Performance Assessment in Fingerprinting and Multi Component Quantitative NMR Analyses

An interlaboratory comparison (ILC) was organized with the aim to set up quality control indicators suitable for multicomponent quantitative analysis by nuclear magnetic resonance (NMR) spectroscopy. A total of 36 NMR data sets (corresponding to 1260 NMR spectra) were produced by 30 participants using 34 NMR spectrometers. The calibration line method was chosen for the quantification of a five-component model mixture. Results show that quantitative NMR is a robust quantification tool and that 26 out of 36 data sets resulted in statistically equivalent calibration lines for all considered NMR signals. The performance of each laboratory was assessed by means of a new performance index (named Qp-score) which is related to the difference between the experimental and the consensus values of the slope of the calibration lines. Laboratories endowed with a Qp-score falling within the suitable acceptability range are qualified to produce NMR spectra that can be considered statistically equivalent in terms of relative intensities of the signals. In addition, the specific response of nuclei to the experimental excitation/relaxation conditions was addressed by means of the parameter named NR. NR is related to the difference between the theoretical and the consensus slopes of the calibration lines and is specific for each signal produced by a well-defined set of acquisition parameters

Competitive Na+ and Rb+ binding in the minor groove of DNA

Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. Here, we present new Na-23 and Rb-87 magnetic relaxation dispersion (MRD) data that demonstrate competitive and long-lived binding of Na+ and Rb+ ions in the minor groove of the B-DNA duplex [d(CGCGAATTCGCG)](2). The Na+/Rb+ selectivity of the minor groove is found to be weak, consistent with local structural flexibility. The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. For example, in the presence of 0.20 M Na+ and 0.56 M Rb+ at 4 degreesC, the ApT site in the minor groove is occupied by a Rb+ ion, a Na+ ion, or a water molecule 40, 10, and 50% of the time, respectively. In the absence of Rb+, the Na+ occupancy increases to 50%. At 4 degreesC, the mean residence time of groove-bound ions is 0.2 +/- 0.1 mus for Rb+ and 10 ns to 100 mus for Na+. A shorter correlation time of 2 ns is attributed to counterions bridging cross-strand phosphate groups

An energy dispersive x-ray scattering and molecular dynamics study of liquid dimethyl carbonate

In this work, we report on the first x-ray diffraction study on liquid dimethyl carbonate. Diffraction spectra were collected with an energy-dispersive instrument, whose wide Q-range allows the structure determination of weakly ordered systems (such as liquids). The structural correlation in this liquid ranges up to about 20 A degrees. The observed patterns are interpreted with a structural model derived from classical molecular dynamics simulations. The simulations were run using OPLS force field, only slightly modified to restrain bond distances to the experimental values. The model structure function and radial distribution functions, averaged among the productive trajectory frames, are in very good agreement with the corresponding experimental ones. Molecular dynamics results show that the deviations from C(2v) cis-cis structure, predicted by ab initio calculations and observed by electron diffraction in the gas phase, are small. By analyzing the intra- and intermolecular pair distribution functions, it was possible to assign the peaks of the experimental radial distribution function to specific structural correlations, and to compute the different average intermolecular coordination numbers. The intermolecular methyl-carbonyl oxygen distance is thoroughly discussed to assess the presence of weak C-H center dot center dot O hydrogen bonds

Effect of rubidium and cesium ions on the dimeric quaduplex formed by the Oxytricha nova telomeric repeat oligonucleotide d(GGGGTTTTGGGG)

The DNA sequence d(GGGGTTTTGGGG) consists of 1.5 units of the repeat in telomeres of Oxytricha nova. It has been shown by NMR and x-ray crystallographic analysis that it is capable to form a dimeric quadruplex structure and that a variety of cations, namety K+, Na+, and NH4+, are able to interact with this complex with different affinity, leading to complexes characterized by different local conformations. Thus, in order to improve the knowledge of this kind of molecule, and in particular to Providejurther insight into the role of monovalent cations in the G-quadruplex folding and conformation, we have investigated by H-1-NMR the effect of the addition of Rb+ and Cs+ to the quadruplex formed by the oligonucleotide d(GGGGTTTTGGGG)

Metabolic responses of clams, Ruditapes decussatus and Ruditapes philippinarum, to short-term exposure to lead and zinc

This study investigated the effects of 48h heavy metal exposure upon the metabolic profiles of Ruditapes decussatus and Ruditapes philippinarum using 1H NMR metabolomics. Both species were exposed to increasing concentrations of lead nitrate (10, 40, 60 and 100μg/L) and zinc chloride (20, 50, 100 and 150μg/L), under laboratory conditions. ICP-OES analysis was further performed on the clams' samples in order to verify the occurrence of heavy metal bioaccumulation. With respect to the controls, the metabolic profiles of treated R. decussatus exhibited higher levels of organic osmolytes and lower contents of free amino acids. An opposite behavior was shown by R. philippinarum. In terms of heavy metal, the exposure effects were more evident in the case of Pb rather than Zn. These findings show that NMR-based metabolomics has the required sensitivity and specificity for the identification of metabolites that can act as sensitive indicators of contaminant-induced stres

Definition of food quality by NMR-based foodomics

Quality definition of food includes several complex factors like physical, compositional and microbial features, modifications induced by technological processes or storage, nutritional value and safety. Foodomics is a holistic approach applying omics technologies to observe food along the entire production/consumption chain. In the present review, we present key applications of nuclear magnetic resonance in foodomics described in the 2012–2015 period, in the quest for robust and thorough information required by the scientific community. In doing so, we summarize the issues connected to food traceability and authenticity, composition and physical characteristics, processing and storage and health, that mostly impact food qualit

NMR, calorimetry, and computational studies of aqueous solutions of N-methyl-2-pyrrolidone

N-Methyl-2-pyrrolidone (NMP) is a solvent with applications in different industrial fields. Although largely employed in aqueous mixtures, little is known on the structural and dynamic properties of this system. In order to improve the knowledge on NMP aqueous solutions, useful to the development of their applications, NMR spectroscopy, calorimetric titration, and puckering analysis of molecular dynamics (MD) simulations were employed in this work. Our calorimetric study evidenced the presence of strong interactions between NMP and water and revealed that, under comparable conditions, the solvation of NMP by water results in an interaction stronger than the solvation of water by NMP. Overall, the changes of H-1 and C-13 chemical shifts and 2D ROESY spectra upon dilution suggested a preferential location of water nearby the carbonyl group of NMP and the formation of hydrogen bonding between these two molecules. In parallel, observation of correlation times by C-13 NMR spectroscopy evidenced a different dynamic behavior moving from the NMP-rich region to the water-rich region, characterized by a maximum value at about 0.7 water mole fraction. MD simulations showed that the NMP conformation remains the same over the whole concentration range. Our results were discussed in terms of changes in the NMP assembling upon dilution

The structural organization of N -methyl-2-pyrrolidone + water mixtures: a densitometry, x-ray diffraction, and molecular dynamics study

A combined approach of molecular dynamics simulations, wide angle X-ray scattering experiments, and density measurements was employed to study the structural properties of N-methyl-2-pyrrolidone (NMP) + water mixtures over the whole concentration range. Remarkably, a very good agreement between computed and experimental densities and diffraction patterns was achieved, especially if the effect of the mixture composition on NMP charges is taken into account. Analysis of the inter- molecular organization, as revealed by the radial and spatial distribution functions of relevant solvent atoms, nicely explained the density maximum observed experimentally

A spectroscopic study on ionization of 2-, 3- and 4-aminopyridines

The first ionization constants of the 2-, 3-, and 4-aminopyridines were evaluated by spectrophotometric methods using Evolving Factor Analysis approach. The ionization constants of aniline and pyridine were estimated by potentiometric methods in the same experimental conditions for comparison. A C-13 NMR spectroscopy study is here presented to assess the protonation site in aminopyridines and to evaluate the resonance effects