Frequency (250 MHz to 9.2 GHz) and viscosity dependence of electron spin relaxation of triarylmethyl radicals at room temperature

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.

Toward a Nanoencapsulated EPR Imaging Agent for Clinical Use

PURPOSE

Progress toward developing a novel radiocontrast agent for determining pO2 in tumors in a clinical setting is described. The imaging agent is designed for use with electron paramagnetic resonance imaging (EPRI), in which the collision of a paramagnetic probe molecule with molecular oxygen causes a spectroscopic change which can be calibrated to give the real oxygen concentration in the tumor tissue.

PROCEDURES

The imaging agent is based on a nanoscaffold of aluminum hydroxide (boehmite) with sizes from 100 to 200 nm, paramagnetic probe molecule, and encapsulation with a gas permeable, thin (10-20 nm) polymer layer to separate the imaging agent and body environment while still allowing O2 to interact with the paramagnetic probe. A specially designed deuterated Finland trityl (dFT) is covalently attached on the surface of the nanoparticle through 1,3-dipolar addition of the alkyne on the dFT with an azide on the surface of the nanoscaffold. This click-chemistry reaction affords 100% efficiency of the trityl attachment as followed by the complete disappearance of the azide peak in the infrared spectrum. The fully encapsulated, dFT-functionalized nanoparticle is referred to as RADI-Sense.

RESULTS

Side-by-side in vivo imaging comparisons made in a mouse model made between RADI-Sense and free paramagnetic probe (OX-071) showed oxygen sensitivity is retained and RADI-Sense can create 3D pO2 maps of solid tumors CONCLUSIONS: A novel encapsulated nanoparticle EPR imaging agent has been described which could be used in the future to bring EPR imaging for guidance of radiotherapy into clinical reality.

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.

Steady state effects introduced by local relaxation modes on J-driven DNP-enhanced NMR

One of solution-state Nuclear Magnetic Resonance (NMR)'s main weaknesses, is its relative insensitivity. J-driven Dynamic Nuclear Polarization (JDNP) was recently proposed for enhancing solution-state NMR's sensitivity, by bypassing the limitations faced by conventional Overhauser DNP (ODNP), at the high magnetic fields where most analytical research is performed. By relying on biradicals with inter-electron exchange couplings Jex on the order of the electron Larmor frequency ωE, JDNP was predicted to introduce a transient enhancement in NMR's nuclear polarization at high magnetic fields, and for a wide range of rotational correlation times of medium-sized molecules in conventional solvents. This communication revisits the JDNP proposal, including additional effects and conditions that were not considered in the original treatment. These include relaxation mechanisms arising from local vibrational modes that often dominate electron relaxation in organic radicals, as well as the possibility of using biradicals with Jex of the order of the nuclear Larmor frequency ωN as potential polarizing agents. The presence of these new relaxation effects lead to variations in the JDNP polarization mechanism originally proposed, and indicate that triplet-to-singlet cross-relaxation processes may lead to a nuclear polarization enhancement that persists even at steady states. The physics and potential limitations of the ensuing theoretical derivations, are briefly discussed.

Microwave-free J-driven dynamic nuclear polarization: A proposal for enhancing the sensitivity of solution-state NMR

J-driven dynamic nuclear polarization (JDNP) was recently proposed for enhancing the sensitivity of solution-state nuclear magnetic resonance (NMR), while bypassing the limitations faced by conventional (Overhauser) DNP at magnetic fields of interest in analytical applications. Like Overhauser DNP, JDNP also requires saturating the electronic polarization using high-frequency microwaves known to have poor penetration and associated heating effects in most liquids. The present microwave-free JDNP (MF-JDNP) proposal seeks to enhance solution NMR's sensitivity by shuttling the sample between higher and lower magnetic fields, with one of these fields providing an electron Larmor frequency that matches the interelectron exchange coupling J_{ex}. If spins cross this so-called JDNP condition sufficiently fast, we predict that a sizable nuclear polarization will be created without microwave irradiation. This MF-JDNP proposal requires radicals whose singlet-triplet self-relaxation rates are dominated by dipolar hyperfine relaxation, and shuttling times that can compete with these electron relaxation processes. This paper discusses the theory behind the MF-JDNP, as well as proposals for radicals and conditions that could enable this new approach to NMR sensitivity enhancement.

Observation of slow magnetic relaxation phenomena in spatially isolated π-radical ions

The use of molecular spins as quantum bits is fascinating because it offers a wide range of strategies through chemical modifications. In this regard, it is very interesting to search for organic radical ions that have small spin-orbit coupling values. On the other hand, the feature of the magnetic relaxation of π-organic radical ions is rarely exploited due to the difficulty of spin dilution, and π-stacking interaction. In this study, we focus on N,N',N''-tris(2,6-dimethylphenyl)benzenetriimide (BTI-xy), where three xylene moieties connected to the imide groups cover the π-plane of the BTI core. As a result, BTI-xy radical anions without π-stacking interaction were obtained. This led to the slow magnetization relaxation, which is reported for the first time in organic radicals. Furthermore, the relaxation times in a solution state revealed the importance of spin interaction.

A new 13C trityl-based spin label enables the use of DEER for distance measurements

Triarylmethyl (TAM)-based labels, while still underutilized, are a powerful class of labels for pulsed-Electron Spin Resonance (ESR) distance measurements. They feature slow relaxation rates for long-lasting signals, high stability for cellular experiments, and narrow spectral features for efficient excitation of the spins. However, the typical narrow line shape limits the available distance measurements to only single-frequency experiments, such as Double Quantum Coherence (DQC) and Relaxation Induced Dipolar Modulation Enhancement (RIDME), which can be complicated to perform or hard to process. Therefore, widespread usage of TAM labels can be enhanced by the use of Double Electron-Electron Resonance (DEER) distance measurements. In this work, we developed a new spin label, 13C1-mOX063-d24, with a 13C isotope as the radical center. Due to the resolved hyperfine splitting, the spectrum is sufficiently broadened to permit DEER-based experiments at Q-band spectrometers. Additionally, this new label can be incorporated orthogonally with Cu(II)-based protein label. The orthogonal labeling scheme enables DEER distance measurement at X-band frequencies. Overall, the new trityl label allows for DEER-based distance measurements that complement existing TAM-label DQC and RIDME experiments.

Impact of Chlorine Substitution on Electron Spin Relaxation of a Trityl Radical

A perchlorotriarylmethyl tricarboxylic acid radical 99% enriched in ¹³C at the central carbon (¹³C₁-PTMTC) was characterized in phosphate buffered saline solution (pH = 7.2) (PBS) at ambient temperature. Samples immobilized in 1:1 PBS:glycerol or in 9:1 trehalose:sucrose were studied as a function of temperature. Isotope enrichment at C₁ creates a trityl that can be used to accurately measure microscopic viscosity. Understanding of the impact of the ¹³C hyperfine interaction on electron spin relaxation is important for application of this trityl in oximetry and distance measurements. The anisotropic ¹³C₁ hyperfine couplings (A_x = A_y = 24 ± 2 MHz, A_z = 200 ± 1 MHz) are larger than for the related ¹³C₁-perdeuterated Finland trityl (¹³C₁-dFT) and the g anisotropy (g_x = 2.0013, g_y = 2.0016, g_z = 2.0042) is slightly larger than for ¹³C₁-dFT. The tumbling correlation times (τ_R) for ¹³C₁-PTMTC are 0.20 ± 0.02 ns in PBS and 0.40 ± 0.05 ns in 3:1 PBS:glycerol, which are shorter than for ¹³C₁-dFT in the same solutions. T₁ for ¹³C₁-PTMTC is 3.5 ± 0.5 μs in PBS and 5.3 ± 0.4 μs in 3:1 PBS:glycerol, which are shorter than for ¹³C₁-dFT due to faster tumbling, larger anisotropy of the ¹³C₁ hyperfine, and about 30% larger contribution from the local mode. In immobilized samples T₁ for ¹³C₁-PTMTC is similar to that for ¹³C₁-dFT and other trityls without chlorine or ¹³C₁ substituents, indicating that the ¹³C₁ and Cl substituents on the phenyl rings have little impact on T₁. The temperature dependence of T₁ was modeled with contributions from the direct, Raman, and local mode processes. Broadening of CW linewidths of about 0.6 G in fluid solution and about 2 G in rigid lattice is attributed to unresolved ^35,37Cl hyperfine couplings.

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.

Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides?

Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron-electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.

J-Driven dynamic nuclear polarization for sensitizing high field solution state NMR

Dynamic nuclear polarization (DNP) is widely used to enhance solid state nuclear magnetic resonance (NMR) sensitivity. Its efficiency as a generic signal-enhancing approach for liquid state NMR, however, decays rapidly with magnetic field B₀, unless mediated by scalar interactions arising only in exceptional cases. This has prevented a more widespread use of DNP in structural and dynamical solution NMR analyses. This study introduces a potential solution to this problem, relying on biradicals with exchange couplings J_ex of the order of the electron Larmor frequency ω_E. Numerical and analytical calculations show that in such J_ex ≈ ±ω_E cases a phenomenon akin to that occurring in chemically induced DNP (CIDNP) happens, leading to different relaxation rates for the biradical singlet and triplet states which are hyperfine-coupled to the nuclear α or β states. Microwave irradiation can then generate a transient nuclear polarization build-up with high efficiency, at all magnetic fields that are relevant in contemporary NMR, and for all rotational diffusion correlation times that occur in small- and medium-sized molecules in conventional solvents.

Spin-spin interaction and relaxation in two trityl-nitroxide diradicals

Trityl-nitroxides show substantial promise as polarizing agents in solid state dynamic nuclear polarization. To optimize performance it is important to understand the impact of spin-spin interactions on relaxation times of the diradicals. CW spectra and electron spin relaxation were measured for two trityl-nitroxides that differ in the substituents on the amide linker and have different strengths of the exchange interaction J. Analysis of the EPR spectra in terms of overlapping AB spin-spin splitting patterns explains the impact of J on various regions of the spectra. Even modest values of J are large relative to the separation between trityl and nitroxide resonances for some nitrogen nuclear spin state. Two conformations for each diradical were observed in CW spectra in fluid solution at X-band and Q-band. For one diradical J = 15 G (83%) and 5 G (17%) at 293 K, and J = 27 G (67%) and 3 G (33%) with interspin distances of 16 Å and 12 Å, respectively, at 80 K. For the second diradical the exchange interaction is stronger: the two conformations in fluid solution at 293 K had J = 113 G (67%) and 59 G (33%) and at 80 K the value of J was 43 G and there were two conformations with interspin distances of 13 and 11.5 Å. The observation of two conformations for each diradical, with different values of J, demonstrates the dependence of their exchange interactions on through-bond orbital interactions. X-band values of spin relaxation rates 1/T₁ and 1/T_m at 80 to 120 K for the trityl-nitroxides are similar to values for nitroxide mono-radicals, and faster than for trityl radicals. These observations show that even for a relatively small value of J, the nitroxide is very effective in enhancing the relaxation of the more slowly relaxing trityl.

dHis-troying Barriers: Deuteration Provides a Pathway to Increase Sensitivity and Accessible Distances for Cu2+ Labels

Recently, site-directed Cu²⁺ labeling has emerged as an incisive biophysical tool to directly report on distance constraints that pertain to the structure, conformational transitions, and dynamics of proteins and nucleic acids. However, short phase memory times inherent to the Cu²⁺ labels limit measurable distances to 4-5 nm. In this work we systematically examine different methods to dampen electron-nuclear and electron-electron coupled interactions to decrease rapid relaxation. We show that using Cu²⁺ spin concentrations up to ca. 800 μM has an invariant effect on relaxation and that increasing the cryoprotectant concentration reduces contributions of solvent protons to relaxation. On the other hand, the deuteration of protein and solvent dramatically increases the duration of the dipolar modulated signal by over 6-fold to 32 μs. Based on this increase in signal longevity, distances up to 9 nm and beyond can potentially be measured with Cu²⁺ labels.

Molecular Dynamics in Ionic Liquid/Radical Systems

Molecular dynamics of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethyl sulfonyl)imide (Emim-Tf₂N) with either of the four organic stable radicals, TEMPO, 4-benzoyloxy-TEMPO, BDPA, and DPPH, is studied by using Nuclear Magnetic Resonance (NMR) and Dynamic Nuclear Polarization (DNP). In complex fluids at ambient temperature, NMR signal enhancement by DNP is frequently obtained by a combination of several mechanisms, where the Overhauser effect and solid effect are the most common. Understanding the interactions of free radicals with ionic liquid molecules is of particular significance due to their complex dynamics in these systems, influencing the properties of the ion-radical interaction. A combined analysis of EPR, DNP, and NMR relaxation dispersion is carried out for cations and anions containing, respectively, the NMR active nuclei ¹H or ¹⁹F. Depending on the size and the chemical properties of the radical, different interaction processes are distinguished, namely, the Overhauser effect and solid effect, driven by dominating dipolar or scalar interactions. The resulting NMR relaxation dispersion is decomposed into rotational and translational contributions, allowing the identification of the corresponding correlation times of motion and interactions. The influence of electron relaxation time and electron-nuclear spin hyperfine coupling is discussed.

Cleavage-Resistant Protein Labeling With Hydrophilic Trityl Enables Distance Measurements In-Cell

Sensitive in-cell distance measurements in proteins using pulsed-electron spin resonance (ESR) require reduction-resistant and cleavage-resistant spin labels. Among the reduction-resistant moieties, the hydrophilic trityl core known as OX063 is promising due to its long phase-memory relaxation time (T_m). This property leads to a sufficiently intense ESR signal for reliable distance measurements. Furthermore, the T_m of OX063 remains sufficiently long at higher temperatures, opening the possibility for measurements at temperatures above 50 K. In this work, we synthesized deuterated OX063 with a maleimide linker (mOX063-d₂₄). We show that the combination of the hydrophilicity of the label and the maleimide linker enables high protein labeling that is cleavage-resistant in-cells. Distance measurements performed at 150 K using this label are more sensitive than the measurements at 80 K. The sensitivity gain is due to the significantly short longitudinal relaxation time (T₁) at higher temperatures, which enables more data collection per unit of time. In addition to in vitro experiments, we perform distance measurements in Xenopus laevis oocytes. Interestingly, the T_m of mOX063-d₂₄ is sufficiently long even in the crowded environment of the cell, leading to signals of appreciable intensity. Overall, mOX063-d₂₄ provides highly sensitive distance measurements both in vitro and in-cells.

In Situ Labeling and Distance Measurements of Membrane Proteins in E. coli Using Finland and OX063 Trityl Labels

In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (TM ) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.

A 13 C-Labeled Triarylmethyl Radical as an EPR Spin Probe Highly Sensitive to Molecular Tumbling

A stable triarylmethyl spin probe whose electron paramagnetic resonance (EPR) spectrum is highly sensitive to molecular tumbling is reported. The strong anisotropy of the hyperfine coupling tensor with the central carbon of a 13 C1 -labeled triarylmethyl radical enables the measurement of the probe rotational correlation time with applications to measure microviscosity and molecular dynamics.

13C isotope enrichment of the central trityl carbon decreases fluid solution electron spin relaxation times

Electron spin relaxation times for perdeuterated Finland trityl 99% enriched in ¹³C at the central carbon (¹³C₁-dFT) were measured in phosphate buffered saline (pH = 7.2) (PBS) solution at X-band. The anisotropic ¹³C₁ hyperfine (A_x = A_y = 18 ± 2, A_z = 162 ± 1 MHz) and g values (2.0033, 2.0032, 2.00275) in a 9:1 trehalose:sucrose glass at 293 K and in 1:1 PBS:glycerol at 160 K were determined by simulation of spectra at X-band and Q-band. In PBS at room temperature the tumbling correlation time, τ_R, is 0.29 ± 0.02 ns. The linewidths are broadened by incomplete motional averaging of the hyperfine anisotropy and T₂ is 0.13 ± 0.02 µs, which is shorter than the T₂ ~ 3.8 µs for natural abundance dFT at low concentration in PBS. T₁ for ¹³C₁-dFT in deoxygenated PBS is 5.9 ± 0.5 µs, which is shorter than for natural abundance dFT in PBS (16 µs) but much longer than in air-saturated solution (0.48 ± 0.04 µs). The tumbling dependence of T₁ in PBS, 3:1 PBS:glycerol (τ_R = 0.80 ± 0.05 ns, T₁ = 9.7 ± 0.7 µs) and 1:1 PBS:glycerol (τ_R = 3.4 ± 0.3 ns, T₁ = 12.0 ± 1.0 µs) was modeled with contributions to the relaxation predominantly from modulation of hyperfine anisotropy and a local mode. The 1/T₁ rate for the 1% ¹²C₁-dFT in the predominantly ¹³C labeled sample is about a factor of 6 more strongly concentration dependent than for natural abundance ¹²C₁-trityl, which reflects the importance of Heisenberg exchange with molecules with different resonance frequencies and faster relaxation rates. In glassy matrices at 160 K, T₁ and T_m for ¹³C₁-dFT are in good agreement with previously reported values for ¹²C₁-dFT consistent with the expectation that modulation of nuclear hyperfine does not contribute to electron spin relaxation in a rigid lattice.

Methanethiosulfonate Derivative of OX063 Trityl: A Promising and Efficient Reagent for Side-Directed Spin Labeling of Proteins

Trityl radicals (TAMs) have recently appeared as an alternative source of spin labels for measuring long distances in biological systems. Finland trityl radical (FTAM) served as the basis for this new generation of spin labels, but FTAM is rather lipophilic and susceptible to self-aggregation, noncovalent binding with lipophilic sites of proteins, and noncovalent docking at the termini of duplex DNA. In this paper the very hydrophilic OX063 TAM with very low toxicity and little tendency for aggregation is used as the basis for a spin label. Human serum albumin (HSA) labeled with OX063 has an intense narrow line typical of TAM radicals in solution, whereas HSA labeled with FTAM shows broad lines and extensive aggregation. In pulse EPR measurements, the measured phase memory time T_M for HSA labeled with OX063 is 6.3 μs at 50 K, the longest yet obtained with a TAM-based spin label. The lowered lipophilicity also decreases side products in the labeling reaction.

Photochemistry of tris(2,3,5,6-tetrathiaaryl)methyl radicals in various solutions

A detailed mechanism of TAM photolysis was studied and includes photoionization of the TAM radical with the formation of carbocation and further conversion of the carbocation under aerobic conditions into quinone-methide and under anaerobic conditions supposedly into an aromatic carbene.

Rapid-scan EPR imaging of a phantom comprised of species with different linewidths and relaxation times

As a demonstration of the application of rapid-scan EPR to imaging at low frequency and magnetic field, a multi-compartment phantom containing six different samples was imaged. The samples were nitroxide radicals, trityl (substituted triarylmethyl) radicals, and the oxygen-sensitive solid lithium phthalocyanine (LiPc), all of which are useful for in vivo imaging. The 2D spectral-spatial image demonstration was performed at 250 MHz, with samples in sealed tubes of various sizes arranged in a 3D-printed plastic holder. Maximum gradients of 10 G/cm gave a spatial resolution of about 0.1 mm for the narrow trityl and LiPc signals and about 1 mm for the nitroxide. The importance of proper selection of resonator bandwidth and scan rate for obtaining accurate linewidth information is demonstrated for a case in which the phantom is composed of species with signal linewidths and relaxation times that differ by more than a factor of 10.

Site Selective and Efficient Spin Labeling of Proteins with a Maleimide-Functionalized Trityl Radical for Pulsed Dipolar EPR Spectroscopy

Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) in combination with site-directed spin labeling (SDSL) of proteins and oligonucleotides is a powerful tool in structural biology. Instead of using the commonly employed gem-dimethyl-nitroxide labels, triarylmethyl (trityl) spin labels enable such studies at room temperature, within the cells and with single-frequency electron paramagnetic resonance (EPR) experiments. However, it has been repeatedly reported that labeling of proteins with trityl radicals led to low labeling efficiencies, unspecific labeling and label aggregation. Therefore, this work introduces the synthesis and characterization of a maleimide-functionalized trityl spin label and its corresponding labeling protocol for cysteine residues in proteins. The label is highly cysteine-selective, provides high labeling efficiencies and outperforms the previously employed methanethiosulfonate-functionalized trityl label. Finally, the new label is successfully tested in PDS measurements on a set of doubly labeled Yersinia outer protein O (YopO) mutants.

Synthesis and Characterization of Hydrophilic Trityl Radical TFO for Biomedical and Biophysical Applications

Tetrathiatriarylmethyl (TAM, trityl) radicals have found wide applications as spin probes/labels for EPR spectroscopy and imaging, and as polarizing agents for dynamic nuclear polarization. The high hydrophilicity of TAM radicals is essential for their biomedical applications. However, the synthesis of hydrophilic TAM radicals (e.g., OX063) is extremely challenging and has only been reported in the patent literature, to date. Herein, an efficient synthesis of a highly water-soluble TAM radical bis(8-carboxyl-2,2,6,6-tetramethylbenzo[1,2-d:4,5-d']bis([1,3]dithiol-4-yl)-mono-(8-carboxyl-2,2,6,6-tetrakis(2-hydroxyethyl)benzo[1,2-d:4,5-d']bis([1,3]dithiol-4-yl)methyl (TFO), which contains four additional hydroxylethyl groups, relative to the Finland trityl radical CT-03, is reported. Similar to OX063, TFO exhibits excellent properties, including high water solubility in phosphate buffer, low log P, low pK_a , long relaxation times, and negligible binding with bovine serum albumin. On the other hand, TFO has a sharper EPR line and higher O₂ sensitivity than those of OX063. Therefore, in combination with its facile synthesis, TFO should find wide applications in magnetic resonance related fields and this synthetic approach would shed new light on the synthesis of other hydrophilic TAM radicals.

An x-band continuous wave saturation recovery electron paramagnetic resonance spectrometer based on an arbitrary waveform generator

An X-band (ca. 9-10 GHz) continuous wave saturation recovery spectrometer to measure electron spin-lattice relaxation (T1) was designed around an arbitrary waveform generator (AWG). The AWG is the microwave source and is used for timing of microwave pulses, generation of control signals, and digitizer triggering. Use of the AWG substantially simplifies the hardware in the bridge relative to that in conventional spectrometers and decreases the footprint. The bridge includes selectable paths with different power amplifications to permit experiments requiring hundreds of milliwatts to fractions of nanowatts for the pump and observe periods. The signal is detected with either a single or quadrature-output double balanced mixer. The system can operate with reflection or crossed-loop resonators. The source noise from the AWG was decreased by addition of a Wenzel high-stability clock. The source is sufficiently stable that automatic frequency control is not needed. The spectrometer was tested with samples that contained 1 × 1015 to 8 × 1017 spins and have T1 between a few hundred ns and hundreds of μs. Excellent signal-to-noise ratio was obtained with acquisition times of 2-90 s. Signal-to-noise performance is similar to that of a conventional saturation recovery spectrometer with a solid-state source. The stability and data reproducibility are better than with conventional sources. With replacement of frequency-sensitive components, this spectrometer can be used to perform saturation recovery measurements at any frequency within the range of the AWG.

Pulse EPR of Triarylmethyl Probes: A New Approach for the Investigation of Molecular Motions in Soft Matter

Triarylmethyl (TAM) radicals have become widely used free radicals in the past few years. Their electron spins have long relaxation times and narrow electron paramagnetic resonance (EPR) lines, which make them an important class of probes and tags in biological applications and materials science. In this work, we propose a new approach to characterize librations by means of TAM radicals. The temperature dependence of motional parameter ⟨α²⟩τ_c, where ⟨α²⟩ is the mean-squared amplitude of librations and τ_c is their characteristic time, is obtained by comparison of the 1/ T_m phase-relaxation rates at X- and Q-band EPR frequencies. We study three soft matrixes, viz., glassy trehalose and two ionic liquids, using TAMs with optimized relaxation properties OX063D and a dodeca- n-butyl homologue of Finland trityl (DBT). The motional parameters ⟨α²⟩τ_c obtained using TAMs are in excellent agreement with those obtained by means of nitroxide radicals. At the same time, the new TAM-based approach has (1) greater sensitivity due to the narrower EPR spectrum and (2) greater measuring accuracy and broader temperature range due to longer relaxation times. The developed approach may be fruitfully implemented to probe low-temperature molecular motions of TAM-labeled biopolymers, membrane systems, polymers, molecules in glassy media, and ionic liquids.

Multi-step phase-cycling in a free-electron laser-powered pulsed electron paramagnetic resonance spectrometer

Electron paramagnetic resonance (EPR) is a powerful tool for research in chemistry, biology, physics and materials science, which can benefit significantly from moving to frequencies above 100 GHz. In pulsed EPR spectrometers driven by powerful sub-THz oscillators, such as the free electron laser (FEL)-powered EPR spectrometer at UCSB, control of the duration, power and relative phases of the pulses in a sequence must be performed at the frequency and power level of the oscillator. Here we report on the implementation of an all-quasioptical four-step phase cycling procedure carried out directly at the kW power level of the 240 GHz pulses used in the FEL-powered EPR spectrometer. Phase shifts are introduced by modifying the optical path length of a 240 GHz pulse with precision-machined dielectric plates in a procedure we call phase cycling with optomechanical phase shifters (POPS), while numerical receiver phase cycling is implemented in post-processing. The POPS scheme was successfully used to reduce experimental dead times, enabling pulsed EPR of fast-relaxing spin systems such as gadolinium complexes at temperatures above 190 K. Coherence transfer pathway selection with POPS was used to perform spin echo relaxation experiments to measure the phase memory time of P1 centers in diamond in the presence of a strong unwanted FID signal in the background. The large excitation bandwidth of FEL-EPR, together with phase cycling, enabled the quantitative measurement of instantaneous electron spectral diffusion, from which the P1 center concentration was estimated to within 10%. Finally, phase cycling enabled saturation-recovery measurements of T1 in a trityl-water solution at room temperature - the first FEL-EPR measurement of electron T1.

Room-temperature distance measurements using RIDME and the orthogonal spin labels trityl/nitroxide

Electron paramagnetic resonance (EPR) based nanometer distance measurements at ambient temperatures are of particular interest for structural biology applications. The nitroxide spin labels commonly used in EPR reveal relatively short transverse relaxation under these conditions, which limits their use for detecting static dipolar interactions. At the same time, the longitudinal relaxation of nitroxide spin labels is still long enough to allow using them as 'pumped' species in the relaxation induced dipolar modulation enhancement (RIDME) experiment where the detection is carried out on the slower relaxing triarylmethyl (TAM) spin labels. In the present study, we report the first demonstration of room-temperature RIDME distance measurements in nucleic acids using TAM as the slow-relaxing detected species and traditional nitroxide as the fast-relaxing partner spin. Two types of immobilizers, glassy trehalose and the modified silica gel Nucleosil, were used for immobilization of the spin-labeled biomolecules. The room-temperature RIDME-based distance distributions are in good agreement with those measured at 80 K by other techniques. Room-temperature RIDME on the spin pairs trityl/nitroxide may become a useful method for the structural characterization of biomacromolecules and biomolecular complexes at near physiological temperatures.

Tabletop 700 MHz electron paramagnetic resonance imaging spectrometer

Low frequency electron paramagnetic resonance imaging is a powerful tool to non-invasively measure the physiological status of tumors. Here, we report on the design and functionality of a rapid scan and pulse table-top imaging spectrometer based around an arbitrary waveform generator and 25mm cross-loop resonator operating at 700 MHz. Two and four-dimensional rapid scan spectral-spatial images are presented. This table-top imager is a prototype for future pre-clinical imagers.

Synthesis of Nanometer Sized Bis- and Tris-trityl Model Compounds with Different Extent of Spin-Spin Coupling

Tris(2,3,5,6-tetrathiaaryl)methyl radicals, so-called trityl radicals, are emerging as spin labels for distance measurements in biological systems based on Electron Paramagnetic Resonance (EPR). Here, the synthesis and characterization of rigid model systems carrying either two or three trityl moieties is reported. The monofunctionalized trityl radicals are connected to the molecular bridging scaffold via an esterification reaction employing the Mukaiyama reagent 2-chloro-methylpyridinium iodide. The bis- and tris-trityl compounds exhibit different inter-spin distances, strength of electron-electron exchange and dipolar coupling and can give rise to multi-spin effects. They are to serve as benchmark systems in comparing EPR distance measurement methods.

Synthesis and EPR-spectroscopic characterization of the perchlorotriarylmethyl tricarboxylic acid radical (PTMTC) and its 13C labelled analogue (13C-PTMTC)

A hydrophilic tris(tetrachlorotriaryl)methyl (tetrachloro-TAM) radical labelled 50% with ¹³C at the central carbon atom was prepared. The mixture of isotopologue radicals was characterised by continuous wave and pulsed X-band electron paramagnetic spectroscopy (EPS). For the pharmaceutical and medical applications planned, the quantitative influence of oxygen, viscosity, temperature and pH on EPR line widths was studied in aqueous buffer, DMSO, water-methanol and water-glycerol mixtures. Under in vivo conditions, pH can be disregarded. There is a clear oxygen dependence of the width of the ¹²C isotopologue single EPR line in aqueous solutions while changes in rotational motion (viscosity) are observable only in the doublet lines of the central carbon of the ¹³C isotopologue. The tetrachloro-TAM proved to be very stable as a solid. Its thermal decay was determined quantitatively by thermal annealing. Towards ascorbic acid as a reducing agent and towards an oocyte cell extract it had a half-life of approx. 60 and 10 min. Thus for in vivo applications, 50% ¹³C tetrachloro-TAMs are suitable for selective and simultaneous oxygen and macroviscosity measurements in a formulation, e.g. nanocapsules.

Triarylmethyl Radical OX063d24 Oximetry: Electron Spin Relaxation at 250 MHz and RF Frequency Dependence of Relaxation and Signal-to-Noise

The triarylmethyl radical OX063d24 is currently used for pulsed electron paramagnetic resonance oximetry at 250 MHz. Both 1/T ₁ and 1/T ₂ increase with increasing oxygen concentration. The dependence of 1/T ₁ on probe concentration is smaller than for 1/T ₂. To inform the selection of the optimum frequency for in vivo oximetry 1/T ₁, 1/T ₂ and signal-to-noise were measured as a function of frequency between 400 and 1000 MHz on a variable-frequency spectrometer with an adjustable-frequency cross-loop resonator. 1/T ₁ and 1/T ₂ decrease with increasing frequency and signal-to-noise increases with increasing frequency, which are all favourable for imaging at higher frequencies. However, depth of penetration of the radio frequency (RF) into an animal decreases with increasing frequency. Assuming that the RF loss in the animal to be studied determines the resonator Q, our results indicate that the optimum frequency for in vivo imaging will be determined by the desired depth of penetration in the tissue.

High-frequency pulsed electron–electron double resonance spectroscopy on DNA duplexes using trityl tags and shaped microwave pulses

Distances between trityl spin labels attached to DNA duplexes were determined by 180 GHz and 260 GHz PELDOR spectroscopy applying broadband pump pulse at higher frequency.

Performance of PELDOR, RIDME, SIFTER, and DQC in measuring distances in trityl based bi- and triradicals: exchange coupling, pseudosecular coupling and multi-spin effects

The performance of pulsed EPR methods for distance measurements is evaluated on three different trityl model systems.

A Versatile Approach to Attachment of Triarylmethyl Labels to DNA for Nanoscale Structural EPR Studies at Physiological Temperatures

Triarylmethyl (trityl, TAM) radicals are a promising class of spin labels for nanometer-scale distance measurements in biomolecules at physiological temperatures. However, to date, existing approaches to site-directed TAM labeling of DNA have been limited to label attachment at the termini of oligonucleotides, thus hindering a majority of demanded applications. Herein, we report a new versatile strategy for TAM attachment at arbitrary sites of nucleic acids. It utilizes an achiral non-nucleoside phosphoramidite monomer for automated solid-phase synthesis of oligonucleotides, which are then postsynthetically functionalized with TAM. We demonstrate a synthesis of a set of oligonucleotide complexes that are TAM-labeled at internal or terminal sites, as well as the possibility of measuring interspin distances up to ∼5-6 nm at 298 K using double quantum coherence electron paramagnetic resonance (EPR). Implementation of the developed approach strongly broadens the scope of nucleic acids and nucleoprotein complexes available for nanoscale structural EPR studies at room temperatures.

EPR-based distance measurements at ambient temperature

Pulsed dipolar (PD) EPR spectroscopy is a powerful technique allowing for distance measurements between spin labels in the range of 2.5-10.0nm. It was proposed more than 30years ago, and nowadays is widely used in biophysics and materials science. Until recently, PD EPR experiments were limited to cryogenic temperatures (T<80K). Recently, application of spin labels with long electron spin dephasing time at room temperature such as triarylmethyl radicals and nitroxides with bulky substituents at a position close to radical centers enabled measurements at room temperature and even at physiologically relevant temperatures by PD EPR as well as other approaches based on EPR (e.g., relaxation enhancement; RE). In this paper, we review the features of PD EPR and RE at ambient temperatures, in particular, requirements on electron spin phase memory time, ways of immobilization of biomolecules, the influence of a linker between the spin probe and biomolecule, and future opportunities.

Triarylmethyl Radicals: EPR Study of 13C Hyperfine Coupling Constants

Triarylmethyl (TAM) radicals are widely used in Electron Paramagnetic Resonance (EPR) spectroscopy as spin labels and in EPR imaging as spin probes for in vivo oxymetry. One of the key advantages of TAMs is extremely narrow EPR line, especially in case of deuterated analogues (~5 μT). Another advantage is their slow spin relaxation even at physiological temperatures allowing, in particular, application of pulsed dipolar EPR methods for distance measurements in biomolecules. In this paper a large series of TAM radicals and their deuterated analogues is synthesized, and corresponding spectroscopic parameters including 13C hyperfine constants are obtained for the first time. The negligible dependence of 13C hyperfine constants on solvent, as well as on structure and number of substituents at para-C atoms of aromatic rings, has been found. In addition, we have demonstrated that 13C signals at natural abundance can be employed for successful room-temperature distance measurements using Pulsed Electron Double Resonance (PELDOR or DEER).

Designing Molecular Probes To Prolong Intracellular Retention: Application to Nitroxide Spin Probes

Targeted delivery of molecular probes into cells enables cellular imaging through optical and magnetic modalities. Probe molecules that are well retained by cells can accumulate to higher intracellular concentrations, and thus increase the signal-to-noise ratio of, and widen the temporal window for, imaging. Here we synthesize a paramagnetic spin probe bearing six ionic functional groups and show that it has long intracellular half-life (>12 h) and exceptional biostability in living cells. We demonstrate that judicious incorporation of ionic substituents on probe molecules systematically increases intracellular retention time, and should therefore be beneficial to imaging experiments.

Triarylmethyl Radical: EPR Signal to Noise at Frequencies between 250 MHz and 1.5 GHz and Dependence of Relaxation on Radical and Salt Concentration and on Frequency

In vivo oximetry by pulsed electron paramagnetic resonance is based on measurements of changes in electron spin relaxation rates of probe molecules, such as the triarylmethyl radicals. A series of experiments was performed at frequencies between 250 MHz and 1.5 GHz to assist in the selection of an optimum frequency for oximetry. Electron spin relaxation rates for the triarylmethyl radical OX063 as a function of radical concentration, salt concentration, and resonance frequency were measured by electron spin echo 2-pulse decay and 3-pulse inversion recovery in the frequency range of 250 MHz-1.5 GHz. At constant OX063 concentration, 1/T₁ decreases with increasing frequency because the tumbling dependent processes that dominate relaxation at 250 MHz are less effective at higher frequency. 1/T₂ also decreases with increasing frequency because 1/T₁ is a significant contribution to 1/T₂ for trityl radicals in fluid solution. 1/T₂-1/T₁, the incomplete motional averaging contribution to 1/T₂, increases with increasing frequency. At constant frequency, relaxation rates increase with increasing radical concentration due to contributions from collisions that are more effective for 1/T₂ than 1/T₁. The collisional contribution to relaxation increases as the concentration of counter-ions in solution increases, which is attributed to interactions of cations with the negatively charged radicals that decrease repulsion between trityl radicals. The Signal-to-Noise ratio (S/N) of field-swept echo-detected spectra of OX063 were measured in the frequency range of 400 MHz-1 GHz. S/N values, normalized by √Q, increase as frequency increases. Adding salt to the radical solution decreased S/N because salt lowers the resonator Q. Changing the temperature from 19 to 37 °C caused little change in S/N at 700 MHz. Both slower relaxation rates and higher S/N at higher frequencies are advantageous for oximetry. The potential disadvantage of higher frequencies is the decreased depth of penetration into tissue.

A triarylmethyl spin label for long-range distance measurement at physiological temperatures using T1 relaxation enhancement

Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy has become an important tool for measuring distances in proteins on the order of a few nm. For this purpose pairs of spin labels, most commonly nitroxides, are site-selectively introduced into the protein. Recent efforts to develop new spin labels are focused on tailoring the intrinsic properties of the label to either extend the upper limit of measurable distances at physiological temperature, or to provide a unique spectral lineshape so that selective pairwise distances can be measured in a protein or complex containing multiple spin label species. Triarylmethyl (TAM) radicals are the foundation for a new class of spin labels that promise to provide both capabilities. Here we report a new methanethiosulfonate derivative of a TAM radical that reacts rapidly and selectively with an engineered cysteine residue to generate a TAM containing side chain (TAM1) in high yield. With a TAM1 residue and Cu(2+) bound to an engineered Cu(2+) binding site, enhanced T1 relaxation of TAM should enable measurement of interspin distances up to 50Å at physiological temperature. To achieve favorable TAM1-labeled protein concentrations without aggregation, proteins are tethered to a solid support either site-selectively using an unnatural amino acid or via native lysine residues. The methodology is general and readily extendable to complex systems, including membrane proteins.

Saccharides as Prospective Immobilizers of Nucleic Acids for Room-Temperature Structural EPR Studies

Pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for structural studies of biomolecules and their complexes. This method, whose applicability has been recently extended to room temperatures, requires immobilization of the studied biosystem to prevent averaging of dipolar couplings; at the same time, the modification of native conformations by immobilization must be avoided. In this work, we provide first demonstration of room-temperature EPR distance measurements in nucleic acids using saccharides trehalose, sucrose, and glucose as immobilizing media. We propose an approach that keeps structural conformation and unity of immobilized double-stranded DNA. Remarkably, room-temperature electron spin dephasing time of triarylmethyl-labeled DNA in trehalose is noticeably longer compared to previously used immobilizers, thus providing a broader range of available distances. Therefore, saccharides, and especially trehalose, can be efficiently used as immobilizers of nucleic acids, mimicking native conditions and allowing wide range of structural EPR studies at room temperatures.

UHF EPR spectrometer operating at frequencies between 400 MHz and 1 GHz

A spectrometer was designed and constructed to facilitate measurements of T₁, T₂, spin echo signal-to-noise, and resonator quality factor, Q, between about 400 and 1000 MHz. Pulse patterns are generated at 250 MHz and mixed with the output from a second source to perform excitation and detection. A cross-loop resonator was constructed in which the same sample could be measured in the same resonator over the full range of frequencies. An air-core, 4-coil, water-cooled electromagnet with a large experimental volume was built.

Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels

Pulse dipole-dipole electron paramagnetic resonance (EPR) spectroscopy (double electron-electron resonance [DEER] or pulse electron-electron double resonance [PELDOR] and double quantum coherence [DQC]) allows for measurement of distances in biomolecules and can be used at low temperatures in a frozen solution. Recently, the possibility of distance measurement in a nucleic acid at a physiological temperature using pulse EPR was demonstrated. In these experiments, triarylmethyl (TAM) radicals with long memory time of the electron spin served as a spin label. In addition, the duplex was immobilized on modified silica gel particles (Nucleosil DMA); this approach enables measurement of interspin distances close to 4.5 nm. Nevertheless, the possible influence of TAM on the structure of a biopolymer under study and validity of the data obtained by DQC are debated. In this paper, a combination of molecular dynamics (MD) and nuclear magnetic resonance (NMR) methods was used for verification of interspin distances measured by the X-band DQC method. NMR is widely used for structural analysis of biomolecules under natural conditions (room temperature and an aqueous solution). The ultraviolet (UV) melting method and thermal series (1)H NMR in the range 5-95 °C revealed the presence of only the DNA duplex in solution at oligonucleotide concentrations 1 μM to 1.1 mM at temperatures below 40 °C. The duplex structures and conformation flexibility of native and TAM-labeled DNA complexes obtained by MD simulation were the same as the structure obtained by NMR refinement. Thus, we showed that distance measurements at physiological temperatures by the X-band DQC method allow researchers to obtain valid structural information on an unperturbed DNA duplex using terminal TAM spin labels.

Paramagnetic spherical nanoparticles by the self-assembly of persistent trityl radicals

The self-association of a water-soluble persistent trityl radical gives rise to paramagnetic nanoparticles: a new class of non-metallic high spin systems.