Advances in the synthesis of nitroxide radicals for use in biomolecule spin labelling

Sigmatropic rearrangement enables access to a highly stable spirocyclic nitroxide for protein spin labelling

Spin labelling enables the study of biomolecules using electron paramagnetic resonance (EPR) spectroscopy. Here, we describe the synthesis of a cysteine-reactive spin label based on a spirocyclic pyrrolidinyl nitroxide containing an iodoacetamide moiety. The spin label was shown to be highly persistent under reducing conditions while maintaining excellent EPR relaxation parameters up to a temperature of 180 K. After successful double spin labelling of a calmodulin variant, interspin distances were measured by the EPR experiment double electron-electron resonance (DEER) at 120 K.

Nitroxide radical contrast agents for safe magnetic resonance imaging: progress, challenges, and perspectives

Magnetic resonance imaging (MRI) is considered one of the most valuable diagnostic technologies in the 21st century. To enhance the image contrast of anatomical features, MRI contrast agents have been widely used in clinical MRI diagnosis, especially those based on gadolinium, manganese, and iron oxide. However, these metal-based MRI contrast agents show potential toxicity to patients, which urges researchers to develop novel MRI contrast agents that can replace metal-based MRI contrast agents. Metal-free nitroxide radical contrast agents (NRCAs) effectively overcome the shortcomings of metal-based contrast agents and also have many advantages, including good biocompatibility, prolonged systemic circulation time, and easily functionalized structures. Importantly, since NRCAs acquire MRI signals with standard tissue water 1H relaxation mechanisms, they have great potential to realize clinical translation among many metal-free MRI contrast agents. At present, NRCAs have been proposed as an effective substitute for metal-based MRI contrast agents. Herein, this review first briefly introduces NRCAs, including their composition, classification, mechanism of action, application performances and advantages. Then, this review highlights the progress of NRCAs, including small molecule-based NRCAs and polymer-based NRCAs. Finally, this review also discusses the challenges and future perspectives of NRCAs.

Research progress of nitroxide radical-based MRI contrast agents: from structure design to application

Magnetic resonance imaging (MRI) remains a cornerstone of diagnostic imaging, offering unparalleled insights into anatomical structures and pathological conditions. Gadolinium-based contrast agents have long been the standard in MRI enhancement, yet concerns over nephrogenic systemic fibrosis have spurred interest in metal-free alternatives. Nitroxide radical-based MRI contrast agents (NO-CAs) have emerged as promising candidates, leveraging their biocompatibility and imaging capabilities. This review summaries the latest advancements in NO-CAs, focusing on synthesis methodologies, influencing effects of structures of NO-CAs on relaxation efficiency and their applications across various clinical contexts. Comprehensive discussions encompass small molecular, polymeric, and nano-sized NO-CAs, detailing their unique properties and potential clinical utilities. Despite challenges, NO-CAs represent a dynamic area of research poised to revolutionize MRI diagnostics. This review serves as a critical resource for researchers and practitioners seeking to navigate the evolving landscape of MRI contrast agents.

Probing the Effects of Multisite Mutations in the Lipoic Acid Region of the BCOADC-E2 Protein

Primary biliary cholangitis (PBC) is a chronic disease, the prevalence of which has been increasing in recent years. And the prevalence of patients who test negative with existing diagnostic techniques remains high. It was found that the antigenic BCOADC-E2 protein could detect patients with a negative original test. And experiments revealed that the lipoyl domain of BCOADC-E2 plays an important role. The present study was carried out to verify the necessity of maintaining the folding conformation of the lipoyl β-sheet of the protein in the lipoyl domain during the recognition of the BCOADC-E2 protein and the importance of the glutamic acid and isoleucine residues at position 4 and position 13, respectively. In order to search for a new pathway for the pre-detection of patients with PBC, firstly, the mutant proteins were subjected to an enzyme-linked immunosorbent assay (ELISA) with serum. Then, MTSSL spin tags were positioned at specific sites of the Cys mutant and reacted with serum samples from PBC patients and controls, and EPR spectroscopic data were measured. The multiple mutant proteins all reacted less specifically with the serum than the wild-type protein in the ELISA; the spectra measured for the pGEX-BCKD-E4A-I13A mutant were severely broadened, and the compactness at the conformational position of the lipoyl β-sheet structural conformation of the proteins of amino acids 4 and 13 remained unchanged. The EPR spectral data validate the importance of the glutamate and isoleucine residues at position 4 and position 13 and their necessity in the maintenance of the lipoyl β-sheet structural conformation of proteins in the lipoyl domain in anti-BCOADC-E2 recognition.

Spirocyclic Pyrrolidinyl Nitroxides with Exo-Methylene Substituents

Nitroxides are stable organic radicals with exceptionally long lifetimes, which render them uniquely suitable as observable probes or polarising agents for spectroscopic investigation of biomolecular structure and dynamics. Radical-based probes for biological applications are ideally characterized by both robustness towards reductive degradation and beneficial electron spin relaxation parameters. These properties are largely influenced by the molecular structure of the nitroxide scaffold, and also by the conformations it prefers to adopt. In this study we present the synthesis of the first nitroxides based on a spirocyclic pyrrolidine scaffold with an exocyclic methylene substituent. The conformations adopted by these nitroxides were evaluated by X-ray crystallography, both with single nitroxide crystals and by inclusion of nitroxides in a microporous crystalline sponge. The kinetic and thermodynamic stability of the new nitroxides towards reduction was investigated by electron paramagnetic resonance (EPR) spectroscopy and cyclic voltammetry (CV). In combination with EPR measurements of electron spin relaxation properties, these results suggest that this new family of nitroxides can provide access to multifunctionalized probes and polarising agents suitable for use in biological environments at elevated temperatures.

Advancements in electron paramagnetic resonance (EPR) spectroscopy: A comprehensive tool for pharmaceutical research

Electron paramagnetic resonance (EPR) spectroscopy has long been established across various scientific disciplines for characterizing organic radicals, organometallic complexes, protein structures and dynamics, polymerization processes, and radical degradation phenomena. Despite its extensive utility in these areas, EPR spectroscopy's application within pharmaceutical science has historically been constrained, primarily due to factors such as high equipment costs, a steep learning curve, complex spectral deconvolution and analysis, and a traditional lack of emphasis on single-electron chemistry in pharmaceutical research. This review aims to provide a thorough examination of EPR spectroscopy's applications in analyzing a wide array of para-magnetic species relevant to pharmaceutical research. We detail how EPR spectroscopy can be employed to assess free radical scavenging properties in pharmaceutical compounds, elucidate drug mechanisms of action, and explore pharmacokinetics. Additionally, we investigate the role of free radicals in drug-induced toxicity and drug-membrane interactions, while also covering the application of EPR spectroscopy in drug delivery research, advanced studies of metallodrugs, and monitoring of oxygen levels in biological systems through EPR oximetry. The recent advancements in the miniaturization of EPR spectro meters have paved the way for their application in on-site and in-line mo nitoring during the manufacturing process and quality control of pharmaceutical substances and final drug formulations due to being the only direct and non-invasive detection technique for radical detection. Through these discussions, we highlight the substantial contributions of EPR spectroscopy to the advancement of pharmaceutical sciences.

Comprehensive Insight into the Common Organic Radicals in Advanced Oxidation Processes for Water Decontamination

Radical-based advanced oxidation processes (AOPs) are among the most effective technologies employed to destroy organic pollutants. Compared to common inorganic radicals, such as •OH, O2•-, and SO4•-, organic radicals are widespread, and more selective, but are easily overlooked. Furthermore, a systematic understanding of the generation and contributions of organic radicals remains lacking. In this review, we systematically summarize the properties, possible generation pathways, detection methods, and contributions of organic radicals in AOPs. Notably, exploring organic radicals in AOPs is challenging due to (1) limited detection methods for generated organic radicals; (2) controversial organic radical-mediated reaction mechanisms; and (3) rapid transformation of organic radicals as reaction intermediates. In addition to their characteristics and reactivity, we examine potential scenarios of organic radical generation in AOPs, including during the peroxide activation process, in water matrices or with coexisting organic pollutants, and due to the addition of quenching agents. Subsequently, we summarize various methods for organic radical detection as reported previously, such as electron paramagnetic resonance spectroscopy (EPR), 31P nuclear magnetic resonance spectroscopy (31P NMR), liquid/gas chromatography-mass spectroscopy (GC/LC-MS), and fluorescence probes. Finally, we review the contributions of organic radicals to decontamination processes and provide recommendations for future research.

A Spin-Labeled Derivative of Gossypol

Gossypol and its derivatives arouse interest due to their broad spectrum of biological activities. Despite its wide potential application, there is no reported example of gossypol derivatives bearing stable radical functional groups. The first gossypol nitroxide hybrid compound was prepared here via formation of a Schiff base. By this approach, synthesis of a gossypol nitroxide conjugate was performed by condensation of gossypol with a 4-amino-TEMPO (4-amino-2,2,6,6-tetramethylpiperidin-1-oxyl) free radical, which afforded the target product in high yield. Its structure was proven by a combination of NMR and EPR spectroscopy, infrared spectroscopy, mass spectrometry, and high-resolution mass spectrometry. In addition, the structure of the gossypol nitroxide was determined by single-crystal X-ray diffraction measurements. In crystals, the paramagnetic Schiff base exists in an enamine-enamine tautomeric form. The tautomer is strongly stabilized by the intra- and intermolecular hydrogen bonds promoted by the resonance of π-electrons in the aromatic system. NMR analyses of the gossypol derivative proved that in solutions, the enamine-enamine tautomeric form prevailed. The gossypol nitroxide at micromolar concentrations suppressed the growth of tumor cells; however, compared to gossypol, the cytotoxicity of the obtained conjugate was substantially lower.

Uncovering Factors Controlling Reactivity of Metal-TEMPO Reaction Systems in the Solid State and Solution

Nitroxides find application in various areas of chemistry, and a more in-depth understanding of factors controlling their reactivity with metal complexes is warranted to promote further developments. Here, we report on the effect of the metal centre Lewis acidity on both the distribution of the O- and N-centered spin density in 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO) and turning TEMPO from the O- to N-radical mode scavenger in metal-TEMPO systems. We use Et(Cl)Zn/TEMPO model reaction system with tuneable reactivity in the solid state and solution. Among various products, a unique Lewis acid-base adduct of Cl2Zn with the N-ethylated TEMPO was isolated and structurally characterised, and the so-called solid-state 'slow chemistry' reaction led to a higher yield of the N-alkylated product. The revealed structure-activity/selectivity correlations are exceptional yet are entirely rationalised by the mechanistic underpinning supported by theoretical calculations of studied model systems. This work lays a foundation and mechanistic blueprint for future metal/nitroxide systems exploration.

Stable organic radical qubits and their applications in quantum information science

The past century has witnessed the flourishing of organic radical chemistry. Stable organic radicals are highly valuable for quantum technologies thanks to their inherent room temperature quantum coherence, atomic-level designability, and fine tunability. In this comprehensive review, we highlight the potential of stable organic radicals as high-temperature qubits and explore their applications in quantum information science, which remain largely underexplored. Firstly, we summarize known spin dynamic properties of stable organic radicals and examine factors that influence their electron spin relaxation and decoherence times. This examination reveals their design principles and optimal operating conditions. We further discuss their integration in solid-state materials and surface structures, and present their state-of-the-art applications in quantum computing, quantum memory, and quantum sensing. Finally, we analyze the primary challenges associated with stable organic radical qubits and provide tentative insights to future research directions.

Structure-property-function relationships of stabilized and persistent C- and N-based triaryl radicals

Structurally similar C- and N-based triaryl radicals are among the most commonly used structural motifs in stable, open-shell, organic molecules. The application of such species is associated with their stability, properties and structural design. This study summarizes the basic stabilization and persistence principles of C- and N-based triaryl radicals and highlights recent advances in design strategies of radicals tailored for specific applications.

Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics

Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large-amplitude conformational transition, a coarse-grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE-MD including all intermediate states.

Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins

We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least 1 order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase in the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of interspin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4-9, compared to the common spin label such as MTSL, which is not affected by CB-7. Interspin distances of 3 nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating an undisturbed structure and conformation of the protein.

From Stable Radicals to Thermally Robust High-Spin Diradicals and Triradicals

Stable radicals and thermally robust high-spin di- and triradicals have emerged as important organic materials due to their promising applications in diverse fields. New fundamental properties, such as SOMO/HOMO inversion of orbital energies, are explored for the design of new stable radicals, including highly luminescent ones with good photostability. A relation with the singlet-triplet energy gap in the corresponding diradicals is proposed. Thermally robust high-spin di- and triradicals, with energy gaps that are comparable to or greater than a thermal energy at room temperature, are more challenging to synthesize but more rewarding. We summarize a number of high-spin di- and triradicals, based on nitronyl nitroxides that provide a relation between the experimental pairwise exchange coupling constant J/k in the high-spin species vs experimental hyperfine coupling constants in the corresponding monoradicals. This relation allows us to identify outliers, which may correspond to radicals where J/k is not measured with sufficient accuracy. Double helical high-spin diradicals, in which spin density is delocalized over the chiral π-system, have been barely explored, with the sole example of such high-spin diradical possessing alternant π-system with Kekulé resonance form. Finally, we discuss a high-spin diradical with electrical conductivity and derivatives of triangulene diradicals.

Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins

We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least one order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase of the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of inter-spin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4 - 9, compared to the common spin label such as MTSL, which is not affected by CB-7. Inter-spin distances of 3-nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating undisturbed structure and conformation of the protein.

Two Discoveries in One Crystal: σ-Type Oxime Radical as an Unforeseen Building Block in Molecular Magnetics and Its Spatial Structure

In the present work, the study of the unusual interaction between copper hexafluoroacetylacetonate and the diacetyliminoxyl radical resulted in two discoveries from different fields: the determination of the oxime radical spatial structure and the introduction of an oxime radical into the field of molecular magnetic material design. Oxime radicals are key plausible intermediates in the processes of oxidative CH-functionalization and in the synthesis of functionalized isoxazolines from oximes. Due to the lack of X-ray diffraction data for oxime radicals, the knowledge about their structure is based mainly on indirect approaches, spectroscopic methods (electron paramagnetic resonance and IR), and quantum chemical calculations. The structure of the oxime radical was determined for the first time by stabilizing the diacetyliminoxyl radical in the form of its complex with copper (II) hexafluoroacetylacetonate (Cu(hfac)₂), followed by single-crystal X-ray diffraction analysis. Although oxime radicals are known to undergo oxidative coupling with acetylacetonate ligands in transition-metal complexes, a complex is formed with intact hfac ligands. X-ray diffraction studies have shown that the oxime radical is coordinated with copper ions through the oxygen atoms of the carbonyl groups without the direct involvement of the C═N-O^• radical moiety. The structure of the coordinated diacetyliminoxyl is in good agreement with the density functional theory (DFT) prediction for free diacetyliminoxyl due to the very weak interaction of the radical molecule with copper ions. Remarkably, both weak ferromagnetic and antiferromagnetic interactions between Cu (II) and oxime radicals have been revealed by modeling the temperature dependence of magnetic susceptibility and confirmed by DFT calculations, rendering diacetyliminoxyl a promising building block for the design of molecular magnets.

Conformational tuning improves the stability of spirocyclic nitroxides with long paramagnetic relaxation times

Nitroxides are widely used as probes and polarization transfer agents in spectroscopy and imaging. These applications require high stability towards reducing biological environments, as well as beneficial relaxation properties. While the latter is provided by spirocyclic groups on the nitroxide scaffold, such systems are not in themselves robust under reducing conditions. In this work, we introduce a strategy for stability enhancement through conformational tuning, where incorporating additional substituents on the nitroxide ring effects a shift towards highly stable closed spirocyclic conformations, as indicated by X-ray crystallography and density functional theory (DFT) calculations. Closed spirocyclohexyl nitroxides exhibit dramatically improved stability towards reduction by ascorbate, while maintaining long relaxation times in electron paramagnetic resonance (EPR) spectroscopy. These findings have important implications for the future design of new nitroxide-based spin labels and imaging agents.

Role of membrane mimetics on biophysical EPR studies of membrane proteins

Biological membranes are essential in providing the stability of membrane proteins in a functional state. Functionally stable homogeneous sample is required for biophysical electron paramagnetic resonance (EPR) studies of membrane proteins for obtaining pertinent structural dynamics of the protein. Significant progresses have been made for the optimization of the suitable membrane environments required for biophysical EPR measurements. However, no universal membrane mimetic system is available that can solubilize all membrane proteins suitable for biophysical EPR studies while maintaining the functional integrity. Great efforts are needed to optimize the sample condition to obtain better EPR data quality of membrane proteins that can provide meaningful information on structural dynamics. In this mini-review, we will discuss important aspects of membrane mimetics for biophysical EPR measurements and current progress with some of the recent examples.

Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes

Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.

Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block

The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.

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.

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

Orthogonal spin labeling and pulsed dipolar spectroscopy for protein studies

Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.

Light-induced pulsed dipolar EPR spectroscopy for distance and orientation analysis

Measuring distances in biology at the molecular level is of great importance for understanding the structure and function of proteins, nucleic acids and other biological molecules and their complexes. Pulsed Dipolar Spectroscopy (PDS) offers advantages with respect to other methods as it is uniquely sensitive and specific to electronic spin centers and allows measurements in near-native conditions, comprising the in-cell environment. PDS methods measure the electron spin-spin dipolar interaction, therefore they require the presence of at least two paramagnetic centers, which are often stable radicals. Recent developments have introduced transient triplet states, photo-activated by a laser pulse, as spin labels and probes, thereby establishing a new family of techniques-Light-induced PDS (LiPDS). In this chapter, an overview of these methods is provided, looking at the chromophores that can be used for LiPDS and some of the technical aspects of the experiments. A guide to the choice of technique that can yield the best results, depending on the type of system studied and the information required, is provided. Examples of previous LiPDS studies of model systems and proteins are given. Characterization data for the chromophores used in these studies is tabulated to help selection of appropriate triplet state probes in future studies.

Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement

Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.

Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation

Electron paramagnetic resonance (EPR) is a spectroscopic method for investigating structures, conformational changes, and dynamics of biomacromolecules, for example, oligonucleotides. In order to be applicable, the oligonucleotide has to be labeled site-specifically with paramagnetic tags, the so-called spin labels. Here, we provide a protocol for spin labeling of long oligonucleotides with nitroxides. In the first step, a short and commercially available RNA strand is labeled with a nitroxide via a copper-(I)-catalyzed azide-alkyne cycloaddition (CuAAC), also referred to as "click" reaction. In the second step, the labeled RNA strand is fused to another RNA sequence by means of enzymatic ligation to obtain the labeled full-length construct. The protocol is robust and has been shown experimentally to deliver high yields for RNA sequences up to 81 nucleotides, but longer strands are in principle also feasible. Moreover, it sets the path to label, for example, long riboswitches, ribozymes, and DNAzymes for coarse-grained structure determination and enables to investigate mechanistical features of these systems.

Stabilization of radical active species in a MOF nanospace to exploit unique reaction pathways

We synthesized a metal-organic framework (MOF) using a ligand bearing haloalkoxy chains as a radical precursor. The radicals generated in the MOF upon photoirradiation were stable even at 250 K or under an O₂ atmosphere, despite radicals generated from the ligand decomposing at 200 K; thus, the regular arrangement of radicals effectively stabilized them. Moreover, a unique photoproduct was obtained only in the MOF, indicating that the confinement effect in the nanospace enabled a specific reaction that did not occur in the bulk state. We propose a new platform for exploring chemical reactions and materials based on reactive species.

Three-dimensional electron paramagnetic resonance imaging of mice using ascorbic acid sensitive nitroxide imaging probes

Nitroxide compounds have been used as redox-sensitive imaging probes by electron paramagnetic resonance (EPR) for assessing oxidative stress in vivo. Fast redox reactions of nitroxide radicals are favorable for assessment of higher redox sensitivity; however, a variety of nitroxides have not been trialed for use as imaging probes due to their very rapid in vivo reduction, which cannot be captured at the slow operation speed of existing EPR imagers. To overcome this limitation, we improved our EPR system to provide a stable and highly sensitive imaging operation. We challenged the improved EPR imager to perform three-dimensional (3D) EPR imaging of mouse brain using two useful nitroxide imaging probes, 4-hydroxy-2,2,6,6-tetramethylpiperidine 1-oxyl (Tempol) and 2,6-dispiro-4',4"-dipyrane-piperidine-4-one-N-oxyl (DiPy). The second-order rate constant of DiPy with ascorbic acid is 10 times larger than that of Tempol. The improved EPR imager obtained clear 3D EPR images of mouse brain and demonstrated that Tempol could exist with an unpaired electron. The imager also successfully obtained 3D EPR images of mouse head after administration of DiPy. As 126 projections can be acquired in a period of 6 s, 3D EPR imaging can visualize the sequential process of DiPy entering the brain, being distributed within the brain, and being reduced within the brain. These improvements to the EPR imager will enable useful nitroxide imaging probes that were previously unsuitable as imaging probes due to their rapid reduction to be considered for use for sensitive redox assessment in an in vivo system.

Molecular structures and magnetic properties of endohedral metallofullerenes

Endohedral metallofullerenes have fascinating core-shell structures, with metal atoms or metal clusters encaged in fullerene cages, and they display various chemical, optical and magnetic properties derived from different types of fullerene cages and metal moieties. Fullerene cages can act as carriers to stabilize unusual cluster moieties. Many bizarre species that are hard to produce via synthetic methods survive well under the protection of a fullerene cage, making metallofullerenes ideal platforms for generating new clusters and bonds. Fullerene cages can also be carriers to hold active unpaired electrons. Some metallofullerenes possess electron spin and show intriguing magnetic properties, making them applicable for use in quantum computing, high density information storage and magnetoreception systems. The exploration of new metallofullerenes is still ongoing, while function-oriented studies are also promoted for the future application of metallofullerenes. Herein, we highlight the recent progress in the synthesis, electron spin characteristics and magnetic properties of metallofullerenes. Discussions and an outlook on the future development of metallofullerenes are also stated.

Bis-Spiro-Oxetane and Bis-Spiro-Tetrahydrofuran Pyrroline Nitroxide Radicals: Synthesis and Electron Spin Relaxation Studies

Synthesis of bis-spiro-oxetane and bis-spiro-tetrahydrofuran pyrroline nitroxide radicals relies on the Mitsunobu reaction-mediated double cyclizations of N-Boc protected pyrroline tetraols. Structures of the nitroxide radicals are supported by X-ray crystallography. In a trehalose/sucrose matrix at room temperature, the bis-spiro-oxetane nitroxide radical possesses electron spin coherence time, Tm ≈ 0.7 μs. The observed enhanced Tm is most likely associated with strong hydrogen bonding of oxetane moieties to the trehalose/sucrose matrix.

Uptake of Cell-Penetrating Peptide RL2 by Human Lung Cancer Cells: Monitoring by Electron Paramagnetic Resonance and Confocal Laser Scanning Microscopy

RL2 is a recombinant analogue of a human κ-casein fragment, capable of penetrating cells and inducing apoptosis of cancer cells with no toxicity to normal cells. The exact mechanism of RL2 penetration into cells remains unknown. In this study, we investigated the mechanism of RL2 penetration into human lung cancer A549 cells by a combination of electron paramagnetic resonance (EPR) spectroscopy and confocal laser scanning microscopy. EPR spectra of A549 cells incubated with RL2 (sRL2) spin-labeled by a highly stable 3-carboxy-2,2,5,5-tetraethylpyrrolidine-1-oxyl radical were found to contain three components, with their contributions changing with time. The combined EPR and confocal-microscopy data allowed us to assign these three forms of sRL2 to the spin-labeled protein sticking to the membrane of the cell and endosomes, to the spin-labeled protein in the cell interior, and to spin labeled short peptides formed in the cell because of protein digestion. EPR spectroscopy enabled us to follow the kinetics of transformations between different forms of the spin-labeled protein at a minimal spin concentration (3-16 μM) in the cell. The prospects of applications of spin-labeled cell-penetrating peptides to EPR imaging, DNP, and magnetic resonance imaging are discussed, as is possible research on an intrinsically disordered protein in the cell by pulsed dipolar EPR spectroscopy.

A Carbazole-Derived Nitroxide That Is an Analogue of Cytidine: A Rigid Spin Label for DNA and RNA

A variety of semirigid and rigid spin labels comprise a valuable arsenal for measurements of biomolecular structures and dynamics by electron paramagnetic resonance (EPR) spectroscopy. Here, we report the synthesis and characterization of rigid spin labels Ċ and Ċm for DNA and RNA, respectively, that are carbazole-derived nitroxides and analogues of cytidine. Ċ and Ċm were converted to their phosphoramidites and used for their incorporation into oligonucleotides by solid-phase synthesis. Analysis of Ċ and Ċm by single-crystal X-ray crystallography verified their identity and showed little deviation from planarity of the nucleobase. Analysis of the continuous-wave (CW) EPR spectra of the spin-labeled DNA and RNA duplexes confirmed their incorporation into the nucleic acids and the line-shape was characteristic of rigid spin labels. Circular dichroism (CD) and thermal denaturation studies of the Ċ-labeled DNAs and Ċm-labeled RNAs indicated that the labels are nonperturbing of duplex structure.

Stable Bicyclic Functionalized Nitroxides: The Synthesis of Derivatives of Aza-nortropinone-5-Methyl-3-oxo-6,8-diazabicyclo[3.2.1]-6-octene 8-oxyls

In recent decades, bicyclic nitroxyl radicals have caught chemists’ attention as selective catalysts for the oxidation of alcohols and amines and as additives and mediators in directed C-H oxidative transformations. In this regard, the design and development of synthetic approaches to new functional bicyclic nitroxides is a relevant and important issue. It has been reported that imidazo[1,2-b]isoxazoles formed during the condensation of acetylacetone with 2-hydroxyaminooximes having a secondary hydroxyamino group are recyclized under mild basic catalyzed conditions to 8-hydroxy-5-methyl-3-oxo-6,8-diazabicyclo[3.2.1]-6-octenes. The latter, containing a sterically hindered cyclic N-hydroxy group, upon oxidation with lead dioxide in acetone, virtually quantitatively form stable nitroxyl bicyclic radicals of a new class, which are derivatives of both 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl (TEMPON) and 3-imidazolines.

Revealing the Structure of Transition Metal Complexes of Formaldoxime

Aerobic reactions of iron(III), nickel(II), and manganese(II) chlorides with formaldoxime cyclotrimer (tfoH₃) and 1,4,7-triazacyclononane (tacn) produce indefinitely stable complexes of general formula [M(tacn)(tfo)]Cl. Although the formation of formaldoxime complexes has been known since the end of 19th century and applied in spectrophotometric determination of d-metals (formaldoxime method), the structure of these coordination compounds remained elusive until now. According to the X-ray analysis, [M(tacn)(tfo)]⁺ cation has a distorted adamantane-like structure with the metal ion being coordinated by three oxygen atoms of deprotonated tfoH₃ ligand. The metal has a formal +4 oxidation state, which is atypical for organic complexes of iron and nickel. Electronic structure of [M(tacn)(tfo)]⁺ cations was studied by XPS, NMR, cyclic (CV) and differential pulse (DPV) voltammetries, Mössbauer spectroscopy, and DFT calculations. Unusual stabilization of high-valent metal ion by tfo^3- ligand was explained by the donation of electron density from the nitrogen atom to the antibonding orbital of the metal-oxygen bond via hyperconjugation as confirmed by the NBO analysis. All complexes [M(tacn)(tfo)]Cl exhibited high catalytic activity in the aerobic dehydrogenative dimerization of p-thiocresol under ambient conditions.

Probing Structural Dynamics of Membrane Proteins Using Electron Paramagnetic Resonance Spectroscopic Techniques

Membrane proteins are essential for the survival of living organisms. They are involved in important biological functions including transportation of ions and molecules across the cell membrane and triggering the signaling pathways. They are targets of more than half of the modern medical drugs. Despite their biological significance, information about the structural dynamics of membrane proteins is lagging when compared to that of globular proteins. The major challenges with these systems are low expression yields and lack of appropriate solubilizing medium required for biophysical techniques. Electron paramagnetic resonance (EPR) spectroscopy coupled with site directed spin labeling (SDSL) is a rapidly growing powerful biophysical technique that can be used to obtain pertinent structural and dynamic information on membrane proteins. In this brief review, we will focus on the overview of the widely used EPR approaches and their emerging applications to answer structural and conformational dynamics related questions on important membrane protein systems.

Nitroxide spin labels and EPR spectroscopy: A powerful association for protein dynamics studies

Site-Directed Spin Labelling (SDSL) technique is based on the attachment of a paramagnetic label onto a specific position of a protein (or other bio-molecules) and the subsequent study by Electron Paramagnetic Resonance (EPR) spectroscopy. In particular, continuous-wave EPR (cw-EPR) spectra can detect the local conformational dynamics for proteins under various conditions. Moreover, pulse-EPR experiments on doubly spin-labelled proteins allow measuring distances between spin centres in the 1.5-8 nm range, providing information about structures and functions. This review focuses on SDSL-EPR spectroscopy as a structural biology tool to investigate proteins using nitroxide labels. The versatility of this spectroscopic approach for protein structural characterization has been demonstrated through the choice of recent studies. The main aim is to provide a general overview of the technique, particularly for non-experts, to spread the applicability of this technique in various fields of structural biology.

Polyradical PROXYL/TEMPO Conjugates Connected by Ester/Amide Bridges: Synthesis, Physicochemical Studies, and DFT Calculations

A series of di-/trinitroxide esters and amides featuring PROXYL and/or TEMPO radicals connected with alicyclic bridges were prepared in 61-92 % yields and their properties were analysed by using multiple experimental techniques. The examination of EPR spectra of radicals in organic solvents augmented with DFT calculations brought valuable information on the conformational dynamics and spin exchange mechanisms. Cyclic voltammetry investigations revealed (quasi)reversible electrochemical behaviour of studied nitroxides with their half-wave potentials ranging from -51 to -17 mV. SQUID measurements of selected radicals revealed that the magnetism of di- and trinitroxides is significantly different, since antiferromagnetic coupling in biradicals is notably larger than in triradicals. The single-crystal X-ray analysis of selected biradicals revealed the existence of 3D supramolecular networks of molecules linked through hydrogen-bonding interactions. These polynitroxide radicals can serve as promising bridging or chelating ligands in the synthesis of transition-metal-based molecular magnets.

Cell-Free Synthesis of Selenoproteins in High Yield and Purity for Selective Protein Tagging

The selenol group of selenocysteine is much more nucleophilic than the thiol group of cysteine. Selenocysteine residues in proteins thus offer reactive points for rapid post-translational modification. Herein, we show that selenoproteins can be expressed in high yield and purity by cell-free protein synthesis by global substitution of cysteine by selenocysteine. Complete alkylation of solvent-exposed selenocysteine residues was achieved in 10 minutes with 4-chloromethylene dipicolinic acid (4Cl-MDPA) under conditions that left cysteine residues unchanged even after overnight incubation. Gd^III -Gd^III distances measured by double electron-electron resonance (DEER) experiments of maltose binding protein (MBP) containing two selenocysteine residues tagged with 4Cl-MDPA-Gd^III were indistinguishable from Gd^III -Gd^III distances measured of MBP containing cysteine reacted with 4Br-MDPA tags.

Spirocyclic Nitroxides as Versatile Tools in Modern Natural Sciences: From Synthesis to Applications. Part I. Old and New Synthetic Approaches to Spirocyclic Nitroxyl Radicals

Spirocyclic nitroxyl radicals (SNRs) are stable paramagnetics bearing spiro-junction at a-, b-, or g-carbon atom of the nitroxide fragment, which is part of the heterocyclic system. Despite the fact that the first representatives of SNRs were obtained about 50 years ago, the methodology of their synthesis and their usage in chemistry and biochemical applications have begun to develop rapidly only in the last two decades. Due to the presence of spiro-function in the SNRs molecules, the latter have increased stability to various reducing agents (including biogenic ones), while the structures of the biradicals (SNBRs) comprises a rigid spiro-fused core that fixes mutual position and orientation of nitroxide moieties that favors their use in dynamic nuclear polarization (DNP) experiments. This first review on SNRs will give a glance at various strategies for the synthesis of spiro-substituted, mono-, and bis-nitroxides on the base of six-membered (piperidine, 1,2,3,4-tetrahydroquinoline, 9,9'(10H,10H')-spirobiacridine, piperazine, and morpholine) or five-membered (2,5-dihydro-1H-pyrrole, pyrrolidine, 2,5-dihydro-1H-imidazole, 4,5-dihydro-1H-imidazole, imidazolidine, and oxazolidine) heterocyclic cores.

Molecular S = 2 High-Spin, S = 0 Low-Spin and S = 0 ⇄ 2 Spin-Transition/-Crossover Nickel(II)-Bis(nitroxide) Coordination Compounds

Heterospin systems have a great advantage in frontier orbital engineering since they utilize a wide diversity of paramagnetic chromophores and almost infinite combinations and mutual geometries. Strong exchange couplings are expected in 3d–2p heterospin compounds, where the nitroxide (aminoxyl) oxygen atom has a direct coordination bond with a nickel(II) ion. Complex formation of nickel(II) salts and tert-butyl 2-pyridyl nitroxides afforded a discrete 2p–3d–2p triad. Ferromagnetic coupling is favored when the magnetic orbitals, nickel(II) dσ and radical π*, are arranged in a strictly orthogonal fashion, namely, a planar coordination structure is characterized. In contrast, a severe twist around the coordination bond gives an orbital overlap, resulting in antiferromagnetic coupling. Non-chelatable nitroxide ligands are available for highly twisted and practically diamagnetic complexes. Here, the Ni–O–N–Csp2 torsion (dihedral) angle is supposed to be a useful metric to describe the nickel ion dislocated out of the radical π* nodal plane. Spin-transition complexes exhibited a planar coordination structure in a high-temperature phase and a nonplanar structure in a low-temperature phase. The gradual spin transition is described as a spin equilibrium obeying the van’t Hoff law. Density functional theory calculation indicates that the energy level crossing of the high- and low-spin states. The optimized structures of diamagnetic and high-spin states well agreed with the experimental large and small torsions, respectively. The novel mechanism of the present spin transition lies in the ferro-/antiferromagnetic coupling switch. The entropy-driven mechanism is plausible after combining the results of the related copper(II)-nitroxide compounds. Attention must be paid to the coupling parameter J as a variable of temperature in the magnetic analysis of such spin-transition materials. For future work, the exchange coupling may be tuned by chemical modification and external stimulus, because it has been clarified that the parameter is sensitive to the coordination structure and actually varies from 2J/kB = +400 K to −1400 K.

A metabolically engineered spin-labeling approach for studying glycans on cells

Metabolic glycan engineering (MGE) coupled with nitroxide spin-labeling (SL) was utilized to investigate the heterogeneous environment of cell surface glycans in select cancer and normal cells. This approach exploited the incorporation of azides into cell surface glycans followed by a click reaction with a new nitroxide spin label. Both sialic acid and N-acetylglucosamine (GlcNAc) were targeted for spin labelling. Although each of these moieties experiences a diverse and heterogeneous glycan environment, their EPR spectra and hence mobility are both characterized as a linear combination of two distinct spectra where one component reflects a highly mobile or uncrowded micro-environment with the second component reflecting more restricted motion, reflective of increased crowding and packing within the glycocalyx. What differs among the spectra of the targeted glycans is the relative percentage of each component, with sialic acid moieties experiencing on average an ∼80% less crowded environment, where conversely GlcNAc/GalNAz labeled sites reported on average a ∼50% more crowded environment. These distinct environments are consistent with the organization of sugar moieties within cellular glycans where some residues occur close to the cell membrane/protein backbone (i.e. more restricted) and others are more terminal in the glycan (i.e. more mobile). Strikingly, different cell lines displayed varied relative populations of these two components, suggesting distinctive glycan packing, organization, and composition of different cells. This work demonstrates the capability of SDSL EPR to be a broadly useful tool for studying glycans on cells, and interpretation of the results provides insights for distinguishing the differences and changes in the local organization and heterogeneity of the cellular glycocalyx.

Nitroxide-Derived N-Oxide Phenazines for Noncovalent Spin-Labeling of DNA

Two o-benzoquinone derivatives of isoindoline were synthesized for use as building blocks to incorporate isoindoline nitroxides into different compounds and materials. These o-quinones were condensed with a number of o-phenylenediamines to form isoindoline-phenazines in high yields. Subsequent oxidation gave phenazine-di-N-oxide isoindoline nitroxides that were evaluated for noncovalent and site-directed spin-labeling of duplex DNA and RNA that contained abasic sites. Although only minor binding was observed for RNA, the unsubstituted phenazine-N,N-dioxide tetramethyl isoindoline nitroxide showed high binding affinity and selectivity towards abasic sites in duplex DNA that contained cytosine as the orphan base.

Progress Toward Sustainable Reversible Deactivation Radical Polymerization

The recent focus of media and governments on renewability, green chemistry, and circular economy has led to a surge in the synthesis of renewable monomers and polymers. In this review, focussing on renewable monomers for reversible deactivation radical polymerizations (RDRP), it is highlighted that for the majority of the monomers and polymers reported, the claim to renewability is not always accurate. By closely examining the sustainability of synthetic routes and the renewability of starting materials, fully renewable monomers are identified and discussed in terms of sustainability, polymerization behavior, and properties obtained after polymerization. The holistic discussion considering the overall preparation process of polymers, that is, monomer syntheses, origin of starting materials, solvents used, the type of RDRP technique utilized, and the purification method, allows to highlight certain topics which need to be addressed in order to progress toward not only (partially) renewable, but sustainable monomers and polymers using RDRPs.