Low-resolution NMR Research Articles

A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias

We introduce PMF*, a novel potential of mean force (PMF) for the Ramachandran ϕ/Ψ dihedral plot of the 20 standard amino acids and assess its relevance to the conformation of polypeptides by scoring structures in the protein data bank and decoy datasets. The new energy function is a linear combination of the conventional, unreferenced PMF and the ΔPMF relative to the free energy of all amino acids in the parameterization set of structures, effectively removing their respective biases toward α-helix and β-strand. It is shown that low-resolution crystal structures, NMR structures, and theoretical models have on average significantly higher energies than high-resolution crystal structures; also PMF* is more discriminative for structure quality than the individual PMF and ΔPMF energy functions. PMF* may be well suited for use as a restraint energy term in the refinement of experimental structures and theoretical models.

Glycerol as a reference material for fecal fat quantitation using low-resolution time domain 1H NMR spectroscopy

Objectives To assess glycerol as reference material for low-resolution time-domain 1H NMR analysis of fecal fat. Design and methods NMR analysis of fecal fat in stool samples with added glycerol was used to assess linearity, recovery, and relationship with NMR lipid signal. Results The study revealed for added glycerol excellent linearity (r = 0.9998), recovery (101–104%), and linear relationship with simulated fecal fat content. Conclusions Glycerol is an effective reference material for NMR fecal fat analysis.

Monitoring the Transesterification Reaction Used in Biodiesel Production, with a Low Cost Unilateral Nuclear Magnetic Resonance Sensor

The transesterification reaction used to produce biodiesel was monitored with 1H high-resolution nuclear magnetic resonance (HRNMR), conventional low-resolution NMR (LRNMR), and unilateral NMR (UNM...

Applicability of solid state fast field cycling NMR relaxometry in understanding relaxation properties of leaves and leaf-litters

Inversion recovery high field solid state (SS) 1H NMR spectroscopy and fast field cycling (FFC) NMR relaxometry have been applied on dried leaves and leaf-litters from a reafforestated area in central Sicily (Italy) in order to evaluate relaxation properties in both slow ( 1 ≪ ω 0 2 τ C 2 ) and fast ( 1 ≫ ω 0 2 τ C 2 ) motion regimes. Namely, SS 1H NMR spectroscopy (i.e. slow motion regime conditions) revealed that two relaxation components (a fast and a slow one) can be identified in all the leaves and leaf-litter samples. The fast component was assigned to small sized plant metabolites, whereas the slow one was attributed to slowly tumbling macropolymeric molecules. FFC NMR relaxometry (i.e. fast motion regime conditions) indicated that intra- and inter-segmental motional contributions to plant relaxation occur, depending on the nature of the plant sample under investigation. The present study represents the first example of a combination of high and low resolution NMR techniques for the understanding of the dynamics properties of environmentally relevant soft matter such as leaves and leaf-litters. These materials are considered among the main contributors for the synthesis of natural organic matter. For this reason, a comprehension of their basic molecular dynamics properties is a crucial point to evaluate their effect on, e.g., carbon cycle, fate of organic and inorganic pollutants, and microbial biomass grow.

Enclosed Volume Determination of Concentrated Dioctadecyldimethylammonium Chloride (DODAC) Vesicular Dispersions by Low-Resolution Proton NMR Diffusometry and T2 Relaxometry

The enclosed volume of concentrated dioctadecyldimethylammonium chloride (DODAC) dispersions has been determined by means of low-resolution NMR pfg-diffusometry and T(2) relaxometry. The pfg-NMR diffusometry method is based on the different diffusion behaviors of water in the external and internal phases and as such does not require the addition of a tracer. On the other hand, T(2) relaxometry is based on the different relaxation behaviors of water fractions upon addition of manganese chloride as external (paramagnetic) probe. It was noticed that reliable results are found only for temperatures below the phase transition temperature of DODAC, when the exchange between the two water compartments can be neglected. At 5 °C, these two independent methods resulted in similar enclosed volume values, meaning that the results are reliable and reflect the real enclosed volume. In addition, the T(2) relaxometry method has been proven to be useful in the investigation of the DODAC membrane permeability.

Qualitative analysis by online nuclear magnetic resonance using Carr–Purcell–Meiboom–Gill sequence with low refocusing flip angles

The Carr–Purcell–Meiboom–Gill (CPMG) pulse sequence has been used in many applications of magnetic resonance imaging (MRI) and low-resolution NMR (LRNMR) spectroscopy. Recently, CPMG was used in online LRNMR measurements that use long RF pulse trains, causing an increase in probe temperature and, therefore, tuning and matching maladjustments. To minimize this problem, the use of a low-power CPMG sequence based on low refocusing pulse flip angles (LRFA) was studied experimentally and theoretically. This approach has been used in several MRI protocols to reduce incident RF power and meet the specific absorption rate. The results for CPMG with LRFA of 3 π/4 (CPMG 135), π/2 (CPMG 90) and π/4 (CPMG 45) were compared with conventional CPMG with refocusing π pulses. For a homogeneous field, with linewidth equal to Δ υ = 15 Hz, the refocusing flip angles can be as low as π/4 to obtain the transverse relaxation time ( T 2) value with errors below 5%. For a less homogeneous magnetic field, Δ υ = 100 Hz, the choice of the LRFA has to take into account the reduction in the intensity of the CPMG signal and the increase in the time constant of the CPMG decay that also becomes dependent on longitudinal relaxation time ( T 1). We have compared the T 2 values measured by conventional CPMG and CPMG 90 for 30 oilseed species, and a good correlation coefficient, r = 0.98, was obtained. Therefore, for oilseeds, the T 2 measurements performed with π/2 refocusing pulses (CPMG 90), with the same pulse width of conventional CPMG, use only 25% of the RF power. This reduces the heating problem in the probe and reduces the power deposition in the samples.

Polystyrene microsphere-ferritin conjugates: A robust phantom for correlation of relaxivity and size distribution

In vivo iron load must be monitored to prevent complications from iron overload diseases such as hemochromatosis or transfusion-dependent anemias. While liver biopsy is the gold standard for determining in vivo iron load, MRI offers a noninvasive approach. MR phantoms have been reported that estimate iron concentration in the liver and mimic relaxation characteristics of in vivo deposits of hemosiderin. None of these phantoms take into account the size distribution of hemosiderin, which varies from patient to patient based on iron load. We synthesized stable and reproducible microsphere-ferritin conjugates (ferribeads) of different sizes that are easily characterized for several parameters that are necessary for modeling such as iron content and bead fraction. T(1) s and T(2) s were measured on a 1.41-T low-resolution NMR spectrometer and followed a size-dependent trend. Ferribeads imaged at 4.7 and 14.1 T showed that signal intensities are dependent on the distribution of ferritin around the bead rather than the iron concentration alone. These particles can be used to study the effects of particle size, ferritin distribution, and bead fraction on proton relaxation and may be of use in mimicking hemosiderin in a phantom for estimating iron concentration.

Proton Spin−Lattice Relaxation in Silkworm Cocoons: Physisorbed Water and Serine Side-Chain Motions

The molecular dynamic behavior of silkworm cocoons produced by a single Bombyx mori strain was investigated by means of high- and low-resolution solid-state NMR experiments. Cocoons with different moisture content were prepared to study the effects of physisorbed water on their molecular dynamics in the MHz regime, which was probed through the measurement of (1)H T(1) relaxation times at 25 MHz in the 25-95 degrees C temperature range. The water content of the different samples was determined from the analysis of (1)H free-induction decays. In addition to the rotation of methyl groups, mostly from alanine, and to the reorientation of physisorbed water molecules, already identified in previous works as relaxation sinks, the reorientation of serine side-chains was here found to contribute to (1)H T(1) above room temperature. The analysis of the trends of (1)H T(1) versus temperature was carried out in terms of semiempirical models describing the three main motional processes, and indicated that methyl rotation, water reorientation and serine side-chain motions are the most efficient relaxation mechanisms below 0 degrees C, between 0 and 60 degrees C, and above 60 degrees C, respectively. The activation energies were found to decrease passing from serine to water to methyl motions.

Supressão das anomalias de fase e batimentos laterais em espectros de RMN 13c obtidos com a sequência de precessão livre no estado estacionário

The Steady-State Free Precession (SSFP) sequence has been widely used in low-field and low-resolution imaging NMR experiments to increase the signal-to-noise ratio (s/n) of the signals. Here, we analyzed the Scrambled Steady State - SSS and Unscrambled Steady State - USS sequences to suppress phase anomalies and sidebands of the 13C NMR spectrum acquired in the SSFP regime. The results showed that the application of the USS sequence allowed a uniform distribution of the time interval between pulses (Tp), in the established time range, allowing a greater suppression of phase anomalies and sidebands, when compared with the SSS sequence.

Application of low field and solid-state NMR spectroscopy to study the liquid/liquid interface in porous space of clay minerals and shales

In petroleum research understanding displacement, redistribution, and adsorption of oil and water plays an important role. To study complex multi-component systems such as liquid/liquid/mineral interactions in the porous space of clays and shales we applied low field (2 – 15 MHz) and high resolution (300 MHz) NMR spectroscopy. The detailed NMR analysis shows that the results from low field NMR measurements are in good correlation with the solid-state data. Consequently the process of liquid/liquid displacement can be characterised by considering the relaxation times, signal amplitudes and chemical shifts together.

Porosities accessible to HTO and iodide on water-saturated compacted clay materials and relation with the forms of water: A low field proton NMR study

The aim of the present work was to quantify accessible porosities for iodide and for a water tracer (HTO) on water-saturated compacted clay samples (illite, montmorillonite and MX-80 bentonite) and to relate these macroscopic values to the forms of water in these porosities (surface/bulk water, external/internal water). Low field proton NMR was used to characterise and quantify the forms of water. This enabled the three different populations (structural OH, external surface and internal surface water) to be differentiated on hydrated clays by considering the difference in proton mobility. An accurate description of the water forms within the different populations did not appear possible when water molecules of these populations were in contact because of the occurrence of rapid exchange reactions. For this reason, it was not possible to use the low resolution NMR method to quantify external surface and bulk water in fully water-saturated compacted clay media at room temperature. This latter information could however be estimated when analysing the samples at –25 °C. At this temperature, a distinction based on the difference in mobility could be made since surface water remained in a semi-liquid state whereas bulk water froze. In parallel, accessible porosities for anions and HTO were determined by an isotopic dilution method using capillaries to confine the materials. HTO was shown to probe the whole pore volume (i.e. the space made of surface and bulk water). When the surface water volume was mainly composed of interlayer water (case of montmorillonite and bentonite), iodide was shown to be located in the pore space made of bulk water. When the interlayer water was not present (case of illite), the results showed that iodide could access a small fraction of the surface water volume localised at the external surface of the clay particles.

Hill Coefficient Analysis of Transmembrane Helix Dimerization

Here, we employed the Hill equation, used broadly to characterize cooperativity in protein-ligand binding, to describe the dimerization of transmembrane (TM) helices in hydrophobic environments. The Hill analysis of wild-type fibroblast growth factor receptor 3 (FGFR3) TM domain dimerization gives a Hill coefficient of approximately 1 for lipid bilayers but only approximately 0.2 for sodium dodecyl sulfate (SDS) micelles. We propose that this finding is indicative of heterogeneity in FGFR3 TM dimer structure and stability in SDS micelles. We further speculate that (1) the Hill equation can be used as a tool to assess the existence of multiple structural states of TM dimers in different hydrophobic environments and (2) the structural heterogeneity, detectable by Hill analysis, may be the underlying reason for the broad peaks and the low resolution NMR studies of peptides in detergents.

Effect of initial estimates and constraints selection in multivariate curve resolution—Alternating least squares. Application to low-resolution NMR data

A comprehensive study of the applicability of multivariate curve resolution (MCR) methods to series of T 2-relaxation filtered 1H NMR spectra of a cross-linked polymer network is presented. A collection of Hahn-echo NMR spectra is obtained at different echo times, yielding two-way data. In this study the applicability of two different types of orthogonal-projection approach (OPA1 and OPA2) (column-wise and row-wise) were tested. Four different strategies of alternating least squares methods were also examined (ALS1, ALS2, ALS3 and ALS4). These strategies differed on the order of measurement for which the constraints were applied in the final output, and the way in which SSR was calculated to monitor for convergence. In the spectral order of measurement, a non-negativity constraint was imposed, whereas in the time order of measurement, the signal was forced to follow an exponential decay. This yielded up to eight MCR configurations, giving different results. For solid-state NMR, the dissimilarity in NMR profiles is significantly lower than the dissimilarity in signal decays, and therefore OPA2 performed better. A final output with a constrained solution in relaxation time was preferred (instead of a constrained solution in NMR spectra) for practical purposes. Differences between the solutions given from the two ALS configurations can be interpreted as a sign of lack of fit.

The study of water behaviour in regenerated cellulosic fibres by low-resolution proton NMR

Regenerated cellulosic fibres and comparative materials were studied in the hydrated state by low-resolution proton NMR. Experiments at variable pH and temperatures have shown that the shortened T2 relaxation times of water within fully swollen cellulosic fibres are dominated by proton exchange with accessible cellulose hydroxyl groups. Proton exchange is accelerated by both acid and base catalysis, with relaxation data used to estimate rate constants for acid, base and neutral mechanisms. Complementary deuterium exchange measurements suggest that accessible cellulose regions below the immediate water interface may not contribute effectively to the proton exchange relaxation mechanism, with two-site relaxation models sensitive only to the direct pore surface area. Differences between surface-relaxing water and deuterium-exchanging water can therefore be used to determine an apparent depth of the accessible cellulose, which is greater for viscose and modal compared to lyocell. However, from relaxation data lyocell has a higher pore surface area. This work also confirmed that water interacting with accessible cellulose experiences motional restriction, allowing an intra-molecular dipolar contribution to relaxation. However, in the fully swollen state water molecules are diffusing rapidly between all internal fibre environments and there is no evidence of specific binding.

The binary phase behavior of 1,3-dicaproyl-2-stearoyl- sn-glycerol and 1,2-dicaproyl-3-stearoyl- sn-glycerol

The phase behavior of a binary system constituted of purified 1,3-dicaproyl-2-stearoyl- sn-glycerol (CSC) and 1,2-dicaproyl-3-stearoyl- sn-glycerol (CCS) was investigated at a very slow (0.1 °C/min) and a relatively fast (3.0 °C/min) cooling rate using differential scanning calorimetry (DSC), low resolution NMR, X-ray diffraction (XRD), and polarized light microscopy (PLM). Related forms of the β′ polymorph were detected for all mixtures as well as a β form for CSC-rich mixtures. A double chain length (DCL) stacking of the non-mixed CCS–CCS and CSC–CSC phases and a triple chain length (TCL) stacking of mixed CCS–CSC structure were detected for the different β′ forms. The kinetic phase diagram demonstrated an apparent eutectic at the 0.5 CSC composition when cooled at 0.1 °C/min and at the 0.25 CSC composition when cooled at 3.0 °C/min. The application of a thermodynamic model based on the Hildebrand equation suggests that compounds CSC and CCS are not fully miscible. In addition, the miscibility changes according to the structure of the growing solid phase which is dependent on CSC molar ratio as well as on the kinetics. It was also shown that the miscibility is concentration dependent and that the solid phase, which is growing at conditions well away from equilibrium, is determined kinetically. The molecular interactions were found to be strong and to favor the formation of CSC–CCS pairs in the liquid state. CSC and CCS were also shown to be immiscible in the solid state. Depressions in solid fat content (SFC) were observed for both rates. Relatively complex networks made of needle-like, spherulitic and granular crystals were observed in the CSC/CCS system. A pure CSC phase was found to be instrumental in promoting a higher SFC, and more stable polymorphic forms. The microstructure was shown to be strongly dependent on the cooling rate and was linked to the different polymorphic forms observed by DSC and XRD. Correlations between SFC and the eutectic behavior have been observed for the 3.0 °C/min cooling rate, but not directly in the case of the 0.1 °C/min cooling rate, where slower kinetics which favors the metastable to stable phase conversion processes prevented the same shifts in behavior.

A rapid and automated low resolution NMR method to analyze oil quality in intact oilseeds

Oilseeds with modified fatty acid profiles have been the genetic alternative for high quality vegetable oil for food and biodiesel applications. They can provide stable, functional oils for the food industry, without the hydrogenation process that produces trans-fatty acid, which has been linked to cardiovascular disease. High yield and high quality oilseeds are also necessary for the success of biodiesel programs, as polyunsatured or saturated fatty acid oil produces biofuel with undesirable properties. In this paper, a rapid and automated low resolution NMR method to select intact oilseeds with a modified fatty acid profile is introduced, based on 1H transverse relaxation time ( T 2). The T 2 weighted NMR signal, obtained by a CPMG pulse sequence and processed by chemometric methods was able to determine the oil quality in intact seeds by its fatty composition, cetane number, iodine value and kinematic viscosity with a correlation coefficient r > 0.9. The automated system has the potential to analyze more than 1000 samples per hour and is a powerful tool to speed up the selection of high quality oilseeds for food and biodiesel applications.

Methods for peak assignment in low-resolution multidimensional NMR cross-correlation relaxometry

Several NMR protocols are presented for assigning peaks in complex T 1– T 2 spectra, including the effects of varying the spectrometer frequency and the CPMG pulsing rate. Extensions into a third dimension based on chemical-shift; diffusion- and field-cycled weighted T 1– T 2 cross-correlation methods are also explored as a means of peak assignment. We illustrate the power of these novel techniques with reference to simple aqueous sucrose solutions, but the methodology should be generally applicable.

Interactions at the Surface of Organophilic-Modified Laponites: A Multinuclear Solid-State NMR Study

Organically modified clays are largely employed in the preparation of nanostructured materials. The structural and dynamic characterization of the clay surface appears very important in the perspective of understanding the molecular mechanisms determining the improvement of the material properties. To this aim, in this work, a synthetic clay, Laponite, was studied in its untreated hydrophilic Na+-form, after ion exchange with alkylammonium cations and after subsequent grafting reaction with an alkoxysilane. These three samples were characterized by IR, SEM, TGA, and X-ray techniques and were deeply investigated by means of a wide combination of 29Si, 13C, and 1H high- and low-resolution solid-state NMR experiments. The grafting reaction with alkoxysilanes, occurring at the clay platelet edges, resulted in a reduction of the clay inter-platelet distances, and in an increased disorder in both the arrangement of the platelets and the conformational structure of the intercalated organic cation chains, probably due to the relative twisting of adjacent platelets.

Molecular Properties of Flurbiprofen and its Solid Dispersions with Eudragit RL100 Studied by High- and Low-Resolution Solid-State Nuclear Magnetic Resonance

Investigation of the conformational and molecular dynamic properties of the acidic and sodium salt forms of Flurbiprofen and their solid dispersions with Eudragit RL100, obtained by two different preparation methods (physical mixtures and coevaporates), and of the mixing degree between the two components in the dispersions. 1H and 13C high-resolution solid state NMR techniques, including Single Pulse Excitation-MAS, CP-MAS, FSLG-HETCOR; low-resolution 1H FID analysis; 1H spin-lattice relaxation time measurements. Conformational, molecular packing and dynamic differences were observed between the two pure forms of flurbiprofen, as well as between the pure drugs and the corresponding coevaporates. In the coevaporates of the two flurbiprofen forms, drug and polymer appear intimately mixed; their chemical interactions were detected and characterized. A combined analysis of several 13C and 1H high- and low-resolution solid state NMR experiments allowed the investigation of the conformational and dynamic properties of the pure drugs and of the solid dispersions with the polymer, as well as of the degree of mixing between drug and polymer and of the chemical nature of their interaction. Such information could be compared to the in vitro drug release profiles given by these solid dispersions.

Water, Solute, and Segmental Dynamics in Polysaccharide Hydrogels

Polysaccharide hydrogels have found several applications in the food industry, in biomedicine, and cosmetics. The study of polysaccharide hydrogels offers a challenging scenario of intrinsic heterogeneities in the crosslinking density and large time and space ranges that characterize a number of dynamic processes entailing segmental motions, water diffusion, and small-molecule diffusion. The understanding of such complex features is essential because of the extensive use of polysaccharidic moieties in the food industry, biomedical devices, and cosmetics. The study of phenomena occurring at the nanoscale to the mesoscale requires the combination of investigative tools to probe different time and distance scales and the structural characterization of the networks by established methodologies such as swelling and elastic modulus measurements. Elastic and quasielastic neutron scattering, and fluorescence recovery after photobleaching are emerging methodologies in this field. In this feature article we focus, somewhat arbitrarily, on these new approaches because other techniques, such as low-resolution proton NMR relaxometry and rheology, have been already described thoroughly in the literature. Case examples of polysaccharide hydrogels studied by neutron scattering and fluorescence recovery are presented here as contributions to the comprehension of the dynamic behavior of physical and chemical hydrogels based on polysaccharides. Quasielastic incoherent neutron scattering experiment on a Sephadex hydrogel sample at different temperatures.