Efficient 18.8 T MAS-DNP NMR reveals hidden side chains in amyloid fibrils.

Amyloid fibrils are large and insoluble protein assemblies composed of a rigid core associated with a cross-ß arrangement rich in ß-sheet structural elements. It has been widely observed in solid-state NMR experiments that semi-rigid protein segments or side chains do not yield easily observable NMR signals at room temperature. The reasons for the missing peaks may be due to the presence of unfavorable dynamics that interfere with NMR experiments, which result in very weak or unobservable NMR signals. Therefore, for amyloid fibrils, semi-rigid and dynamically disordered segments flanking the amyloid core are very challenging to study. Here, we show that high-field dynamic nuclear polarization (DNP), an NMR hyperpolarization technique typically performed at low temperatures, can circumvent this issue because (i) the low-temperature environment (~ 100 K) slows down the protein dynamics to escape unfavorable detection regime, (ii) DNP improves the overall NMR sensitivity including those of flexible side chains, and (iii) efficient cross-effect DNP biradicals (SNAPol-1) optimized for high-field DNP (≥ 18.8 T) are employed to offer high sensitivity and resolution suitable for biomolecular NMR applications. By combining these factors, we have successfully established an impressive enhancement factor of ε ~ 50 on amyloid fibrils using an 18.8 T/ 800 MHz magnet. We have compared the DNP efficiencies of M-TinyPol, NATriPol-3, and SNAPol-1 biradicals on amyloid fibrils. We found that SNAPol-1 (with ε ~ 50) outperformed the other two radicals. The MAS DNP experiments revealed signals of flexible side chains previously inaccessible at conventional room-temperature experiments. These results demonstrate the potential of MAS-DNP NMR as a valuable tool for structural investigations of amyloid fibrils, particularly for side chains and dynamically disordered segments otherwise hidden at room temperature.

Room-Temperature Quantitative Quantum Sensing of Lithium Ions with a Radical-Embedded Metal-Organic Framework.

Recent advancements in quantum sensing have sparked transformative detection technologies with high sensitivity, precision, and spatial resolution. Owing to their atomic-level tunability, molecular qubits and ensembles thereof are promising candidates for sensing chemical analytes. Here, we show quantum sensing of lithium ions in solution at room temperature with an ensemble of organic radicals integrated in a microporous metal-organic framework (MOF). The organic radicals exhibit electron spin coherence and microwave addressability at room temperature, thus behaving as qubits. The high surface area of the MOF promotes accessibility of the guest analytes to the organic qubits, enabling unambiguous identification of lithium ions and quantitative measurement of their concentration through relaxometric and hyperfine spectroscopic methods based on electron paramagnetic resonance (EPR) spectroscopy. The sensing principle presented in this work is applicable to other metal ions with nonzero nuclear spin.

Observing Nearby Nuclei on Paramagnetic Trityls and MOFs via DNP and Electron Decoupling.

Dynamic nuclear polarization (DNP) is an NMR sensitivity enhancement technique that mediates polarization transfer from unpaired electrons to NMR-active nuclei. Despite its success in elucidating important structural information on biological and inorganic materials, the detailed polarization-transfer pathway from the electrons to the nearby and then the bulk solvent nuclei, and finally to the molecules of interest-remains unclear. In particular, the nuclei in the paramagnetic polarizing agent play significant roles in relaying the enhanced NMR polarizations to more remote nuclei. Despite their importance, the direct NMR observation of these nuclei is challenging because of poor sensitivity. Here, we show that a combined DNP and electron decoupling approach can facilitate direct NMR detection of these nuclei. We achieved an ∼80 % improvement in NMR intensity via electron decoupling at 0.35 T and 80 K on trityl radicals. Moreover, we recorded a DNP enhancement factor of ϵ ${\varepsilon{} }$ ∼90 and ∼11 % higher NMR intensity using electron decoupling on paramagnetic metal-organic framework, magnesium hexaoxytriphenylene (MgHOTP MOF).

Observation of a four-spin solid effect.

The two-spin solid effect (2SSE) is one of the established continuous wave dynamic nuclear polarization mechanisms that enables enhancement of nuclear magnetic resonance signals. It functions via a state-mixing mechanism that mediates the excitation of forbidden transitions in an electron-nuclear spin system. Specifically, microwave irradiation at frequencies ωµw ∼ ω0S ± ω0I, where ω0S and ω0I are electron and nuclear Larmor frequencies, respectively, yields enhanced nuclear spin polarization. Following the recent rediscovery of the three-spin solid effect (3SSE) [Tan et al., Sci. Adv. 5, eaax2743 (2019)], where the matching condition is given by ωµw = ω0S ± 2ω0I, we report here the first direct observation of the four-spin solid effect (4SSE) at ωµw = ω0S ± 3ω0I. The forbidden double- and quadruple-quantum transitions were observed in samples containing trityl radicals dispersed in a glycerol-water mixture at 0.35 T/15 MHz/9.8 GHz and 80 K. We present a derivation of the 4SSE effective Hamiltonian, matching conditions, and transition probabilities. Finally, we show that the experimental observations agree with the results from numerical simulations and analytical theory.

A unified description for polarization-transfer mechanisms in magnetic resonance in static solids: Cross polarization and DNP.

Polarization transfers are crucial building blocks in magnetic resonance experiments, i.e., they can be used to polarize insensitive nuclei and correlate nuclear spins in multidimensional nuclear magnetic resonance (NMR) spectroscopy. The polarization can be transferred either across different nuclear spin species or from electron spins to the relatively low-polarized nuclear spins. The former route occurring in solid-state NMR can be performed via cross polarization (CP), while the latter route is known as dynamic nuclear polarization (DNP). Despite having different operating conditions, we opinionate that both mechanisms are theoretically similar processes in ideal conditions, i.e., the electron is merely another spin-1/2 particle with a much higher gyromagnetic ratio. Here, we show that the CP and DNP processes can be described using a unified theory based on average Hamiltonian theory combined with fictitious operators. The intuitive and unified approach has allowed new insights into the cross-effect DNP mechanism, leading to better design of DNP polarizing agents and extending the applications beyond just hyperpolarization. We explore the possibility of exploiting theoretically predicted DNP transients for electron-nucleus distance measurements-such as routine dipolar-recoupling experiments in solid-state NMR.

Overhauser Dynamic Nuclear Polarization with Selectively Deuterated BDPA Radicals.

The Overhauser effect (OE), commonly observed in NMR spectra of liquids and conducting solids, was recently discovered in insulating solids doped with the radical 1,3-bisdiphenylene-2-phenylallyl (BDPA). However, the mechanism of polarization transfer in OE-DNP in insulators is yet to be established, but hyperfine coupling of the radical to protons in BDPA has been proposed. In this paper we present a study that addresses the role of hyperfine couplings via the EPR and DNP measurements on some selectively deuterated BDPA radicals synthesized for this purpose. Newly developed synthetic routes enable selective deuteration at orthogonal positions or perdeuteration of the fluorene moieties with 2H incorporation of >93%. The fluorene moieties were subsequently used to synthesize two octadeuterated BDPA radicals, 1,3-[α,γ-d8]-BDPA and 1,3-[ß,δ-d8]-BDPA, and a BDPA radical with perdeuterated fluorene moieties, 1,3-[α,ß,γ,δ-d16]-BDPA. In contrast to the strong positive OE enhancement observed in degassed samples of fully protonated h21-BDPA (ε ∼ +70), perdeuteration of the fluorenes results in a negative enhancement (ε ∼ -13), while selective deuteration of α- and γ-positions (aiso ∼ 5.4 MHz) in BDPA results in a weak negative OE enhancement (ε ∼ -1). Furthermore, deuteration of ß- and δ-positions (aiso ∼ 1.2 MHz) results in a positive OE enhancement (ε ∼ +36), albeit with a reduced magnitude relative to that observed in fully protonated BDPA. Our results clearly show the role of the hyperfine coupled α and γ 1H spins in the BDPA radical in determining the dominance of the zero and double-quantum cross-relaxation pathways and the polarization-transfer mechanism to the bulk matrix.

Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.

All cells obtain 2'-deoxyribonucleotides for DNA synthesis through the activity of a ribonucleotide reductase (RNR). The class I RNRs found in humans and pathogenic bacteria differ in (i) use of Fe(II), Mn(II), or both for activation of the dinuclear-metallocofactor subunit, ß; (ii) reaction of the reduced dimetal center with dioxygen or superoxide for this activation; (iii) requirement (or lack thereof) for a flavoprotein activase, NrdI, to provide the superoxide from O2; and (iv) use of either a stable tyrosyl radical or a high-valent dimetal cluster to initiate each turnover by oxidizing a cysteine residue in the α subunit to a radical (Cys•). The use of manganese by bacterial class I, subclass b-d RNRs, which contrasts with the exclusive use of iron by the eukaryotic Ia enzymes, appears to be a countermeasure of certain pathogens against iron deprivation imposed by their hosts. Here, we report a metal-free type of class I RNR (subclass e) from two human pathogens. The Cys• in its α subunit is generated by a stable, tyrosine-derived dihydroxyphenylalanine radical (DOPA•) in ß. The three-electron oxidation producing DOPA• occurs in Escherichia coli only if the ß is coexpressed with the NrdI activase encoded adjacently in the pathogen genome. The independence of this new RNR from transition metals, or the requirement for a single metal ion only transiently for activation, may afford the pathogens an even more potent countermeasure against transition metal-directed innate immunity.

Efficient low-power TOBSY sequences for fast MAS.

Through-bond J-coupling based experiments in solid-state NMR spectroscopy are challenging because the J couplings are typically much smaller than the dipolar couplings. This often leads to a lower transfer efficiency compared to dipolar-coupling based sequences. One of the reasons for the low transfer efficiency are the second-order cross terms involving the strong heteronuclear dipolar couplings leading to fast magnetization decay. Here, we show that by employing a symmetry-based C9 sequence, which was carefully selected to suppress second-order terms, efficient polarization transfers of up to 80% can be achieved without decoupling on fully protonated two-spin model systems at a MAS frequency of 55.5 kHz with rf-field amplitudes of about 25 kHz. In addition, we analyse the effects of rf inhomogeneity and crystallites selection due to the polarization preparation method on the TOBSY transfer efficiency. We demonstrate on small model substances as well as on deuterated and 100% back-exchanged ubiquitin that C9391 and C9481 are efficient and practical TOBSY sequences at experimental conditions ranging from proton Larmor frequencies of 400-850 MHz, and MAS frequencies ranging from 55.5 to 111.1 kHz.

Optimizing symmetry-based recoupling sequences in solid-state NMR by pulse-transient compensation and asynchronous implementation.

Pulse imperfections like pulse transients and radio-frequency field maladjustment or inhomogeneity are the main sources of performance degradation and limited reproducibility in solid-state nuclear magnetic resonance experiments. We quantitatively analyze the influence of such imperfections on the performance of symmetry-based pulse sequences and describe how they can be compensated. Based on a triple-mode Floquet analysis, we develop a theoretical description of symmetry-based dipolar recoupling sequences, in particular, R26411, calculating first- and second-order effective Hamiltonians using real pulse shapes. We discuss the various origins of effective fields, namely, pulse transients, deviation from the ideal flip angle, and fictitious fields, and develop strategies to counteract them for the restoration of full transfer efficiency. We compare experimental applications of transient-compensated pulses and an asynchronous implementation of the sequence to a supercycle, SR26, which is known to be efficient in compensating higher-order error terms. We are able to show the superiority of R26 compared to the supercycle, SR26, given the ability to reduce experimental error on the pulse sequence by pulse-transient compensation and a complete theoretical understanding of the sequence.

A generalized theoretical framework for the description of spin decoupling in solid-state MAS NMR: Offset effect on decoupling performance.

We present a generalized theoretical framework that allows the approximate but rapid analysis of residual couplings of arbitrary decoupling sequences in solid-state NMR under magic-angle spinning conditions. It is a generalization of the tri-modal Floquet analysis of TPPM decoupling [Scholz et al., J. Chem. Phys. 130, 114510 (2009)] where three characteristic frequencies are used to describe the pulse sequence. Such an approach can be used to describe arbitrary periodic decoupling sequences that differ only in the magnitude of the Fourier coefficients of the interaction-frame transformation. It allows a ∼100 times faster calculation of second-order residual couplings as a function of pulse sequence parameters than full spin-dynamics simulations. By comparing the theoretical calculations with full numerical simulations, we show the potential of the new approach to examine the performance of decoupling sequences. We exemplify the usefulness of this framework by analyzing the performance of commonly used high-power decoupling sequences and low-power decoupling sequences such as amplitude-modulated XiX (AM-XiX) and its super-cycled variant SC-AM-XiX. In addition, the effect of chemical-shift offset is examined for both high- and low-power decoupling sequences. The results show that the cross-terms between the dipolar couplings are the main contributions to the line broadening when offset is present. We also show that the SC-AM-XIX shows a better offset compensation.

Improved transfer efficiencies in radio-frequency-driven recoupling solid-state NMR by adiabatic sweep through the dipolar recoupling condition.

The homonuclear radio-frequency driven recoupling (RFDR) experiment is commonly used in solid-state NMR spectroscopy to gain insight into the structure of biological samples due to its ease of implementation, stability towards fluctuations/missetting of radio-frequency (rf) field strength, and in general low rf requirements. A theoretical operator-based Floquet description is presented to appreciate the effect of having a temporal displacement of the π-pulses in the RFDR experiment. From this description, we demonstrate improved transfer efficiency for the RFDR experiment by generating an adiabatic passage through the zero-quantum recoupling condition. We have compared the performances of RFDR and the improved sequence to mediate efficient (13)CO to (13)Cα polarization transfer for uniformly (13)C,(15)N-labeled glycine and for the fibril forming peptide SNNFGAILSS (one-letter amino acid codes) uniformly (13)C,(15)N-labeled at the FGAIL residues. Using numerically optimized sweeps, we get experimental gains of approximately 20% for glycine where numerical simulations predict an improvement of 25% relative to the standard implementation. For the fibril forming peptide, using the same sweep parameters as found for glycine, we have gains in the order of 10%-20% depending on the spectral regions of interest.

Asynchronous symmetry-based sequences for homonuclear dipolar recoupling in solid-state nuclear magnetic resonance.

We show a theoretical framework, based on triple-mode Floquet theory, to analyze recoupling sequences derived from symmetry-based pulse sequences, which have a non-vanishing effective field and are not rotor synchronized. We analyze the properties of one such sequence, a homonuclear double-quantum recoupling sequence derived from the C72 (1) sequence. The new asynchronous sequence outperforms the rotor-synchronized version for spin pairs with small dipolar couplings in the presence of large chemical-shift anisotropy. The resonance condition of the new sequence is analyzed using triple-mode Floquet theory. Analytical calculations of second-order effective Hamiltonian are performed to compare the efficiency in suppressing second-order cross terms. Experiments and numerical simulations are shown to corroborate the results of the theoretical analysis.

A focus on applying 63/65Cu solid-state NMR spectroscopy to characterize Cu MOFs.

Metal-organic frameworks (MOFs) are a class of hybrid organic and inorganic porous materials that have shown prospects in applications ranging from gas storage, separation, catalysis, etc. Although they can be studied using various characterization techniques, these methods often do not provide local structural details that help explain their functionality. Zhang et al. (W. Zhang, B. E. G. Lucier, V. V. Terskikh, S. Chen and Y. Huang, Chem. Sci., 2024, https://doi.org/10.1039/D4SC00782D) have recently exploited 63/65Cu solid-state NMR spectroscopy (for the first time) and DFT calculations to elucidate the structures of Cu(i) centers in MOFs. While there are still many challenges in overcoming issues in resolution and sensitivity, this work lays the foundation for further development of solid-state NMR technology in characterizing copper in MOFs or other amorphous solids.

In-house fabrication of 1.3 to 7 mm MAS drive caps using desktop 3D printers.

The 3D-printing technology has emerged as a well-developed method to produce parts with considerably low cost and yet with high precision (<100 µm). Recent literature has shown that the 3D-printing technology can be exploited to fabricate a magic-angle spinning (MAS) system in solid-state nuclear magnetic resonance (NMR) spectroscopy. In particular, it was demonstrated that advanced industry-grade 3D printers could fabricate 3.2 mm MAS drive caps with intricate features, and the caps were shown to spin > 20 kHz. Here, we show that not only lab-affordable benchtop 3D printers can produce 3.2 mm drive caps with a similar quality as the commercialized version, but also smaller 2.5 mm and 1.3 mm MAS drive caps-despite a slight compromise in performance. All in-house fabricated drive caps (1.3 to 7 mm) can be consistently reproduced (>90 %) and achieve excellent spinning performances. In summary, the > 3.2 mm systems have similar performances as the commercial systems, while the 2.5- and 1.3-mm caps can spin up to 26 kHz ± 2 Hz, and 46 kHz ± 1 Hz, respectively. The low-cost and fast in-house fabrication of MAS drive caps allows easy prototyping of new MAS drive cap models and, possibly, new NMR applications. For instance, we have fabricated a 4 mm drive cap with a center hole that could allow better light penetration or sample insertion during MAS. Besides, an added groove design on the drive cap allows an airtight seal suitable for probing air- or moisture-sensitive materials. Moreover, the 3D-printed cap was shown to be robust for low-temperature MAS experiments at âˆ¼ 100 K, making it suitable for DNP experiments.

Integrated, Stretched, and Adiabatic Solid Effects.

This paper presents a theory describing the dynamic nuclear polarization (DNP) process associated with an arbitrary frequency swept microwave pulse. The theory is utilized to explain the integrated solid effect (ISE) as well as the newly discovered stretched solid effect (SSE) and adiabatic solid effect (ASE). It is verified with experiments performed at 9.4 GHz (0.34 T) on single crystals of naphthalene doped with pentacene-d14. It is shown that the SSE and ASE can be more efficient than the ISE. Furthermore, the theory predicts that the efficiency of the SSE improves at high magnetic fields, where the EPR line width is small compared to the nuclear Larmor frequency. In addition, we show that the ISE, SSE, and ASE are based on similar physical principles and we suggest definitions to distinguish among them.

Designing broadband pulsed dynamic nuclear polarization sequences in static solids.

Dynamic nuclear polarization (DNP) is a nuclear magnetic resonance (NMR) hyperpolarization technique that mediates polarization transfer from unpaired electrons with large thermal polarization to NMR-active nuclei via microwave (mw) irradiation. The ability to generate arbitrarily shaped mw pulses using arbitrary waveform generators allows for remarkable improvement of the robustness and versatility of DNP. We present here novel design principles based on single-spin vector effective Hamiltonian theory to develop new broadband DNP pulse sequences, namely, an adiabatic version of XiX (X-inverse X)-DNP and a broadband excitation by amplitude modulation (BEAM)-DNP experiment. We demonstrate that the adiabatic BEAM-DNP pulse sequence may achieve a 1H enhancement factor of ∼360, which is better than ramped-amplitude NOVEL (nuclear spin orientation via electron spin locking) at ∼0.35 T and 80 K in static solids doped with trityl radicals. In addition, the bandwidth of the BEAM-DNP experiments (~50 MHz) is about three times the 1H Larmor frequency. The generality of our theoretical approach will be helpful in the development of new pulsed DNP sequences.

Adiabatic Solid Effect.

The solid effect (SE) is a two spin dynamic nuclear polarization (DNP) mechanism that enhances the sensitivity in NMR experiments by irradiation of the electron-nuclear spin transitions with continuous wave (CW) microwaves at ω0S ± ω0I, where ω0S and ω0I are electron and nuclear Larmor frequencies, respectively. Using trityl (OX063), dispersed in a 60/40 glycerol/water mixture at 80 K, as a polarizing agent, we show here that application of a chirped microwave pulse, with a bandwidth comparable to the EPR line width applied at the SE matching condition, improves the enhancement by a factor of 2.4 over the CW method. Furthermore, the chirped pulse yields an enhancement that is ∼20% larger than obtained with the ramped-amplitude NOVEL (RA-NOVEL), which to date has achieved the largest enhancements in time domain DNP experiments. Numerical simulations suggest that the spins follow an adiabatic trajectory during the polarization transfer; hence, we denote this sequence as an adiabatic solid effect (ASE). We foresee that ASE will be a practical pulsed DNP experiment to be implemented at higher static magnetic fields due to the moderate power requirement. In particular, the ASE uses only 13% of the maximum microwave power required for RA-NOVEL.

Three-spin solid effect and the spin diffusion barrier in amorphous solids.

Dynamic nuclear polarization (DNP) has evolved as the method of choice to enhance NMR signal intensities and to address a variety of otherwise inaccessible chemical, biological and physical questions. Despite its success, there is no detailed understanding of how the large electron polarization is transferred to the surrounding nuclei or where these nuclei are located relative to the polarizing agent. To address these questions we perform an analysis of the three-spin solid effect, and show that it is exquisitely sensitive to the electron-nuclear distances. We exploit this feature and determine that the size of the spin diffusion barrier surrounding the trityl radical in a glassy glycerol-water matrix is <6 Å, and that the protons involved in the initial transfer step are on the trityl molecule. 1H ENDOR experiments indicate that polarization is then transferred in a second step to glycerol molecules in intimate contact with the trityl.

Time-optimized pulsed dynamic nuclear polarization.

Pulsed dynamic nuclear polarization (DNP) techniques can accomplish electron-nuclear polarization transfer efficiently with an enhancement factor that is independent of the Zeeman field. However, they often require large Rabi frequencies and, therefore, high-power microwave irradiation. Here, we propose a new low-power DNP sequence for static samples that is composed of a train of microwave pulses of length τp spaced with delays d. A particularly robust DNP condition using a period τm = τp + d set to ~1.25 times the Larmor period τLarmor is investigated which is a time-optimized pulsed DNP sequence (TOP-DNP). At 0.35 T, we obtained an enhancement of ~200 using TOP-DNP compared to ~172 with nuclear spin orientation via electron spin locking (NOVEL), a commonly used pulsed DNP sequence, while using only ~7% microwave power required for NOVEL. Experimental data and simulations at higher fields suggest a field-independent enhancement factor, as predicted by the effective Hamiltonian.

Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR.

In DNP MAS NMR experiments at ∼80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H decoupling. Here we investigate the effect of these dynamic processes on the NMR line shapes and signal intensities in several typical systems: (1) microcrystalline APG, (2) membrane protein bR, (3) amyloid fibrils PI3-SH3, (4) monomeric alanine-CD3, and (5) the protonated and deuterated dipeptide N-Ac-VL over 78-300 K. In APG, the three-site hopping of the Ala-Cß peak disappears completely at 112 K, concomitant with the attenuation of CP signals from other 13C's and 15N's. Similarly, the 15N signal from Ala-NH3+ disappears at ∼173 K, concurrent with the attenuation in CP experiments of other 15N's as well as 13C's. In bR and PI3-SH3, the methyl groups are attenuated at ∼95 K, while all other 13C's remain unaffected. However, both systems exhibit substantial losses of intensity at ∼243 K. Finally, with spectra of Ala and N-Ac-VL, we show that it is possible to extract site specific dynamic data from the temperature dependence of the intensity losses. Furthermore, 2H labeling can assist with recovering the spectral intensity. Thus, our study provides insight into the dynamic behavior of biological systems over a wide range of temperatures, and serves as a guide to optimizing the sensitivity and resolution of structural data in low temperature DNP MAS NMR spectra.