NMR spectroscopy as a tool to investigate the degradation of aromatic compounds by a Pseudomonas putida strain

Pseudomonas putida strain KT2442, harbouring the pWW0 TOL plasmid, was grown with a number of different homologous aromatic acids as carbon sources. Small samples of liquid culture supernatant were collected and directly analysed by 2D NMR spectroscopy. In all cases similar compounds with olefinic signals were observed to accumulate. To elucidate the structures of these compounds, 2D NMR experiments with 500 and 600 MHz spectrometers equipped with a CryoProbe (Bruker BioSpin) were performed on samples obtained from a culture growing on 4‐methylbenzoate and, for ¹³C spectroscopy, on ¹³C‐labelled 4‐methylbenzoate. In all cases a 1,2‐dihydroxycyclohexa‐3,5‐diene‐carboxylate derivative was identified. The use of this technique helped us to identify easily some metabolites that were released into the solution by bacteria and to follow their secretion as a function of time. The high sensitivity of the present approach allowed a clear and rapid acquisition of spectra, notwithstanding the low concentration of the compounds. The benefits of introducing the use of NMR cryoprobes to perform metabolic pathway studies is demonstrated. Copyright © 2003 John Wiley & Sons, Ltd.     

UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates

Following unidirectional biophysical events such as the folding of proteins or the equilibration of binding interactions, requires experimental methods that yield information at both atomic-level resolution and at high repetition rates. Toward this end a number of different approaches enabling the rapid acquisition of 2D NMR spectra have been recently introduced, including spatially encoded "ultrafast" 2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions by reducing the number of scans that are necessary for completing arbitrary 2D NMR experiments, the latter operates by reducing the delay between consecutive scans while preserving sensitivity. Given the complementarities between these two approaches it seems natural to combine them into a single tool, enabling the acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate here this capability with the introduction of "ultraSOFAST" HMQC NMR, a spatially encoded and relaxation-optimized approach that can provide 2D protein correlation spectra at approximately 1 s repetition rates for samples in the approximately 2 mM concentration range. The principles, relative advantages, and current limitations of this new approach are discussed, and its application is exemplified with a study of the fast hydrogen-deuterium exchange characterizing amide sites in Ubiquitin.     

Real-time monitoring of chemical transformations by ultrafast 2D NMR spectroscopy

An approach enabling the acquisition of 2D nuclear magnetic resonance (NMR) spectra within a single scan has been recently proposed. A promising application opened up by this "ultrafast" data acquisition format concerns the monitoring of chemical transformations as they happen, in real time. The present paper illustrates some of this potential with two examples: (i) following an H/D exchange process that occurs upon dissolving a protonated protein in D2O, and (ii) real-time in situ tracking of a transient Meisenheimer complex that forms upon rapidly mixing two organic reactants inside the NMR observation tube. The first of these measurements involved acquiring a train of 2D 1H-15N HSQC NMR spectra separated by ca. 4 s; following an initial dead time, this allowed us to monitor the kinetics of hydrogen exchange in ubiquitin at a site-resolved level. The second approach enabled us to observe, within ca. 2 s after the triggering of the reaction, a competition between thermodynamic and kinetic controls via changes in a series of 2D TOCSY patterns. The real-time dynamic experiments hereby introduced thus add to an increasing family of fast characterization techniques based on 2D NMR; their potential and limitations are briefly discussed.     

Using pure shift HSQC to characterize microgram samples of drug metabolites

Difficulties in isolating samples from complex biological matrices and sensitivity limitations have long stymied the utilization of heteronuclear 2D NMR for the characterization of drug metabolites. Small diameter cryogenic NMR probes have largely ameliorated sensitivity limitations and the recently reported pure shift HSQC 2D NMR pulse sequence offers a further and marked improvement in both resolution and sensitivity. Using a 7.4 μg sample of the commercially available metabolite 3-hydroxy carbamazepine dissolved in 30 μL of deuterated solvent and a 600 MHz NMR equipped with a 1.7 mm cryogenic NMR probe, it was possible to acquire high signal-to-noise pure shift HSQC data in just over 30 min. A conventional HSQC spectrum acquired with identical parameters had approximately half the signal-to-noise of the pure shift HSQC spectrum. Collapsing the vicinal homonuclear couplings in the pure shift HSQC spectrum also significantly improves resolution. A practical, real world application of the technique is illustrated with the chromatographically isolated metabolite 3-hydroxy amiodarone from incubation with CYP2J2 recombinant enzyme. High quality pure shift HSQC data were recorded in slightly over 14 h for a 3 μg sample of the metabolite.     

HOBS methods for enhancing resolution and sensitivity in small DNA oligonucleotide NMR studies

¹H NMR spectra from biopolymers give chemical shifts classified according to proton type and often suffer from signal degeneracy. Data from nucleic acids are particularly prone to this failing. Recent developments in proton broadband decoupling techniques with the promise of enhanced resolution at full sensitivity have allowed us to investigate the application of homonuclear band‐selective (HOBS) decoupling to the study of small synthetic DNA molecules and to compare these with results from classical and pure shift techniques. Improved signal resolution at full sensitivity in both HOBS‐1D ¹H and HOBS‐2D [¹H, ¹H] NOESY NMR data is reported for three example small DNA molecules. Comparisons of ¹H T₁ and integrals of signals from HOBS‐1D ¹H and HOBS‐2D [¹H, ¹H] NOESY NMR data with those of standard data collection methods are also reported. The results show that homonuclear HOBS‐NOESY data are useful for data assignment purposes and have some merit for quantification purposes. In general, we show that resolution and sensitivity enhancement of ¹H NMR data for small DNA samples may be achieved without recourse to higher magnetic field strength at full sensitivity in a band‐selected manner. Copyright © 2014 John Wiley & Sons, Ltd.     

Practical aspects of the simultaneous collection of COSY and TOCSY spectra

The practical aspects of some NMR experiments designed for the simultaneous acquisition of 2D COSY and 2D TOCSY spectra are presented and discussed. Several techniques involving afterglow-based, coherence transfer pathway (CTP)-based, and NMR by Ordered Acquisition using ¹H-detection (NOAH)-based strategies for the collection of different free-induction signal decays (FIDs) within the same scan are evaluated and compared. These methods offer a faster recording of these spectra in small-molecule NMR when sensitivity is not a limiting factor, with a reduction in spectrometer time about 45–60% when compared with the conventional sequential acquisition of the parent experiments. It is also shown how the optimized design of an extended three-FID approach yields one COSY and two TOCSY spectra simultaneously by combining CTP and NOAH principles in the same experiment, affording substantial sensitivity enhancements per time unit.     

Structural characterization of monomeric and oligomeric arylamides by solution and solid‐state NMR spectroscopy

An extensive study of both liquid‐ and solid‐state NMR spectroscopy was undertaken in order to elucidate the structural features of a phenyleneterephthalamide oligomer (OPTA) and of some related diarylamides. 1D‐ and 2D‐COSY measurements allowed us to assign completely the proton signals of the title compounds in solution, while 1D‐, 2D‐HETCOR and 2D‐COLOC measurements were used to assign ¹³C resonances. Solid‐state ¹³C NMR experiments, by conventional cross‐polarization (CP) at different contact times and with the dipolar dephased CP technique, were used to characterize these molecules in the solid state. Such techniques allowed us to differentiate among different carbon atoms; in the resulting spectra it was then possible to observe the selective appearance of signals from protonated and quaternary carbon atoms. It was also ascertained that the limited structural mobility of the insoluble OPTA, existing as a single monophasic species, can be explained in terms of hydrogen‐type bonds present in the solid state. Copyright © 2002 John Wiley & Sons, Ltd.     

Merging Gradient-Based Methods to Improve Benchtop NMR Spectroscopy: A New Tool for Flow Reaction Optimization

Emerging low cost, compact NMR spectrometers that can be connected in-line to a flow reactor are suited to study reaction mixtures. The main limitation of such spectrometers arises from their lower magnetic field inducing a reduced sensitivity and a weaker spectral resolution. For enhancing the spectral resolution, the merging of Pure-Shift methods recognized for line narrowing with solvent elimination schemes was implemented in the context of mixtures containing protonated solvents. One more step was achieved to further enhance the resolution power on compact systems, thanks to multiple elimination schemes prior to Pure-Shift pulse sequence elements. For the first time, we were able to remove up to 6 protonated solvent signals simultaneously by dividing their intensity by 500 to 1700 with a concomitant spectral resolution enhancement for signals of interest from 9 to 12 as compared to the standard 1D ¹H. Then, the potential of this new approach was shown on the flow synthesis of a complex benzoxanthenone structure.     

Single-Scan Diffusion-Ordered NMR Spectroscopy of SABRE-Hyperpolarized Mixtures

The analysis of complex mixtures of dissolved molecules is a major challenge, especially for systems that gradually evolve, e. g., in the course of a chemical reaction or in the case of chemical instability. 1D NMR is a fast and non-invasive method suitable for detailed molecular analysis, though of low sensitivity. Moreover, the spectral resolution of proton, the most commonly used and most sensitive stable isotope in NMR, is also quite limited. Spatially encoded (SPEN) experiments aim at creating in one acquisition a 2D data set by simultaneously performing different 1D sub-experiments on different slices of the NMR tube, at the price of an extra loss of sensitivity. Choosing translational diffusion coefficients as the additional dimension (the so-called DOSY approach) helps to recover proton spectra of each molecule in a mixture. The sensitivity limitation of SPEN NMR can, on the other hand, be addressed with hyperpolarization methods. Within hyperpolarization methods, signal amplification by reversible exchange (SABRE), based on parahydrogen, is the cheapest and the easiest one to set up, and allows multi-shot experiments. Here we show that the spectra of a mixture's components at millimolar concentration are resolved in few seconds by combining the SABRE, SPEN and DOSY concepts.     

Ultrafast Multidimensional Laplace NMR Using a Single‐Sided Magnet

Laplace NMR (LNMR) consists of relaxation and diffusion measurements providing detailed information about molecular motion and interaction. Here we demonstrate that ultrafast single‐ and multidimensional LNMR experiments, based on spatial encoding, are viable with low‐field, single‐sided magnets with an inhomogeneous magnetic field. This approach shortens the experiment time by one to two orders of magnitude relative to traditional experiments, and increases the sensitivity per unit time by a factor of three. The reduction of time required to collect multidimensional data opens significant prospects for mobile chemical analysis using NMR. Particularly tantalizing is future use of hyperpolarization to increase sensitivity by orders of magnitude, allowed by single‐scan approach.     

Ultrafast Single-Scan 2D NMR Spectroscopic Detection of a PHIP-Hyperpolarized Protease Inhibitor

Two-dimensional NMR spectroscopy is one of the most important spectroscopic tools for the investigation of biological macromolecules. However, due to the low sensitivity of NMR spectroscopy, it takes usually from several minutes to many hours to record such spectra. Here, the possibility of detecting a bioactive derivative of the sunflower trypsin inhibitor-1 (SFTI-1), a tetradecapeptide, by combining parahydrogen-induced polarization (PHIP) and ultrafast 2D NMR spectroscopy is shown. The PHIP activity of the inhibitor was achieved by labeling with O-propargyl-l -tyrosine. In 1D PHIP experiments a signal enhancement of a factor of approximately 1200 compared to standard NMR was found. This enhancement permits measurement of 2D NMR correlation spectra of low-concentrated SFTI-1 in less than 10 seconds, employing ultrafast single-scan 2D NMR detection. As experimental examples PHIP-assisted ultrafast single-scan TOCSY spectra of SFTI-1 are shown.     

Newly Applied Two-Dimensional Solid-State NMR Correlation Techniques for the Characterization of Organically Modified Silicates

This paper highlights the use of two-dimensional (2D) solid-state NMR correlation techniques to probe the chemical homogeneity of organically modified silicate networks. Specifically, ²⁹Si{¹H} heteronuclear correlation (HETCOR) NMR experiments have revealed the spatial proximity of the two types of Si units present in a gel obtained from co-hydrolysis of methyldiethoxysilane and triethoxysilane. Similar information has also been obtained by using 2D ¹H homonuclear correlation NMR spectroscopy. Such experiments were only possible by combining the use of high magnetic field (14.10 T) with fast MAS spinning rate (30 kHz).     

NMR crystallography of zeolites: How far can we go without diffraction data?

Nuclear magnetic resonance (NMR) crystallography—an approach to structure determination that seeks to integrate solid-state NMR spectroscopy, diffraction, and computation methods—has emerged as an effective strategy to determine structures of difficult-to-characterize materials, including zeolites and related network materials. This paper explores how far it is possible to go in determining the structure of a zeolite framework from a minimal amount of input information derived only from solid-state NMR spectroscopy. It is shown that the framework structure of the fluoride-containing and tetramethylammonium-templated octadecasil clathrasil material can be solved from the 1D ²⁹Si NMR spectrum and a single 2D ²⁹Si NMR correlation spectrum alone, without the space group and unit cell parameters normally obtained from diffraction data. The resulting NMR-solved structure is in excellent agreement with the structures determined previously by diffraction methods. It is anticipated that NMR crystallography strategies like this will be useful for structure determination of other materials, which cannot be solved from diffraction methods alone.     

Molecular dynamics and composition of crude oil by low‐field nuclear magnetic resonance

Nuclear magnetic resonance (NMR) techniques are widely used to identify pure substances and probe protein dynamics. Oil is a complex mixture composed of hydrocarbons, which have a wide range of molecular size distribution. Previous work show that empirical correlations of relaxation times and diffusion coefficients were found for simple alkane mixtures, and also the shape of the relaxation and diffusion distribution functions are related to the composition of the fluids. The 2D NMR is a promising qualitative evaluation method for oil composition. But uncertainty in the interpretation of crude oil indicated further study was required. In this research, the effect of each composition on relaxation distribution functions is analyzed in detail. We also suggest a new method for prediction of the rotational correlation time distribution of crude oil molecules using low field NMR (LF‐NMR) relaxation time distributions. A set of down‐hole NMR fluid analysis system is independently designed and developed for fluid measurement. We illustrate this with relaxation–relaxation correlation experiments and rotational correlation time distributions on a series of hydrocarbon mixtures that employ our laboratory‐designed downhole NMR fluid analyzer. The LF‐NMR is a useful tool for detecting oil composition and monitoring oil property changes. Copyright © 2016 John Wiley & Sons, Ltd.     

Sensitivity and lineshape improvement in ultrafast 2D NMR by optimized apodization in the spatially encoded dimension

Ultrafast 2D NMR allows the acquisition of a 2D spectrum in a single scan. However, even when the acquisition of ultrafast spectra is carried out under optimized conditions, the appearance and the sensitivity of 2D spectra are often not satisfactory compared with what one could expect from this promising methodology. This is due to limitations in terms of sensitivity, spectral width and resolution, and also to non-ideal lineshapes characterized by asymmetric sinc wiggles. Here, we identify the origin of these distortions by means of numerical simulations compared with experimental data. We then propose a processing approach to improve lineshapes while increasing the sensitivity of ultrafast experiments. The method consists in multiplying the Fourier transform of ultrafast echoes by an optimized apodization function. The principles of the method are described, and a variety of window functions are tested to determine optimum processing conditions. The approach is finally applied to ultrafast 2D spectra, leading to symmetric lineshapes with a sensitivity increased by a factor of 2.     

Probing Cell-Surface Interactions in Fungal Cell Walls by High-Resolution 1H-Detected Solid-State NMR Spectroscopy

Solid-state NMR (ssNMR) spectroscopy facilitates the non-destructive characterization of structurally heterogeneous biomolecules in their native setting, for example, comprising proteins, lipids and polysaccharides. Here we demonstrate the utility of high and ultra-high field ¹H-detected fast MAS ssNMR spectroscopy, which exhibits increased sensitivity and spectral resolution, to further elucidate the atomic-level composition and structural arrangement of the cell wall of Schizophyllum commune, a mushroom-forming fungus from the Basidiomycota phylum. These advancements allowed us to reveal that Cu(II) ions and the antifungal peptide Cathelicidin-2 mainly bind to cell wall proteins at low concentrations while glucans are targeted at high metal ion concentrations. In addition, our data suggest the presence of polysaccharides containing N-acetyl galactosamine (GalNAc) and proteins, including the hydrophobin proteins SC3, shedding more light on the molecular make-up of cells wall as well as the positioning of the polypeptide layer. Obtaining such information may be of critical relevance for future research into fungi in material science and biomedical contexts.     

Progress in Hyperpolarized Ultrafast 2D NMR Spectroscopy

An important development in the field of NMR spectroscopy has been the advent of hyperpolarization approaches, capable of yielding nuclear spin states whose value exceeds by orders‐of‐magnitude what even the highest‐field spectrometers can afford under Boltzmann equilibrium. Included among these methods is an ex situ dynamic nuclear polarization (DNP) approach, which yields liquid‐phase samples possessing spin polarizations of up to 50 %. Although capable of providing an NMR sensitivity equivalent to the averaging of about 1 000 000 scans, this methodology is constrained to extract its “superspectrum” within a single—or at most a few—transients. This makes it a poor starting point for conventional 2D NMR acquisition experiments, which require a large number of scans that are identical to one another except for the increment of a certain t₁ delay. It has been recently suggested that by merging this ex situ DNP approach with spatially encoded “ultrafast” methods, a suitable starting point could arise for the acquisition of 2D spectra on hyperpolarized liquids. Herein, we describe the experimental principles, potential features, and current limitations of such integration between the two methodologies. For a variety of small molecules, these new hyperpolarized ultrafast experiments can, for equivalent overall durations, provide heteronuclear correlation spectra at significantly lower concentrations than those currently achievable by conventional 2D NMR acquisitions. A variety of challenges still remain to be solved before bringing the full potential of this new integrated 2D NMR approach to fruition; these outstanding issues are discussed.     

Study of near‐symmetric cyclodextrins by compressed sensing 2D NMR

The compressed sensing NMR (CS‐NMR) is an approach to processing of nonuniformly sampled NMR data. Its idea is to introduce minimal l_p‐norm (0 < p ≤ 1) constraint to a penalty function used in a reconstruction algorithm. Here, we demonstrate that 2D CS‐NMR spectra allow the full spectral assignment of near‐symmetric β‐cyclodextrin derivatives (mono‐modified at the C6 position). The application of CS‐NMR ensures experimental time saving and the resolution improvement, necessary because of very low chemical shift dispersion. In the overnight experimental time, the set of properly resolved 2D NMR spectra required for the unambiguous assignment of mono(6‐deoxy‐6‐(1‐1,2,3‐triazo‐4‐yl)‐1‐propane‐3‐O‐(phenyl)) β‐cyclodextrin was obtained. The highly resolved HSQC spectrum was reconstructed from 5.12% of the data. Moreover, reconstructed 2D HSQC–TOCSY spectrum yielded information about the correlations within one sugar unit, and 2D HSQC–NOESY technique allowed the sequential assignment of the glucosidic units. Copyright © 2013 John Wiley & Sons, Ltd.     

Evaluation of double-tuned single-sided planar microcoils for the analysis of small 13C enriched biological samples using 1H-13C 2D heteronuclear correlation NMR spectroscopy

Microcoils provide a cost-effective approach to improve detection limits for mass-limited samples. Single-sided planar microcoils are advantageous in comparison to volume coils, in that the sample can simply be placed on top. However, the considerable drawback is that the RF field that is produced by the coil decreases with distance from the coil surface, which potentially limits more complex multi-pulse NMR pulse sequences. Unfortunately, ¹H NMR alone is not very informative for intact biological samples due to line broadening caused by magnetic susceptibility distortions, and ¹H-¹³C 2D NMR correlations are required to provide the additional spectral dispersion for metabolic assignments in vivo or in situ. To our knowledge, double-tuned single-sided microcoils have not been applied for the 2D ¹H-¹³C analysis of intact ¹³C enriched biological samples. Questions include the following: Can ¹H-¹³C 2D NMR be performed on single-sided planar microcoils? If so, do they still hold sensitivity advantages over conventional 5 mm NMR technology for mass limited samples? Here, 2D ¹H-¹³C HSQC, HMQC, and HETCOR variants were compared and then applied to ¹³C enriched broccoli seeds and Daphnia magna (water fleas). Compared to 5 mm NMR probes, the microcoils showed a sixfold improvement in mass sensitivity (albeit only for a small localized region) and allowed for the identification of metabolites in a single intact D. magna for the first time. Single-sided planar microcoils show practical benefit for ¹H-¹³C NMR of intact biological samples, if localized information within ~0.7 mm of the 1 mm I.D. planar microcoil surface is of specific interest.     

Modern proton‐detected 1D 1H–15N NMR experiments. Application to the measurement of 1H,15N coupling constants at natural abundance

Non‐selective and selective versions of several proton‐detected 1D NMR experiments to be applied to ¹⁵N are proposed. Clean, artifact‐free 1D spectra are easily obtained by the effective coherence selection by pulsed‐field gradients and the attainable sensitivity is maximized using modern pulse schemes. Despite the low sensitivity inherent to ¹⁵N NMR spectroscopy, the successful application of these experiments is demonstrated for resonance assignments and accurate measurement of both one‐bond and long‐range proton–nitrogen coupling constants on a model tripeptide at natural abundance. Copyright © 2001 John Wiley & Sons, Ltd.