Multidimensional Nuclear Magnetic Resonance Research Articles

Using NMR to study changes in the characteristic constituents of stored rice

This study investigated constituent differences between stored and fresh rice using multidimensional solution-state nuclear magnetic resonance (NMR) spectroscopy. Fourier transform infrared (FTIR) spectroscopy and gas chromatography–mass spectrometry (GC-MS) was also used to determine constituent changes during storage.Signal variations in alkyl, alkoxy, acyl, hydroxyl, amine, and amino groups revealed hydrolysis of neutral fats and phospholipids to free fatty acids or lower esters. Signals from double bonds showed changes in unsaturated substances, such as glycerides and phospholipids, which correspond to a phenomenon exposed by GC-MS detection, that is, a reduction in polyunsaturated fatty acids occurs on storage. Moreover, the hydrolysis or oxidation of unstable lipids result in a conversion from fresh to aging rice with respect to the development of disagreeable flavors. Results from this study can both aid in our understanding and further the research into the progression and phenomenon of aging rice.

Applications of the New Family of Coherent Multidimensional Spectroscopies for Analytical Chemistry.

A new family of vibrational and electronic spectroscopies has emerged, comprising the coherent analogs of traditional analytical methods. These methods are also analogs of coherent multidimensional nuclear magnetic resonance (NMR) spectroscopy. This new family is based on creating the same quantum mechanical superposition states called multiple quantum coherences (MQCs). NMR MQCs are mixtures of nuclear spin states that retain their quantum mechanical phase information for milliseconds. The MQCs in this new family are mixtures of vibrational and electronic states that retain their phases for picoseconds or shorter times. Ultrafast, high-intensity coherent beams rapidly excite multiple states. The excited MQCs then emit bright beams while they retain their phases. Time-domain methods measure the frequencies of the MQCs by resolving their phase oscillations, whereas frequency-domain methods measure the resonance enhancements of the output beam while scanning the excitation frequencies. The resulting spectra provide multidimensional spectral signatures that increase the spectroscopic selectivity required for analyzing complex samples.

Residual Structure in the Denatured State of a Three-Helix Bundle Protein

The denatured state of a protein is canonically described as an ensemble of non-interacting random coil conformations. By studying a helical bundle protein under denaturing conditions, we have found that residual structure persists in its denatured state. Our work uses the upstream Ubiquitin-Associated domain, UBA(1), of the HHR23A protein as a model system to study residual structure in the denatured state ensemble. Multi-dimensional nuclear magnetic resonance (NMR) experiments 1H-15N HSQC, HNCO, and HNCA were used to find backbone atom secondary chemical shifts which correspond to protein secondary structure with amino acid resolution. By comparing chemical shifts in moderate- to highly denaturing conditions of 4M, 5M, and 6M guanidine HCl to a reference state of 7M GdnHCl, UBA(1) shows residual helical content among all three helices. In contrast, the helical propensity is predicted by the program Agadir to be higher in helix 2 and negligible elsewhere, with the assumption that helices do not interact. The presence of relatively uniform helical content among all three helices may indicate stabilizing tertiary interactions despite highly denaturing conditions. To further probe tertiary interactions, single-residue mutants of UBA(1) will be used to determine if residues in the hydrophobic core or turn regions are contributing to stability of residual structure in the denatured state.

Protein Sculpting: Probing the Interplay between the Ribosome and Molecular Chaperones in Protein Folding in the Cell

Understanding the way in which proteins fold inside the cell is of fundamental importance to both biology and medicine. In the E. Coli cell, proteins are synthesized on the ribosome in the presence of molecular chaperones, Trigger Factor and DnaK. While both the ribosome and molecular chaperones are known to be important to protein folding in the cell, it has been nearly impossible to isolate their independent roles in the folding process since cells die at temperatures over 30C when Trigger Factor and DnaK are deleted simultaneously. In this work, we are able to access this challenging experimental condition and study the interplay between the ribosome and chaperones by synthesizing a model globin protein in a bacterial cell-free system derived from a Trigger Factor- deleted cell strain in the presence of an in-house- designed peptide inhibitor of DnaK. Surprisingly, we find that translation through the ribosome is sufficient to grant solubility to the full-length newly synthesized protein. Ongoing studies based on time-resolved fluorescence anisotropy in the frequency-domain and multidimensional nuclear magnetic resonance yield additional details on the quality of the de novo-produced protein, and on the intriguing interplay between the ribosome and chaperones in ensuring its correct folding.

Novel methodology for accurate resolution of fluid signatures from multi-dimensional NMR well-logging measurements

A novel methodology for accurate fluid characterization from multi-dimensional nuclear magnetic resonance (NMR) well-logging measurements is introduced. This methodology overcomes a fundamental challenge of poor resolution of features in multi-dimensional NMR distributions due to low signal-to-noise ratio (SNR) of well-logging measurements. Based on an unsupervised machine-learning concept of blind source separation, the methodology resolves fluid responses from simultaneous analysis of large quantities of well-logging data. The multi-dimensional NMR distributions from a well log are arranged in a database matrix that is expressed as the product of two non-negative matrices. The first matrix contains the unique fluid signatures, and the second matrix contains the relative contributions of the signatures for each measurement sample. No a priori information or subjective assumptions about the underlying features in the data are required. Furthermore, the dimensionality of the data is reduced by several orders of magnitude, which greatly simplifies the visualization and interpretation of the fluid signatures. Compared to traditional methods of NMR fluid characterization which only use the information content of a single measurement, the new methodology uses the orders-of-magnitude higher information content of the entire well log. Simulations show that the methodology can resolve accurate fluid responses in challenging SNR conditions. The application of the methodology to well-logging data from a heavy oil reservoir shows that individual fluid signatures of heavy oil, water associated with clays and water in interstitial pores can be accurately obtained.

A Proposed Computed Tomography Contrast Agent Using Carboxybetaine Zwitterionic Tantalum Oxide Nanoparticles

The aim of this study was to produce and evaluate a proposed computed tomography (CT) contrast agent based on carboxybetaine zwitterionic (CZ)-coated soluble tantalum oxide (TaO) nanoparticles (NPs). We chose tantalum to provide superior imaging performance compared with current iodine-based clinical CT contrast agents. We developed the CZ coating to provide biological and physical performance similar to that of current iodinated contrast agents. In addition, the aim of this study was to evaluate the imaging, biological, and physicochemical performance of this proposed contrast agent compared with clinically used iodinated agents. We evaluated CT imaging performance of our CZ-TaO NPs compared with that of an iodinated agent in live rats, imaged centrally located within a tissue-equivalent plastic phantom that simulated a large patient. To evaluate vascular contrast enhancement, we scanned the rats' great vessels at high temporal resolution during and after contrast agent injection. We performed several in vivo CZ-TaO NP studies in healthy rats to evaluate tolerability. These studies included injecting the agent at the anticipated clinical dose (ACD) and at 3 times and 6 times the ACD, followed by longitudinal hematology to assess impact to blood cells and organ function (from 4 hours to 1 week). Kidney histological analysis was performed 48 hours after injection at 3 times the ACD. We measured the elimination half-life of CZ-TaO NPs from blood, and we monitored acute kidney injury biomarkers with a kidney injury assay using urine collected from 4 hours to 1 week. We measured tantalum retention in individual organs and in the whole carcass 48 hours after injection at ACD. Carboxybetaine zwitterionic TaO NPs were synthesized and analyzed in detail. We used multidimensional nuclear magnetic resonance to determine surface functionality of the NPs. We measured NP size and solution properties (osmolality and viscosity) of the agent over a range of tantalum concentrations, including the high concentrations required for standard clinical CT imaging. Computed tomography imaging studies demonstrated image contrast improvement of approximately 40% to 50% using CZ-TaO NPs compared with an iodinated agent injected at the same mass concentration. Blood and organ analyses showed no adverse effects after injection in healthy naive rats at 3 times the ACD. Retention of tantalum at 48 hours after injection was less than 2% of the injected dose in the whole carcass, which very closely matched the reported retention of existing commercial iodine-based contrast agents. Urine analysis of sensitive markers for acute kidney injury showed no responses at 1 week after injection at 3 times the ACD; however, a moderate response in the neutrophil gelatinase-associated lipocalin biomarker was measured at 24 and 48 hours. Compared with other TaO NPs reported in the literature, CZ-TaO NPs had relatively low osmolality and viscosity at concentrations greater than 200 mg Ta/mL and were similar in these physical properties to dimeric iodine-based contrast agents. We found that a CZ-TaO NP-based contrast agent is potentially viable for general-purpose clinical CT imaging. Our results suggest that such an agent can be formulated with clinically viable physicochemical properties, can be biologically safe and cleared rapidly in urine, and can provide substantially improved image contrast at CT compared with current iodinated agents.

An Introduction to Coherent Multidimensional Spectroscopy.

Coherent multidimensional spectroscopy is a field that has drawn much attention as an optical analogue to multidimensional nuclear magnetic resonance imaging. Coherent multidimensional spectroscopic techniques produce spectra that show the magnitude of an optical signal as a function of two or more pulsed laser frequencies. Spectra can be collected in either the frequency or the time domain. In addition to improving resolution and overcoming spectral congestion, coherent multidimensional spectroscopy provides the ability to investigate and conduct studies based upon the relationship between different peaks. The purpose of this paper is to provide a general introduction to the area of coherent multidimensional spectroscopy, to provide a brief overview of current experimental approaches, and to discuss some emerging developments in this relatively young field.

A fast approach to 3D HSQC-based spectroscopy based on a Fourier phase encoding of pre-targeted resonances

Multidimensional Nuclear Magnetic Resonance (NMR) provides a unique window into structure and dynamics at an atomic level. Traditionally, given the scan-by-scan time modulation involved in these experiments, the duration of nD NMR increases exponentially with spectral dimensionality. In addition, acquisition times increase as the number of spectral elements being sought in each indirect domain – given by the ratio between the spectral bandwidth being targeted and the resolution desired. These long sampling times can be substantially reduced by exploiting information that is often available from lower-dimensionality acquisitions. This work presents a novel approach that exploits previous 2D information to speed up the acquisition of 3D spectra, based on what we denote as a Time-Optimized FouriEr Encoding (TOFEE) of pre-targeted peaks. Such 3D TOFEE experiments, which present points in common with Hadamard-encoded 3D acquisitions, do not necessarily require more scans than their 2D counterparts. This is here demonstrated based on extensions of 2D Heteronuclear Single-quantum Coherence (HSQC) experiments, to 3D HSQC-TOCSY or 3D HSQC-NOESY acquisitions. The theoretical basis of this new approach is given, and experimental demonstrations are presented on small molecule and protein-based model systems.

Parsimony and goodness-of-fit in multi-dimensional NMR inversion

Multi-dimensional nuclear magnetic resonance (NMR) experiments are often used for study of molecular structure and dynamics of matter in core analysis and reservoir evaluation. Industrial applications of multi-dimensional NMR involve a high-dimensional measurement dataset with complicated correlation structure and require rapid and stable inversion algorithms from the time domain to the relaxation rate and/or diffusion domains. In practice, applying existing inverse algorithms with a large number of parameter values leads to an infinite number of solutions with a reasonable fit to the NMR data. The interpretation of such variability of multiple solutions and selection of the most appropriate solution could be a very complex problem. In most cases the characteristics of materials have sparse signatures, and investigators would like to distinguish the most significant relaxation and diffusion values of the materials.To produce an easy to interpret and unique NMR distribution with the finite number of the principal parameter values, we introduce a new method for NMR inversion. The method is constructed based on the trade-off between the conventional goodness-of-fit approach to multivariate data and the principle of parsimony guaranteeing inversion with the least number of parameter values. We suggest performing the inversion of NMR data using the forward stepwise regression selection algorithm. To account for the trade-off between goodness-of-fit and parsimony, the objective function is selected based on Akaike Information Criterion (AIC). The performance of the developed multi-dimensional NMR inversion method and its comparison with conventional methods are illustrated using real data for samples with bitumen, water and clay.

Rapid T 1–T 2 Measurement Using Drive Equilibrium Pulse Sequence

In the last decade, multidimensional Laplace nuclear magnetic resonance (NMR) was widely used in laboratory and oil industry. Compared to one-dimensional NMR, multidimensional NMR measurements have advantages in fluid recognition and content calculation, etc. However, the applications are limited due to its long measurement time. The paper presents a rapid T1–T2 measurement pulse sequence—drive equilibrium (DE) pulse sequence which can obtain fluid T1–T2 distribution down to two one-dimensional measurements and the obtained correlation maps are in good consistency with the results by traditional T1 encoding pulse sequence. It is found that the performance of DE pulse sequence is related to measurement times. If we add measurement times, DE pulse sequence will work better. The sequence can be used in time limit experiments, like downhole fluid analysis and online reaction monitoring.

Angstrom-Resolution Magnetic Resonance Imaging of Single Molecules via Wave-Function Fingerprints of Nuclear Spins

Nuclear magnetic resonance (NMR) with single-molecule sensitivity and magnetic resonance imaging (MRI) with atomic-scale resolution are the prime challenges in magnetic microscopy. The authors advance leading-edge quantum sensing by developing a scheme for MRI with angstrom-level resolution. This would determine the position and conformation of a single isotopically labeled molecule, using the response of an $N\phantom{\rule{0}{0ex}}V$ center in diamond to the characteristic wave-function signatures of target nuclear spins. This approach differs from typical multidimensional NMR, and beats the resolution limit set by frequency gradients in conventional MRI.

Ramsey-type phase control of free-electron beams

Interference between multiple distinct paths is a defining property of quantum physics, where "paths" may involve actual physical trajectories, as in interferometry, or transitions between different internal (e.g. spin) states, or both. A hallmark of quantum coherent evolution is the possibility to interact with a system multiple times in a phase-preserving manner. This principle underpins powerful multi-dimensional optical and nuclear magnetic resonance spectroscopies and related techniques, including Ramsey's method of separated oscillatory fields used in atomic clocks. Previously established for atomic, molecular and quantum dot systems, recent developments in the optical quantum state preparation of free electron beams suggest a transfer of such concepts to the realm of ultrafast electron imaging and spectroscopy. Here, we demonstrate the sequential coherent interaction of free electron states with two spatially separated, phase-controlled optical near-fields. Ultrashort electron pulses are acted upon in a tailored nanostructure featuring two near-field regions with anisotropic polarization response. The amplitude and relative phase of these two near-fields are independently controlled by the incident polarization state, allowing for constructive and destructive quantum interference of the subsequent interactions. Future implementations of such electron-light interferometers may yield unprecedented access to optically phase-resolved electronic dynamics and dephasing mechanisms with attosecond precision.

Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies.

The HIV-1 capsid protein (CA) forms the capsid shell that encloses RNA within a mature HIV-1 virion. Previous studies by electron microscopy have shown that the capsid shell is primarily a triangular lattice of CA hexamers, with variable curvature that destroys the ideal symmetry of a planar lattice. The mature CA lattice depends on CA dimerization, which occurs through interactions between helix 9 segments of the C-terminal domain (CTD) of CA. Several high-resolution structures of the CTD-CTD dimerization interface have been reported, based on X-ray crystallography and multidimensional solution nuclear magnetic resonance (NMR), with significant differences in amino acid side chain conformations and helix 9-helix 9 orientations. In a structural model for tubular CA assemblies based on cryogenic electron microscopy (cryoEM) [Zhao et al. Nature, 2013, 497, 643-646], the dimerization interface is substantially disordered. The dimerization interface structure in noncrystalline CA assemblies and the extent to which this interface is structurally ordered within a curved lattice have therefore been unclear. Here we describe solid state NMR measurements on the dimerization interface in tubular CA assemblies, which contain the curved triangular lattice of a mature virion, including quantitative measurements of intermolecular and intramolecular distances using dipolar recoupling techniques, solid state NMR chemical shifts, and long-range side chain-side chain contacts. When combined with restraints on the distance and orientation between helix 9 segments from the cryoEM study, the solid state NMR data lead to a unique high-resolution structure for the dimerization interface in the noncrystalline lattice of CA tubes. These results demonstrate that CA lattice curvature is not dependent on disorder or variability in the dimerization interface. This work also demonstrates the feasibility of local structure determination within large noncrystalline assemblies formed by high-molecular-weight proteins, using modern solid state NMR methods.

NMR pioneers reflect on Silicon Valley: a conversation with Martin Packard and Weston Anderson.

NMR pioneers reflect on Silicon Valley: a conversation with Martin Packard and Weston Anderson.

Major Variations in HIV-1 Capsid Assembly Morphologies Involve Minor Variations in Molecular Structures of Structurally Ordered Protein Segments

We present the results of solid state nuclear magnetic resonance (NMR) experiments on HIV-1 capsid protein (CA) assemblies with three different morphologies, namely wild-type CA (WT-CA) tubes with 35-60 nm diameters, planar sheets formed by the Arg(18)-Leu mutant (R18L-CA), and R18L-CA spheres with 20-100 nm diameters. The experiments are intended to elucidate molecular structural variations that underlie these variations in CA assembly morphology. We find that multidimensional solid state NMR spectra of (15)N,(13)C-labeled CA assemblies are remarkably similar for the three morphologies, with only small differences in (15)N and (13)C chemical shifts, no significant differences in NMR line widths, and few differences in the number of detectable NMR cross-peaks. Thus, the pronounced differences in morphology do not involve major differences in the conformations and identities of structurally ordered protein segments. Instead, morphological variations are attributable to variations in conformational distributions within disordered segments, which do not contribute to the solid state NMR spectra. Variations in solid state NMR signals from certain amino acid side chains are also observed, suggesting differences in the intermolecular dimerization interface between curved and planar CA lattices, as well as possible differences in intramolecular helix-helix packing.

Solution Structure and Dynamics of LptE from Pseudomonas aeruginosa.

LptE is an outer membrane (OM) lipoprotein found in Gram-negative bacteria, where it forms a complex with the β-barrel lipopolysaccharide (LPS) transporter LptD. The LptD/E complex plays a key role in OM biogenesis, by translocating newly synthesized LPS molecules from the periplasm into the external leaflet of the asymmetric OM during cell growth. The LptD/E complex in Pseudomonas aeruginosa (Pa) is a target for macrocyclic β-hairpin-shaped peptidomimetic antibiotics, which inhibit the transport of LPS to the cell surface. So far, the three-dimensional structure of the Pa LptD/E complex and the mode of interaction with these antibiotics are unknown. Here, we report the solution structure of a Pa LptE derivative lacking the N-terminal lipid membrane anchor, determined by multidimensional solution nuclear magnetic resonance (NMR) spectroscopy. The structure reveals a central five-stranded β-sheet against which pack a long C-terminal and a short N-terminal α-helix, as found in homologues of LptE from other Gram-negative bacteria. One unique feature is an extended C-terminal helix in Pa LptE, which in a model of the Pa LptD/E complex appears to be long enough to contact the periplasmic domain of LptD. Chemical shift mapping experiments suggest only weak interactions occur between LptE and the oligosaccharide chains of LPS. The NMR structure of Pa LptE will be valuable for more detailed structural studies of the LptD/E complex from P. aeruginosa.

Numerical simulation of multi-dimensional NMR response in tight sandstone

Conventional logging methods have limitations in the evaluation of tight sandstone reservoirs. The multi-dimensional nuclear magnetic resonance (NMR) logging method has the advantage that it can simultaneously measure transverse relaxation time (T 2), longitudinal relaxation time (T 1) and diffusion coefficient (D). In this paper, we simulate NMR measurements of tight sandstone with different wettability and saturations by the random walk method and obtain the magnetization decays of Carr–Purcell–Meiboom–Gill pulse sequences with different wait times (TW) and echo spacings (TE) under a magnetic field gradient, resulting in D-T 2-T 1 maps by the multiple echo trains joint inversion method. We also study the effects of wettability, saturation, signal-to-noise ratio (SNR) of data and restricted diffusion on the D-T 2-T 1 maps in tight sandstone. The results show that with decreasing wetting fluid saturation, the surface relaxation rate of the wetting fluid gradually increases and the restricted diffusion phenomenon becomes more and more obvious, which leads to the wetting fluid signal moving along the direction of short relaxation and the direction of the diffusion coefficient decreasing in D-T 2-T 1 maps. Meanwhile, the non-wetting fluid position in D-T 2-T 1 maps does not change with saturation variation. With decreasing SNR, the ability to identify water and oil signals based on NMR maps gradually decreases. The wetting fluid D-T 1 and D-T 2 correlations in NMR diffusion-relaxation maps of tight sandstone are obtained through expanding the wetting fluid restricted diffusion models, and are further applied to recognize the wetting fluid in simulated D-T 2 maps and D-T 1 maps.

Solid-State NMR Characterization of Mixed Phosphonic Acid Ligand Binding and Organization on Silica Nanoparticles.

As ligand functionalization of nanomaterials becomes more complex, methods to characterize the organization of multiple ligands on surfaces is required. In an effort to further the understanding of ligand-surface interactions, a combination of multinuclear ((1)H, (29)Si, (31)P) and multidimensional solid-state nuclear magnetic resonance (NMR) techniques was utilized to characterize the phosphonic acid functionalization of fumed silica nanoparticles using methylphosphonic acid (MPA) and phenylphosphonic acid (PPA). (1)H → (29)Si cross-polarization (CP)-magic angle spinning (MAS) solid-state NMR was used to selectively detect silicon atoms near hydrogen atoms (primarily surface species); these results indicate that geminal silanols are preferentially depleted during the functionalization with phosphonic acids. (1)H → (31)P CP-MAS solid-state NMR measurements on the functionalized silica nanoparticles show three distinct resonances shifted upfield (lower ppm) and broadened compared to the resonances of the crystalline ligands. Quantitative (31)P MAS solid-state NMR measurements indicate that ligands favor a monodentate binding mode. When fumed silica nanoparticles were functionalized with an equal molar ratio of MPA and PPA, the MPA bound the nanoparticle surface preferentially. Cross-peaks apparent in the 2D (1)H exchange spectroscopy (EXSY) NMR measurements of the multiligand sample at short mixing times indicate that the MPA and PPA are spatially close (≤5 Å) on the surface of the nanostructure. Furthermore, (1)H-(1)H double quantum-single quantum (DQ-SQ) back-to-back (BABA) 2D NMR spectra further confirmed that MPA and PPA are strongly dipolar coupled with observation of DQ intermolecular contacts between the ligands. DQ experimental buildup curves and simulations indicate that the average distance between MPA and PPA is no further than 4.2 ± 0.2 Å.

Partial-Homogeneity-Based Two-Dimensional High-Resolution Nuclear Magnetic Resonance Spectroscopy under Inhomogeneous Magnetic Fields.

High-resolution multidimensional nuclear magnetic resonance (NMR) spectroscopy serves as an irreplaceable and versatile tool in various chemical investigations. In this study, a method based on the concept of partial homogeneity is developed to offer two-dimensional (2D) high-resolution NMR spectra under inhomogeneous fields. Oscillating gradients are exerted to encode the high-resolution information, and a field-inhomogeneity correction algorithm based on pattern recognition is designed to recover high-resolution spectra. Under fields where inhomogeneity primarily distributes along a single orientation, the proposed method will improve performances of 2D NMR spectroscopy without increasing the experimental duration or significant loss in sensitivity, and thus may open important perspectives for studies of inhomogeneous chemical systems.

Ultrafast multidimensional nuclear magnetic resonance technique: A proof of concept based on inverse-k-space for convenient and efficient performance

Ultrafast multidimensional nuclear magnetic resonance (NMR) technique serves as an important and powerful tool for analyzing chemical and biological systems. Here, we propose an inverse-k-space along with a systematic processing strategy to improve quality of the ultrafast spectrum in terms of lineshape, signal-to-noise ratio, and adaptability to magnetic-field inhomogeneity. Experiments on phantom solutions and a chemical reaction system were performed to validate the effectiveness of inverse-k-space in enhancing the spectral quality of ultrafast technique. On the basis of its versatility, the inverse-k-space will facilitate applications of multidimensional NMR spectra in the rapid characterization of homogeneous chemical systems as well as in the real-time detection of inhomogeneous reaction systems.