intermolecular interactions in more detail. The structure is unique among pharmaceutical cocrystals because each carboxyl group of the two naproxens formed different intermolecular synthons. Copyright © 2012 Wiley Periodicals, Inc.

High-Resolution Magic-Angle-Spinning NMR and Magnetic Resonance Imaging Spectroscopies Distinguish Metabolome and Structural Properties of Maize Seeds from Plants Treated with Different Fertilizers and Arbuscular mycorrhizal fungi.

PubMed

Mazzei, Pierluigi; Cozzolino, Vincenza; Piccolo, Alessandro

2018-03-21

Both high-resolution magic-angle-spinning (HRMAS) and magnetic resonance imaging (MRI) NMR spectroscopies were applied here to identify the changes of metabolome, morphology, and structural properties induced in seeds (caryopses) of maize plants grown at field level under either mineral or compost fertilization in combination with the inoculation by arbuscular mycorrhizal fungi (AMF). The metabolome of intact caryopses was examined by HRMAS-NMR, while the morphological aspects, endosperm properties and seed water distribution were investigated by MRI. Principal component analysis (PCA) was applied to evaluate 1 H CPMG (Carr-Purcel-Meiboom-Gill) HRMAS spectra as well as several MRI-derived parameters ( T 1 , T 2 , and self-diffusion coefficients) of intact maize caryopses. PCA score-plots from spectral results indicated that both seeds metabolome and structural properties depended on the specific field treatment undergone by maize plants. Our findings show that a combination of multivariate statistical analyses with advanced and nondestructive NMR techniques, such as HRMAS and MRI, enables the evaluation of the effects induced on maize caryopses by different fertilization and management practices at field level. The spectroscopic approach adopted here may become useful for the objective appraisal of the quality of seeds produced under a sustainable agriculture.

¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

PubMed

Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

2016-04-15

Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Acid-base equilibrium in aqueous solutions of 1,3-dimethylbarbituric acid as studied by 13C NMR spectroscopy

NASA Astrophysics Data System (ADS)

Gryff-Keller, A.; Kraska-Dziadecka, A.

2011-12-01

13C NMR spectra of 1,3-dimethylbarbituric acid in aqueous solutions of various acidities and for various solute concentrations have been recorded and interpreted. The spectra recorded at pH = 2 and below contain the signals of the neutral solute molecule exclusively, while the ones recorded at pH = 7 and above only the signals of the appropriate anion, which has been confirmed by theoretical GIAO-DFT calculations. The signals in the spectra recorded for solutions of pH < 7 show dynamic broadenings. The lineshape analysis of these signals has provided information on the kinetics of the processes running in the dynamic acid-base equilibrium. The kinetic data determined this way have been used to clarify the mechanisms of these processes. The numerical analysis has shown that under the investigated conditions deprotonation of the neutral solute molecules undergoes not only via a simple transfer of the C-H proton to water molecules but also through a process with participation of the barbiturate anions. Moreover, the importance of tautomerism, or association, or both these phenomena for the kinetics of the acid-base transformations in the investigated system has been shown. Qualitatively similar changes of 13C NMR spectra with the solution pH variation have been observed for the parent barbituric acid.

Structural analysis of fructans from Agave americana grown in South Africa for spirit production.

PubMed

Ravenscroft, Neil; Cescutti, Paola; Hearshaw, Meredith A; Ramsout, Ronica; Rizzo, Roberto; Timme, Elizabeth M

2009-05-27

Fructans isolated from Agave americana grown in South Africa are currently used for spirit production. Structural studies on water-soluble fructans were performed to facilitate the development of other applications including its use as a prebiotic. Acid hydrolysis followed by HPAEC-PAD analysis confirmed that the fructan was composed of glucose and fructose, and size analysis by HPAEC-PAD and size exclusion chromatography indicated that the saccharides have a DP range from 6 to 50. An average DP of 14 was estimated by (1)H NMR analysis. Linkage analysis and ESI-MS studies suggest that A. americana has a neofructan structure consisting of a central sucrose to which (2 → 1)- and (2 → 6)-linked β-D-Fruf chains are attached. The (2 → 1)-linked units extend from C-1 of Fru and C-6 of glucose, whereas the (2 → 6)-linked β-D-Fruf units are attached to C-6 of the central Fru. This structure accounts for the presence of equimolar amounts of 1,6-linked Glu and 1,2,6-linked Fru found in linkage analysis and the multiplicity of the NMR signals observed. Detailed ESI-MS studies were performed on fructan fractions: native, periodate oxidized/reduced, and permethylated oligomers. These derivatizations introduced mass differences between Glc and Fru following oxidation and between 1,2-, 1,6-, 2,6-, and 1,2,6-linked units after methylation. Thus, ESI-MS showed the presence of a single Glc per fructan chain and that it is predominantly internal, rather than terminal as found in inulin. These structural features were confirmed by the use of 1D and 2D NMR experiments.

Nuclear Magnetic Resonance Spectroscopy-Based Identification of Yeast.

PubMed

Himmelreich, Uwe; Sorrell, Tania C; Daniel, Heide-Marie

2017-01-01

Rapid and robust high-throughput identification of environmental, industrial, or clinical yeast isolates is important whenever relatively large numbers of samples need to be processed in a cost-efficient way. Nuclear magnetic resonance (NMR) spectroscopy generates complex data based on metabolite profiles, chemical composition and possibly on medium consumption, which can not only be used for the assessment of metabolic pathways but also for accurate identification of yeast down to the subspecies level. Initial results on NMR based yeast identification where comparable with conventional and DNA-based identification. Potential advantages of NMR spectroscopy in mycological laboratories include not only accurate identification but also the potential of automated sample delivery, automated analysis using computer-based methods, rapid turnaround time, high throughput, and low running costs.We describe here the sample preparation, data acquisition and analysis for NMR-based yeast identification. In addition, a roadmap for the development of classification strategies is given that will result in the acquisition of a database and analysis algorithms for yeast identification in different environments.

Expedited Selection of NMR Chiral Solvating Agents for Determination of Enantiopurity

PubMed Central

2016-01-01

The use of NMR chiral solvating agents (CSAs) for the analysis of enantiopurity has been known for decades, but has been supplanted in recent years by chromatographic enantioseparation technology. While chromatographic methods for the analysis of enantiopurity are now commonplace and easy to implement, there are still individual compounds and entire classes of analytes where enantioseparation can prove extremely difficult, notably, compounds that are chiral by virtue of very subtle differences such as isotopic substitution or small differences in alkyl chain length. NMR analysis using CSAs can often be useful for such problems, but the traditional approach to selection of an appropriate CSA and the development of an NMR-based analysis method often involves a trial-and-error approach that can be relatively slow and tedious. In this study we describe a high-throughput experimentation approach to the selection of NMR CSAs that employs automation-enabled screening of prepared libraries of CSAs in a systematic fashion. This approach affords excellent results for a standard set of enantioenriched compounds, providing a valuable comparative data set for the effectiveness of CSAs for different classes of compounds. In addition, the technique has been successfully applied to challenging pharmaceutical development problems that are not amenable to chromatographic solutions. Overall, this methodology provides a rapid and powerful approach for investigating enantiopurity that compliments and augments conventional chromatographic approaches. PMID:27280168

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, R.E.

This report describes the analysis of carbonxyl-terminated butadiene (CTB), carboxyl-terminated butadiene/acrylonitrile (CTBN), and a CTBN adduct prepared by reaction with Epon 828. Data from gel permeation chromatography, nuclear magnetic resonance spectroscopy, high performance liquid chromatography, and ion chromatography are presented and discussed. Quantitative methods based on carbon-13 and proton NMR for analyzing CTBN are described. Proton NMR was found to be useful in identifying lots that have an abnormal amount of CTBN protons. One such lot exhibited a phase separation of a polybutadiene impurity. Carbon-13 NMR was found to be capable of determining nitrile content directly. Carbon-13 NMR had amore » relative standard deviation of 8.3% and a proton NMR of 3.9%. Proton NMR was found to be useful in identifying lots that have 5% more CTBN protons than other lots. 3 refs., 11 figs., 4 tabs.« less

The new Schiff base 4-[(4-Hydroxy-3-fluoro-5-methoxy-benzylidene)amino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one: Experimental, DFT calculational studies and in vitro antimicrobial activity

NASA Astrophysics Data System (ADS)

İskeleli, Nazan Ocak; Alpaslan, Yelda Bingöl; Direkel, Şahin; Ertürk, Aliye Gediz; Süleymanoğlu, Nevin; Ustabaş, Reşat

2015-03-01

The synthesized Schiff base, 4-[(4-Hydroxy-3-fluoro-5-methoxy-benzylidene)amino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one (I), has been characterized by 13C NMR, 1H NMR, 2D NMR (1H-1H COSY and 13C APT), FT-IR, UV-vis and X-ray single-crystal techniques. Molecular geometry of the compound I in the ground state, vibrational frequencies and chemical shift values have been calculated by using the density functional method (DFT) with 6-311++G(d,p) basis set. The obtained results indicate that optimized geometry can well reflect the crystal structural parameters. The differences between experimental and calculated results of FT-IR and NMR have supported the existence of intermolecular (O-H⋯O type) and intramolecular (C-H⋯O type) hydrogen bonds in the crystal structure. Molecular electrostatic potential (MEP), frontier molecular orbital analysis (HOMO-LUMO) and electronic absorption spectra were carried out at B3LYP/6-311G++(d,p). HOMO-LUMO electronic transition of 3.92 eV is due to contribution of the bands the n → π∗. The antimicrobial activity of the compound I was determined against the selected 11 bacteria and 8 fungi by microdilution broth assay with Alamar Blue. In vitro studies showed that the compound I has no antifungal effect for selected fungal isolates. However, the compound I shows remarkable antibacterial effect for the bacteria; Streptococcus pneumoniae, Haemophilus influenzae and Enterococcus faecalis.

Studies of Secondary Melanoma on C57BL/6J Mouse Liver Using 1H NMR Metabolomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Ju; Isern, Nancy G.; Burton, Sarah D.

2013-10-31

NMR metabolomics, consisting of solid state high resolution (hr) magic angle spinning (MAS) 1H NMR (1H hr-MAS), liquid state high resolution 1H-NMR, and principal components analysis (PCA) has been used to study secondary metastatic B16-F10 melanoma in C57BL/6J mouse liver . The melanoma group can be differentiated from its control group by PCA analysis of the absolute concentrations or by the absolute peak intensities of metabolites from either 1H hr-MAS NMR data on intact liver tissues or liquid state 1H-NMR spectra on liver tissue extracts. In particular, we found that the absolute concentrations of alanine, glutamate, creatine, creatinine, fumarate andmore » cholesterol are elevated in the melanoma group as compared to controls, while the absolute concentrations of succinate, glycine, glucose, and the family of linear lipids including long chain fatty acids, total choline and acylglycerol are decreased. The ratio of glycerophosphocholine to phosphocholine is increased by about 1.5 fold in the melanoma group, while the absolute concentration of total choline is actually lower in melanoma mice. These results suggest the following picture in secondary melanoma metastasis: Linear lipid levels are decreased by beta oxidation in the melanoma group, which contributes to an increase in the synthesis of cholesterol, and also provides an energy source input for TCA cycle. These findings suggest a link between lipid oxidation, the TCA cycle and the hypoxia-inducible factors (HIF) signal pathway in tumor metastases. Thus this study indicates that the metabolic profile derived from NMR analysis can provide a valuable bio-signature of malignancy and cell hypoxia in metastatic melanoma.« less

Proton Nuclear Magnetic Resonance-Spectroscopic Discrimination of Wines Reflects Genetic Homology of Several Different Grape (V. vinifera L.) Cultivars.

PubMed

Hu, Boran; Yue, Yaqing; Zhu, Yong; Wen, Wen; Zhang, Fengmin; Hardie, Jim W

2015-01-01

Proton nuclear magnetic resonance spectroscopy coupled multivariate analysis (1H NMR-PCA/PLS-DA) is an important tool for the discrimination of wine products. Although 1H NMR has been shown to discriminate wines of different cultivars, a grape genetic component of the discrimination has been inferred only from discrimination of cultivars of undefined genetic homology and in the presence of many confounding environmental factors. We aimed to confirm the influence of grape genotypes in the absence of those factors. We applied 1H NMR-PCA/PLS-DA and hierarchical cluster analysis (HCA) to wines from five, variously genetically-related grapevine (V. vinifera) cultivars; all grown similarly on the same site and vinified similarly. We also compared the semi-quantitative profiles of the discriminant metabolites of each cultivar with previously reported chemical analyses. The cultivars were clearly distinguishable and there was a general correlation between their grouping and their genetic homology as revealed by recent genomic studies. Between cultivars, the relative amounts of several of the cultivar-related discriminant metabolites conformed closely with reported chemical analyses. Differences in grape-derived metabolites associated with genetic differences alone are a major source of 1H NMR-based discrimination of wines and 1H NMR has the capacity to discriminate between very closely related cultivars. The study confirms that genetic variation among grape cultivars alone can account for the discrimination of wine by 1H NMR-PCA/PLS and indicates that 1H NMR spectra of wine of single grape cultivars may in future be used in tandem with hierarchical cluster analysis to elucidate genetic lineages and metabolomic relations of grapevine cultivars. In the absence of genetic information, for example, where predecessor varieties are no longer extant, this may be a particularly useful approach.

[Non-invasive analysis of proteins in living cells using NMR spectroscopy].

PubMed

Tochio, Hidehito; Murayama, Shuhei; Inomata, Kohsuke; Morimoto, Daichi; Ohno, Ayako; Shirakawa, Masahiro

2015-01-01

NMR spectroscopy enables structural analyses of proteins and has been widely used in the structural biology field in recent decades. NMR spectroscopy can be applied to proteins inside living cells, allowing characterization of their structures and dynamics in intracellular environments. The simplest "in-cell NMR" approach employs bacterial cells; in this approach, live Escherichia coli cells overexpressing a specific protein are subjected to NMR. The cells are grown in an NMR active isotope-enriched medium to ensure that the overexpressed proteins are labeled with the stable isotopes. Thus the obtained NMR spectra, which are derived from labeled proteins, contain atomic-level information about the structure and dynamics of the proteins. Recent progress enables us to work with higher eukaryotic cells such as HeLa and HEK293 cells, for which a number of techniques have been developed to achieve isotope labeling of the specific target protein. In this review, we describe successful use of electroporation for in-cell NMR. In addition, (19)F-NMR to characterize protein-ligand interactions in cells is presented. Because (19)F nuclei rarely exist in natural cells, when (19)F-labeled proteins are delivered into cells and (19)F-NMR signals are observed, one can safely ascertain that these signals originate from the delivered proteins and not other molecules.

Rates and Mechanisms of Oil Shale Pyrolysis: A Chemical Structure Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fletcher, Thomas; Pugmire, Ronald

2015-01-01

Three pristine Utah Green River oil shale samples were obtained and used for analysis by the combined research groups at the University of Utah and Brigham Young University. Oil shale samples were first demineralized and the separated kerogen and extracted bitumen samples were then studied by a host of techniques including high resolution liquid-state carbon-13 NMR, solid-state magic angle sample spinning 13C NMR, GC/MS, FTIR, and pyrolysis. Bitumen was extracted from the shale using methanol/dichloromethane and analyzed using high resolution 13C NMR liquid state spectroscopy, showing carbon aromaticities of 7 to 11%. The three parent shales and the demineralized kerogensmore » were each analyzed with solid-state 13C NMR spectroscopy. Carbon aromaticity of the kerogen was 23-24%, with 10-12 aromatic carbons per cluster. Crushed samples of Green River oil shale and its kerogen extract were pyrolyzed at heating rates from 1 to 10 K/min at pressures of 1 and 40 bar and temperatures up to 1000°C. The transient pyrolysis data were fit with a first-order model and a Distributed Activation Energy Model (DAEM). The demineralized kerogen was pyrolyzed at 10 K/min in nitrogen at atmospheric pressure at temperatures up to 525°C, and the pyrolysis products (light gas, tar, and char) were analyzed using 13C NMR, GC/MS, and FTIR. Details of the kerogen pyrolysis have been modeled by a modified version of the chemical percolation devolatilization (CPD) model that has been widely used to model coal combustion/pyrolysis. This refined CPD model has been successful in predicting the char, tar, and gas yields of the three shale samples during pyrolysis. This set of experiments and associated modeling represents the most sophisticated and complete analysis available for a given set of oil shale samples.« less

Green coffee oil analysis by high-resolution nuclear magnetic resonance spectroscopy.

PubMed

D'Amelio, Nicola; De Angelis, Elisabetta; Navarini, Luciano; Schievano, Elisabetta; Mammi, Stefano

2013-06-15

In this work, we show how an extensive and fast quantification of the main components in green coffee oil can be achieved by NMR, with minimal sample manipulation and use of organic solvents. The approach is based on the integration of characteristic NMR signals, selected because of their similar relaxation properties and because they fall in similar spectral regions, which minimizes offset effects. Quantification of glycerides, together with their fatty acid components (oleic, linoleic, linolenic and saturated) and minor species (caffeine, cafestol, kahweol and 16-O-methylcafestol), is achieved in less than 1h making use of (1)H and (13)C spectroscopy. The compositional data obtained are in reasonable agreement with classical chromatographic analyses. Copyright © 2013 Elsevier B.V. All rights reserved.

Synthesis and biological evaluation of Raddeanin A, a triterpene saponin isolated from Anemone raddeana.

PubMed

Qian, Shan; Chen, Quan Long; Guan, Jin Long; Wu, Yong; Wang, Zhou Yu

2014-01-01

First, Raddeanin A, a cytotoxic oleanane-type triterpenoid saponin isolated from Anemone raddeana REGEL, was synthesized. Stepwise glycosylation was adopted in the synthesis from oleanolic acid, employing arabinosyl, glucosyl and rhamnosyl trichloroacetimidate as donors. The chemical structure of Raddeanin A was confirmed by means of (1)H-NMR, (13)C-NMR, IR, MS and elemental analysis, which elucidated the structure to be 3-O-α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranosyl-(1→2)-α-L-arabinopyranoside oleanolic acid. Biological activity tests showed that in the range of low concentrations, Raddeanin A displayed moderate inhibitory activity against histone deacetylases (HDACs), indicating that the HDACs' inhibitory activity of Raddeanin A may contribute to its cytotoxicity.

Direct synthesis of acid-base bifunctionalized hexagonal mesoporous silica and its catalytic activity in cascade reactions.

PubMed

Shang, Fanpeng; Sun, Jianrui; Wu, Shujie; Liu, Heng; Guan, Jingqi; Kan, Qiubin

2011-03-01

A series of efficient acid-base bifunctionalized hexagonal mesoporous silica (HMS) catalysts contained aminopropyl and propanesulfonic acid have been synthesized through a simple co-condensation by protection of amino group. The results of small-angle XRD, TEM, and N(2) adsorption-desorption measurements show that the resultant materials have mesoscopic structures. X-ray photoelectron spectroscopies, elemental analysis (EA), back titration, (29)Si NMR and (13)C NMR confirm that the organosiloxanes were condensed as a part of the silica framework. The resultant catalysts exhibit excellent acid-basic properties, which make them possess high activity for one-pot deacetalization-Knoevenagel and deacetalization-nitroaldol (Henry) reactions. Copyright © 2010 Elsevier Inc. All rights reserved.

Crystallographic identification of an unexpected by-product in an Ullman's reaction toward biphenyls: 1-(4-hexyloxy-3-hydroxyphenyl)ethanone.

PubMed

Manzano, Veronica E; Baggio, Ricardo; Cukiernik, Fabio D

2015-11-01

The synthesis of 3,3'-diacetoxy-4,4'-bis(hexyloxy)biphenyl following the nickel-modified Ullmann reaction yielded a by-product which was identified successfully by crystallographic analysis as 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C14H20O3. This unexpected nonbiphenyl by-product exhibited IR, (1)H NMR, (13)C NMR and COSY (correlation spectroscopy) spectra fully consistent with the proposed structure. The compound crystallized in the orthorombic Pbca space group, with two independent formula units in the asymmetric unit (one of which was slightly disordered), and showed a supramolecular architecture in which molecules linked by hydroxy-ethanone O-H···O interactions are organized in columns separated by the aliphatic tails.

Androgen Receptor Antagonists and Anti-Prostate Cancer Activities of Some Newly Synthesized Substituted Fused Pyrazolo-, Triazolo- and Thiazolo-Pyrimidine Derivatives

PubMed Central

Bahashwan, Saleh A.; Fayed, Ahmed A.; Ramadan, Mohamed A.; Amr, Abd El-Galil E.; Al-Harbi, Naif O.

2014-01-01

A series of substituted pyrazole, triazole and thiazole derivatives (2–13) were synthesized from 1-(naphtho[1,2-d]thiazol-2-yl)hydrazine as starting material and evaluated as androgen receptor antagonists and anti-prostate cancer agents. The newly synthesized compounds showed potent androgen receptor antagonists and anti-prostate cancer activities with low toxicity (lethal dose 50 (LD50)) comparable to Bicalutamide as reference drug. The structures of newly synthesized compounds were confirmed by IR, 1H-NMR, 13C-NMR, and MS spectral data and elemental analysis. The detailed synthesis, spectroscopic data, LD50 values and pharmacological activities of the synthesized compounds are reported. PMID:25421248

Phthalocyaninatoruthenium(II), Hexakis(dimethylsulfoxide)Phthalocyaninatoruthenium(II), and Hexadis(dimethylsulfoxide-d6)phthalocyanin-atoruthenium(II), Three Highly Selective NMR Shift Reagents.

DTIC Science & Technology

1977-07-18

dimethylsu lfoxi de-d6) phthalocyanin — atoruthenium (II), Three Highly Selective NMR Shift Reagents ( ~‘ iby j \\ / Clement K. Choy and F•lalcolm E. Kenney...Running head : Phthalocyaninatorut henium( II) Shift Reagents I NTRODUCT ION Previously, work on FePc (Pc = phthalocyanine li gand , C32H16N8) show- ing...RuPc and dimethylsulfoxide -d 6 were re cted together and the product isolated, An nmr spectrum of the product showed only phthalocyanine resorar.ces

NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds.

PubMed

Ortegón-Reyna, David; Garcías-Morales, Cesar; Padilla-Martínez, Itzia; García-Báez, Efren; Aríza-Castolo, Armando; Peraza-Campos, Ana; Martínez-Martínez, Francisco

2013-12-31

An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.

Improving reliability of chemometric models for authentication of species origin of heparin by switching from 1D to 2D NMR experiments.

PubMed

Monakhova, Yulia B; Fareed, Jawed; Yao, Yiming; Diehl, Bernd W K

2018-05-10

Nuclear magnetic resonance (NMR) spectroscopy is regarded as one of the most powerful and versatile analytical approaches to assure the quality of heparin preparations. In particular, it was recently demonstrated that by using 1 H NMR coupled with chemometrics heparin and low molecular weight heparin (LMWH) samples derived from three major animal species (porcine, ovine and bovine) can be differentiated [Y.B. Monakhova et al. J. Pharm. Anal. 149 (2018) 114-119]. In this study, significant improvement of existing chemometric models was achieved by switching to 2D NMR experiments (heteronuclear multiple-quantum correlation (HMQC) and diffusion-ordered spectroscopy (DOSY)). Two representative data sets (sixty-nine heparin and twenty-two LMWH) belonged to different batches and distributed by different commercial companies were investigated. A trend for animal species differentiation was observed in the principal component analysis (PCA) score plot built based on the DOSY data. A superior model was constructed using HMQC experiments, where individual heparin (LMWH) clusters as well as their blends were clearly differentiated. The predictive power of different classification methods as well as unsupervised techniques (independent components analysis, ICA) clearly proved applicability of the model for routine heparin and LMWH analysis. The switch from 1D to 2D NMR techniques provides a wealth of additional information, which is beneficial for multivariate modeling of NMR spectroscopic data for heparin preparations. Copyright © 2018 Elsevier B.V. All rights reserved.

LEGO-NMR spectroscopy: a method to visualize individual subunits in large heteromeric complexes.

PubMed

Mund, Markus; Overbeck, Jan H; Ullmann, Janina; Sprangers, Remco

2013-10-18

Seeing the big picture: Asymmetric macromolecular complexes that are NMR active in only a subset of their subunits can be prepared, thus decreasing NMR spectral complexity. For the hetero heptameric LSm1-7 and LSm2-8 rings NMR spectra of the individual subunits of the complete complex are obtained, showing a conserved RNA binding site. This LEGO-NMR technique makes large asymmetric complexes accessible to detailed NMR spectroscopic studies. © 2013 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of Creative Commons the Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

N-(4-Nitrobenzoyl)-N'-(1,5-dimethyl-3-oxo-2-phenyl-1H-3(2H)-pyrazolyl)-thiourea hydrate: Synthesis, spectroscopic characterization, X-ray structure and DFT studies

NASA Astrophysics Data System (ADS)

Arslan, N. Burcu; Kazak, Canan; Aydın, Fatma

2012-04-01

The title molecule (C19H17N5O4S·H2O) was synthesized and characterized by IR-NMR spectroscopy, MS and single-crystal X-ray diffraction. The molecular geometry, vibrational frequencies and gauge-independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method with 6-31G(d) basis set, and compared with the experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies and 1H and 13C NMR chemical shift values show good agreement with experimental data. To determine conformational flexibility, the molecular energy profile of the title compound was obtained with respect to the selected torsion angle, which was varied from -180° to +180° in steps of 10°. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and thermodynamic properties of the compound were investigated by theoretical calculations.

Solid-state NMR investigations of cellulose structure and interactions with matrix polysaccharides in plant primary cell walls.

PubMed

Wang, Tuo; Hong, Mei

2016-01-01

Until recently, the 3D architecture of plant cell walls was poorly understood due to the lack of high-resolution techniques for characterizing the molecular structure, dynamics, and intermolecular interactions of the wall polysaccharides in these insoluble biomolecular mixtures. We introduced multidimensional solid-state NMR (SSNMR) spectroscopy, coupled with (13)C labelling of whole plants, to determine the spatial arrangements of macromolecules in near-native plant cell walls. Here we review key evidence from 2D and 3D correlation NMR spectra that show relatively few cellulose-hemicellulose cross peaks but many cellulose-pectin cross peaks, indicating that cellulose microfibrils are not extensively coated by hemicellulose and all three major polysaccharides exist in a single network rather than two separate networks as previously proposed. The number of glucan chains in the primary-wall cellulose microfibrils has been under active debate recently. We show detailed analysis of quantitative (13)C SSNMR spectra of cellulose in various wild-type (WT) and mutant Arabidopsis and Brachypodium primary cell walls, which consistently indicate that primary-wall cellulose microfibrils contain at least 24 glucan chains. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Atomic site preferences and structural evolution in vanadium-doped ZrSiO4 from multinuclear solid-state NMR

NASA Astrophysics Data System (ADS)

Dajda, N.; Dixon, J. M.; Smith, M. E.; Carthey, N.; Bishop, P. T.

2003-01-01

Solid state NMR spectra of 29Si are reported from pure and vanadium-doped zircon (V-ZrSiO4) samples. The vanadium concentration is varied up to ˜1-mol % V4+ by using both conventional-firing and sol-gel routes, and 51V NMR data are also recorded. 17O NMR of 17O isotopically enriched samples shows that the initial gel is completely amorphous with the whole range of possible M-O-M' linkages detected, and that this structure evolves into a fully ordered ZrSiO4 structure with calcination. Static 91Zr NMR data is reported from a pure zircon sample. The NMR data are used to quantify the amount of vanadium entering the zircon structure, and to elucidate its site preference within the lattice. Two contact shifted peaks with very different T1 relaxation from the main zircon peak but attributable to the zircon lattice are observed in the 29Si NMR spectra for all samples. These spectra are consistent with vanadium substitution on both the tetrahedral and dodecahedral sites, with a slight preference for the silicon site. The data show that the relative occupation of these two sites is almost independent of the preparation method and vanadium concentration. At a higher vanadium concentration a third additional peak is observed which may indicate another substitution site. Variable temperature NMR and susceptibility measurements indicate the hyperfine nature of the interactions influencing silicon from V4+ ions in the different sites.

A Solid-State NMR Study of Selenium Substitution into Nanocrystalline Hydroxyapatite

PubMed Central

Kolmas, Joanna; Kuras, Marzena; Oledzka, Ewa; Sobczak, Marcin

2015-01-01

The substitution of selenium oxyanions in the hydroxyapatite structure was examined using multinuclear solid-state resonance spectroscopy (ssNMR). The study was supported by powder X-ray diffractometry (PXRD) and wavelength dispersion X-ray fluorescence (WD-XRF). Samples of pure hydroxyapatite (HA300) and selenate (HA300-1.2SeO4) or selenite (HA300-1.2SeO3) substituted hydroxyapatites were synthesized using the standard wet method and heated at 300 °C to remove loosely bonded water. PXRD data showed that all samples are single-phase, nanocrystalline hydroxyapatite. The incorporation of selenite and selenate ions affected the lattice constants. In selenium-containing samples the concentration of Se was very similar and amounted to 9.55% and 9.64%, for HA300-1.2SeO4 and HA300-1.2SeO3, respectively. PXRD and ssNMR data showed that the selenite doping significantly decreases the crystallite size and crystallinity degree. 31P and 1H NMR experiments demonstrated the developed surface hydrated layer in all samples, especially in HA300-1.2SeO3. 1H NMR studies showed the dehydroxylation of HA during the selenium oxyanions substitution and the existence of hydrogen bonding in structural hydroxyl group channels. 1H→77Se cross polarization NMR experiments indicated that selenites and selenates are located in the crystal lattice and on the crystal surface. PMID:25997001

Quantitative analysis of protein-ligand interactions by NMR.

PubMed

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

NMR doesn't lie or how solid-state NMR spectroscopy contributed to a better understanding of the nature and function of soil organic matter (Philippe Duchaufour Medal Lecture)

NASA Astrophysics Data System (ADS)

Knicker, Heike

2016-04-01

"Nuclear magnetic resonance (NMR) does not lie". More than anything else, this statement of a former colleague and friend has shaped my relation to solid-state NMR spectroscopy. Indeed, if this technique leads to results which contradict the expectations, it is because i) some parts of the instrument are broken, ii) maladjustment of the acquisition parameters or iii) wrong preparation or confusion of samples. However, it may be even simpler, namely that the expectations were wrong. Of course, for researchers, the latter is the most interesting possibility since it forces to reassess accepted views and to search for new explanations. As my major analytical tool, NMR spectroscopy has confronted me with this challenge often enough to turn this issue into the main subject of my talk and to share with the audience how it formed my understanding of function and nature of soil organic matter (SOM). Already shortly after its introduction into soil science in the 1980's, the data obtained with solid-state 13C NMR spectroscopy opened the stage for ongoing discussions, since they showed that in humified SOM aromatic carbon is considerably less important than previously thought. This finding had major implications regarding the understanding of the origin of SOM and the mechanisms by which it is formed. Certainly, the discrepancy between the new results and previous paradigms contributed to mistrust in the reliability of solid-state NMR techniques. The respective discussion has survived up to our days, although already in the 1980's and 1990's fundamental studies could demonstrate that quantitative solid-state NMR data can be obtained if i) correct acquisition parameters are chosen, ii) the impact of paramagnetic compounds is reduced and iii) the presence of soot in soils can be excluded. On the other hand, this mistrust led to a detailed analysis of the impact of paramagnetics on the NMR behavior of C groups which then improved our understanding of the role of carbohydrates for organo-mineral interactions. Since decent solid-state NMR spectra cannot be obtained from graphenic components, the successful acquisition of solid-state 13C and 15N NMR spectra of charcoals challenged the well accepted model of their chemical nature. Application of advanced 2D NMR approaches confirmed the new view of charcoal as a heterogeneous material, the composition of which depends upon the feedstock and charring condition. The respective consequences of this alternative for the understanding of C sequestration are still matter of ongoing debates. Although the sensitivity of 15N for NMR spectroscopy is 50 times lower than that of 13C, first solid-state 15N NMR spectra of soils with natural 15N abundance were already published in the 1990's. They clearly identified peptide-like structures as the main organic N form in unburnt soils. However, in spite of their high contribution to SOM, the role of peptides in soils is far from understood. Considering the new technological developments in the field of NMR spectroscopy, this technique will certainly not stop to contribute to unexpected results.

Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

PubMed

Markin, Craig J; Spyracopoulos, Leo

2012-12-01

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements from NMR-monitored chemical shift titrations, for which the dependence of K ( D ) on the chemical shift difference (Δω) between free and bound states is extrapolated to Δω = 0. The demonstrated accuracy and precision for k ( off ) will be valuable for the interpretation of biological kinetics in weakly interacting protein-protein networks, where a small change in the magnitude of the underlying kinetics of a given pathway may lead to large changes in the associated downstream signaling cascade.

In-depth investigation on quantitative characterization of pyrolysis oil by 31P NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben, Haoxi; Ferrell, III, Jack R.

The characterization of different heteroatom functional groups by employing 31P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigatedmore » by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.« less

In-depth investigation on quantitative characterization of pyrolysis oil by 31P NMR

DOE PAGES

Ben, Haoxi; Ferrell, III, Jack R.

2016-01-29

The characterization of different heteroatom functional groups by employing 31P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigatedmore » by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.« less

An integrated analysis for determining the geographical origin of medicinal herbs using ICP-AES/ICP-MS and (1)H NMR analysis.

PubMed

Kwon, Yong-Kook; Bong, Yeon-Sik; Lee, Kwang-Sik; Hwang, Geum-Sook

2014-10-15

ICP-MS and (1)H NMR are commonly used to determine the geographical origin of food and crops. In this study, data from multielemental analysis performed by ICP-AES/ICP-MS and metabolomic data obtained from (1)H NMR were integrated to improve the reliability of determining the geographical origin of medicinal herbs. Astragalus membranaceus and Paeonia albiflora with different origins in Korea and China were analysed by (1)H NMR and ICP-AES/ICP-MS, and an integrated multivariate analysis was performed to characterise the differences between their origins. Four classification methods were applied: linear discriminant analysis (LDA), k-nearest neighbour classification (KNN), support vector machines (SVM), and partial least squares-discriminant analysis (PLS-DA). Results were compared using leave-one-out cross-validation and external validation. The integration of multielemental and metabolomic data was more suitable for determining geographical origin than the use of each individual data set alone. The integration of the two analytical techniques allowed diverse environmental factors such as climate and geology, to be considered. Our study suggests that an appropriate integration of different types of analytical data is useful for determining the geographical origin of food and crops with a high degree of reliability. Copyright © 2014 Elsevier Ltd. All rights reserved.

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

Chemometric Methods to Quantify 1D and 2D NMR Spectral Differences Among Similar Protein Therapeutics.

PubMed

Chen, Kang; Park, Junyong; Li, Feng; Patil, Sharadrao M; Keire, David A

2018-04-01

NMR spectroscopy is an emerging analytical tool for measuring complex drug product qualities, e.g., protein higher order structure (HOS) or heparin chemical composition. Most drug NMR spectra have been visually analyzed; however, NMR spectra are inherently quantitative and multivariate and thus suitable for chemometric analysis. Therefore, quantitative measurements derived from chemometric comparisons between spectra could be a key step in establishing acceptance criteria for a new generic drug or a new batch after manufacture change. To measure the capability of chemometric methods to differentiate comparator NMR spectra, we calculated inter-spectra difference metrics on 1D/2D spectra of two insulin drugs, Humulin R® and Novolin R®, from different manufacturers. Both insulin drugs have an identical drug substance but differ in formulation. Chemometric methods (i.e., principal component analysis (PCA), 3-way Tucker3 or graph invariant (GI)) were performed to calculate Mahalanobis distance (D M ) between the two brands (inter-brand) and distance ratio (D R ) among the different lots (intra-brand). The PCA on 1D inter-brand spectral comparison yielded a D M value of 213. In comparing 2D spectra, the Tucker3 analysis yielded the highest differentiability value (D M  = 305) in the comparisons made followed by PCA (D M  = 255) then the GI method (D M  = 40). In conclusion, drug quality comparisons among different lots might benefit from PCA on 1D spectra for rapidly comparing many samples, while higher resolution but more time-consuming 2D-NMR-data-based comparisons using Tucker3 analysis or PCA provide a greater level of assurance for drug structural similarity evaluation between drug brands.

Epoxy monomers derived from tung oil fatty acids and its regulable thermosets cured in two synergistic ways

USDA-ARS?s Scientific Manuscript database

A new bio-based epoxy monomer with conjugated double bonds, glycidyl ester of eleostearic acid (GEEA), was synthesized from tung oil fatty acids and characterized by 1H-NMR, 13C-NMR and Mass Spectrometry Analysis (MSA). Differential Scanning Calorimetry (DSC) analysis and FT-IR were utilized to inve...

Analysis of ethanol-soluble extractives in southern pine wood by low-field proton NMR

Treesearch

Thomas L. Eberhardt; Thomas Elder; Nicole Labbe

2007-01-01

Low-field portion NMR was evaluated as a nondestructive and rapid technique for measuring ethanol-soluble extractives in southern pine wood. Matchstick-sized wood specimens were steeped in extractive-containing solutions to generate extractive-enriched samples for analysis. decay curves obtained by the Carr-Purcell-Meiboom-gill (CPMG) pulse sequence were analyzed with...

Discrimination of Aurantii Fructus Immaturus and Fructus Poniciri Trifoliatae Immaturus by Flow Injection UV Spectroscopy (FIUV) and 1H NMR using Partial Least-squares Discriminant Analysis (PLS-DA)

USDA-ARS?s Scientific Manuscript database

Two simple fingerprinting methods, flow-injection UV spectroscopy (FIUV) and 1H nuclear magnetic resonance (NMR), for discrimination of Aurantii FructusImmaturus and Fructus Poniciri TrifoliataeImmaturususing were described. Both methods were combined with partial least-squares discriminant analysis...

Fraction of boroxol rings in vitreous boron oxide from a first-principles analysis of Raman and NMR spectra.

PubMed

Umari, P; Pasquarello, Alfredo

2005-09-23

We determine the fraction f of B atoms belonging to boroxol rings in vitreous boron oxide through a first-principles analysis. After generating a model structure of vitreous B2O3 by first-principles molecular dynamics, we address a large set of properties, including the neutron structure factor, the neutron density of vibrational states, the infrared spectra, the Raman spectra, and the 11B NMR spectra, and find overall good agreement with corresponding experimental data. From the analysis of Raman and 11B NMR spectra, we yield consistently for both probes a fraction f of approximately 0.75. This result indicates that the structure of vitreous boron oxide is largely dominated by boroxol rings.

Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR.

PubMed

Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter

2012-06-06

Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data. Copyright © 2012 Elsevier Ltd. All rights reserved.

Stereochemistry of C18 monounsaturated cork suberin acids determined by spectroscopic techniques including (1) H-NMR multiplet analysis of olefinic protons.

PubMed

Santos, Sara; Graça, José

2014-01-01

Suberin is a biopolyester responsible for the protection of secondary plant tissues, and yet its molecular structure remains unknown. The C18:1 ω-hydroxyacid and the C18:1 α,ω-diacid are major monomers in the suberin structure, but the configuration of the double bond remains to be elucidated. To unequivocally define the configuration of the C18:1 suberin acids. Pure C18:1 ω-hydroxyacid and C18:1 α,ω-diacid, isolated from cork suberin, and two structurally very close C18:1 model compounds of known stereochemistry, methyl oleate and methyl elaidate, were analysed by NMR spectroscopy, Fourier transform infrared (FTIR) and Raman spectroscopy, and GC-MS. The GC-MS analysis showed that both acids were present in cork suberin as only one geometric isomer. The analysis of dimethyloxazoline (DMOX) and picolinyl derivatives proved the double bond position to be at C-9. The FTIR spectra were concordant with a cis-configuration for both suberin acids, but their unambiguous stereochemical assignment came from the NMR analysis: (i) the chemical shifts of the allylic (13) C carbons were shielded comparatively to the trans model compound, and (ii) the complex multiplets of the olefinic protons could be simulated only with (3) JHH and long-range (4) JHH coupling constants typical of a cis geometry. The two C18:1 suberin acids in cork are (Z)-18-hydroxyoctadec-9-enoic acid and (Z)-octadec-9-enedoic acid. Copyright © 2013 John Wiley & Sons, Ltd.

Capillary toroid cavity detector for high pressure NMR

DOEpatents

Gerald, II, Rex E.; Chen, Michael J.; Klingler, Robert J.; Rathke, Jerome W.; ter Horst, Marc

2007-09-11

A Toroid Cavity Detector (TCD) is provided for implementing nuclear magnetic resonance (NMR) studies of chemical reactions under conditions of high pressures and temperatures. A toroid cavity contains an elongated central conductor extending within the toroid cavity. The toroid cavity and central conductor generate an RF magnetic field for NMR analysis. A flow-through capillary sample container is located within the toroid cavity adjacent to the central conductor to subject a sample material flowing through the capillary to a static magnetic field and to enable NMR spectra to be recorded of the material in the capillary under a temperature and high pressure environment.

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

(13)C NMR substituent-induced chemical shifts in 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-ones (thiones).

PubMed

Kara, Yesim Saniye

2015-01-01

In the present, study mostly novel ten 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-ones and ten 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-thiones were synthesized. These oxadiazole derivatives were characterized by IR, (1)H NMR, (13)C NMR and elemental analyses. Their (13)C NMR spectra were measured in Deuterochloroform (CDCl3). The correlation analysis for the substituent-induced chemical shift (SCS) with Hammett substituent constants (σ), Brown Okamoto substituent constants (σ(+), σ(-)), inductive substituent constants (σI) and different of resonance substituent constants (σR, σR(o)) were performed using SSP (single substituent parameter), DSP (dual substituent parameter) and DSP-NLR (dual substituent parameter-non-linear resonance) methods, as well as single and multiple regression analysis. Negative ρ values were found for all correlations (reverse substituent effect). The results of all statistical analyses, (13)C NMR chemical shift of CN, CO and CS carbon of oxadiazole rings have shown satisfactory correlation. Copyright © 2015 Elsevier B.V. All rights reserved.

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.

PubMed

Emwas, Abdul-Hamid; Roy, Raja; McKay, Ryan T; Ryan, Danielle; Brennan, Lorraine; Tenori, Leonardo; Luchinat, Claudio; Gao, Xin; Zeri, Ana Carolina; Gowda, G A Nagana; Raftery, Daniel; Steinbeck, Christoph; Salek, Reza M; Wishart, David S

2016-02-05

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.

Note: Commercial SQUID magnetometer-compatible NMR probe and its application for studying a quantum magnet.

PubMed

Vennemann, T; Jeong, M; Yoon, D; Magrez, A; Berger, H; Yang, L; Živković, I; Babkevich, P; Rønnow, H M

2018-04-01

We present a compact nuclear magnetic resonance (NMR) probe which is compatible with a magnet of a commercial superconducting quantum interference device magnetometer and demonstrate its application to the study of a quantum magnet. We employ trimmer chip capacitors to construct an NMR tank circuit for low temperature measurements. Using a magnetic insulator MoOPO 4 with S = 1/2 (Mo 5+ ) as an example, we show that the T-dependence of the circuit is weak enough to allow the ligand-ion NMR study of magnetic systems. Our 31 P NMR results are compatible with previous bulk susceptibility and neutron scattering experiments and furthermore reveal unconventional spin dynamics.

Note: Commercial SQUID magnetometer-compatible NMR probe and its application for studying a quantum magnet

NASA Astrophysics Data System (ADS)

Vennemann, T.; Jeong, M.; Yoon, D.; Magrez, A.; Berger, H.; Yang, L.; Živković, I.; Babkevich, P.; Rønnow, H. M.

2018-04-01

We present a compact nuclear magnetic resonance (NMR) probe which is compatible with a magnet of a commercial superconducting quantum interference device magnetometer and demonstrate its application to the study of a quantum magnet. We employ trimmer chip capacitors to construct an NMR tank circuit for low temperature measurements. Using a magnetic insulator MoOPO4 with S = 1/2 (Mo5+) as an example, we show that the T-dependence of the circuit is weak enough to allow the ligand-ion NMR study of magnetic systems. Our 31P NMR results are compatible with previous bulk susceptibility and neutron scattering experiments and furthermore reveal unconventional spin dynamics.

NMR study of the gelation of a designed gelator.

PubMed

Brand, Torsten; Nolis, Pau; Richter, Sven; Berger, Stefan

2008-06-01

The gelation of a designed gelator was investigated by different NMR methods, which showed a clear thermal hysteresis. Two very simple approaches for the NMR determination of the gelation point are suggested. One involves the observation of the NMR integral, and the other records the ratio of the diffusion coefficients between the gelator and the solvent. Differential behavior of the gelator protons are interpreted as a hint that a part of the gelator molecule might still be flexible as in the dissolved state. Copyright (c) 2008 John Wiley & Sons, Ltd

Perspectives on NMR in drug discovery: a technique comes of age

PubMed Central

Pellecchia, Maurizio; Bertini, Ivano; Cowburn, David; Dalvit, Claudio; Giralt, Ernest; Jahnke, Wolfgang; James, Thomas L.; Homans, Steve W.; Kessler, Horst; Luchinat, Claudio; Meyer, Bernd; Oschkinat, Hartmut; Peng, Jeff; Schwalbe, Harald; Siegal, Gregg

2009-01-01

In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility. PMID:19172689

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

DOE PAGES

Boiteau, Rene M.; Hoyt, David W.; Nicora, Carrie D.; ...

2018-01-17

Here, we introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS 2), and NMR in a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS 2 approach is well suited for discovery ofmore » new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases.« less

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boiteau, Rene M.; Hoyt, David W.; Nicora, Carrie D.

Here, we introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS 2), and NMR in a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS 2 approach is well suited for discovery ofmore » new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases.« less

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

PubMed Central

Hoyt, David W.; Nicora, Carrie D.; Kinmonth-Schultz, Hannah A.; Ward, Joy K.

2018-01-01

We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS2), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS2 approach is well suited to the discovery of new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases. PMID:29342073

Assessment of higher order structure comparability in therapeutic proteins using nuclear magnetic resonance spectroscopy.

PubMed

Amezcua, Carlos A; Szabo, Christina M

2013-06-01

In this work, we applied nuclear magnetic resonance (NMR) spectroscopy to rapidly assess higher order structure (HOS) comparability in protein samples. Using a variation of the NMR fingerprinting approach described by Panjwani et al. [2010. J Pharm Sci 99(8):3334-3342], three nonglycosylated proteins spanning a molecular weight range of 6.5-67 kDa were analyzed. A simple statistical method termed easy comparability of HOS by NMR (ECHOS-NMR) was developed. In this method, HOS similarity between two samples is measured via the correlation coefficient derived from linear regression analysis of binned NMR spectra. Applications of this method include HOS comparability assessment during new product development, manufacturing process changes, supplier changes, next-generation products, and the development of biosimilars to name just a few. We foresee ECHOS-NMR becoming a routine technique applied to comparability exercises used to complement data from other analytical techniques. Copyright © 2013 Wiley Periodicals, Inc.

Purity assessment of organic calibration standards using a combination of quantitative NMR and mass balance.

PubMed

Davies, Stephen R; Jones, Kai; Goldys, Anna; Alamgir, Mahuiddin; Chan, Benjamin K H; Elgindy, Cecile; Mitchell, Peter S R; Tarrant, Gregory J; Krishnaswami, Maya R; Luo, Yawen; Moawad, Michael; Lawes, Douglas; Hook, James M

2015-04-01

Quantitative NMR spectroscopy (qNMR) has been examined for purity assessment using a range of organic calibration standards of varying structural complexities, certified using the traditional mass balance approach. Demonstrated equivalence between the two independent purity values confirmed the accuracy of qNMR and highlighted the benefit of using both methods in tandem to minimise the potential for hidden bias, thereby conferring greater confidence in the overall purity assessment. A comprehensive approach to purity assessment is detailed, utilising, where appropriate, multiple peaks in the qNMR spectrum, chosen on the basis of scientific reason and statistical analysis. Two examples are presented in which differences between the purity assignment by qNMR and mass balance are addressed in different ways depending on the requirement of the end user, affording fit-for-purpose calibration standards in a cost-effective manner.

Thermal and spectroscopic analysis of organic matter degradation and humification during composting of pig slurry in different scenarios.

PubMed

Martín-Mata, J; Lahoz-Ramos, C; Bustamante, M A; Marhuenda-Egea, F C; Moral, R; Santos, A; Sáez, J A; Bernal, M P

2016-09-01

In this work, different analytical techniques (thermal analysis, (13)C cross-polarization magic angle spinning (CPMAS) NMR and Fourier transform infrared (FT-IR) spectroscopy) have been used to study the organic matter changes during the co-composting of pig slurry with cotton gin waste. To ensure the validity of the findings, the composting process was developed in different scenarios: under experimental pilot plant conditions, using the static pile system, and under real conditions on a pig farm, using the turning pile system. Also, the thermal stability index (R1) was determined before and after an extraction with water, to evaluate the effect of eliminating water-soluble inorganic salts on the thermal analysis. The results of the thermal methods showed the degradation of the most labile organic matter during composting; R1 increased during composting in all piles, without any influence of the presence of water-soluble inorganic ions in the sample. The NMR showed a decrease in the abundance of the carbohydrate molecules and an increase in the aliphatic materials during composting, due to a concentration effect. Also, FT-IR spectroscopy was a useful technique to study the trends of polysaccharides and nitrate, as indicators of organic matter transformations during composting.

Theoretical NMR correlations based Structure Discussion.

PubMed

Junker, Jochen

2011-07-28

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction.

Molecular structures of fructans from Agave tequilana Weber var. azul.

PubMed

Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

2003-12-31

Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

Interaction of lafutidine in binding to human serum albumin in gastric ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY, molecule docking, and spectroscopic studies.

PubMed

Yang, Hongqin; Huang, Yanmei; He, Jiawei; Li, Shanshan; Tang, Bin; Li, Hui

2016-09-15

In this study, lafutidine (LAF) was used as a model compound to investigate the binding mechanism between antiulcer drugs and human serum albumin (HSA) through various techniques, including STD-NMR, WaterLOGSY-NMR, (1)H NMR relaxation times, tr-NOESY, molecule docking calculation, FT-IR spectroscopy, and CD spectroscopy. The analyses of STD-NMR, which derived relative STD (%) intensities, and WaterLOGSY-NMR, determined that LAF bound to HSA. In particular, the pyridyl group of LAF was in close contact with HSA binding pocket, whereas furyl group had a secondary binding. Competitive STD-NMR and WaterLOGSY-NMR experiments, with warifarin and ibuprofen as site-selective probes, indicated that LAF preferentially bound to site II in the hydrophobic subdomains IIIA of HSA. The bound conformation of LAF at the HSA binding site was further elucidated by transferred NOE effect (tr-NOESY) experiment. Relaxation experiments provided quantitative information about the relationship between the affinity and structure of LAF. The molecule docking simulations conducted with AutoDock and the restraints derived from STD results led to three-dimensional models that were consistent with the NMR spectroscopic data. The presence of hydrophobic forces and hydrogen interactions was also determined. Additionally, FT-IR and CD spectroscopies showed that LAF induced secondary structure changes of HSA. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthesis and molecular structure of a zinc complex of the vitamin K3 analogue phthiocol

NASA Astrophysics Data System (ADS)

Kathawate, Laxmi; Sproules, Stephen; Pawar, Omkar; Markad, Ganesh; Haram, Santosh; Puranik, Vedavati; Salunke-Gawali, Sunita

2013-09-01

The complex [Zn(phthiocol)2(H2O)2]; 1, where phthiocol is 2-hydroxy-3-methyl-1,4-naphthoquinone, has been synthesized and characterized by elemental analysis, FT-IR, 1H NMR, UV-vis spectroscopy, thermogravimetric (TG) analysis, electrochemical and single crystal X-ray diffraction studies. The νCO stretch shifts to lower frequencies upon complexation of phthiocol to Zn2+. 1H NMR spectra show an upfield shift of the benzenoid ring protons in 1. There is a bathochromic shift of the LMCT band in the UV-vis spectra of 1. Single crystal X-ray structure of 1 show distorted octahedral geometry around Zn2+. Two phthiocol ligands are in plane with the metal, while water molecules are trans to this plane. Coordination of deprotonated phthiocol ligands is 'trans, trans' to Zn2+. Intra as well as intermolecular interactions are observed in 1. Molecules of 1 show three dimensional network through CH⋯O and OH⋯O interactions. Additional anodic peaks are observed in cyclic voltammogram of phthiocol ligand due to oxidation of reduced species formed during reduction. One-electron reduction of 1 is shown to be reversible and DFT studies define this redox event as ligand-centered.

Magic Angle Spinning NMR of Viruses

PubMed Central

Quinn, Caitlin; Lu, Manman; Suiter, Christopher L.; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

2015-01-01

Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies. PMID:25919197

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

PubMed

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

Automatic analysis of quantitative NMR data of pharmaceutical compound libraries.

PubMed

Liu, Xuejun; Kolpak, Michael X; Wu, Jiejun; Leo, Gregory C

2012-08-07

In drug discovery, chemical library compounds are usually dissolved in DMSO at a certain concentration and then distributed to biologists for target screening. Quantitative (1)H NMR (qNMR) is the preferred method for the determination of the actual concentrations of compounds because the relative single proton peak areas of two chemical species represent the relative molar concentrations of the two compounds, that is, the compound of interest and a calibrant. Thus, an analyte concentration can be determined using a calibration compound at a known concentration. One particularly time-consuming step in the qNMR analysis of compound libraries is the manual integration of peaks. In this report is presented an automated method for performing this task without prior knowledge of compound structures and by using an external calibration spectrum. The script for automated integration is fast and adaptable to large-scale data sets, eliminating the need for manual integration in ~80% of the cases.

NMR-based urine analysis in rats: prediction of proximal tubule kidney toxicity and phospholipidosis.

PubMed

Lienemann, Kai; Plötz, Thomas; Pestel, Sabine

2008-01-01

The aim of safety pharmacology is early detection of compound-induced side-effects. NMR-based urine analysis followed by multivariate data analysis (metabonomics) identifies efficiently differences between toxic and non-toxic compounds; but in most cases multiple administrations of the test compound are necessary. We tested the feasibility of detecting proximal tubule kidney toxicity and phospholipidosis with metabonomics techniques after single compound administration as an early safety pharmacology approach. Rats were treated orally, intravenously, inhalatively or intraperitoneally with different test compounds. Urine was collected at 0-8 h and 8-24 h after compound administration, and (1)H NMR-patterns were recorded from the samples. Variation of post-processing and feature extraction methods led to different views on the data. Support Vector Machines were trained on these different data sets and then aggregated as experts in an Ensemble. Finally, validity was monitored with a cross-validation study using a training, validation, and test data set. Proximal tubule kidney toxicity could be predicted with reasonable total classification accuracy (85%), specificity (88%) and sensitivity (78%). In comparison to alternative histological studies, results were obtained quicker, compound need was reduced, and very importantly fewer animals were needed. In contrast, the induction of phospholipidosis by the test compounds could not be predicted using NMR-based urine analysis or the previously published biomarker PAG. NMR-based urine analysis was shown to effectively predict proximal tubule kidney toxicity after single compound administration in rats. Thus, this experimental design allows early detection of toxicity risks with relatively low amounts of compound in a reasonably short period of time.

Molecular structure, NMR, UV-Visible, vibrational spectroscopic and HOMO, LUMO analysis of (E)-1-(2, 6-bis (4-methoxyphenyl)-3, 3-dimethylpiperidine-4-ylidene)-2-(3-(3, 5-dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl) hydrazine by DFT method

NASA Astrophysics Data System (ADS)

Alphonsa, A. Therasa; Loganathan, C.; Anand, S. Athavan Alias; Kabilan, S.

2016-02-01

We have synthesized (E)-1-(2, 6-bis (4-methoxyphenyl)-3, 3-dimethylpiperidine-4-ylidene)-2-(3-(3, 5-dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl) hydrazine (PM6). It was characterized using FT-IR, FT-Raman, 1H NMR, 13C NMR techniques. To interpret the experimental data, ab initio computations of the vibrational frequencies were carried out using the Gaussian 09 program followed by the full optimizations done using Density Functional Theory (DFT) at B3LYP/6-311 G(d,p) level. The combined use of experiments and computations allowed a firm assignment of the majority of observed bands for the compound. The calculated stretching frequencies have been found to be in good agreement with the experimental frequencies. The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs) and density of states (DOS). The absorption spectra have been computed by using time dependent density functional theory (TD-DFT). 1H and 13C NMR spectra were recorded and 1H and 13C NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. From the optimized geometry of the molecule, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMOs) of the title compound have been calculated in the ground state theoretically. The theoretical results showed good agreement with the experimental values.

Is Institutional Delivery Protective Against Neonatal Mortality Among Poor or Tribal Women? A Cohort Study From Gujarat, India.

PubMed

Altman, Rebecca; Sidney, Kristi; De Costa, Ayesha; Vora, Kranti; Salazar, Mariano

2017-05-01

Objectives In low-income settings, neonatal mortality rates (NMR) are higher among socioeconomically disadvantaged groups. Institutional deliveries have been shown to be protective against neonatal mortality. In Gujarat, India, the access of disadvantaged women to institutional deliveries has increased. However, the impact of increased institutional delivery on NMR has not been studied here. This paper examined if institutional childbirth is associated with lower NMR among disadvantaged women in Gujarat, India. Methods A community-based prospective cohort of pregnant women was followed in three districts in Gujarat, India (July 2013-November 2014). Two thousand nine hundred and nineteen live births to disadvantaged women (tribal or below poverty line) were included in the study. Data was analyzed using multivariable logistic regression. Results The overall NMR was 25 deaths per 1000 live births. Multivariable analysis showed that institutional childbirth was protective against neonatal mortality only among disadvantaged women with obstetric complications during delivery. Among mothers with obstetric complications during delivery, those who gave birth in a private or public facility had significantly lower odds of having a neonatal death than women delivering at home (AOR 0.07 95% CI 0.01-0.45 and AOR 0.03, 95% CI 0.00-0.33 respectively). Conclusions for Practice Our findings highlight the crucial role of institutional delivery to prevent neonatal deaths among those born to disadvantaged women with complications during delivery in this setting. Efforts to improve disadvantaged women's access to good quality obstetric care must continue in order to further reduce the NMR in Gujarat, India.

Using solid 13C NMR coupled with solution 31P NMR spectroscopy to investigate molecular species and lability of organic carbon and phosphorus from aquatic plants in Tai Lake, China.

PubMed

Liu, Shasha; Zhu, Yuanrong; Wu, Fengchang; Meng, Wei; Wang, Hao; He, Zhongqi; Guo, Wenjing; Song, Fanhao; Giesy, John P

2017-01-01

Forms and labilities of plant-derived organic matters (OMs) including carbon (C) and phosphorus (P) were fundamental for understanding their release, degradation and environmental behaviour in lake ecosystems. Thus, solid 13 C and solution 31 P nuclear magnetic resonance (NMR) spectroscopy were used to characterize biomass of six aquatic plants in Tai Lake, China. The results showed that carbohydrates (61.2% of the total C) were predominant C functional group in the solid 13 C NMR spectra of plant biomass, which may indicate high lability and bioavailability of aquatic plants-derived organic matter in lakes. There was 72.6-103.7% of the total P in aquatic plant biomass extracted by NaOH-EDTA extracts. Solution 31 P NMR analysis of these NaOH-EDTA extracts further identified several molecular species of P including orthophosphate (50.1%), orthophosphate monoesters (46.8%), DNA (1.6%) and pyrophosphate (1.4%). Orthophosphate monoesters included β-glycerophosphate (17.7%), hydrolysis products of RNA (11.7%), α-glycerophosphate (9.2%) and other unknown monoesters (2.1%). Additionally, phytate, the major form of organic P in many lake sediments, was detected in floating plant water poppy. These inorganic P (e.g. orthophosphate and pyrophosphate) and organic P (e.g. diester and its degradation products) identified in plant biomass were all labile and bioavailable P, which would play an important role in recycling of P in lakes. These results increased knowledge of chemical composition and bioavailability of OMs derived from aquatic plants in lakes.

Chiral lactic hydrazone derivatives as potential bioactive antibacterial agents: Synthesis, spectroscopic, structural and molecular docking studies

NASA Astrophysics Data System (ADS)

Noshiranzadeh, Nader; Heidari, Azam; Haghi, Fakhri; Bikas, Rahman; Lis, Tadeusz

2017-01-01

A series of novel chiral lactic-hydrazone derivatives were synthesized by condensation of (S)-lactic acid hydrazide with salicylaldehyde derivatives and characterized by elemental analysis and spectroscopic studies (FT-IR, 1H NMR and 13C NMR spectroscopy). The structure of one compound was determined by single crystal X-ray analysis. Antibacterial activity of the synthesized compounds was studied against Staphylococcus aureus, Streptococcus pneumonia, Escherichia coli and Pseudomonas aeruginosa as bacterial cultures by broth microdilution method. All of the synthesized compounds showed good antibacterial activity with MIC range of 64-512 μg/mL. Compounds (S,E)-2-hydroxy-N-(2-hydroxy-5-nitrobenzylidene)propanehydrazide (5) and (S,E)-2-hydroxy-N-((3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)propanehydrazide (7) were the most effective antibacterial derivatives against S. aureus and E. coli respectively with a MIC value of 64 μg/mL. Bacterial biofilm formation assay showed that these compounds significantly inhibited biofilm formation of P. aeruginosa. Also, in silico molecular docking studies were performed to show lipoteichoic acid synthase (LtaS) inhibitory effect of lactic hydrazone derivatives. The association between electronic and structural effects of some substituents on the benzylidene moiety and the biological activity of these chiral compounds were studied. Structural studies show that compound with higher hydrogen bonding interactions show higher antibacterial activity. The results show chiral hydrazone derivatives based on lactic acid hydrazide could be used as potential lead compounds for developing novel antibacterial agents.

X-ray and 1H-NMR spectroscopic studies of the structures and conformations of the new nootropic agents RU-35929, RU-47010 and RU-35965

NASA Astrophysics Data System (ADS)

Amato, Maria E.; Bandoli, Giuliano; Casellato, Umberto; Pappalardo, Giuseppe C.; Toja, Emilio

1990-10-01

The crystal and molecular structures of the nootropics (±)1-benzenesulphonyl-2-oxo-5-ethoxypyrrolidine ( 1), (±)1-(3-pyridinylsulphonyl)-2-oxo-5-ethoxypyrrolidine ( 2) and (±)1-benzenesulphonyl-2-oxo-5-isopropyloxypyrrolidine ( 3) have been determined by X-ray analysis. The solution conformation of 1, 2 and 3 has been investigated by 1H NMR spectroscopy. In the solid state, the main feature consists of the similar structural parameters and conformations, with the exception of the conformation adopted by the 5-ethoxy moiety which changes on passing from 1 to 2. The solid state overall enveloped conformation of the 2-pyrrolidinone ring for the three nootropics is found to be retained in solution on the basis of NMR evidence. Comparison between calculated and experimental coupling constant values shows that one of the two possible puckered opposite conformational isomers (half-chair shapes) occurs in solution. The relative pharmacological potencies of 1, 2 and 3 cannot therefore be interpreted in terms of the different conformation features presently detectable by available experimental methods.

Synthesis, Characterization, and Anti-Cancer Activity of Some New N'-(2-Oxoindolin-3-ylidene)-2-propylpentane hydrazide-hydrazones Derivatives.

PubMed

El-Faham, Ayman; Farooq, Muhammad; Khattab, Sherine N; Abutaha, Nael; Wadaan, Mohammad A; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-08-13

Eight novel N'-(2-oxoindolin-3-ylidene)-2-propylpentane hydrazide-hydrazone derivatives 4a-h were synthesized and fully characterized by IR, NMR ((1)H-NMR and (13)C-NMR), elemental analysis, and X-ray crystallography. The cyto-toxicity and in vitro anti-cancer evaluation of the prepared compounds have been assessed against two different human tumour cell lines including human liver (HepG2) and leukaemia (Jurkat), as well as in normal cell lines derived from human embryonic kidney (HEK293) using MTT assay. The compounds 3e, 3f, 4a, 4c, and 4e revealed promising anti-cancer activities in tested human tumour cells lines (IC50 values between 3 and 7 μM) as compared to the known anti-cancer drug 5-Fluorouracil (IC50 32-50 μM). Among the tested compounds, 4a showed specificity against leukaemia (Jurkat) cells, with an IC50 value of 3.14 μM, but this compound was inactive in liver cancer and normal cell lines.

Automation of peak-tracking analysis of stepwise perturbed NMR spectra.

PubMed

Banelli, Tommaso; Vuano, Marco; Fogolari, Federico; Fusiello, Andrea; Esposito, Gennaro; Corazza, Alessandra

2017-02-01

We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TINT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered. TINT was applied successfully to several protein systems during a temperature ramp in isotope exchange experiments. A comparison with a state-of-the-art algorithm showed promising results for great numbers of spectra and low signal to noise ratios, when the graduality of the perturbation is appropriate. TINT can be applied to different kinds of high throughput chemical shift mapping experiments, with quasi-continuous variations, in which a quantitative automated recognition is crucial.

Metabolomics by Proton High-Resolution Magic-Angle-Spinning Nuclear Magnetic Resonance of Tomato Plants Treated with Two Secondary Metabolites Isolated from Trichoderma.

PubMed

Mazzei, Pierluigi; Vinale, Francesco; Woo, Sheridan Lois; Pascale, Alberto; Lorito, Matteo; Piccolo, Alessandro

2016-05-11

Trichoderma fungi release 6-pentyl-2H-pyran-2-one (1) and harzianic acid (2) secondary metabolites to improve plant growth and health protection. We isolated metabolites 1 and 2 from Trichoderma strains, whose different concentrations were used to treat seeds of Solanum lycopersicum. The metabolic profile in the resulting 15 day old tomato leaves was studied by high-resolution magic-angle-spinning nuclear magnetic resonance (HRMAS NMR) spectroscopy directly on the whole samples without any preliminary extraction. Principal component analysis (PCA) of HRMAS NMR showed significantly enhanced acetylcholine and γ-aminobutyric acid (GABA) content accompanied by variable amount of amino acids in samples treated with both Trichoderma secondary metabolites. Seed germination rates, seedling fresh weight, and the metabolome of tomato leaves were also dependent upon doses of metabolites 1 and 2 treatments. HRMAS NMR spectroscopy was proven to represent a rapid and reliable technique for evaluating specific changes in the metabolome of plant leaves and calibrating the best concentration of bioactive compounds required to stimulate plant growth.

Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae—A 2D NMR Metabolomics Study

PubMed Central

Vergara, Fredd; Shino, Amiu; Kikuchi, Jun

2016-01-01

Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of 1H-13C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae. PMID:27598144

Synthesis of flexirubin-mediated silver nanoparticles using Chryseobacterium artocarpi CECT 8497 and investigation of its anticancer activity.

PubMed

Venil, Chidambaram Kulandaisamy; Sathishkumar, Palanivel; Malathi, Mahalingam; Usha, Rajamanickam; Jayakumar, Rajarajeswaran; Yusoff, Abdull Rahim Mohd; Ahmad, Wan Azlina

2016-02-01

In this work, the synthesis of silver nanoparticles from a pigment produced by a recently-discovered bacterium, Chryseobacterium artocarpi CECT 8497, was achieved, followed by an investigation of its anticancer properties. The bacterial pigment was identified as flexirubin following NMR ((1)H NMR and (13)C NMR), UV-Vis, and LC-MS analysis. An aqueous silver nitrate solution was treated with isolated flexirubin to produce silver nanoparticles. The synthesised silver nanoparticles were subsequently characterised by UV-Vis spectroscopy, Scanning Electron Microscopy (SEM), Energy Dispersive X-ray Spectroscopy (EDX), X-Ray Diffraction (XRD), and Fourier Transform Infrared (FTIR) Spectroscopy methodologies. Furthermore, the anticancer effects of synthesised silver nanoparticles in a human breast cancer cell line (MCF-7) were evaluated. The tests showed significant cytotoxicity activity of the silver nanoparticles in the cultured cells, with an IC50 value of 36μgmL(-1). This study demonstrates that silver nanoparticles, synthesised from flexirubin from C. artocarpi CECT 8497, may have potential as a novel chemotherapeutic agent. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

NASA Astrophysics Data System (ADS)

Madanagopal, A.; Periandy, S.; Gayathri, P.; Ramalingam, S.; Xavier, S.

2017-01-01

The pharmaceutical compound; Phenacetin was investigated by analyzing FT-IR, FT-Raman and 1H &13C NMR spectra. The hybrid efficient computational calculations performed for computing physical and chemical parameters. The cause of pharmaceutical activity due to the substitutions; carboxylic, methyl and amine groups in appropriate positions on the pedestal compound was deeply investigated. Moreover, 13C NMR and 1H NMR chemical shifts correlated with TMS standard to explain the truth of compositional ratio of base and ligand groups. The bathochromic shift due to chromophores over the energy levels in UV-Visible region was strongly emphasized the Anti-inflammatory chemical properties. The chemical stability was pronounced by the strong kubo gap which showed the occurring of charge transformation within the molecule. The occurrence of the chemical reaction was feasibly interpreted by Gibbs free energy profile. The standard vibrational analysis stressed the active participation of composed ligand groups for the existence of the analgesic as well as antipyretic properties of the Phenacetin compound. The strong dipole interaction energy utilization for the transition among non-vanishing donor and acceptor for composition of the molecular structure was interpreted.

Development and Validation of Quantitative (1)H NMR Spectroscopy for the Determination of Total Phytosterols in the Marine Seaweed Sargassum.

PubMed

Zhang, Xiu-Li; Wang, Cong; Chen, Zhen; Zhang, Pei-Yu; Liu, Hong-Bing

2016-08-10

Knowledge of phytosterol (PS) contents in marine algae is currently lacking compared to those in terrestrial plants. The present studies developed a quantitative (1)H NMR method for the determination of the total PSs in Sargassum. The characteristic proton signal H-3α in PSs was used for quantification, and 2,3,4,5-tetrachloro-nitrobenzene was used as an internal standard. Seaweed samples could be recorded directly after total lipid extraction and saponification. The results showed that the PS contents in Sargassum fusiforme (788.89-2878.67 mg/kg) were significantly higher than those in Sargassum pallidum (585.33-1596.00 mg/kg). The variable contents in both species suggested that fixed raw materials are very important for future research and development. Orthogonal projection to latent structures discriminant analysis was carried out in the spectral region of δ 3.00-6.50 in the (1)H NMR spectrum. S. fusiforme and S. pallidum could be separated well, and the key sterol marker was fucosterol.

Synthesis of Polystyrene and Molecular Weight Determination by [superscript 1]H NMR End-Group Analysis

ERIC Educational Resources Information Center

Wackerly, Jay Wm.; Dunne, James F.

2017-01-01

A procedure for the solution polymerization of styrene using di-"tert"-butyl peroxide (DTBP) as the initiator is described. The use of DTBP allows for end-group analysis by [superscript 1]H NMR spectroscopy and calculation of the number-average molecular weight of the polymer. This experiment was designed as a laboratory introduction to…

Sealed magic angle spinning nuclear magnetic resonance probe and process for spectroscopy of hazardous samples

DOEpatents

Cho, Herman M.; Washton, Nancy M.; Mueller, Karl T.; Sears, Jr., Jesse A.; Townsend, Mark R.; Ewing, James R.

2016-06-14

A magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) probe is described that includes double containment enclosures configured to seal and contain hazardous samples for analysis. The probe is of a modular design that ensures containment of hazardous samples during sample analysis while preserving spin speeds for superior NMR performance and convenience of operation.

A simple protocol for NMR analysis of the enantiomeric purity of chiral hydroxylamines.

PubMed

Tickell, David A; Mahon, Mary F; Bull, Steven D; James, Tony D

2013-02-15

A practically simple three-component chiral derivatization protocol for determining the enantiopurity of chiral hydroxylamines by (1)H NMR spectroscopic analysis is described, involving their treatment with 2-formylphenylboronic acid and enantiopure BINOL to afford a mixture of diastereomeric nitrono-boronate esters whose ratio is an accurate reflection of the enantiopurity of the parent hydroxylamine.

NMR and IR Spectroscopy for the Structural Characterization of Edible Fats and Oils: An Instrumental Analysis Laboratory

ERIC Educational Resources Information Center

Crowther, Molly W.

2008-01-01

This article describes an upper-level instrumental laboratory for undergraduates that explores the complementary nature of IR and NMR spectroscopy for analysis of several edible fats and oils that are structurally similar but differ in physical properties and health implications. Five different fats and oils are analyzed for average chain length,…

A Protocol for NMR Analysis of the Enantiomeric Excess of Chiral Diols Using an Achiral Diboronic Acid Template.

PubMed

Tickell, David A; Lampard, Emma V; Lowe, John P; James, Tony D; Bull, Steven D

2016-08-05

A practically simple derivatization protocol for determining the enantiopurity of chiral diols by (1)H NMR spectroscopic analysis is described. Diols were treated with 0.5 equiv of 1,3-phenyldiboronic acid to afford mixtures of diastereomeric boronate esters whose homochiral/heterochiral ratios are an accurate reflection of the diol's enantiopurity.

Synthesis, high-resolution NMR spectroscopic analysis, and single-crystal X-ray diffraction of isoxazoline tetracycles.

PubMed

Fascio, Mirta L; Alvarez-Larena, Angel; D'Accorso, Norma B

2002-11-29

Three isoxazoline tetracycles were obtained enantiomerically pure by intramolecular 1,3-dipolar cycloaddition. The characterization of the new compounds was performed by high-resolution 1H and 13C NMR spectroscopy. The relative configuration of the new chiral centers was determined by NOESY experiments and confirmed by single-crystal X-ray structural analysis.

Chemical tagging of chlorinated phenols for their facile detection and analysis by NMR spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valdez, Carlos A.; Leif, Roald N.

2015-03-22

A derivatization method that employs diethyl (bromodifluoromethyl) phosphonate (DBDFP) to efficiently tag the endocrine disruptor pentachlorophenol (PCP) and other chlorinated phenols (CPs) along with their reliable detection and analysis by NMR is presented. The method accomplishes the efficient alkylation of the hydroxyl group in CPs with the difluoromethyl (CF 2H) moiety in extremely rapid fashion (5 min), at room temperature and in an environmentally benign manner. The approach proved successful in difluoromethylating a panel of 18 chlorinated phenols, yielding derivatives that displayed unique 1H, 19F NMR spectra allowing for the clear discrimination between isomerically related CPs. Due to its biphasicmore » nature, the derivatization can be applied to both aqueous and organic mixtures where the analysis of CPs is required. Furthermore, the methodology demonstrates that PCP along with other CPs can be selectively derivatized in the presence of other various aliphatic alcohols, underscoring the superiority of the approach over other general derivatization methods that indiscriminately modify all analytes in a given sample. The present work demonstrates the first application of NMR on the qualitative analysis of these highly toxic and environmentally persistent species.« less

Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

PubMed

Jeannerat, Damien

2017-01-01

The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Combined Application of UHPLC-QTOF/MS, HPLC-ELSD and 1 H-NMR Spectroscopy for Quality Assessment of DA-9801, A Standardised Dioscorea Extract.

PubMed

Kang, Kyo Bin; Ryu, Jayoung; Cho, Youngwoong; Choi, Sang-Zin; Son, Miwon; Sung, Sang Hyun

2017-05-01

DA-9801, a standardised 50% aqueous ethanolic extract of a mixture of Dioscorea japonica and D. nipponica, is a botanical drug candidate for the treatment of diabetic neuropathy, which finished its US phase II clinical trials recently. An advanced quality control method is needed for further development of DA-9801, considering its high contents of both primary and secondary metabolites. Development of a quality assessment strategy for DA-9801, based on the combination of UHPLC-QTOF/MS, HPLC-ELSD, and 1 H-NMR spectroscopy. The method was developed and tested with 15 batch products of DA-9801. The steroidal saponins of DA-9801 were tentatively identified by UHPLC-QTOF/MS and were quantified with the validated HPLC-ELSD method. Primary metabolites of DA-9801 were identified and profiled using 1 H-NMR spectrometry. The batch-to-batch equivalence of DA-9801 was tested with the 1 H-NMR spectra using spectral binning, correlation analysis, and principal component analysis. Six major saponins of DA-9801 were tentatively identified by UHPLC-QTOF/MS. Among them, protodioscin and dioscin were quantified by the validated HPLC-ELSD method. Twenty-six metabolites were identified in 1 H-NMR spectra. The similarity between DA-9801 batches could be evaluated with the NMR spectra of DA-9801. The 1 H-NMR method also revealed that two Dioscorea species contributed distinct amino acids to the contents of DA-9801. This study validates the effectiveness of UHPLC-QTOF/MS, HPLC-ELSD, and 1 H NMR-combined method for quality control of DA-9801 and its crude materials. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Conformational Aspects of the O-acetylation of C-tetra(phenyl)calixpyrogallol[4]arene.

PubMed

Casas-Hinestroza, José Luis; Maldonado, Mauricio

2018-05-20

Reaction between pyrogallol and benzaldehyde results in a conformational mixture of C- tetra(phenyl)pyrogallol[4]arene (crown and chair). The conformer mixture was separated using crystallization procedures and the structures were determined using FTIR, ¹H-NMR, and 13 C-NMR. O -acetylation of C- tetra(phenyl)pyrogallol[4]arene (chair) with acetic anhydride, in pyridine results in the formation of dodecaacetyl-tetra(phenyl)pyrogallol[4]arene. The structure was determined using ¹H-NMR and 13 C-NMR finding that the product maintains the conformation of the starting conformer. On the other hand, the O -acetylation reaction of C- tetra(phenyl)pirogallol[4]arene (crown) under same conditions proceeded efficiently, and its structure was determined using ¹H-NMR and 13 C-NMR. Dynamic ¹H-NMR of acetylated pyrogallolarene was studied by means of variable temperature in DMSO- d ₆ solution, and it revealed that two conformers are formed in the solution. Boat conformations for acetylated pyrogallolarene showed a slow interconversion at room temperature.

High-sensitivity NMR beyond 200,000 atmospheres of pressure

NASA Astrophysics Data System (ADS)

Meier, T.; Reichardt, S.; Haase, J.

2015-08-01

Pressure-induced changes in the chemical or electronic structure of solids require pressures well into the Giga-Pascal (GPa) range due to the strong bonding. Anvil cell designs can reach such pressures, but their small and mostly inaccessible sample chamber has severely hampered NMR experiments in the past. With a new cell design that has a radio frequency (RF) micro-coil in the high pressure chamber, NMR experiments beyond 20 Giga-Pascal are reported for the first time. 1 H NMR of water shows sensitivity and resolution obtained with the cells, and 63 Cu NMR on a cuprate superconductor (YBa2Cu3O7-δ) demonstrates that single-crystals can be investigated, as well. 115 In NMR of the ternary chalcogenide AgInTe2 discovers an insulator-metal transition with shift and relaxation measurements. The pressure cells can be mounted easily on standard NMR probes that fit commercial wide-bore magnets with regular cryostats for field- and temperature-dependent measurements ready for many applications in physics and chemistry.

Comparing pharmacophore models derived from crystallography and NMR ensembles

NASA Astrophysics Data System (ADS)

Ghanakota, Phani; Carlson, Heather A.

2017-11-01

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225-8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the "extra" pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor-Pashow, K.; Fondeur, F.; White, T.

Savannah River National Laboratory (SRNL) was tasked with identifying and developing at least one, but preferably two methods for quantifying the suppressor in the Next Generation Solvent (NGS) system. The suppressor is a guanidine derivative, N,N',N"-tris(3,7-dimethyloctyl)guanidine (TiDG). A list of 10 possible methods was generated, and screening experiments were performed for 8 of the 10 methods. After completion of the screening experiments, the non-aqueous acid-base titration was determined to be the most promising, and was selected for further development as the primary method. {sup 1}H NMR also showed promising results from the screening experiments, and this method was selected formore » further development as the secondary method. Other methods, including {sup 36}Cl radiocounting and ion chromatography, also showed promise; however, due to the similarity to the primary method (titration) and the inability to differentiate between TiDG and TOA (tri-n-ocytlamine) in the blended solvent, {sup 1}H NMR was selected over these methods. Analysis of radioactive samples obtained from real waste ESS (extraction, scrub, strip) testing using the titration method showed good results. Based on these results, the titration method was selected as the method of choice for TiDG measurement. {sup 1}H NMR has been selected as the secondary (back-up) method, and additional work is planned to further develop this method and to verify the method using radioactive samples. Procedures for analyzing radioactive samples of both pure NGS and blended solvent were developed and issued for the both methods.« less

Crossover from Commensurate to Incommensurate Antiferromagnetism in Stoichiometric NaFeAs Revealed by Single-Crystal 23Na,75As-NMR Experiments

NASA Astrophysics Data System (ADS)

Kitagawa, Kentaro; Mezaki, Yuji; Matsubayashi, Kazuyuki; Uwatoko, Yoshiya; Takigawa, Masashi

2011-03-01

We report the results of 23Na and 75As nuclear magnetic resonance (NMR) experiments on a self-flux grown high-quality single crystal of stoichiometric NaFeAs. The NMR spectra reveal a tetragonal to twinned-orthorhombic structural phase transition at TO = 57 K and an antiferromagnetic (AF) transition at TAF = 45 K. The divergent behavior of nuclear relaxation rate near TAF shows significant anisotropy, indicating that the critical slowing down of stripe-type AF fluctuations are strongly anisotropic in spin space. The NMR spectra at sufficiently low temperatures consist of sharp peaks showing a commensurate stripe AF order with a small moment of ˜0.3 μB. However, the spectra just below TAF exhibit a highly asymmetric broadening pointing to an incommensurate modulation. The commensurate-incommensurate crossover in NaFeAs shows a certain similarity to the behavior of SrFe2As2 under high pressure.

Metabolomic differentiation of maca (Lepidium meyenii) accessions cultivated under different conditions using NMR and chemometric analysis.

PubMed

Zhao, Jianping; Avula, Bharathi; Chan, Michael; Clément, Céline; Kreuzer, Michael; Khan, Ikhlas A

2012-01-01

To gain insights on the effects of color type, cultivation history, and growing site on the composition alterations of maca (Lepidium meyenii Walpers) hypocotyls, NMR profiling combined with chemometric analysis was applied to investigate the metabolite variability in different maca accessions. Maca hypocotyls with different colors (yellow, pink, violet, and lead-colored) cultivated at different geographic sites and different areas were examined for differences in metabolite expression. Differentiations of the maca accessions grown under the different cultivation conditions were determined by principle component analyses (PCAs) which were performed on the datasets derived from their ¹H NMR spectra. A total of 16 metabolites were identified by NMR analysis, and the changes in metabolite levels in relation to the color types and growing conditions of maca hypocotyls were evaluated using univariate statistical analysis. In addition, the changes of the correlation pattern among the metabolites identified in the maca accessions planted at the two different sites were examined. The results from both multivariate and univariate analysis indicated that the planting site was the major determining factor with regards to metabolite variations in maca hypocotyls, while the color of maca accession seems to be of minor importance in this respect. © Georg Thieme Verlag KG Stuttgart · New York.

A biofilm microreactor system for simultaneous electrochemical and nuclear magnetic resonance techniques.

PubMed

Renslow, R S; Babauta, J T; Majors, P D; Mehta, H S; Ewing, R J; Ewing, T W; Mueller, K T; Beyenal, H

2014-01-01

Nuclear magnetic resonance (NMR) techniques are ideally suited for the study of biofilms and for probing their microenvironments because these techniques allow for noninvasive interrogation and in situ monitoring with high resolution. By combining NMR with simultaneous electrochemical techniques, it is possible to sustain and study live biofilms respiring on electrodes. Here, we describe a biofilm microreactor system, including a reusable and a disposable reactor, that allows for simultaneous electrochemical and NMR techniques (EC-NMR) at the microscale. Microreactors were designed with custom radio frequency resonator coils, which allowed for NMR measurements of biofilms growing on polarized gold electrodes. For an example application of this system we grew Geobacter sulfurreducens biofilms on electrodes. EC-NMR was used to investigate growth medium flow velocities and depth-resolved acetate concentration inside the biofilm. As a novel contribution we used Monte Carlo error analysis to estimate the standard deviations of the acetate concentration measurements. Overall, we found that the disposable EC-NMR microreactor provided a 9.7 times better signal-to-noise ratio over the reusable reactor. The EC-NMR biofilm microreactor system can ultimately be used to correlate extracellular electron transfer rates with metabolic reactions and explore extracellular electron transfer mechanisms.

Metabolomics analysis of follicular fluid in women with ovarian endometriosis undergoing in vitro fertilization.

PubMed

Karaer, Abdullah; Tuncay, Gorkem; Mumcu, Akın; Dogan, Berat

2018-05-28

The purpose of this study was to investigate whether a change in the follicular fluid metabolomics profile due to endometrioma is identifiable. Twelve women with ovarian endometriosis (aged<40 years, with a body mass index [BMI] of <30 kg/m 2 ) and 12 age- and BMI-matched controls (women with infertility purely due to a male factor) underwent ovarian stimulation for intracytoplasmic sperm injection (ICSI). Follicular fluid samples were collected from both of groups at the time of oocyte retrieval for ICSI. Next, nuclear magnetic resonance (NMR) spectroscopy was performed for the collected follicular fluids. The metabolic compositions of the follicular fluids were then compared using univariate and multivariate statistical analyses of NMR data. Univariate and multivariate statistical analyses of NMR data showed that the metabolomic profiles of the follicular fluids obtained from the women with ovarian endometriosis were distinctly different from those obtained from the control group. In comparison with the controls, the follicular fluids of the women with ovarian endometriosis had statistically significant elevated levels of lactate, β-glucose, pyruvate, and valine. We conclude that the levels of lactate, β-glucose, pyruvate, and valine in the follicular fluid of the women with endometrioma were higher than those of the controls. ASRM: American Society for Reproductive Medicine; BMI: body mass index; CPMG: Carr-Purcell-Meiboom-Gill; E 2 : estradiol; ESHRE: European Society of Human Reproduction and Embryology; ERETIC: electronic to access in vivo concentration; FF: follicular fluid; FSH: follicle-stimulating hormone; hCG: human chorionic gonadotropin; HEPES: 2-hydroxyethyl-1-piperazineethanesulfonic acid; ICSI: intracytoplasmic sperm injection; IVF: in vitro fertilization; NMR: nuclear magnetic resonance spectroscopy; PCA: principal component analysis; PCOS: polycystic ovary syndrome; PLS-DA: partial least squares discriminant analysis; ppm: parts per million; PULCON: pulse length-based concentration determination; TSP: 3-(trimethylsilyl)-1-propanesulfonic acid sodium salt; VIP: variable importance in projection.

Advances in the Determination of the Speciation of the Carbon Associated with Biogenic Silica Produced by Plants

NASA Astrophysics Data System (ADS)

Masion, A.; Alexandre, A. E.; Ziarelli, F.; Viel, S.; Santos, G.

2016-12-01

Biogenic silica resulting from the precipitation of dissolved Si through biological processes in plants, often contains small amounts of occluded organic carbon. These phases, called phytoliths, have a long persistence in soils, making them tracers of past conditions. In this context, the knowledge of the carbon speciation associated with phytoliths bears significant importance in examining the carbon dynamics in soils. With carbon concentrations as low as the 0.1% range, examining the nature of organic carbon remains very challenging, and available tools (e.g. pyrolysis) are often prone to serious artifacts. Recent improvements of microwave sources enabled the application of the Dynamic Nuclear Polarization (DNP) technique to NMR, thereby establishing a new non-destructive tool for the qualitative and quantitative determination of the carbon speciation. Applied to the analysis of phytoliths, this method showed the presence of carbons from different sources within the sample: About 20% of the signal correspond to carbohydrates, and are assigned to photosynthetic carbon; the marked alkyl, N-alkyl and carbonyl signals indicate a significant proportion of proteins. This is consistent with the hypothesis that parts of the carbon associated with the phytoliths is imported into the host plant via uptake from the soil. Finally, lignins, glomalin-like and/or humic-like compounds are minor species associated with biogenic silica. This speciation was obtained overnight with a DNP-NMR set-up with an excellent sensitivity (few tens of weight ppm); the same spectrum on a standard NMR spectrometer would have required at least 250 days of data acquisition. The considerable gain in sensitivity associated with the use of DNP now makes NMR a relevant technique for the analysis of environmental samples.

pH optimization for a reliable quantification of brain tumor cell and tissue extracts with (1)H NMR: focus on choline-containing compounds and taurine.

PubMed

Robert, O; Sabatier, J; Desoubzdanne, D; Lalande, J; Balayssac, S; Gilard, V; Martino, R; Malet-Martino, M

2011-01-01

The aim of this study was to define the optimal pH for (1)H nuclear magnetic resonance (NMR) spectroscopy analysis of perchloric acid or methanol-chloroform-water extracts from brain tumor cells and tissues. The systematic study of the proton chemical shift variations as a function of pH of 13 brain metabolites in model solutions demonstrated that recording (1)H NMR spectra at pH 10 allowed resolving resonances that are overlapped at pH 7, especially in the 3.2-3.3 ppm choline-containing-compounds region. (1)H NMR analysis of extracts at pH 7 or 10 showed that quantitative measurements of lactate, alanine, glutamate, glutamine (Gln), creatine + phosphocreatine and myo-inositol (m-Ino) can be readily performed at both pHs. The concentrations of glycerophosphocholine, phosphocholine and choline that are crucial metabolites for tumor brain malignancy grading were accurately measured at pH 10 only. Indeed, the resonances of their trimethylammonium moieties are cleared of any overlapping signal, especially those of taurine (Tau) and phosphoethanolamine. The four non-ionizable Tau protons resonating as a singlet in a non-congested spectral region permits an easier and more accurate quantitation of this apoptosis marker at pH 10 than at pH 7 where the triplet at 3.43 ppm can be overlapped with the signals of glucose or have an intensity too low to be measured. Glycine concentration was determined indirectly at both pHs after subtracting the contribution of the overlapped signals of m-Ino at pH 7 or Gln at pH 10.

Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

NASA Astrophysics Data System (ADS)

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-02-01

In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

PubMed Central

Verdi, Kacy K; Ellis, Heidi JC; Gryk, Michael R

2007-01-01

Background Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. Results We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Conclusion Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment. PMID:17263870

Combination of 1H nuclear magnetic resonance spectroscopy and principal component analysis to evaluate the lipid fluidity of flutamide-encapsulated lipid nanoemulsions.

PubMed

Takegami, Shigehiko; Ueyama, Keita; Konishi, Atsuko; Kitade, Tatsuya

2018-06-06

The lipid fluidity of various lipid nanoemulsions (LNEs) without and with flutamide (FT) and containing one of two neutral lipids, one of four phosphatidylcholines as a surfactant, and sodium palmitate as a cosurfactant was investigated by the combination of 1 H nuclear magnetic resonance (NMR) spectroscopy and principal component analysis (PCA). In the 1 H NMR spectra, the peaks from the methylene groups of the neutral lipids and surfactants for all LNE preparations showed downfield shifts with increasing temperature from 20 to 60 °C. PCA was applied to the 1 H NMR spectral data obtained for the LNEs. The PCA resulted in a model in which the first two principal components (PCs) extracted 88% of the total spectral variation; the first PC (PC-1) axis and second PC (PC-2) axis accounted for 73 and 15%, respectively, of the total spectral variation. The Score-1 values for PC-1 plotted against temperature revealed the existence of two clusters, which were defined by the neutral lipid of the LNE preparations. Meanwhile, the Score-2 values decreased with rising temperature and reflected the increase in lipid fluidity of each LNE preparation, consistent with fluorescence anisotropy measurements. In addition, the changes of Score-2 values with temperature for LNE preparations with FT were smaller than those for LNE preparations without FT. This indicates that FT encapsulated in LNE particles markedly suppressed the increase in lipid fluidity of LNE particles with rising temperature. Thus, PCA of 1 H NMR spectra will become a powerful tool to analyze the lipid fluidity of lipid nanoparticles. Graphical abstract ᅟ.

NMR-based metabolomic urinalysis: a rapid screening test for urinary tract infection.

PubMed

Lam, Ching-Wan; Law, Chun-Yiu; To, Kelvin Kai-Wang; Cheung, Stanley Kwok-Kuen; Lee, Kim-Chung; Sze, Kong-Hung; Leung, Ka-Fai; Yuen, Kwok-Yung

2014-09-25

Urinary tract infection (UTI) is one of the most common bacterial infections in humans; however, there is no accurate and fast quantitative test to detect UTI. Dipstick urinalysis is semi-quantitative with a limited diagnostic accuracy, while urine culture is accurate but takes time. We described a quantitative biochemical method for the diagnosis of bacteriuria using a single marker. We compared the urine metabolomes from 88 patients with bacterial UTI and 61 controls using (1)H NMR spectroscopy followed by principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA). The biomarker identified was subsequently validated using independent samples. The urine acetic acid/creatinine (mmol/mmol) level was determined to be the most discriminatory marker for bacterial UTI with an area-under-receiver operating characteristic curve=0.97, sensitivity=91% and specificity=95% at the optimal cutoff 0.03 mmol/mmol. For validation, 60 samples were recruited prospectively. Using the optimal cutoff for acetic acid/creatinine, this method showed sensitivity=96%, specificity=94%, positive predictive value=92%, negative predictive value=97% and an overall accuracy=95%. The diagnostic performance was superior to dipstick urinalysis or microscopy. In addition, we also observed an increase of urinary trimethylamine (TMA) in patients with Escherichia coli-associated UTI. TMA is a mammalian-microbial co-metabolite and the high level of TMA generated is related to the bacterial enzyme, trimethylamine N-oxide (TMAO) reductase which reduces TMAO to TMA. Urine acetic acid is a neglected metabolite that can be used for rapid diagnosis of UTI and TMA can be used for etiologic diagnosis of UTI. With the introduction of NMR-based clinical analyzers to clinical laboratories, NMR-based urinalysis can be translated for clinical use. Copyright © 2014 Elsevier B.V. All rights reserved.

Conceptual-level workflow modeling of scientific experiments using NMR as a case study.

PubMed

Verdi, Kacy K; Ellis, Heidi Jc; Gryk, Michael R

2007-01-30

Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment.

A Quick and Easy Simplification of Benzocaine's NMR Spectrum

NASA Astrophysics Data System (ADS)

Carpenter, Suzanne R.; Wallace, Richard H.

2006-04-01

The preparation of benzocaine is a common experiment used in sophomore-level organic chemistry. Its straightforward procedure and predictable good yields make it ideal for the beginning organic student. Analysis of the product via NMR spectroscopy, however, can be confusing to the novice interpreter. An inexpensive, quick, and effective method for simplifying the NMR spectrum is reported. The method results in a spectrum that is cleanly integrated and more easily interpreted.

Biodiversity in targeted metabolomics analysis of filamentous fungal pathogens by 1H NMR-based studies.

PubMed

Ząbek, Adam; Klimek-Ochab, Magdalena; Jawień, Ewa; Młynarz, Piotr

2017-07-01

The taxonomical classification among fungi kingdom in the last decades was evolved. In this work the targeted metabolomics study based on 1 H NMR spectroscopy combined with chemometrics tools was reported to be useful for differentiation of three model of fungal strains, which represent various genus of Ascomycota (Aspergillus pallidofulvus, Fusarium oxysporum, Geotrichum candidum) were selected in order to perform metabolomics studies. Each tested species, revealed specific metabolic profile of primary endo-metabolites. The species of A. pallidofulvus is represented by the highest concentration of glycerol, glucitol and Unk5. While, F. oxysporum species is characterised by increased level of propylene glycol, ethanol, 4-aminobutyrate, succinate, xylose, Unk1 and Unk4. In G. candidum, 3-methyl-2-oxovalerate, glutamate, pyruvate, glutamine and citrate were elevated. Additionally, a detailed analysis of metabolic changes among A. pallidofulvus, F. oxysporum and G. candidum showed that A. pallidofulvus seems to be the most pathogenic fungi. The obtained results demonstrated that targeted metabolomics analysis could be utilized in the future as a supporting taxonomical tool for currently methods.

Metabolomics study of Saw palmetto extracts based on 1H NMR spectroscopy.

PubMed

de Combarieu, Eric; Martinelli, Ernesto Marco; Pace, Roberto; Sardone, Nicola

2015-04-01

Preparations containing Saw palmetto extracts are used in traditional medicine to treat benign prostatic hyperplasia. According to the European and the American Pharmacopoeias, the extract is obtained from comminuted Saw palmetto berries by a suitable extracting procedure using ethanol or supercritical carbon dioxide or a mixture of n-hexane and methylpentanes. In the present study an approach to metabolomics profiling using nuclear magnetic resonance (NMR) has been used as a finger-printing tool to assess the overall composition of the extracts. The phytochemical analysis coupled with principal component analysis (PCA) showed the same composition of the Saw palmetto extracts obtained with carbon dioxide and hexane with minor not significant differences for extracts obtained with ethanol. In fact these differences are anyhow lower than the batch-to-batch variability ascribable to the natural-occurring variability in the Saw palmetto fruits' phytochemical composition. The fingerprinting analysis combined with chemometric method, is a technique, which would provide a tool to comprehensively assess the quality control of Saw palmetto extracts. Copyright © 2015 Elsevier B.V. All rights reserved.

NMR analysis of compositional heterogeneity in polysaccharides

USDA-ARS?s Scientific Manuscript database

Many copolysaccharides are compositionally heterogeneous, and the composition determined by the usual analytical or spectroscopic methods provides only an average value. For some polysaccharides, the NMR data contain copolymer sequence information, such as diad, triad, and tetrad sequence intensiti...

Advanced Laboratory NMR Spectrometer with Applications.

ERIC Educational Resources Information Center

Biscegli, Clovis; And Others

1982-01-01

A description is given of an inexpensive nuclear magnetic resonance (NMR) spectrometer suitable for use in advanced laboratory courses. Applications to the nondestructive analysis of the oil content in corn seeds and in monitoring the crystallization of polymers are presented. (SK)

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

DOE PAGES

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao; ...

2017-12-05

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

Structural investigation, spectroscopic and energy level studies of Schiff base: 2-[(3‧-N-salicylidenephenyl)benzimidazole] using experimental and DFT methods

NASA Astrophysics Data System (ADS)

Suman, G. R.; Bubbly, S. G.; Gudennavar, S. B.; Muthu, S.; Roopashree, B.; Gayatri, V.; Nanje Gowda, N. M.

2017-07-01

The Schiff base 2-[(3‧-N-salicylidenephenyl)benzimidazole] (Spbzl) was characterized by FT-Raman, 1H NMR, 13C NMR and single crystal X-ray diffraction technique. Crystallographic studies reveal the presence of two water molecules in the asymmetry unit which aid the intermolecular hydrogen bonding with imidazole ring, and the trans-conformation of the azomethine bond. Theoretical computations conducted using density functional theory (DFT) analysis support the experimental facts. Energy levels estimated by DFT studies are in good agreement with the values obtained from cyclic voltammetry technique. Frontier molecular orbital analysis shows that charge transfer has taken place from donor to acceptor moiety, which is also supported by the high hyperpolarizability values in both gaseous and solution phases, indicating high charge transfer capability of the molecule. A comparative theoretical study of Spbzl with derivative 4-((3-(1H-benzimidazol-2-yl)phenylimino)methyl)-3-hydroxybenzoic acid (Pbzlb) having an added anchor group COOH substituted at para position in the acceptor ring has been made. The result shows the feasibility of charge transfer to the semiconductor surface in dye sensitized solar cell (DSSC) applications for Pbzlb.

Solubilization of ibuprofen with β-cyclodextrin derivatives: energetic and structural studies.

PubMed

di Cagno, Massimiliano; Stein, Paul C; Skalko-Basnet, Nataša; Brandl, Martin; Bauer-Brandl, Annette

2011-06-01

The aim of this work was to investigate the complexation of ibuprofen as model drug with various β-cyclodextrins (native β-cyclodextrin, hydroxypropyl-β-cyclodextrin with two different molar degrees of substitution, and methyl-β-cyclodextrin). Solutions of the commercially available β-cyclodextrins were prepared in phosphate buffer (73mM). The pH value was adjusted to 7.4 and the solutions were isotonized with NaCl. A solution of ibuprofen was prepared in the same way. A thermal activity monitor was used for isothermal titration calorimetry (ITC). (1)H NMR analysis was employed to investigate the structures of the complexes. ITC analysis showed that each type of β-cyclodextrin had its characteristic values of both enthalpy and mass equilibrium constant for the complexation processes with the drug molecules. (1)H NMR spectroscopy of the complexes showed through significant differences in chemical shifts that the physical interaction between the cyclodextrins and ibuprofen molecules were also different, probably due to different three-dimensional arrangements of ibuprofen in the cyclodextrin cavity, induced by the different substituents bonded to the glucose rings. These differences were connected to the thermodynamic parameters of the complexes. Copyright © 2011 Elsevier B.V. All rights reserved.

Real-time oil-saturation monitoring in rock cores with low-field NMR.

PubMed

Mitchell, J; Howe, A M; Clarke, A

2015-07-01

Nuclear magnetic resonance (NMR) provides a powerful suite of tools for studying oil in reservoir core plugs at the laboratory scale. Low-field magnets are preferred for well-log calibration and to minimize magnetic-susceptibility-induced internal gradients in the porous medium. We demonstrate that careful data processing, combined with prior knowledge of the sample properties, enables real-time acquisition and interpretation of saturation state (relative amount of oil and water in the pores of a rock). Robust discrimination of oil and brine is achieved with diffusion weighting. We use this real-time analysis to monitor the forced displacement of oil from porous materials (sintered glass beads and sandstones) and to generate capillary desaturation curves. The real-time output enables in situ modification of the flood protocol and accurate control of the saturation state prior to the acquisition of standard NMR core analysis data, such as diffusion-relaxation correlations. Although applications to oil recovery and core analysis are demonstrated, the implementation highlights the general practicality of low-field NMR as an inline sensor for real-time industrial process control. Copyright © 2015 Elsevier Inc. All rights reserved.

Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pecher, Oliver; Bayley, Paul M.; Liu, Hao

We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insightmore » into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep 7Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, 31P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. 31P in situ NMR with “on-the-fly” re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of 31P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC 23Na in situ NMR on symmetrical Na–Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and electrolyte peak, respectively. Thus, interleaved measurements with different optimal NMR set-ups for the metal and electrolyte, respectively, became possible. This allowed the formation of different Na metal species as well as a quantification of electrolyte consumption during the electrochemical experiment to be monitored. The new approach is likely to benefit a further understanding of Na-ion battery chemistries.« less

Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries

NASA Astrophysics Data System (ADS)

Pecher, Oliver; Bayley, Paul M.; Liu, Hao; Liu, Zigeng; Trease, Nicole M.; Grey, Clare P.

2016-04-01

We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insight into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep 7Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, 31P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. 31P in situ NMR with "on-the-fly" re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of 31P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC 23Na in situ NMR on symmetrical Na-Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and electrolyte peak, respectively. Thus, interleaved measurements with different optimal NMR set-ups for the metal and electrolyte, respectively, became possible. This allowed the formation of different Na metal species as well as a quantification of electrolyte consumption during the electrochemical experiment to be monitored. The new approach is likely to benefit a further understanding of Na-ion battery chemistries.

Decursin: a cytotoxic agent and protein kinase C activator from the root of Angelica gigas.

PubMed

Ahn, K S; Sim, W S; Kim, I H

1996-02-01

A cytotoxic compound was purified from the root of Angelica gigas Nakai by silica gel chromatography and preparative HPLC. As a result of the structure analysis by mass, IR, 1H-NMR, and 13C-NMR spectrometry, the effective compound was identified as decursin, a pyranocoumarin characterized originally from Angelica decursiva Fr. et Sav. In vitro cytotoxicity testing showed that decursin displayed toxic activity against various human cancer cell lines, for which the ED50 of decursin was about 5-16 micrograms/ml. On the other hand, decursin displayed relatively low cytotoxicity against normal fibroblasts. Decursin also activated protein kinase C (PKC) in vitro, which indicates that the cytotoxic activity of decursin may be related to the protein kinase C activation.

Tautomeric equilibria in solutions of 1-methyl-2-phenacylbenzimidazoles

NASA Astrophysics Data System (ADS)

Skotnicka, Agnieszka; Czeleń, Przemysław; Gawinecki, Ryszard

2017-04-01

Until now the susceptibility of 1-methyl-2-phenacylbenzimidazoles to the proton transfer has not been carefully examined. There only have been selective trials to recognize tautomeric equilibrium of substituted compounds. Unfortunately, conclusions of these studies are often conflicting. Therefore, the aim of this work was to analyze the influence of the factors affecting the tautomeric processes of substituted 1-methyl-2-phenacylbenzimidazoles in solutions of chloroform by spectroscopic technique of 1H and 13C NMR. Complex equilibria may only take place when molecules of tautomeric species contain multiple basic and/or acidic centres. Analysis of NMR spectra show unequivocally that 1-methyl-2-phenacylbenzimidazoles (ketimine tautomeric form) are in equilibrium with (Z)-2-(1-methyl-1H-benzo[d]imidazol-2yl)-1-phenylethenols (enolimine).