Natural Abundance, Single-Scan 13C-13C-Based Structural Elucidations by Dissolution DNP NMR

The matrix pencil as a tunable filter

Despite inherent sensitivity constraints, nuclear magnetic resonance (NMR) plays an indispensable role in probing molecular structures and dynamics across scientific disciplines. Remarkably, while extensive efforts have targeted instrumental and experimental sensitivity improvements, comparatively little focus has been dedicated to sensitivity enhancement through signal analysis. Amidst this present gap, the matrix pencil method (MPM) has emerged as a versatile algorithm that offers tunable filtering and phasing capabilities. Extensive prior research has established the MPM as an adept fitting tool in signal analysis. Here, the efficacy of the MPM is investigated by precisely modeling noisy data to separate information-bearing signals from noise, thereby expanding its utility in various magnetic resonance applications. Simulated data is used to confirm the ability of the MPM to discern and separate signals from noise. Comparative analyses against standard Fourier-based filtering methods highlight the superior performance of the matrix pencil filter (MPF) in preserving signal fidelity without introducing aliasing artifacts. A variety of experimental data is then explored to demonstrate the proficiency of the MPF in characterizing signal components and correcting phase distortions. Collectively, these case studies underscore the filtering capacity of the MPM, portending its use for analytical sensitivity improvements in a wide range of NMR applications.

Yeast Solutions and Hyperpolarization Enable Real-Time Observation of Metabolized Substrates Even at Natural Abundance

Metabolic changes in an organism often occur much earlier than macroscopic manifestations of disease, such as invasive tumors. Therefore, noninvasive tools to monitor metabolism are fundamental as they provide insights into in vivo biochemistry. NMR represents one of the gold standards for such insights by observing metabolites. Using nuclear spin hyperpolarization greatly increases the NMR sensitivity, enabling μmol/L sensitivity with a time resolution of about one second. However, a metabolic phantom with reproducible, rapid, and human-like metabolism is needed to progress research in this area. Using baker's yeast as a convenient metabolic factory, we demonstrated in a single study that yeast cells provide a robust and rapidly metabolizing phantom for pyruvate and fumarate, including substrates with a natural abundance of 13C: we observed the production of ethanol, carbon dioxide, bicarbonate, lactate, alanine from pyruvate, malate, and oxaloacetate from fumarate. For observation, we hyperpolarized pyruvate and fumarate via the dissolution dynamic nuclear polarization (dDNP) technique to about 30% 13C polarization that is equivalent to 360,000 signal enhancement at 1 T and 310 K. Major metabolic pathways were observed using tracers at a natural abundance of 13C, demonstrating that isotope labeling is not always essential in vitro. Enriched [1-13C]pyruvate revealed minor lactate production, presumably via the D-lactate dehydrogenase (DLD) enzyme pathway, demonstrating the sensitivity gain using a dense yeast solution. We foresee that yeast as a metabolic factory can find application as an abundant MRI phantom standard to calibrate and optimize molecular MRI protocols. Our study highlights the potential of using hyperpolarization to probe the metabolism of yeast and other microorganisms even with naturally abundant substrates, offering valuable insights into their response to various stimuli such as drugs, treatment, nourishment, and genetic modification, thereby advancing drug development and our understanding of biochemical processes.

Overhauser enhanced liquid state nuclear magnetic resonance spectroscopy in one and two dimensions

Nuclear magnetic resonance (NMR) is fundamental in the natural sciences, from chemical analysis and structural biology, to medicine and physics. Despite its enormous achievements, one of its most severe limitations is the low sensitivity, which arises from the small population difference of nuclear spin states. Methods such as dissolution dynamic nuclear polarization and parahydrogen induced hyperpolarization can enhance the NMR signal by several orders of magnitude, however, their intrinsic limitations render multidimensional hyperpolarized liquid-state NMR a challenge. Here, we report an instrumental design for 9.4 Tesla liquid-state dynamic nuclear polarization that enabled enhanced high-resolution NMR spectra in one and two-dimensions for small molecules, including drugs and metabolites. Achieved enhancements of up to two orders of magnitude translate to signal acquisition gains up to a factor of 10,000. We show that hyperpolarization can be transferred between nuclei, allowing DNP-enhanced two-dimensional 13C-13C correlation experiments at 13C natural abundance. The enhanced sensitivity opens up perspectives for structural determination of natural products or characterization of drugs, available in small quantities. The results provide a starting point for a broader implementation of DNP in liquid-state NMR.

Single-Scan Heteronuclear 13C-15N J-Coupling NMR Observations Enhanced by Dissolution Dynamic Nuclear Polarization

Heteronuclear 13C-15N couplings were measured in single-scan nuclear magnetic resonance (NMR) experiments for a variety of nitrogen-containing chemical compounds with varied structural characteristics, by using a one-dimensional (1D) 13C-15N multiple-quantum (MQ)-filtered experiment. Sensitivity limitations of the MQ filtering were overcome by the combined use of 15N labeling and dissolution dynamic nuclear polarization (dDNP), performed at cryogenic conditions and followed by quick and optimized sample melting and transfer procedures. Coupling information could thus be obtained from nucleotide bases, amino acids, urea, and aliphatic and aromatic amides, including the measurement of relatively small J-couplings directly from the 1D filtered spectra. This experiment could pave the way for NMR-based analytical applications that investigate structural and stereochemical insights into nitrogen-containing compounds, including dipeptides and proteins, while relying on heteronuclear couplings and nuclear hyperpolarization.

Unified understanding of the breakdown of thermal mixing dynamic nuclear polarization: The role of temperature and radical concentration

We reveal an interplay between temperature and radical concentration necessary to establish thermal mixing (TM) as an efficient dynamic nuclear polarization (DNP) mechanism. We conducted DNP experiments by hyperpolarizing widely used DNP samples, i.e., sodium pyruvate-1-13C in water/glycerol mixtures at varying nitroxide radical (TEMPOL) concentrations and microwave irradiation frequencies, measuring proton and carbon-13 spin temperatures. Using a cryogen consumption-free prototype-DNP apparatus, we could probe cryogenic temperatures between 1.5 and 6.5 K, i.e., below and above the boiling point of liquid helium. We identify two mechanisms for the breakdown of TM: (i) Anderson type of quantum localization for low radical concentration, or (ii) quantum Zeno localization occurring at high temperature. This observation allowed us to reconcile the recent diverging observations regarding the relevance of TM as a DNP mechanism by proposing a unifying picture and, consequently, to find a trade-off between radical concentration and electron relaxation times, which offers a pathway to improve experimental DNP performance based on TM.

Spin Hyperpolarization in Modern Magnetic Resonance

Magnetic resonance techniques are successfully utilized in a broad range of scientific disciplines and in various practical applications, with medical magnetic resonance imaging being the most widely known example. Currently, both fundamental and applied magnetic resonance are enjoying a major boost owing to the rapidly developing field of spin hyperpolarization. Hyperpolarization techniques are able to enhance signal intensities in magnetic resonance by several orders of magnitude, and thus to largely overcome its major disadvantage of relatively low sensitivity. This provides new impetus for existing applications of magnetic resonance and opens the gates to exciting new possibilities. In this review, we provide a unified picture of the many methods and techniques that fall under the umbrella term "hyperpolarization" but are currently seldom perceived as integral parts of the same field. Specifically, before delving into the individual techniques, we provide a detailed analysis of the underlying principles of spin hyperpolarization. We attempt to uncover and classify the origins of hyperpolarization, to establish its sources and the specific mechanisms that enable the flow of polarization from a source to the target spins. We then give a more detailed analysis of individual hyperpolarization techniques: the mechanisms by which they work, fundamental and technical requirements, characteristic applications, unresolved issues, and possible future directions. We are seeing a continuous growth of activity in the field of spin hyperpolarization, and we expect the field to flourish as new and improved hyperpolarization techniques are implemented. Some key areas for development are in prolonging polarization lifetimes, making hyperpolarization techniques more generally applicable to chemical/biological systems, reducing the technical and equipment requirements, and creating more efficient excitation and detection schemes. We hope this review will facilitate the sharing of knowledge between subfields within the broad topic of hyperpolarization, to help overcome existing challenges in magnetic resonance and enable novel applications.

Hyperpolarized Solution-State NMR Spectroscopy with Optically Polarized Crystals

Nuclear spin hyperpolarization provides a promising route to overcome the challenges imposed by the limited sensitivity of nuclear magnetic resonance. Here we demonstrate that dissolution of spin-polarized pentacene-doped naphthalene crystals enables transfer of polarization to target molecules via intermolecular cross-relaxation at room temperature and moderate magnetic fields (1.45 T). This makes it possible to exploit the high spin polarization of optically polarized crystals, while mitigating the challenges of its transfer to external nuclei. With this method, we inject the highly polarized mixture into a benchtop NMR spectrometer and observe the polarization dynamics for target ¹H nuclei. Although the spectra are radiation damped due to the high naphthalene magnetization, we describe a procedure to process the data to obtain more conventional NMR spectra and extract the target nuclei polarization. With the entire process occurring on a time scale of 1 min, we observe NMR signals enhanced by factors between -200 and -1730 at 1.45 T for a range of small molecules.

Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water

Nuclear magnetic resonance (NMR) spectroscopy is a powerful and popular technique for probing the molecular structures, dynamics and chemical properties. However the conventional NMR spectroscopy is bottlenecked by its low sensitivity. Dynamic nuclear polarization (DNP) boosts NMR sensitivity by orders of magnitude and resolves this limitation. In liquid-state this revolutionizing technique has been restricted to a few specific non-biological model molecules in organic solvents. Here we show that the carbon polarization in small biological molecules, including carbohydrates and amino acids, can be enhanced sizably by in situ Overhauser DNP (ODNP) in water at room temperature and at high magnetic field. An observed connection between ODNP 13C enhancement factor and paramagnetic 13C NMR shift has led to the exploration of biologically relevant heterocyclic compound indole. The QM/MM MD simulation underscores the dynamics of intermolecular hydrogen bonds as the driving force for the scalar ODNP in a long-living radical-substrate complex. Our work reconciles results obtained by DNP spectroscopy, paramagnetic NMR and computational chemistry and provides new mechanistic insights into the high-field scalar ODNP.

A cryogen-free, semi-automated apparatus for bullet-dynamic nuclear polarization with improved resolution

In dissolution-dynamic nuclear polarization, a hyperpolarized solid is dissolved with a jet of hot solvent. The solution is then transferred to a secondary magnet, where spectra can be recorded with improved sensitivity. In bullet-dynamic nuclear polarization this order is reversed. Pressurized gas is used to rapidly transfer the hyperpolarized solid to the secondary magnet, and the hyperpolarized solid is dissolved only upon arrival. A potential advantage of this approach is that it may avoid excessive dilution and the associated signal loss, in particular for small sample quantities. Previously, we have shown that liquid-state NMR spectra with polarization levels of up to 30 % may be recorded within less than 1 s after the departure of the hyperpolarized solid from the polarizing magnet. The resolution of the recorded spectra however was limited. The system consumed significant amounts of liquid helium, and substantial manual work was required in between experiments to prepare for the next shot. Here, we present a new bullet-DNP (dynamic nuclear polarization) system that addresses these limitations.

Practical dissolution dynamic nuclear polarization

This review article intends to provide insightful advice for dissolution-dynamic nuclear polarization in the form of a practical handbook. The goal is to aid research groups to effectively perform such experiments in their own laboratories. Previous review articles on this subject have covered a large number of useful topics including instrumentation, experimentation, theory, etc. The topics to be addressed here will include tips for sample preparation and for checking sample health; a checklist to correctly diagnose system faults and perform general maintenance; the necessary mechanical requirements regarding sample dissolution; and aids for accurate, fast and reliable polarization quantification. Herein, the challenges and limitations of each stage of a typical dissolution-dynamic nuclear polarization experiment are presented, with the focus being on how to quickly and simply overcome some of the limitations often encountered in the laboratory.

Highly Efficient Determination of Complex NMR Multiplet Structures in Inhomogeneous Magnetic Fields

Proton-proton scalar (J) coupling plays an important role in disentangling molecular structures and spatial conformations. But it is challenging to extract J coupling networks from congested ¹H NMR spectra, especially in inhomogeneous magnetic fields. Herein, we propose a general liquid NMR protocol, named HR-G-SERF, to implement highly efficient determination of individual J couplings and corresponding coupling networks via simultaneously suppressing effects of spectral congestions and magnetic field inhomogeneity. This method records full-resolved 2D absorption-mode spectra to deliver great convenience for multipet analyses on complex samples. More meaningfully, it is capable of disentangling multiplet structures of biological samples, that is, grape sarcocarp, despite of its heterogeneous semisolid state and extensive compositions. In addition, a modification, named AH-G-SERF, is developed to compress experimental acquisition and subsequently improve unit-time SNR, while maintaining satisfactory spectral performance. This accelerated variant may further boost the applicability for rapid NMR detections and afford the possibility of adopting hyperpolarized substances to enhance the overall sensitivity. Therefore, this study provides a promising tool for molecular structure elucidations and composition analyses in chemistry, biochemistry, and metabonomics among others.

Application of INADEQUATE NMR techniques for directly tracing out the carbon skeleton of a natural product

INTRODUCTION

Nuclear magnetic resonance (NMR) measurement of ¹ J_CC coupling by two-dimensional (2D) INADEQUATE (incredible natural abundance double quantum transfer experiment), which is a special case of double-quantum (DQ) spectroscopy that offers unambiguous determination of ¹³ C-¹³ C spin-spin connectivities through the DQ transitions of the spin system, is especially suited to solving structures rich in quaternary carbons and poor in hydrogen content (Crews rule).

OBJECTIVE

To review published literature on the application of NMR methods to determine structure in the liquid-state, which specifically considers the interaction of a pair of carbon-13 (¹³ C) nuclei adjacent to one another, to allow direct tracing out of contiguous carbon connectivity using 2D INADEQUATE.

METHODOLOGY

A comprehensive literature search was implemented with various databases: Web of Knowledge, PubMed and SciFinder, and other relevant published materials including published monographs. The keywords used, in various combinations, with INADEQUATE being present in all combinations, in the search were 2D NMR, ¹ J_CC coupling, natural product, structure elucidation, ¹³ C-¹³ C connectivity, cryoprobe and CASE (computer-assisted structure elucidation)/PANACEA (protons and nitrogen and carbon et alia).

RESULTS

The 2D INADEQUATE continues to solve "intractable" problems in natural product chemistry, and using milligram quantities with cryoprobe techniques combined with CASE/PANACEA experiments can increase machine time efficiency. The ¹³ C-¹³ C-based structural elucidation by dissolution single-scan dynamic nuclear polarisation NMR can overcome disadvantages of ¹³ C insensitivity at natural abundance. Selected examples have demonstrated the trajectory of INADEQUATE spectroscopy from structural determination to clarification of metabolomics analysis and use of DFT (density functional theory) and coupling constants to clarify the connectivity, hybridisation and stereochemistry within natural products.

CONCLUSIONS

Somewhat neglected over the years because of perceived lack of sensitivity, the 2D INADEQUATE NMR technique has re-emerged as a useful tool for solving natural products structures, which are rich in quaternary carbons and poor in hydrogen content.