Design, construction, and validation of a 1-mm triple-resonance high-temperature-superconducting probe for NMR

To flame-seal or not to flame-seal NMR tubes: The role of liquid-vapor equilibria on the accuracy of variable temperature experiments

In NMR experiments, it is crucial to control the temperature of the sample, especially when measuring kinetic parameters. Usually, it takes 2 to 5 min for the temperature of the sample inside the NMR probe to stabilize at a fixed value set for the experiment. However, the NMR sample tubes are flame-sealed in some cases, such as when working with volatile solvents, atmosphere-sensitive samples, or calibration samples for long-term use. When these samples are placed inside the NMR probe, the spectrometer controls the lower portion (liquid phase) of the NMR sample tube with a gas flow at a fixed temperature, while the upper portion (vapor) is at ambient temperature. This probe design creates a unique temperature gradient across the sample, leading to vapor pressure build-up, particularly inside a sealed NMR tube. By analyzing the temperature-dependent spectral line shape changes of a chemical exchange process, we report that under standard experimental conditions, the sample temperature can take up to 2 to 3 h (instead of minutes) to stabilize. The time scale of the liquid-vapor equilibrium process is much slower, with a half-life exceeding 35 min, in contrast to the 2-min duration required to obtain each spectrum. This phenomenon is exclusively due to the liquid-vapor equilibrium process of the flame-sealed NMR tube and is not observable otherwise.

A roadmap to high-resolution standard microcoil MAS NMR spectroscopy for metabolomics

Current microcoil probe technology has emerged as a significant advancement in NMR applications to biofluids research. It has continued to excel as a hyphenated tool with other prominent microdevices, opening many new possibilities in multiple omics fields. However, this does not hold for biological samples such as intact tissue or organisms, due to the considerable challenges of incorporating the microcoil in a magic-angle spinning (MAS) probe without relinquishing the high-resolution spectral data. Not until 2012 did a microcoil MAS probe show promise in profiling the metabolome in a submilligram tissue biopsy with spectral resolution on par with conventional high-resolution MAS (HR-MAS) NMR. This result subsequently triggered a great interest in the possibility of NMR analysis with microgram tissues and striving toward the probe development of "high-resolution" capable microcoil MAS NMR spectroscopy. This review gives an overview of the issues and challenges in the probe development and summarizes the advancements toward metabolomics.

Implementing High Q-Factor HTS Resonators to Enhance Probe Sensitivity in 13C NMR Spectroscopy

Nuclear magnetic resonance spectroscopy (NMR) probes using thin-film high temperature superconducting (HTS) resonators provide exceptional mass sensitivity in small-sample NMR experiments for natural products chemistry and metabolomics. We report improvements in sensitivity to our 1.5 mm 13C-optimized NMR probe based on HTS resonators. The probe has a sample volume of 35 microliters and operates in a 14.1 T magnet. The probe also features HTS resonators for 1H transmission and detection and the 2H lock. The probe utilizes a 13C resonator design that provides greater efficiency than our previous design. The quality factor of the new resonator in the 14.1 T background field was measured to be 4,300, which is over 3x the value of the previous design. To effectively implement the improved quality factor, we demonstrate the effect of adding a shorted transmission line stub to increase the bandwidth and reduce the rise/fall time of 13C irradiation pulses. Initial NMR measurements verify 13C NMR sensitivity is significantly improved while preserving detection bandwidth. The probe will be used for applications in metabolomics.

Application of Counter-wound Multi-arm Spirals in HTS Resonator Design

Significant sensitivity improvements have been achieved by utilizing high temperature superconducting (HTS) resonators in nuclear magnetic resonance (NMR) probes. Many nuclei such as ¹³C benefit from strong excitation fields which cannot be produced by traditional HTS resonator designs. We investigate the use of double-sided, counter-wound multi-arm spiral HTS resonators with the aim of increasing the excitation field at the required nuclear Larmor frequency for ¹³C. When compared to double-sided, counter-wound spiral resonators with similar geometry, simulations indicate that the multi-arm spiral version develops a more uniform current distribution. Preliminary tests of a two-arm resonator indicate that it may produce a stronger excitation field.

Progress Towards a Higher Sensitivity 13C-Optimized 1.5 mm HTS NMR Probe

Nuclear magnetic resonance (NMR) probes using thin-film high temperature superconducting (HTS) resonators offer high sensitivity and are particularly suitable for small-sample applications. We are developing an improved 1.5 mm HTS NMR probe designed for operation at 14.1 T and optimized for 13C detection. The total sample volume is about 35 μL and the active sample volume is 20 μL. The probe employs HTS resonators for 13C and 1H transmission and detection and the 2H lock. We examine the interactions of multiple superconducting resonators and normal metal tuning loops on coil resonance frequency and probe sensitivity. We test a recently introduced 13C resonator design, engineered to significantly increase 13C detection sensitivity over previous all-HTS probes. At zero field, we observe a 13C quality factor of 6000 which is several times higher than previous resonators. In this work the coil design considerations and probe build-out procedure are discussed.

13C-Optimized HTS NMR RF Coil Design at 21.1 T

We present the design of a novel high-temperature superconductor double-sided racetrack resonator for a ¹³C optimized nuclear magnetic resonance (NMR) transmitter/receiver coil. The coils operate in a 21.1 T magnet and accommodate a 3 mm × 6.2 mm cross-section rectangular sample tube. The design includes the incorporation of revised finger lengths to improve the homogeneity of current density across the fingers, a new laser trimming approach for adjusting the resonance frequency, and improved ability to shift higher-order modes for suitability in ¹H/¹³C NMR probes. Resonator design methodology, simulations and experimental results are presented.

The integration of LC-MS and NMR for the analysis of low molecular weight trace analytes in complex matrices

This review discusses the integration of liquid chromatography (LC), mass spectrometry (MS), and nuclear magnetic resonance (NMR) in the comprehensive analysis of small molecules from complex matrices. We first discuss the steps taken toward making the three technologies compatible, so as to create an efficient analytical platform. The development of online LC-MS-NMR, highlighted by successful applications in the profiling of highly concentrated analytes (LODs 10 μg) is discussed next. This is followed by a detailed overview of the alternative approaches that have been developed to overcome the challenges associated with online LC-MS-NMR that primarily stem from the inherently low sensitivity of NMR. These alternative approaches include the use of stop-flow LC-MS-NMR, loop collection of LC peaks, LC-MS-SPE-NMR, and offline NMR. The potential and limitations of all these approaches is discussed in the context of applications in various fields, including metabolomics and natural product discovery.

Modeling the Resonance Shifts Due to Coupling Between HTS Coils in NMR Probes

Nuclear magnetic resonance (NMR) probes using thin-film HTS coils offer high sensitivity and are particularly suitable for small-sample applications. Typically, HTS probes are optimized for the detection of multiple nuclei and require several coils to be located within a small volume near the sample. Coupling between the coils shifts coil resonances and complicates coil trimming when tuning HTS probes. We have modeled the magnetic coupling between the coils of a 1.5-mm all-HTS NMR probe with ¹³C, ¹H, and ²H channels. By measuring the magnetic coupling coefficients between individual coils, we solve the general coupling matrix given by KVL for six coupled resonators. Our results indicate that required trims can be accurately predicted by applying single coil trimming simulations to this magnetic coupling model. Use of the magnetic coupling model significantly improves the efficiency of tuning HTS probes.

Time and Frequency Domain Response of HTS Resonators for Use as NMR Transmit Coils

Replacing normal metal NMR coils with thin-film high-temperature superconductor (HTS) resonators can significantly improve the sensitivity of analytical NMR. To study the use of these resonators for excitation as well as detection, we investigated the radio frequency properties of the HTS NMR coils in both frequency and time domain at a variety of transmit power levels. Experiments were conducted on a double-sided, counter wound spiral resonator designed to detect NMR signals from ¹³C nuclei at 14.1 T. Power-dependent nonlinearity was observed in the transmission coefficient and quality factor. The ability of the HTS resonators to accurately generate short pulses was studied in the time domain over the range power levels. The results of this study show that some form of Q switching is needed to get good transmit performance from HTS coils for ¹³C. For that purpose, the effect of adding a shorted transmission line stub to improve the pulse shapes and reduce phase transients was studied.

Practical Guidelines for 13C-Based NMR Metabolomics

We present an overview of ¹³C-based NMR metabolomics. At first glance, the low sensitivity of ¹³C relative to ¹H NMR might seem like too great an obstacle to use this approach. However, there are several advantages to ¹³C NMR, whether samples can be isotopically enriched or not. At natural abundance, peaks are sharp and largely resolved, and peak frequencies are more stable to pH and other sample conditions. Statistical approaches can be used to obtain C-C and C-H correlation maps, which greatly aid in compound identification. With ¹³C isotopic enrichment, other experiments are possible, including both ¹³C-J-RES and INADEQUATE, which can be used for de novo identification of metabolites not in databases.NMR instrumentation and software has significantly improved, and probes are now commercially available that can record useful natural abundance 1D ¹³C spectra from real metabolomics samples in 2 h or less. Probe technology continues to improve, and the next generation should be even better. Combined with new methods of simultaneous data acquisition, which allows for two or more 1D or 2D NMR experiments to be collected using multiple receivers, very rich datasets can be collected in a reasonable amount of time that should improve metabolomics data analysis and compound identification.

Guide to Simulating Complex NMR Probe Circuits

S‐parameter‐based circuit simulators are well suited to obtaining accurate solutions of even the most complex rf probe circuits. The basic theory necessary for determining the relative S/N of the probe circuit, based on B1/P0.5, from the voltage, current, impedance, and S‐parameter data that come from circuit simulators, is presented. Examples of simulator applications to circuits of increasing complexity are presented. A key requirement for effective utilization of circuit simulators in probe circuit optimizations is constructing an approximate analytical solution of the circuit, or an inverse simulation program, to accompany the direct circuit simulation, that calculates all the needed circuit component values based on minimal input data, such as B0, desired nuclides, sample coil description, and hardware options and details such as characteristics of various leads. A method of developing the needed inverse simulation program is presented for a simplified single‐coil HXY probe circuit. The inverse program is validated by the direct simulation itself. The methods are then applied to a detailed circuit that includes all significant leads, stray capacitances, couplings, and losses for a NB 28.2‐T 1‐mm HXYZ MAS probe. Similar HXY circuit models were validated by NMR experiments with rotor sizes from 0.75 mm to 3.2 mm at fields from 11.7 T to 21 T. Detailed HXYZ circuit model results at 11.7 T, including pulse widths, component values, voltages, and port isolations, agreed with experimental results within a few per cent. The 1200‐MHz HXYZ simulation predicted a 1H π/2 pulse of 1.3 μs at 25 W.

Inductively-coupled Frequency Tuning and Impedance Matching in HTS-based NMR Probes

Nuclear Magnetic Resonance (NMR) probes based on High Temperature Superconducting (HTS) resonators have demonstrated significant gains in detection sensitivity. However, the widespread acceptance of this technology has been limited by some unresolved issues including the mechanical unreliability of the moveable inductive loops used to adjust tuning and matching. In order to improve reliability, we propose to implement frequency tuning and impedance matching of HTS resonators using fixed inductively coupled loops and variable capacitors. By analyzing the loss mechanisms associated with inductive loops, we predict that using a superconducting inductive loop for tuning and matching will not only improve the reliability of HTS probes, but also provide improvements in sensitivity.

Heteronuclear 1D and 2D NMR Resonances Detected by Chemical Exchange Saturation Transfer to Water

A method to detect NMR spectra from heteronuclei through the modulation that they impose on a water resonance is exemplified. The approach exploits chemical exchange saturation transfers, which can magnify the signal of labile protons through their influence on a water peak. To impose a heteronuclear modulation on water, an HMQC-type sequence was combined with the FLEX approach. 1D ¹⁵ N NMR spectra of exchanging sites could thus be detected, with about tenfold amplifications over the ¹⁵ N modulations afforded by conventionally detected HMQC NMR spectroscopy. Extensions of this approach enable 2D heteronuclear acquisitions on directly bonded ¹ H-¹⁵ N spin pairs, also with significant signal amplification. Despite the interesting limits of detection that these signal enhancements could open in NMR spectroscopy, these gains are constrained by the rates of solvent exchange of the targeted heteronuclear pairs, as well as by spectrometer instabilities affecting the intense water resonances detected in these experiments.

Determination of the Nucleic Acid Adducts Structure at the Nucleoside/Nucleotide Level by NMR Spectroscopy

All living organisms are exposed to xenobiotics from the environment. The exposure can lead to the formation of covalent adducts of xenobiotics or their metabolites with nucleic acids (NAs).The knowledge of NA adduct structure provides valuable information n the mechanism of carcinogenesis on a molecular level. While NMR spectroscopy is extremely successful in structural analysis of many classes of molecules ranging from small inorganic and organic molecules to large biomacromolecules, the structural analysis of NA adducts by NMR spectroscopy is accompanied by some challenges. First, the structural diversity of the adducts is very large; the electrophilic species generated from the metabolism of xenobiotics can attack various atoms of the nucleobases, and new rings are frequently formed. The second challenge in the DNA adducts structure determination is the low sensitivity of NMR spectroscopy and low amount of the adducts isolated from in vivo experiments. Recent developments of NMR hardware and experimental methods have led, however, to unprecedented sensitivity. This contribution reviews NMR techniques that are commonly applied in the determination of nucleic acid adducts structure at the nucleoside/nucleotide level. These NMR techniques and the large structural heterogeneity of NA adducts are demonstrated on recent examples (mostly published after 2000) of NA adducts structure determined by NMR. Most of the examples report 2′-deoxyribonucles(t)ide derivatives, but RNA adducts are also briefly discussed. The influence of the formation of NA adducts on nucleoside conformation (particularly syn/anti orientation of the base) is also demonstrated on recent examples.

Applications of NMR spectroscopy to systems biochemistry

The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.

Application of high-field NMR spectroscopy for characterization and quantitation of submilligram quantities of isolated natural products

We have investigated and compared a number of sample conditions on different NMR platforms in the search of maximum SNR and optimal experiment time efficiency for structure elucidation and quantitation of natural products. Using restricted volume 3 mm Shigemi microcell assembly in conjunction with a 900 MHz NMR spectrometer equipped with a 5 mm carbon-sensitive inverse cryoprobe, it was possible to achieve a substantial increase in SNR (46-fold) as compared with a conventional room temperature 400 MHz instrument. Switching from standard 5 mm NMR tube to 3 mm Shigemi microcell assembly typically improved SNR by threefold on either 600 or 900 MHz cryoplatform. A quantitation method that relies on a calibrated residual protonated NMR solvent signal as internal standard was developed using the same hardware setup and restricted sample volume tubes. Linearity of the method spans over 3 orders of magnitude, from low microgram to milligram quantities. We successfully applied this method to quantify a low micrgram sample of paclitaxel, verified by a UV/VIS quantitation measurement.

Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy

In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed.

Metabolomics and Natural-Products Strategies to Study Chemical Ecology in Nematodes

This review provides an overview of two complementary approaches to identify biologically active compounds for studies in chemical ecology. The first is activity-guided fractionation and the second is metabolomics, particularly focusing on a new liquid chromatography–mass spectrometry-based method called isotopic ratio outlier analysis. To illustrate examples using these approaches, we review recent experiments using Caenorhabditis elegans and related free-living nematodes.

An Empirical Expression to Predict the Resonant Frequencies of Archimedean Spirals

This work presents an empirical formula to accurately determine the frequencies of the fundamental and higher order resonances of an Archimedean spiral in a uniform dielectric medium in the absence of a ground plane. The formula is based on method-of-moments simulations which have been experimentally validated. This empirical formula is widely applicable to a broad range of spirals from thin-ring to disk-shaped (ratio of inner to outer radii 0 to 1), with 10 or more turns.

Recent advances and applications of experimental technologies in marine natural product research

Marine natural products are a rich source of novel and biologically active compounds. The number of identified marine natural compounds has grown 20% over the last five years from 2009 to 2013. Several challenges, including sample collection and structure elucidation, have limited the development of this research field. Nonetheless, new approaches, such as sampling strategies for organisms from extreme ocean environments, nanoscale NMR and computational chemistry for structural determination, are now available to overcome the barriers. In this review, we highlight the experimental technology innovations in the field of marine natural products, which in our view will lead to the development of many new drugs in the future.

An overview of methods using (13)C for improved compound identification in metabolomics and natural products

Compound identification is a major bottleneck in metabolomics studies. In nuclear magnetic resonance (NMR) investigations, resonance overlap often hinders unambiguous database matching or de novo compound identification. In liquid chromatography-mass spectrometry (LC-MS), discriminating between biological signals and background artifacts and reliable determination of molecular formulae are not always straightforward. We have designed and implemented several NMR and LC-MS approaches that utilize (13)C, either enriched or at natural abundance, in metabolomics applications. For LC-MS applications, we describe a technique called isotopic ratio outlier analysis (IROA), which utilizes samples that are isotopically labeled with 5% (test) and 95% (control) (13)C. This labeling strategy leads to characteristic isotopic patterns that allow the differentiation of biological signals from artifacts and yield the exact number of carbons, significantly reducing possible molecular formulae. The relative abundance between the test and control samples for every IROA feature can be determined simply by integrating the peaks that arise from the 5 and 95% channels. For NMR applications, we describe two (13)C-based approaches. For samples at natural abundance, we have developed a workflow to obtain (13)C-(13)C and (13)C-(1)H statistical correlations using 1D (13)C and (1)H NMR spectra. For samples that can be isotopically labeled, we describe another NMR approach to obtain direct (13)C-(13)C spectroscopic correlations. These methods both provide extensive information about the carbon framework of compounds in the mixture for either database matching or de novo compound identification. We also discuss strategies in which (13)C NMR can be used to identify unknown compounds from IROA experiments. By combining technologies with the same samples, we can identify important biomarkers and corresponding metabolites of interest.

A microfluidically cryocooled spiral microcoil with inductive coupling for MR microscopy

Magnetic resonance (MR) microscopy typically employs microcoils for enhanced local signal-to-noise ratio (SNR). Planar (surface) microcoils, in particular, offer the potential to be configured into array elements as well as to enable the imaging of extremely small samples because of the uniformity and precision provided by microfabrication techniques. Microcoils, in general, however, are copper-loss dominant, and cryocooling methods have been successfully used to improve the SNR. Cryocooling of the matching network elements, in addition to the coil itself, has shown to provide the most improvement, but can be challenging with respect to cryostat requirements, cabling, and tuning. Here we present the development of a microfluidically cryocooled spiral microcoil with integrated microfabricated parallel plate capacitors, allowing for localized cryocooling of both the microcoil and the on-chip resonating capacitor to increase the SNR while keeping the sample-to-coil distance within the most sensitive imaging range of the microcoil. Inductive coupling was used instead of a direct transmission line connection to eliminate the physical connection between the microcoil and the tuning network so that a single cryocooling microfluidic channel could enclose both the microcoil and the on-chip capacitor with minimum loss in cooling capacity. Comparisons between the cooled and uncooled cases were made via Q-factor measurements and agreed well with the theoretically achievable improvement: the cooled integrated capacitor coil with inductive coupling achieved a factor of 2.6 improvement in Q-factor over a reference coil conventionally matched and tuned with high- Q varactors and capacitively connected to the transmission line.

Nuclear magnetic resonance at the picomole level of a DNA adduct

We investigate the limit of detection for obtaining NMR data of a DNA adduct using modern microscale NMR instrumentation, once the adduct has been isolated at the picomole level. Eighty nanograms (130 pmol) of a DNA adduct standard, N-(2'-deoxyguanosin-8-yl)-2-acetylaminofluorene 5'-monophosphate (AAF-dGMP), in 1.5 μL of D₂O with 10% methanol-d₄, in a vial, was completely picked up as a droplet suspended in a fluorocarbon liquid and loaded efficiently into a microcoil probe. This work demonstrates a practical manual method of droplet microfluidic sample loading, previously demonstrated using automated equipment, which provides a severalfold advantage over conventional flow injection. Eliminating dilution during injection and confining the sample to the observed volume produce the full theoretical mass sensitivity of a microcoil, comparable to that of a microcryo probe. With 80 ng, an NMR spectrum acquired over 40 h showed all of the resonances seen in a standard spectrum of AAF-dGMP, with a signal-to-noise ratio of at least 10, despite broadening due to previously noted effects of conformational exchange. Even with this broadening to 5 Hz, a two-dimensional total correlation spectroscopy spectrum was acquired on 1.6 μg in 18 h. This work helps to define the utility of NMR in combination with other analytical methods for the structural characterization of a small amount of a DNA adduct.

Development of a ¹³C-optimized 1.5-mm high temperature superconducting NMR probe

We report a 1.5-mm NMR probe based on high temperature superconductors operating at 14.1T optimized for (13)C detection. The probe has a total sample volume of about 35 microliters (μL) with an active volume of 20 μL and provides exceptional mass sensitivity for (13)C detection. The probe also has excellent (1)H sensitivity and employs a (2)H lock; (15)N irradiation capability can be added in the future. The coils are cooled to about 20K using a standard Agilent cryogenic refrigeration system, and the sample temperature is regulated near room temperature. The coil design considerations are discussed in detail. This probe is ideal for directly detected (13)C NMR experiments for natural products chemistry and metabolomics applications, for which 35 μL is an optimal sample volume. The outstanding (13)C sensitivity of this probe allowed us to directly determine the (13)C connectivity on 1.1mg of natural abundance histidine using an INADEQUATE experiment. We demonstrated the utility of this probe for (13)C-based metabolomics using a synthetic mixture of common natural abundance metabolites whose concentrations ranged from 1 to 5mM (40-200 nmol).

Using NMR to identify and characterize natural products

Over the past 28 years there have been several thousand publications describing the use of 2D NMR to identify and characterize natural products. During this time period, the amount of sample needed for this purpose has decreased from the 20-50 mg range to under 1 mg. This has been due to both improvements in NMR hardware and methodology. This review will focus on mainly methodology improvements, particularly in pulse sequences, acquisition and processing methods which are particularly relevant to natural product research, with lesser discussion of hardware improvements.

Radiofrequency microcoils for magnetic resonance imaging and spectroscopy

Small radiofrequency coils, often termed "microcoils", have found extensive use in many areas of magnetic resonance. Their advantageous properties include a very high intrinsic sensitivity, a high (several MHz) excitation and reception bandwidth, the fact that large arrays can fit within the homogeneous volume of the static magnetic field, and the very high resonance frequencies (several GHz) that can be achieved. This review concentrates on recent developments in the construction of single and multiple RF microcoil systems, and new types of experiments that can be performed using such assemblies.

Increasing the sensitivity of magnetic resonance spectroscopy and imaging

Nuclear magnetic resonance and magnetic resonance imaging are two of the most important techniques in analytical chemistry and noninvasive medical imaging, respectively. They share a common physical basis, one aspect of which is a low intrinsic sensitivity relative to complementary techniques. Encouragingly, recent advances in physics, chemistry, engineering, and data processing have enabled significant increases in sensitivity, as measured by both increased signal-to-noise and reduced data acquisition times, allowing previously unattainable data to be acquired and also new types of experiments to be designed.

Nanogram-scale preparation and NMR analysis for mass-limited small volatile compounds

Semiochemicals are often produced in infinitesimally small quantities, so their isolation requires large amounts of starting material, not only requiring significant effort in sample preparation, but also resulting in a complex mixture of compounds from which the bioactive compound needs to be purified and identified. Often, compounds cannot be unambiguously identified by their mass spectra alone, and NMR analysis is required for absolute chemical identification, further exacerbating the situation because NMR is relatively insensitive and requires large amounts of pure analyte, generally more than several micrograms. We developed an integrated approach for purification and NMR analysis of <1 µg of material. Collections from high performance preparative gas-chromatography are directly eluted with minimal NMR solvent into capillary NMR tubes. With this technique, ¹H-NMR spectra were obtained on 50 ng of geranyl acetate, which served as a model compound, and reasonable H-H COSY NMR spectra were obtained from 250 ng of geranyl acetate. This simple off-line integration of preparative GC and NMR will facilitate the purification and chemical identification of novel volatile compounds, such as insect pheromones and other semiochemicals, which occur in minute (sub-nanogram), and often limited, quantities.

Hierarchical alignment and full resolution pattern recognition of 2D NMR spectra: application to nematode chemical ecology

Nuclear magnetic resonance (NMR) is the most widely used nondestructive technique in analytical chemistry. In recent years, it has been applied to metabolic profiling due to its high reproducibility, capacity for relative and absolute quantification, atomic resolution, and ability to detect a broad range of compounds in an untargeted manner. While one-dimensional (1D) (1)H NMR experiments are popular in metabolic profiling due to their simplicity and fast acquisition times, two-dimensional (2D) NMR spectra offer increased spectral resolution as well as atomic correlations, which aid in the assignment of known small molecules and the structural elucidation of novel compounds. Given the small number of statistical analysis methods for 2D NMR spectra, we developed a new approach for the analysis, information recovery, and display of 2D NMR spectral data. We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra. Principle component analysis (PCA) and partial least squares (PLS) regression of full resolution total correlation spectroscopy (TOCSY) spectra greatly aid the assignment and interpretation of statistical pattern recognition results by producing back-scaled loading plots that look like traditional TOCSY spectra but incorporate qualitative and quantitative biological information of the resonances. The HATS-PR methodology is demonstrated here using multiple 2D TOCSY spectra of the exudates from two nematode species: Pristionchus pacificus and Panagrellus redivivus. We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds. These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and biological studies in cellular biochemistry, metabolomics, and chemical ecology.

Small-volume nuclear magnetic resonance spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy is one of the most information-rich analytical techniques available. However, it is also inherently insensitive, and this drawback precludes the application of NMR spectroscopy to mass- and volume-limited samples. We review a particular approach to increase the sensitivity of NMR experiments, namely the use of miniaturized coils. When the size of the coil is reduced, the sample volume can be brought down to the nanoliter range. We compare the main coil geometries (solenoidal, planar, and microslot/stripline) and discuss their applications to the analysis of mass-limited samples. We also provide an overview of the hyphenation of microcoil NMR spectroscopy to separation techniques and of the integration with lab-on-a-chip devices and microreactors.

Intermolecular interaction studies using small volumes

We present the use of 1-mm room-temperature probe technology to perform intermolecular interaction studies using chemical shift perturbation methods and saturation transfer difference (STD) spectroscopy using small sample volumes. The use of a small sample volume (5-10 µl) allows for an alternative titration protocol where individual samples are prepared for each titration point, rather than the usual protocol used for a 5-mm probe setup where the ligand is added consecutively to the solution containing the protein or host of interest. This allows for considerable economy in the consumption and cost of the protein and ligand amounts required for interaction studies. For titration experiments, the use of the 1-mm setup consumes less than 10% of the ligand amount required using a 5-mm setup. This is especially significant when complex ligands that are only available in limited quantities, typically because they are obtained from natural sources or through elaborate synthesis efforts, need to be investigated. While the use of smaller volumes does increase the measuring time, we demonstrate that the use of commercial small volume probes allows the study of interactions that would otherwise be impossible to address by NMR.

NMR-spectroscopic analysis of mixtures: from structure to function

NMR spectroscopy as a particularly information-rich method offers unique opportunities for improving the structural and functional characterization of metabolomes, which will be essential for advancing the understanding of many biological processes. Whereas traditionally NMR spectroscopy was mostly relegated to the characterization of pure compounds, the past few years have seen a surge of interest in using NMR-spectroscopic techniques for characterizing complex metabolite mixtures. Development of new methods was motivated partly by the realization that using NMR for the analysis of metabolite mixtures can help identify otherwise inaccessible small molecules, for example compounds that are prone to chemical decomposition and thus cannot be isolated. Furthermore, comparative metabolomics and statistical analyses of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the range of NMR-spectroscopic techniques recently developed for characterizing metabolite mixtures, including methods used in discovery-oriented natural product chemistry, in the study of metabolite biosynthesis and function, or for comparative analyses of entire metabolomes.

Grassypeptolides A-C, cytotoxic bis-thiazoline containing marine cyclodepsipeptides

Grassypeptolides A−C (1−3), a group of closely related bis-thiazoline containing cyclic depsipeptides, have been isolated from extracts of the marine cyanobacterium Lyngbya confervoides. Although structural differences between the analogues are minimal, comparison of the in vitro cytotoxicity of the series revealed a structure−activity relationship. When the ethyl substituent of 1 is changed to a methyl substituent in 2, activity is only slightly reduced (3−4-fold), whereas inversion of the Phe unit flanking the bis-thiazoline moiety results in 16−23-fold greater potency. We show that both 1 and 3 cause G1 phase cell cycle arrest at lower concentrations, followed at higher concentrations by G2/M phase arrest, and that these compounds bind Cu²⁺ and Zn²⁺. The three-dimensional structure of 2 was determined by MS, NMR, and X-ray crystallography, and the structure of 3 was established by MS, NMR, and chemical degradation. The structure of 3 was explored by in silico molecular modeling, revealing subtle differences in overall conformation between 1 and 3. Attempts to interconvert 1 and 3 with base were unsuccessful, but enzymatic conversion may be possible and could be a novel form of activation for chemical defense.

Cytotoxic halogenated macrolides and modified peptides from the apratoxin-producing marine cyanobacterium Lyngbya bouillonii from Guam

Collections of the marine cyanobacterium Lyngbya bouillonii from shallow patch reefs in Apra Harbor, Guam, afforded three hitherto undescribed analogues of the glycosidic macrolide lyngbyaloside, namely, 2-epi-lyngbyaloside (1) and the regioisomeric 18E- and 18Z-lyngbyalosides C (2 and 3). Concurrently we discovered two new analogues of the cytoskeletal actin-disrupting lyngbyabellins, 27-deoxylyngbyabellin A (4) and lyngbyabellin J (5), a novel macrolide of the laingolide family, laingolide B (6), and a linear modified peptide, lyngbyapeptin D (7), along with known lyngbyabellins A and B, lyngbyapeptin A, and lyngbyaloside. The structures of 1-7 were elucidated by a combination of NMR spectroscopic and mass spectrometric analysis. Compounds 1-6 were either brominated (1-3) or chlorinated (4-6), consistent with halogenation being a hallmark of many marine natural products. All extracts derived from these L. bouillonii collections were highly cytotoxic due to the presence of apratoxin A or apratoxin C. Compounds 1-5 showed weak to moderate cytotoxicity to HT29 colorectal adenocarcinoma and HeLa cervical carcinoma cells.

Isolation and biological evaluation of 8-epi-malyngamide C from the Floridian marine cyanobacterium Lyngbya majuscula

A new stereoisomer of malyngamide C, 8-epi-malyngamide C (1), and the known compound lyngbic acid [(4E,7S)-7-methoxytetradec-4-enoic acid] were isolated from a sample of Lyngbya majuscula collected near Bush Key, Dry Tortugas, Florida. The structure of 1 was determined by NMR and MS experiments. The absolute configuration of 1 was determined by selective Mitsunobu inversion of C-8 to give malyngamide C, as determined by NMR, MS, and comparison of specific rotation. Both 1 and malyngamide C were found to be cytotoxic to HT29 colon cancer cells (IC(50) 15.4 and 5.2 microM, respectively) and to inhibit bacterial quorum sensing in a reporter gene assay.

Lyngbyastatins 8-10, elastase inhibitors with cyclic depsipeptide scaffolds isolated from the marine cyanobacterium Lyngbya semiplena

Investigation of an extract from the marine cyanobacterium Lyngbya semiplena, collected in Tumon Bay, Guam, led to the identification of three new cyclodepsipeptides, lyngbyastatins 8-10 (1-3). The structures of 1-3 were determined by NMR, MS, ESIMS fragmentation and chemical degradation. Compounds 1-3 are closely related to lyngbyastatins 4-7. Like the latter compounds, we found 1-3 to inhibit porcine pancreatic elastase, with IC(50) values of 123 nM, 210 nM and 120 nM, respectively.

Grassystatins A-C from marine cyanobacteria, potent cathepsin E inhibitors that reduce antigen presentation

In our efforts to explore marine cyanobacteria as a source of novel bioactive compounds, we discovered a statine unit-containing linear decadepsipeptide, grassystatin A (1), which we screened against a diverse set of 59 proteases. We describe the structure determination of 1 and two natural analogues, grassystatins B (2) and C (3), using NMR, MS, and chiral HPLC techniques. Compound 1 selectively inhibited cathepsins D and E with IC(50)s of 26.5 nM and 886 pM, respectively. Compound 2 showed similar potency and selectivity against cathepsins D and E (IC(50)s of 7.27 nM and 354 pM, respectively), whereas the truncated peptide analogue grassystatin C (3), which consists of two fewer residues than 1 and 2, was less potent against both but still selective for cathepsin E. The selectivity of compounds 1-3 for cathepsin E over D (20-38-fold) suggests that these natural products may be useful tools to probe cathepsin E function. We investigated the structural basis of this selectivity using molecular docking. We also show that 1 can reduce antigen presentation by dendritic cells, a process thought to rely on cathepsin E.

Alkyldimethylpyrazines in the defensive spray of Phyllium westwoodii: a first for order Phasmatodea

Phyllium westwoodii is a phasmid insect (Order Phasmatodea) belonging to the Family Phylliidae (leaf insects). These rather large and ornate creatures are known for their morphological resemblance to plant leaves for camouflage. Pyrazines are a common class of compounds used or produced by a wide variety of organisms, even humans. When an individual of P. westwoodii is disturbed, it sprays an opaque liquid from a pair of prothoracic glands, which are utilized by other phasmid species for defense. The current study has found that this liquid contains glucose and a mixture of 3-isobutyl-2,5-dimethylpyrazine, 2,5-dimethyl-3-(2-methylbutyl)pyrazine, and 2,5-dimethyl-3-(3-methylbutyl)pyrazine. This is the first report of pyrazines found in the defensive gland spray of phasmid insects, and the first chemical analysis of glandular material from family Phylliidae.

Bacterial attraction and quorum sensing inhibition in Caenorhabditis elegans exudates

Caenorhabditis elegans, a bacterivorous nematode, lives in complex rotting fruit, soil, and compost environments, and chemical interactions are required for mating, monitoring population density, recognition of food, avoidance of pathogenic microbes, and other essential ecological functions. Despite being one of the best-studied model organisms in biology, relatively little is known about the signals that C. elegans uses to interact chemically with its environment or as defense. C. elegans exudates were analyzed by using several analytical methods and found to contain 36 common metabolites that include organic acids, amino acids, and sugars, all in relatively high abundance. Furthermore, the concentrations of amino acids in the exudates were dependent on developmental stage. The C. elegans exudates were tested for bacterial chemotaxis using Pseudomonas putida (KT2440), a plant growth promoting rhizobacterium, Pseudomonas aeruginosa (PAO1), a soil bacterium pathogenic to C. elegans, and Escherichia coli (OP50), a non-motile bacterium tested as a control. The C. elegans exudates attracted the two Pseudomonas species, but had no detectable antibacterial activity against P. aeruginosa. To our surprise, the exudates of young adult and adult life stages of C. elegans exudates inhibited quorum sensing in the reporter system based on the LuxR bacterial quorum sensing (QS) system, which regulates bacterial virulence and other factors in Vibrio fischeri. We were able to fractionate the QS inhibition and bacterial chemotaxis activities, thus demonstrating that these activities are chemically distinct. Our results demonstrate that C. elegans can attract its bacterial food and has the potential of partially regulating the virulence of bacterial pathogens by inhibiting specific QS systems.

Active compensation of rf-pulse transients

A new approach to compensate rf-pulse transients is proposed. Based on the idea of the response theory of a linear system, a formula is derived to obtain the required excitation voltage profile back from the intended target rf-pulse shape. The validity of the formula is experimentally confirmed by monitoring the rf-field created inside the sample coil with a pickup coil. Since this approach realizes accurate rf-pulse shapes without reducing the Q-factor of the tank circuit of the probe, it can be used not only to suppress the transient tail of the rf-pulse, but also as a general concept for accurate rf-pulsing.