Pulsed Electron Paramagnetic Resonance Spectroscopy Research Articles

EPR Distance Measurements as a Tool to Characterize Protein‐DNA Interactions

AbstractOver recent decades, electron paramagnetic resonance (EPR) spectroscopy has become an essential tool for exploring complex biological systems. Herein, we discuss the potential of pulsed EPR spectroscopy to shed light on the mechanisms of protein‐DNA interactions. To this end, we first provide an overview of pulsed EPR methodology (and specifically, double electron electron resonance; DEER), with a focus on the various spin‐labeling methods used today both for protein labeling and for DNA labeling. Next, after briefly discussing recent applications of DEER in protein‐DNA studies, we introduce a detailed case study, an example of how EPR spectroscopy has been used to resolve the transcription mechanism of the CueR copper regulator.

Photodriven quantum teleportation of an electron spin state in a covalent donor-acceptor-radical system.

Quantum teleportation transfers the quantum state of a system over an arbitrary distance from one location to another through the agency of quantum entanglement. Because quantum teleportation is essential to many aspects of quantum information science, it is important to establish this phenomenon in molecular systems whose structures and properties can be tailored by synthesis. Here, we demonstrate electron spin state teleportation in an ensemble of covalent organic donor-acceptor-stable radical (D-A-R•) molecules. Following preparation of a specific electron spin state on R• in a magnetic field using a microwave pulse, photoexcitation of A results in the formation of an entangled electron spin pair D•+-A•-. The spontaneous ultrafast chemical reaction D•+-A•--R• → D•+-A-R- constitutes the Bell state measurement step necessary to carry out spin state teleportation. Quantum state tomography of the R• and D•+ spin states using pulse electron paramagnetic resonance spectroscopy shows that the spin state of R• is teleported to D•+ with high fidelity.

Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR Spectroscopy

AbstractPrecise nanoscale distance measurements by pulsed electron paramagnetic resonance (EPR) spectroscopy play a crucial role in structural studies of biomolecules. The properties of the spin labels used in this approach determine the sensitivity limits, attainable distances, and proximity to biological conditions. Herein, we propose and validate the use of photoexcited fullerenes as spin labels for pulsed dipolar (PD) EPR distance measurements. Hyperpolarization and the narrower spectrum of fullerenes compared to other triplets (e.g., porphyrins) boost the sensitivity, and superior relaxation properties allow PD EPR measurements up to a near‐room temperature. This approach is demonstrated using fullerene–nitroxide and fullerene–triarylmethyl pairs, as well as a supramolecular complex of fullerene with nitroxide‐labeled protein. Photoexcited triplet fullerenes can be considered as new spin labels with outstanding spectroscopic properties for future structural studies of biomolecules.

Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR Spectroscopy.

Precise nanoscale distance measurements by pulsed electron paramagnetic resonance (EPR) spectroscopy play a crucial role in structural studies of biomolecules. The properties of the spin labels used in this approach determine the sensitivity limits, attainable distances, and proximity to biological conditions. Herein, we propose and validate the use of photoexcited fullerenes as spin labels for pulsed dipolar (PD) EPR distance measurements. Hyperpolarization and the narrower spectrum of fullerenes compared to other triplets (e.g., porphyrins) boost the sensitivity, and superior relaxation properties allow PD EPR measurements up to a near-room temperature. This approach is demonstrated using fullerene-nitroxide and fullerene-triarylmethyl pairs, as well as a supramolecular complex of fullerene with nitroxide-labeled protein. Photoexcited triplet fullerenes can be considered as new spin labels with outstanding spectroscopic properties for future structural studies of biomolecules.

Cp* Noninnocence Leads to a Remarkably Weak C–H Bond via Metallocene Protonation

Metallocenes, including their permethylated variants, are extremely important in organometallic chemistry. In particular, many are synthetically useful either as oxidants (e.g., Cp2Fe+) or as reductants (e.g., Cp2Co, Cp*2Co, and Cp*2Cr). The latter have proven to be useful reagents in the reductive protonation of small-molecule substrates, including N2. As such, understanding the behavior of these metallocenes in the presence of acids is paramount. In the present study, we undertake the rigorous characterization of the protonation products of Cp*2Co using pulse electron paramagnetic resonance (EPR) techniques at low temperature. We provide unequivocal evidence for the formation of the ring-protonated isomers Cp*( exo/ endo-η4-C5Me5H)Co+. Variable temperature Q-band (34 GHz) pulse EPR spectroscopy, in conjunction with density functional theory (DFT) predictions, are key to reliably assigning the Cp*( exo/ endo-η4-C5Me5H)Co+ species. We also demonstrate that exo-protonation selectivity can be favored by using a bulkier acid and suggest this species is thus likely a relevant intermediate during catalytic nitrogen fixation given the bulky anilinium acids employed. Of further interest, we provide physical data to experimentally assess the C-H bond dissociation free energy (BDFEC-H) for Cp*( exo-η4-C5Me5H)Co+. These experimental data support our prior DFT predictions of an exceptionally weak C-H bond (<29 kcal mol-1), making this system among the most reactive (with respect to C-H bond strength) to be thoroughly characterized. These data also point to the propensity of Cp*( exo-η4-C5Me5H)Co to mediate hydride (H-) transfer. Our findings are not limited to the present protonated metallocene system. Accordingly, we outline an approach to rationalizing the reactivity of arene-protonated metal species, using decamethylnickelocene as an additional example.

Lanthanide Ions as Local Probes in Ionic Hydrides: A Pulsed Electron Nuclear Double Resonance and Thermoluminescence Study of Eu2+-Doped Hydride Perovskites

A model study on the use of pulsed electron paramagnetic resonance spectroscopy and optical spectroscopy of Eu2+ as a local probe in hydrides is presented for the Eu2+-doped (and codoped) perovskites LiMH3 and LiMD3 (M = Sr or Ba). Two-pulse field-swept electron spin echo, Davies and Mims electron nuclear double resonance, Davies-type difference triple resonance experiments, and thermoluminescence spectroscopy, as well as density functional calculations, were carried out. Electron nuclear double resonance spectroscopy allows for an unambiguous determination of the position occupied by the dopant ion, which is important information necessary for the correct interpretation of optical spectra. With regard to the current importance of hydrides and mixed anionic hydrides, doping with rare-earth or transition-metal ions and the combination of pulsed EPR and optical spectroscopy may serve as a promising and convenient tool for studying such materials.

Photogenerated Spin-Entangled Qubit (Radical) Pairs in DNA Hairpins: Observation of Spin Delocalization and Coherence.

The ability to prepare physical qubits in specific initial quantum states is a critical requirement for their use in quantum information science (QIS). Subnanosecond photoinduced electron transfer in a structurally well-defined donor-acceptor system can be used to produce an entangled spin qubit (radical) pair in a pure initial singlet state fulfilling this criterion. Synthetic DNA is a promising platform on which to build spin qubit arrays with fixed spatial relationships; therefore, we have prepared a series of DNA hairpins in which naphthalenediimide (NDI) is the chromophore/acceptor hairpin linker, variable-length diblock A- and G-tracts are intermediate donors, and a stilbenediether (Sd) is the terminal donor. Photoexcitation of NDI in these DNA hairpins generates high-yield, long-lived, entangled spin qubit pairs at 85 K, and time-resolved and pulse electron paramagnetic resonance (EPR) spectroscopies are used to probe their spin dynamics. Specifically, measurements of the distance-dependent dipolar coupling between the two spins are used to obtain the average spin qubit pair distance in the absence of the terminal Sd donor and reveal that one of the spins is fully delocalized across up to five adjacent guanines in a G-tract on the EPR time scale. We have recently shown that extensive spin hopping between degenerate sites accessible to one spin of the pair may result in spin decoherence. However, we observe a strong out-of-phase electron spin echo envelope modulation (OOP-ESEEM) signal from the NDI•--Sd•+ spin qubit pair in DNA hairpins showing that spin coherence is maintained across a 2 adenine A-tract followed by a 2-4 guanine G-tract as a result of rapid spin transport to Sd. These results demonstrate that pulse-EPR can manipulate coherent spin states in DNA hairpins, which is essential for quantum gate operations relevant to QIS applications.

Exploring the Interaction of Ammonia with Supported Vanadia Catalysts by Continuous Wave and Pulsed Electron Paramagnetic Resonance Spectroscopy

Continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) spectroscopy are used to investigate the nature of vanadium species on V2O5/TiO2 catalysts prepared via wet impregnation and gas-phase grafting routes. CW EPR experiments show in both cases the formation of VO2+ vanadyl ions upon reaction with ammonia; moreover, phase memory time filtered echo-detected EPR experiments at X- and Q-band frequencies provide direct experimental evidence for the reduction of the TiO2 substrate and the formation of Ti3+ ions. X-band hyperfine sublevel correlation (HYSCORE) experiments are used to investigate the local environment of VO2+ ions. The direct nitrogen coordination of residual ammonia fragments in the equatorial plane of the vanadyl ion is demonstrated.

Conformationally Unambiguous Spin Label for Exploring the Binding Site Topology of Multivalent Systems.

Multivalent carbohydrate-lectin interactions are a key concept in biological processes mediating, for example, signaling and adhesion. Binding affinities of multivalent ligands often increase by orders of magnitude compared to a monovalent binding situation. Thus, the design of multivalent ligands as potent inhibitors is a highly active field of research, where knowledge about the binding site topology is crucial. Here, we report a general strategy for precise distance measurements between the binding sites of multivalent target proteins using monovalent ligands. We designed and synthesized Monovalent, conformationally Unambiguously Spin-labeled LIgands (MUeSLI). Distances between the binding sites of the multivalent model lectin wheat germ agglutinin in complex with a GlcNAc-derived MUeSLI were determined using pulsed electron paramagnetic resonance spectroscopy. This approach is an efficient method for exploring multivalent systems with monovalent ligands, and it is readily transferable to other target proteins, allowing the targeted design of multivalent ligands without structural information available.

Electronic and Geometric Structures of Paramagnetic Diazadiene Complexes of Lithium and Sodium.

The electronic and molecular structures of the lithium and sodium complexes of 1,4‐bis(2,6‐diisopropylphenyl)‐2,3‐dimethyl‐1,4‐diazabutadiene (Me2DADDipp) were fully characterized by using a multi‐frequency electron paramagnetic resonance (EPR) spectroscopy approach and crystallography, together with density functional theory (DFT) calculations. EPR measurements, using T 1 relaxation‐time‐filtered pulse EPR spectroscopy, revealed the diagonal elements of the A and g tensors for the metal and ligand sites. It was found that the central metals in the lithium complexes had sizable contributions to the SOMO, whereas this contribution was less strongly observed for the sodium complex. Such strong contributions were attributed to structural specifications (e.g. geometrical data and atomic size) rather than electronic effects.

Electronic Structure of Two Catalytic States of the [FeFe] Hydrogenase H-Cluster As Probed by Pulse Electron Paramagnetic Resonance Spectroscopy.

The active site of the [FeFe] hydrogenase (HydA1), the H-cluster, is a 6-Fe cofactor that contains CO and CN- ligands. It undergoes several different oxidation and protonation state changes in its catalytic cycle to metabolize H2. Among them, the well-known Hox state and the recently identified Hhyd state are thought to be directly involved in H2 activation and evolution, and they are both EPR active with net spin S = 1/2. Herein, we report the pulse electronic paramagnetic spectroscopic investigation of these two catalytic states in Chlamydomonas reinhardtii HydA1 ( CrHydA1). Using an in vitro biosynthetic maturation approach, we site-specifically installed 13C into the CO or CN- ligands and 57Fe into the [2Fe]H subcluster of the H-cluster in order to measure the hyperfine couplings to these magnetic nuclei. For Hox, we measured 13C hyperfine couplings (13CO aiso of 25.5, 5.8, and 4.5 MHz) corresponding to all three CO ligands in the H-cluster. We also observed two 57Fe hyperfine couplings (57Fe aiso of ∼17 and 5.7 MHz) arising from the two Fe atoms in the [2Fe]H subcluster. For Hhyd, we only observed two distinct 13CO hyperfine interactions (13CO aiso of 0.16 and 0.08 MHz) and only one for 13CN- (13CN aiso of 0.16 MHz); the couplings to the 13CO/13CN- on the distal Fe of [2Fe]H may be too small to detect. We also observed a very small (<0.3 MHz) 57Fe HFI from the labeled [2Fe]H subcluster and four 57Fe HFI from the labeled [4Fe-4S]H subcluster (57Fe aiso of 7.2, 16.6, 28.2, and 35.3 MHz). These hyperfine coupling constants are consistent with the previously proposed electronic structure of the H-cluster at both Hox and Hhyd states and provide a basis for more detailed analysis.

Probing the coordination and function of Fe4S4 modules in nitrogenase assembly protein NifB

NifB is an essential radical S-adenosylmethionine (SAM) enzyme for nitrogenase cofactor assembly. Previous studies show that NifB couples a putative pair of [Fe4S4] modules (designated K1 and K2) into an [Fe8S9C] cofactor precursor concomitant with radical SAM-dependent carbide insertion through the action of its SAM-binding [Fe4S4] module. However, the coordination and function of the NifB cluster modules remain unknown. Here, we use continuous wave and pulse electron paramagnetic resonance spectroscopy to show that K1- and K2-modules are 3-cysteine-coordinated [Fe4S4] clusters, with a histidine-derived nitrogen serving as the fourth ligand to K1 that is lost upon K1/K2-coupling. Further, we demonstrate that coexistence of SAM/K2-modules is a prerequisite for methyltransfer to K2 and hydrogen abstraction from the K2-associated methyl by a 5′-deoxyadenosyl radical. These results establish an important framework for mechanistic explorations of NifB while highlighting the utility of a synthetic-cluster-based reconstitution approach employed herein in functional analyses of iron–sulfur (FeS) enzymes.

Measurements for Addition Reaction Rate Constants of Organic Free Radicals to Maleic Anhydride by Means of Pulsed EPR Spectroscopy with Laser Excitation

Addition reaction of photo-generated organic radicals to maleic anhydride (MA), that is a common monomer in polymerization, was studied by time-resolved (TR)- and pulsed electron paramagnetic resonance (EPR) spectroscopic methods. The radicals examined are 2-hydroxypropyl (2Hy-Pr), diphenylphosphine oxide (DPPO) and hydroxycyclohexyl (Hy-CyH). Analysis of TR-EPR spectra gave the structures of adduct radicals. The addition rate constants of the radicals generated by the photolysis of initiators were measured by electron spin echo detection method. It was found that the addition reaction rate constants of 2Hy-Pr, DPPO and Hy-CyH radicals to MA show exceptionally smaller values than those estimated by the theoretical reaction model based on enthalpy and polar effects.

A Radical Intermediate in Bacillus subtilis QueE during Turnover with the Substrate Analogue 6-Carboxypterin.

7-Carboxy-7-deazaguanine (CDG) synthase (QueE), a member of the radical S-deoxyadenosyl-l-methionine (SAM) superfamily of enzymes, catalyzes a radical-mediated ring rearrangement required to convert 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) into CDG, forming the 7-dezapurine precursor to all pyrrolopyrimidine metabolites. Members of the radical SAM superfamily bind SAM to a [4Fe-4S] cluster, leveraging the reductive cleavage of SAM by the cluster to produce a highly reactive 5'-deoxyadenosyl radical which initiates chemistry by H atom abstraction from the substrate. QueE has recently been shown to use 6-carboxypterin (6-CP) as an alternative substrate, forming 6-deoxyadenosylpterin as the product. This reaction has been proposed to occur by radical addition between 5'-dAdo· and 6-CP, which upon oxidative decarboxylation yields the modified pterin. Here, we present spectroscopic evidence for a 6-CP-dAdo radical. The structure of this intermediate is determined by characterizing its electronic structure by continuous wave and pulse electron paramagnetic resonance spectroscopy.

Probing Conformational States of the Finger and Thumb Subdomains of HIV-1 Reverse Transcriptase Using Double Electron-Electron Resonance Electron Paramagnetic Resonance Spectroscopy.

The configurational space sampled by the finger and thumb subdomains of the p66 subunit of HIV-1 reverse transcriptase was investigated by Q-band double electron-electron resonance pulsed electron paramagnetic resonance spectroscopy, a method for determining long-range distances between pairs of nitroxide spin-labels introduced via surface-engineered cysteine residues. Four constructs were examined, each containing two spin-labels in the p66 subunit, one in the finger subdomain and the other in the thumb subdomain. In the unliganded state, open and closed configurations for the finger and thumb subdomains are observed with the distribution between these states modulated by the spin-labels and associated mutations, in contrast to crystallographic data in which the unliganded state crystallizes in the closed conformation. Upon addition of double-stranded DNA, all constructs adopt open conformations consistent with previous crystallographic data in which the position of the thumb and finger subdomains is determined by contacts with the bound oligonucleotide duplex (DNA or DNA/RNA). Likewise, binary complexes with five different non-nucleoside reverse transcriptase inhibitors are in open or partially open conformations, indicating that binding of the inhibitor to the palm subdomain indirectly restricts the conformational space sampled by the finger and thumb subdomains.

Heavy-atom effect on optically excited triplet state kinetics

In several fields of research, like e.g. photosensitization, photovoltaics, organic electroluminescent devices, dynamic nuclear polarization, or pulsed dipolar electron paramagnetic resonance spectroscopy, triplet state kinetics play an important role. It is therefore desirable to tailor the kinetics of photoexcited triplet states, e.g. by exploiting the intramolecular heavy-atom effect, and to determine the respective kinetic parameters. In this work, we set out to systematically investigate the photoexcited triplet state kinetics of a series of haloanthracenes by time-resolved electron paramagnetic resonance spectroscopy in combination with synchronized laser excitation. For this purpose, a procedure to simulate time traces by solving the differential equation system governing the triplet kinetics numerically is developed. This way, spin lattice relaxation rates and zero-field triplet life times are obtained concurrently by a global fit to experimental data measured at three different cryogenic temperatures.

Uniform Field Re-entrant Cylindrical TE_{01text {U}} Cavity for Pulse Electron Paramagnetic Resonance Spectroscopy at Q-band

Uniform field (UF) resonators create a region-of-interest, where the sample volume receives a homogeneous microwave magnetic field (B_1) excitation. However, as the region-of-interest is increased, resonator efficiency is reduced. In this work, a new class of uniform field resonators is introduced: the uniform field re-entrant cylindrical TE_{text {01U}} cavity. Here, a UF cylindrical TE_{text {01U}} cavity is designed with re-entrant fins to increase the overall resonator efficiency to match the resonator efficiency maximum of a typical cylindrical TE_{011} cavity. The new UF re-entrant cylindrical TE_{text {01U}} cavity is designed for Q-band (34 GHz) and is calculated to have the same electron paramagnetic resonance (EPR) signal intensity as a TE_{011} cavity, a 60% increase in average resonator efficiency Lambda _mathrm{ave} over the sample, and has a B_1 profile that is 79.8% uniform over the entire sample volume (98% uniform over the region-of-interest). A new H-type T-junction waveguide coupler with inductive obstacles is introduced that increases the dynamic range of a movable short coupler while reducing the frequency shift by 43% during over-coupling. The resonator assembly is fabricated and tested both on the bench and with EPR experiments. This resonator provides a template to improve EPR spectroscopy for pulse experiments at high frequencies.

Monitoring Complex Formation by Relaxation-Induced Pulse Electron Paramagnetic Resonance Distance Measurements.

Biomolecular complexes are often multimers fueling the demand for methods that allow unraveling their composition and geometric arrangement. Pulse electron paramagnetic resonance (EPR) spectroscopy is increasingly applied for retrieving geometric information on the nanometer scale. The emerging RIDME (relaxation‐induced dipolar modulation enhancement) technique offers improved sensitivity in distance experiments involving metal centers (e.g. on metalloproteins or proteins labelled with metal ions). Here, a mixture of a spin labelled ligand with increasing amounts of paramagnetic CuII ions allowed accurate quantification of ligand‐metal binding in the model complex formed. The distance measurement was highly accurate and critical aspects for identifying multimerization could be identified. The potential to quantify binding in addition to the high‐precision distance measurement will further increase the scope of EPR applications.

Probing Nuclear Spin Effects on Electronic Spin Coherence via EPR Measurements of Vanadium(IV) Complexes.

Quantum information processing (QIP) has the potential to transform numerous fields from cryptography, to finance, to the simulation of quantum systems. A promising implementation of QIP employs unpaired electronic spins as qubits, the fundamental units of information. Though molecular electronic spins offer many advantages, including chemical tunability and facile addressability, the development of design principles for the synthesis of complexes that exhibit long qubit superposition lifetimes (also known as coherence times, or T2) remains a challenge. As nuclear spins in the local qubit environment are a primary cause of shortened superposition lifetimes, we recently conducted a study which employed a modular spin-free ligand scaffold to place a spin-laden propyl moiety at a series of fixed distances from an S = 1/2 vanadium(IV) ion in a series of vanadyl complexes. We found that, within a radius of 4.0(4)-6.6(6) Å from the metal center, nuclei did not contribute to decoherence. To assess the generality of this important design principle and test its efficacy in a different coordination geometry, we synthesized and investigated three vanadium tris(dithiolene) complexes with the same ligand set employed in our previous study: K2[V(C5H6S4)3] (1), K2[V(C7H6S6)3] (2), and K2[V(C9H6S8)3] (3). We specifically interrogated solutions of these complexes in DMF-d7/toluene-d8 with pulsed electron paramagnetic resonance spectroscopy and electron nuclear double resonance spectroscopy and found that the distance dependence present in the previously synthesized vanadyl complexes holds true in this series. We further examined the coherence properties of the series in a different solvent, MeCN-d3/toluene-d8, and found that an additional property, the charge density of the complex, also affects decoherence across the series. These results highlight a previously unknown design principle for augmenting T2 and open new pathways for the rational synthesis of complexes with long coherence times.

Studying the Conformation of a Receptor Tyrosine Kinase in Solution by Inhibitor-Based Spin Labeling.

The synthesis of a spin label based on PD168393, a covalent inhibitor of a major anticancer drug target, the epidermal growth factor receptor (EGFR), is reported. The label facilitates the analysis of the EGFR structure in solution by pulsed electron paramagnetic resonance (EPR) spectroscopy. For various EGFR constructs, including near‐full‐length EGFR, we determined defined distance distributions between the two spin labels bound to the ATP binding sites of the EGFR dimer. The distances are in excellent agreement with an asymmetric dimer of the EGFR. Based on crystal structures, this dimer had previously been proposed to reflect the active conformation of the receptor but structural data demonstrating its existence in solution have been lacking. More generally, our study provides proof‐of‐concept that inhibitor‐based spin labeling enables the convenient introduction of site‐specific spin labels into kinases for which covalent or tight‐binding small‐molecule modulators are available.