Pulsed EPR Research Articles

EPR of Type I photosynthetic reaction centers.

Light-induced reactions in photosynthetic reaction centers are initiated by the absorption of a photon, which results in the transfer of a single electron and the generation of radical ions in the donor and acceptor molecules involved in the charge-separated state. Electron paramagnetic resonance (EPR) spectroscopy is the ideal method for the study of such reactions. In addition to measuring spectra of the electron transfer cofactors in continuous light, reactions can be initiated by brief flashes of light, thereby allowing the kinetics of forward electron transfer as well as recombination reactions to be obtained. Because the donor and acceptor pairs are so closely spaced and because light induced charge separation is so rapid, the donor and early acceptors are in a quantum mechanically spin entangled state, which confers properties such as increased sensitivity, the ability to measure reactions on the nanosecond timescale, and the determination of bond angles between cofactors. Additionally, distances between pairs of cofactors can be measured by detecting the modulation of a phase shifted "out-of-phase" electron spin echo signal. In this methods article, we will describe how continuous wave EPR, time resolved EPR, and pulsed EPR can be used to measure these properties in Type I photosynthetic reaction centers. Methods of analysis are described for the bound electron transfer cofactors in the heterodimeric Photosystem I reaction center of plants and cyanobacteria and in the homodimeric reaction centers found in phototrophic members of the phyla Bacillota, Chlorobiota, and Acidobacteriota.

PELDOR Measurements on Nitroxide-Labeled Oligonucleotides.

In the past decades, pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) has emerged as a powerful tool in biophysical chemistry to study the structure, dynamics, and function of biomolecules like oligonucleotides and proteins. Structural information is obtained from PDS methods in form of a distribution of distances between spin centers. Such spin centers can either be intrinsically present paramagnetic metal ions and organic radicals or may be attached to the biomolecule by means of site-directed spin labeling. The most common PDS experiment for probing interspin distances in the nanometer range is pulsed electron-electron double resonance (PELDOR or DEER). In the protocol presented here, we provide a step-by-step workflow on how to set up a PELDOR experiment on a commercially available pulsed EPR spectrometer, outline the data analysis, and highlight potential pitfalls. We suggest PELDOR measurements on nitroxide-labeled oligonucleotides to study the structure of either RNA-cleaving DNAzymes in complex with their RNA targets or modified DNAzymes with different functions and targets, in which deoxynucleotides are substituted by nitroxide-labeled nucleotides.

Fullerene-based triplet spin labels: methodology aspects for pulsed dipolar EPR spectroscopy.

Triplet states of photoexcited organic molecules are promising spin labels with advanced spectroscopic properties for pulsed dipolar electron paramagnetic resonance (PD EPR) spectroscopy. Recently proposed triplet fullerene labels have shown great potential for double electron-electron resonance (DEER) distance measurements as "observer spins" due to a high quantum yield of the triplet state, hyperpolarization and relatively narrow EPR spectra. Here, we demonstrate the applicability of fullerene labels to other PD EPR techniques, such as relaxation induced dipolar modulation enhancement (RIDME) and laser induced magnetic dipolar spectroscopy (LaserIMD). In particular, a specific contaminating signal in LaserIMD experiments was observed, explained and mitigated. Comparative analyses of the signal-to-noise (SNR) ratios were performed for all employed methods. DEER on the fullerene-triarylmethyl pair shows the best performance, which allows state-of-the-art DEER acquisition at 100 nM with a SNR of ∼35 within reasonable 42 hours.

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.

Spins at work: probing charging and discharging of organic radical batteries by electron paramagnetic resonance spectroscopy

A versatile on-substrate electrode setup was developed and used to perform quantitativein operandoEPR as well as low-temperature pulse EPR experiments on electrochemical cells containing a redox conductive polymer as energy-storage material.

The Cu(ii) - dietary fibre interactions at molecular level unveiled via EPR spectroscopy.

While dietary fibres have a reputation of a healthy food component, the interaction between nutrients and neutral fibers is non-covalent, and its characterization is challenging for most analytical techniques. Here, on the example of barley β-glucan (BBG) and paramagnetic Cu(ii) ions we demonstrate the performance of different Electron Paramagnetic Resonance (EPR) methods in the fibre studies. EPR techniques were tested on two spin probe systems with different affinity in the interaction with dietary fibres – Cu(OAc)2 salt, which weakly dissociates under physiological conditions and CuSO4 salt, which easily dissociates, so that in the latter case Cu(ii) can be considered as a ‘free’ ion, only chelated by water molecules. The Cu(ii)-BBG interaction was determined by pulse EPR relaxation measurements, but this interaction appears not strong enough for continuous wave EPR detection. The capability of the fibres for Cu(ii) absorption was successfully analyzed by comparison of the results from the pulse dipolar spectroscopy with numerical simulations. The local distribution of sugar hydrogen atoms around the Cu(ii) ion has been determined by electron spin echo envelope modulation (ESEEM) and electron-nuclei double resonance (ENDOR) techniques.

Structural insights into Lewis acid- and F4TCNQ-doped conjugated polymers by solid-state magnetic resonance spectroscopy.

Molecular doping strategies facilitate orders of magnitude enhancement in the charge carrier mobility of organic semiconductors (OSCs). Understanding the different doping mechanisms and molecular-level constraints on doping efficiency related to the material energy levels is crucial to develop versatile dopants for OSCs. Given the compositional and structural heterogeneities associated with OSC thin films, insight into dopant-polymer interactions by long-range techniques such as X-ray scattering and electron microscopy is exceedingly challenging to obtain. This study employs short-range probes, solid-state (ss)NMR and EPR spectroscopy, to resolve local structures and intermolecular interactions between dopants such as F4TCNQ (2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane), Lewis acid BCF (tris[pentafluorophenyl] borane) and Lewis base conjugated polymer, PCPDTBT (P4) (poly[2,6-(4,4-bis(2-hexadecyl)-4H-cyclopenta[2,1-b;3,4-b']dithiophene)-alt-4,7(2,1,3-benzothiadiazole)]). Analysis of 1H and 13C ssNMR spectra of P4, P4 : F4TCNQ and P4 : BCF blends indicates that the addition of dopants induces local structural changes in the P4 polymer, and causes paramagnetism-induced signal broadening and intensity losses. The hyperfine interactions in P4 : BCF and P4 : F4TCNQ are characterized by two-dimensional pulsed EPR spectroscopy. For P4 : F4TCNQ, 19F ssNMR analysis indicates that the F4TCNQ molecules are distributed and aggregated into different local chemical environments. By comparison, BCF molecules are intermixed with the P4 polymer and interact with traces of water molecules to form BCF-water complexes that serve as Brønsted acid sites, as revealed by 11B ssNMR spectroscopy. These results indicate that the P4-dopant blends exhibit complex morphology with different distributions of dopants, whereby the combined use of ssNMR and EPR provides essential insights into how higher doping efficiency is observed with BCF and a mediocre efficiency is associated with F4TCNQ molecules.

Diffusion equation for the longitudinal spectral diffusion: the case of the RIDME experiment.

Relaxation-induced dipolar modulation enhancement (RIDME) time trace shapes reveal linear scaling with the proton concentration in homogeneous glassy samples. We describe here an approximate diffusion equation-based analysis of such data, which uses only two fit parameters and allows for global data fitting with good accuracy. By construction, the approach should be transferable to other pulse EPR experiments with longitudinal mixing block(s) present. The two fit parameters appear to be sensitive to the type of the glassy matrix and can be thus used for sample characterisation. The estimates suggest that the presented technique should be sensitive to protons at distances up to 3 nm from the electron spin at a 90% matrix deuteration level. We propose that a structural method might be developed based on such an intermolecular hyperfine (ih-)RIDME technique, which would be useful, for instance, in structural biology or dynamic nuclear polarisation experiments.

Effect of the Time Delay between Spin State Preparation and Measurement on Electron Spin Teleportation in a Covalent Donor-Acceptor-Radical System.

We recently demonstrated photodriven quantum teleportation of an electron spin state in a covalent donor-acceptor-radical (D-A-R•) system. Following specific spin state preparation on R• with a microwave pulse, photoexcitation of A results in two-step electron transfer producing D•+-A-R-, where the spin state on R• is teleported to D•+. This study examines the effects of varying the time (τD) between spin state preparation and photoinitiated teleportation. Using pulse electron paramagnetic resonance spectroscopy, the spin echo of D•+ resulting from teleportation shows a damped oscillation as a function of τD that is simulated using a density matrix model, which provides a fundamental understanding of the echo behavior. Teleportation fidelity calculations also show oscillatory behavior as a function of τD due to the accumulation of a phase factor between ⟨Sx⟩ and ⟨Sy⟩. Understanding experimental parameters intrinsic to quantum teleportation in molecular systems is crucial to leveraging this phenomenon for quantum information applications.

Exploring the Solvation Sphere and Spatial Accumulation of Dissolved Transition-Metal Ions in Batteries: A Case Study of Vanadyl Ions Released from V2O5Cathodes

Dissolution of transition-metal ions from Li-ion battery cathodes is a well-known degradation phenomenon. In addition to capacity decrease due to metal loss in the bulk cathode, dissolved transition-metal ions might migrate through the electrolyte and participate in redox reactions resulting in electrolyte decomposition. Aside from the oxidation state and concentration of the transition metal, its ligand sphere and spatial accumulation have to be determined for complete characterization and prediction of possible detrimental impact. Here, pulse electron paramagnetic resonance and density functional theory are exploited to investigate the coordination and location of vanadyl ions, which are a dissolution product of V2O5 cathodes. The solvation sphere is found to be dominated by electrolyte degradation products and also contains contributions from nonelectrolytic sources. Additionally, adjacent lithium and hexafluorophosphate ions are observed.

Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy

Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is powerful in structure and dynamics study of biological macromolecules by providing distance distribution information ranging from 1.8 to 6 nm, providing that the biomolecules are site-specifically labeled with paramagnetic tags. However, long distances up to 16 nm have been measured on perdeuterated and spin-labeled proteins in deuterated solvent by PELDOR. Here we demonstrate long-range distance measurement on a large RNA, the 97-nucleotide 3′SL RNA element of the Dengue virus 2 genome, by combining a posttranscriptional site-directed spin labeling method using an unnatural basepair system with RNA perdeuteration by enzymatic synthesis using deuterated nucleotides. The perdeuteration removes the coupling of the electron spins of the nitroxide spin labels from the proton nuclear spin system of the RNA and does extend the observation time windows of PELDOR up to 50 μs. This enables one to determine long distances up to 14 nm for large RNAs and their conformational flexibility.

Highly fluorine and ytterbium doped polarization maintaining large mode area photonic crystal fiber via the sol-gel process

Highly Yb-doped silica glass with low refractive index for fabrication of Yb-doped large-mode-area photonic crystal fiber (LMA PCF) is in favor of decreasing fiber length and thus increasing the threshold of nonlinear effects in pulse laser amplification. Accordingly, fluorine incorporation in highly Yb-doped silica glass is vitally important to compensate the sharp increase in refractive index caused by ytterbium and aluminum ions. In this work, the fluorine doping concentration in Yb/Al/P/F co-doped silica glass was significantly improved by a modified sol-gel method combined with high temperature sintering. The effects of fluorine doping on glass structure have been investigated in details by Raman spectra, nuclear magnetic resonance (NMR) and advanced pulse electron paramagnetic resonance (EPR) measurements. The incorporation of fluorine yields Si-F bonds and Yb-F bonds formation and leads to the mild change in spectroscopic properties. An optimized silica core glass rod with high Yb (0.77 wt.%) and fluorine (0.8 wt.%) doping concentration, low refractive index and acceptable optical quality was prepared. Based on the highly fluorine and ytterbium doped silica core glass, a polarization maintaining (PM) photonic crystal fiber with 40 µm core was prepared and the pump absorption coefficient at 976 nm was ∼6.5 dB/m. An average amplified power of 103 W was achieved from a 2-m-long PCF with the bend diameter of 23 cm. The slope efficiency (with respect to pump power) was 52% with laser beam quality factor M2 of 1.46.

Probing Redox Non-Innocence in Iron-Carbene Complexes {Fe=C(H)Ar}10-11 by 1,2 H and 13 C Pulse Electron Paramagnetic Resonance.

We report the synthesis and spectroscopic characterization of a series of iron-carbene complexes in redox states {Fe=C(H)Ar}10-11 . Pulse EPR studies of the 1,2 H and 13 C isotopologues of {Fe=C(H)Ar}11 reveal the high covalency of the Fe-carbene bonding, leading to a more even spin distribution than commonly observed for reduced Fischer carbenes.

Probing Redox Non‐Innocence in Iron–Carbene Complexes {Fe=C(H)Ar}10–11by1,2H and13C Pulse Electron Paramagnetic Resonance

AbstractWe report the synthesis and spectroscopic characterization of a series of iron‐carbene complexes in redox states {Fe=C(H)Ar}10–11. Pulse EPR studies of the1,2H and13C isotopologues of {Fe=C(H)Ar}11reveal the high covalency of the Fe–carbene bonding, leading to a more even spin distribution than commonly observed for reduced Fischer carbenes.

Peek Inside the Water Mixtures of Ionic Liquids at Molecular Level: Microscopic Properties Probed by EPR Spectroscopy.

Many ionic liquids (ILs) can be mixed with water, forming either true solutions or emulsions. This favors their applications in many respects, but at the same time might strongly alter their physicochemical properties. A number of methods exist for studying the macroscopic properties of such mixtures, whereas understanding their characteristics at micro/nanoscale is rather challenging. In this work we investigate microscopic properties, such as viscosity and local structuring, in binary water mixtures of IL [Bmim]BF4 in liquid and glassy states. For this sake, we use continuous wave and pulse electron paramagnetic resonance (EPR) spectroscopy with dedicated spin probes, located preferably in IL-rich domains or distributed in IL- and water-rich domains. We demonstrate that the glassy-state nanostructuring of IL-rich domains is very similar to that in neat ILs. At the same time, in liquid state the residual water makes local viscosity in IL-rich domains noticeably different compared to neat ILs, even though the overwhelming amount of water is contained in water-rich domains. These results have to be taken into account in various applications of IL-water mixtures, especially in those cases demanding the combinations of optimum micro- and macroscopic characteristics.

Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.

Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron-electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.

Development and Preclinical Study of Free Radical Imaging Using Field-Cycling Dynamic Nuclear Polarization MRI.

Free radicals, such as metabolic intermediates, reactive oxygen species, and metal enzymes, are key substances in organisms, although they can also cause various oxidative diseases. Thus, in vivo free radical imaging should be considered as the ultimate form of metabolic imaging. Unfortunately, electron spin resonance (ESR) imaging has inherent disadvantages, such as free radicals with large linewidths generating blurred images and the presence of two or more free radicals resulting in a complicated imaging procedure. Dynamic nuclear polarization-magnetic resonance imaging (DNP-MRI) is a noninvasive imaging method to visualize in vivo free radicals, theoretically, with the same resolution as the MRI anatomical resolution, and fixed low-field DNP-MRI provides unique information on oxidative diseases and cancer. However, the large gyromagnetic ratio of the electron spin, which is 660-fold greater than that of a proton, requires field cycling, wherein the external magnetic field should be varied during DNP-MRI observations. This causes difficulties in developing a DNP-MRI system for clinical purposes. We developed a novel field-cycling DNP-MRI system for a preclinical study. In the said system, the magnetic field is switched by rotationally moving two magnets, with a magnetic flux density of 0.3 T for MRI and 5 mT for ESR. The image quality was examined using various pulse sequences and ESR irradiation using nitroxyl radical as the phantom, and the optimum conditions were established. Using the system, we performed a preclinical study involving free radical imaging by placing the free radicals under the palm of a human hand.

Evidence for an Ordering Transition near 120 K in an Intrinsically Disordered Protein, Casein.

Intrinsically disordered proteins (IDPs) are proteins that possess large unstructured regions. Their importance is increasingly recognized in biology but their characterization remains a challenging task. We employed field swept Electron Spin Echoes in pulsed EPR to investigate low-temperature stochastic molecular librations in a spin-labeled IDP, casein (the main protein of milk). For comparison, a spin-labeled globular protein, hen egg white lysozyme, is also investigated. For casein these motions were found to start at 100 K while for lysozyme only above 130 K, which was ascribed to a denser and more ordered molecular packing in lysozyme. However, above 120 K, the motions in casein were found to depend on temperature much slower than those in lysozyme. This abrupt change in casein was assigned to an ordering transition in which peptide residues rearrange making the molecular packing more rigid and/or more cohesive. The found features of molecular motions in these two proteins turned out to be very similar to those known for gel-phase lipid bilayers composed of conformationally ordered and conformationally disordered lipids. This analogy with a simpler molecular system may appear helpful for elucidation properties of molecular packing in IDPs.

Electron nuclear interactions in spin-3/2 color centers in silicon carbide: A high-field pulse EPR and ENDOR study

High-frequency pulsed electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) were used to determine electron nuclear interactions on remote ligand shells of silicon and carbon in spin-3/2 color centers with an optically induced high-temperature spin alignment in hexagonal $4H$-, $6H$-, and rhombic $15R$-silicon carbide (SiC) polytypes. The EPR and ENDOR experimental data relate unambiguously to spin-3/2 centers in which the optically induced alignment of the spin-level populations occurs. The identification is based on resolved ligand hyperfine interactions with carbon and silicon nearest, next-nearest, and the more distant neighbors and on the determination of the unpaired electron spin densities. The hyperfine interactions with $^{29}\mathrm{Si}$ and $^{13}\mathrm{C}$ nuclei are unambiguously separated due to the selective population of the fine-structure levels with certain values of ${\mathrm{M}}_{\mathrm{S}}$. The signs of these interactions and, as a result, the signs of oscillating spin density at $^{29}\mathrm{Si}$ and $^{13}\mathrm{C}$ nuclei, are determined. On the basis of the EPR and optically induced ENDOR measurements, signs of the fine-structure splitting for all the centers were demonstrated, which made it possible to establish the character of optically induced spin alignment, including the inverse populations of the spin levels for these centers. The values of hyperfine interaction with $^{29}\mathrm{Si}$ and $^{13}\mathrm{C}$ nuclei, including those remote from the localization of the spin-3/2 center, are tabulated, which can be used by a number of algorithms in quantum information processing as long-term memory.

Validation of Structural Grounds for Anomalous Molecular Mobility in Ionic Liquid Glasses.

Ionic liquid (IL) glasses have recently drawn much interest as unusual media with unique physicochemical properties. In particular, anomalous suppression of molecular mobility in imidazolium IL glasses vs. increasing temperature was evidenced by pulse Electron Paramagnetic Resonance (EPR) spectroscopy. Although such behavior has been proven to originate from dynamics of alkyl chains of IL cations, the role of electron spin relaxation induced by surrounding protons still remains unclear. In this work we synthesized two deuterated imidazolium-based ILs to reduce electron–nuclear couplings between radical probe and alkyl chains of IL, and investigated molecular mobility in these glasses. The obtained trends were found closely similar for deuterated and protonated analogs, thus excluding the relaxation-induced artifacts and reliably demonstrating structural grounds of the observed anomalies in heterogeneous IL glasses.