Effects in 94 GHz Orientation-Selected PELDOR on a Rigid Pair of Radicals with Non-Collinear Axes

For aromatic organic radicals, pulsed electron-electron double resonance (PELDOR) experiments at high magnetic fields provide information not only about the distance between the paramagnetic species but also about their relative orientation. However, the three-dimensional biradical structure is encoded in a complex pattern of orientation-selected PELDOR traces and the execution of the experiment is generally aggravated by constraints posed by the available hardware and the intrinsically low modulation depth observed. We present a 94 GHz PELDOR experiment performed with a commercial spectrometer and probe heads that permit separation of pump and detection frequencies up to 150 MHz. The setup is employed to examine the orientation selections on a general case of rigid biradicals with non-collinear g axes. The interacting radicals, a tyrosyl radical (Y₁₂₂·) located in the β2 subunit and an 3-aminotyrosyl radical (NH₂Y₇₃₁·) located in the α2 subunit, are generated by Escherichia coli ribonucleotide reductase with a 3-aminotyrosine (NH₂Y) site specifically incorporated into α2 in the presence of cytidine 5′-diphosphate and adenosine 5′-triphosphate. The experimental designs as well as some characteristic features of the observed modulation pattern are discussed.     

High-frequency 263 GHz PELDOR

Pulsed electron–electron double resonance (PELDOR/DEER) at high frequencies can provide information on the relative orientation of paramagnetic centres or spin labels, if those are rigidly oriented in a host biomolecule and experiments are performed with sufficient orientation selectivity. We present the first comparative PELDOR study at 263 and 94 GHz on a model RNA system containing rigid nitroxides. We show that at 263 GHz still considerable modulation depth is observed and orientation selectivity is significant, particularly in g _x–g _y plane of the nitroxides.     

Pulsed EPR Analysis of the Photo-Induced Triplet Radical Pair in the BLUF Protein SyPixD: Determination of the Protein–Protein Distance and Orientation in the Oligomeric Protein

A photo-induced radical pair of FADH^· and Y8^· and in BLUF protein SyPixD was studied by pulsed electron paramagnetic resonance (EPR) spectroscopy. Blue light illumination at 150 K for 30 min followed by cooling to 50 K during illumination induced the stable radical pair. The EPR signal has been characterized by a Pake doublet signal with complete S = 1 spin state. The radical pair was utilized as a probe to analyze the oligomer of SyPixD. The relative arrangement of PixD proteins in the complex was investigated by pulsed electron–electron double resonance (PELDOR) with the orientation selection. Based on the decameric structure in the crystal, the possible structure for the PELDOR results was discussed.     

Pulsed electron double resonance (PELDOR) and its applications in free-radicals research

The papers related to the theoretical background and experimental investigations by pulsed electron double resonance (PELDOR) are reviewed. The main aim of this pulsed ESR application is to study the dipole-dipole spin interaction. In PELDOR the ESR spectrum is excited by two ESE pulses at frequencyω _a and additional pumping pulse atω _b. Decay functionV(T) of the ESE signal, when the time intervalT between the first ESE pulse and pumping pulse is varied, contains the information on dipole-dipole couplings in the spin system. The kinetics ofV(T) decay strongly depends upon distance, mutual orientation inside interacting spin pairs and space distribution of radicals throughout the sample. The distances between spins which were measured or estimated using PELDOR in the papers reviewed are in the range of 15 ÷ 130 Å. This pulsed ESR technique turns now to be a powerful supplement to conventional ESE in studying the free radicals space distribution..     

Visualization of distance distribution from pulsed double electron-electron resonance data

Double electron-electron resonance (DEER), also known as pulsed electron-electron double resonance (PELDOR), is a time-domain electron paramagnetic resonance method that can measure the weak dipole-dipole interactions between unpaired electrons. DEER has been applied to discrete pairs of free radicals in biological macromolecules and to clusters containing small numbers of free radicals in polymers and irradiated materials. The goal of such work is to determine the distance or distribution of distances between radicals, which is an underdetermined problem. That is, the spectrum of dipolar interactions can be readily calculated for any distribution of free radicals, but there are many, quite different distributions of radicals that could produce the same experimental dipolar spectrum. This paper describes two methods that are useful for approximating the distance distributions for the large subset of cases in which the mutual orientations of the free radicals are uncorrelated and the width of the distribution is more than a few percent of its mean. The first method relies on a coordinate transformation and is parameter-free, while the second is based on iterative least-squares with Tikhonov regularization. Both methods are useful in DEER studies of spin-labeled biomolecules containing more than two labels.     

A short note on orientation selection in the DEER experiments on a native cofactor and a spin label in the reaction center ofRhodobacter sphaeroides

The analysis of the two-frequency pulsed electron paramagnetic resonance (EPR) (double electron-electron spin resonance, DEER) investigation on the coupling between the semiquinone anion state of the primary acceptor (Q_A) and the spin label at the cysteine 156 in the H-subunit in the photosynthetic reaction center (RC) fromRhodobacter sphaerodes (R26) (I. V. Borovykh, S. Ceola, P. Gajula, P. Gast, H. J. Steinhoff, M. Huber: J. Magn. Reson. 180, 178–185, 2006) is reinvestigated to include orientation selection. The combination of the EPR properties of the two radicals and the pump and observer frequencies suggests that such an effect could play a role even at the X-band (9 GHz) EPR fields and frequencies employed. The magnitude of the effect is estimated from the structures obtained from the molecular-dynamics (MD) simulations from the previous study: the distance change is small (around 2%) and the distance of 3.05 nm obtained then is possibly underestimated by 0.06 nm. Thus, the difference of at least 0.2 nm between the measured distance and the average distance of 2.8 nm found by the MD simulation remains, suggesting a significant difference between the measurement and the X-ray structure of the RC, as discussed previously.     

Submicrosecond field-jump device for pulsed high-field ELDOR

A field-jump device for fast stepping the electron paramagnetic resonance magnetic field around 3.4 T during pulsed electron-electron double resonance experiments at W-band (95 GHz) is described. Field jumps up to ±160 G and submicrosecond times for the full field-jump cycle allow precession frequency transfer experiments to be made for the determination of the nanometer distance and the orientation of nitroxide spin-label pairs in disordered samples.     

Nonselective excitation of pulsed ELDOR using multi-frequency microwaves

The use of a polychromatic microwave pulse to expand the pumping bandwidth in pulsed electron-electron double resonance (PELDOR) was investigated. The pumping pulse was applied in resonance with the broad (～100 mT) electron paramagnetic resonance (EPR) signal of the manganese cluster of photosystem II in the S2 state. The observation pulses were in resonance with the narrow EPR signal of the tyrosine radical, YD·. It was found that in the case of the polychromatic pumping pulse containing five harmonics with the microwave frequencies between 8.5 and 10.5 GHz the PELDOR effect corresponding to the dipole interaction between the Mn cluster and YD· was about 2.9 times larger than that achieved with a monochromatic pulse. In addition to the dipolar modulation, the nuclear modulation effects were observed. The effects could be suppressed by averaging the PELDOR trace over the time interval between the observation microwave pulses. The polychromatic excitation technique described will be useful for improving the PELDOR sensitivity in the measurements of long distances in biological samples, where the pair consists of a radical with a narrow EPR spectrum and slow phase relaxation, and a metal center that has a broad EPR spectrum and a short phase relaxation time.     

Photo-Induced Electron Spin Polarization in Chemical and Biological Reactions: Probing Structure and Dynamics of Transient Intermediates by Multifrequency EPR Spectroscopy

In this minireview, modern multifrequency electron paramagnetic resonance (EPR) spectroscopy, in particular, at high magnetic fields, is shown to provide detailed information about structure, motional dynamics and spin chemistry of transient radicals and radical pairs occurring in photochemical reactions. Examples discussed comprise spin-polarized radicals and radical pairs in disordered systems, such as ultraviolet-irradiated quinone and ketone compounds in fluid alcohol solutions, green-light initiated electron transfer in biomimetic porphyrin?Cquinone donor?Cacceptor model systems in frozen solution, aiming at artificial photosynthesis, and red-light initiated electron transfer in natural photosynthetic reaction-center protein complexes. The transient paramagnetic states exhibit characteristic electron polarization (CIDEP) effects originating from a triplet mechanism, a radical-pair mechanism or a correlated coupled radical-pair mechanism. They contain valuable information about structure and dynamics of the short-lived reaction intermediates. Moreover, the CIDEP effects can be exploited for signal enhancement. Continuous-wave and pulsed versions of time-resolved high-field EPR spectroscopy, such as transient EPR and electron spin-echo experiments, are compared with respect to their advantages and limitations for the specific photoreaction under study. Furthermore, orientation resolving W-band pulsed electron-electron double resonance (PELDOR) experiments on the spin-correlated coupled radical pair $ {\text{P}}_{865}^{ \cdot + } $ $ {\text{Q}}_{\text{A}}^{ \cdot - } $ in frozen solution reaction centers from the purple photosynthetic bacterium Rb. sphaeroides reveal details of distance and orientation of the pair partners in their charge-separated transient state. The results are compared with those of the ground-state P₈₆₅Q_A. In conjunction with Q-band proton electron-nuclear double resonance (ENDOR) experiments the W-band PELDOR results provide decisive evidence that the local structure of the Q_A binding site does not change under photoreduction of the quinone??in agreement with earlier FTIR studies. The examples given demonstrate that multifrequency EPR experiments on disordered systems add heavily to the capabilities of ??classical?? spectroscopic and diffraction techniques for determining structure?Cdynamics?Cfunction relations of biochemical processes, since short-lived intermediates can be observed in real time while staying in their working states at biologically relevant time scales.     

High-field EPR, ENDOR and ELDOR on bacterial photosynthetic reaction centers

We report on recent 95 and 360 GHz high-field electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR) and pulsed electron-electron double resonance (PELDOR) studies of wild-type and mutant reaction centers (RCs) from the photosynthetic bacteriumRhodobacter sphaeroides. Taking advantage of the excellent spectral and temporal resolution of EPR at 95 and 360 GHz, the electron-transfer (ET) cofactors radical ions and spin-correlated radical pairs were characterized by theirg- and hyperfine-tensor components, their anisotropicT ₂ relaxation as well as by the dipolar interaction between P ₈₆₅ ^?+ Q _A ^?? radical pairs. The goal of these studies is to better understand the dominant factors determining the specificity and directionality of transmembrane ET processes in photosynthetic RC proteins. In particular, our multifrequency experiments elucidate the subtle cofactor-protein interactions, which are essential for fine-tuning the ET characteristics, e.g., the unidirectionality of the light-induced ET pathways along the A branch of the RC protein. By our high-field techniques, frozen-solution RCs of novel site-specific single and double mutants ofR. sphaeroides were studied to modulate the ET characteristics, e.g., even to the extent that dominant B branch ET prevails. The presented multifrequency EPR work culminates in first 360 GHz ENDOR results from organic nitroxide radicals as well as in first 95 GHz high-field PELDOR results from orientationally selected spin-polarized radical pairs P ₈₆₅ ^?+ Q _A ^?? , which allow to determine the full geometrical structure of the pairs even in frozen-solution RCs.     

Orientation Selective 2D-SIFTER Experiments at X-Band Frequencies

Frequency-correlated 2D SIFTER with broadband pulses at X-band frequencies can be used to determine the inter-spin distance and relative orientation of nitroxide moieties in macromolecules when the flexibility of the spin-labels is restricted. At X-band frequencies the EPR spectrum of nitroxides is governed by the strongly anisotropic nitrogen hyperfine coupling. For rigid spin-labels, where the orientation of the inter-connecting vector R correlates to the relative orientations of the nitroxide labels, the dipolar oscillation frequency varies over the EPR spectral line shape. Broadband shaped pulses allow excitation of the complete nitroxide EPR spectra. In this case, Fourier transform of the echo signal gives both fast and direct access to the orientation dependent dipole coupling. This allows determination of not only the inter-spin distance R, but also their mutual orientation. Here, we show the application of the frequency-correlated 2D SIFTER experiment with broadband pulses to a bis-nitroxide model compound and to a double stranded DNA sample. In both molecules, there is restricted internal mobility of the two spin-labels. The experimental results are compared to orientation selective pulsed electron double resonance (PELDOR) experiments and simulations based on a simple geometrical model or MD simulations describing the conformational flexibility of the molecules. Fourier transformation of the SIFTER echo signal yields orientation selective dipolar time traces over the complete EPR-spectral range. This leads to an improved frequency resolution and either to a reduced experimental measurement time or a larger span of frequency offsets measured compared to orientation selective PELDOR experiments. The experimental potential and limitations of the 2D SIFTER method for samples containing rigid spin-labels will be discussed.     

Three-Pulse ELDOR Theory Revisited

The current theory of three-pulse electron double resonance (PELDOR) has been generalized to the case, when paramagnetic particles (spin labels) in pairs or groups have the electron paramagnetic resonance (EPR) spectra, which overlap essentially or coincide. The PELDOR signal modulation induced by the dipole–dipole interaction between paramagnetic spin ½ particles in pairs embedded in disordered systems has been analyzed comprehensively. It has been shown that the PELDOR signal contains additional terms in contrast to the situation considered in the current theory, when the EPR spectra of the spin labels in the pairs do not overlap. In disordered systems, the pairs of spin labels have the characteristic dipolar interaction frequency. According to the current theory for pairs of spin labels, the PELDOR signal reveals the modulation with this characteristic frequency. The additional terms, which are obtained in this work, do not change the modulation frequency of the PELDOR signal for pairs of spin labels. However, these additional terms should be taken into account when analyzing the amplitude of the PELDOR signal and the amplitude of the modulation of the PELDOR signal. The consistent approach to treating the PELDOR data for the groups containing three or more spin labels has been outlined on the basis of the results for pairs of spin labels. It has been also analyzed how the spin flips and molecular motion or molecular isomerization can affect the manifestation of the interaction between the spin labels in PELDOR experiments. PELDOR experiments for the stable biradicals (biradicals I containing 1-oxyl-2,2,5,5-tetramethylpyrroline-3-yl spin labels and biradicals II containing 3-imidazoline spin labels) have been performed. The results have been interpreted within the theory developed in this work.     

PELDOR at S- and X-band frequencies and the separation of exchange coupling from dipolar coupling

A pulsed electron double resonance (PELDOR) setup working at S-band frequencies is introduced and its performance compared with an X-band setup. Furthermore, to verify experimentally that it is possible to disentangle the dipolar coupling nu(Dip) from the exchange coupling J by PELDOR we synthesized and investigated four bisnitroxide radicals. They exhibit in pairs the same distances r(AB) between the nitroxide moieties but only one of each pair possesses a non-zero J. The experimental values for r(AB) match the ones from molecular modeling very well for the molecules without exchange coupling. For one bisnitroxide it was possible to separate nu(Dip) from J and to ascertain the magnitude and sign of J to +11 MHz (antiferromagnetic spin-spin coupling).     

Multifrequency (X-band to W-band) CW EPR of the organic free radical in petroleum asphaltene

Petroleum of Arabian and Colombian origin was studied by electron paramagnetic resonance (EPR) spectroscopy at X- (9 GHz), Q- (34 GHz) and W-bands (94 GHz). The experiments were performed at room temperature (about 300 K) and at 77 K (W-band only). The asymmetry in the lines corresponding to free radicals was observed more intensely in the W-band spectra. The values of the line width ΔH in the spectra increased linearly with the microwave frequency utilized in the EPR experiments. A mathematical simulation of the free radical signal for the EPR spectra in three bands with a set of parameters corresponding to a single species was attempted, but this was not exactly coincident with the experimental signals, suggesting that the hyperfine interaction of the unpaired electron with its neighborhood corresponds to more than one species of radical in the molecular structure of the petroleum asphaltene.     

Effect of Pumping Pulse Duration on Echo Signal Amplitude in Four-Pulse PELDOR

The impact of pumping pulse duration on four-pulse pulsed electron?Celectron double resonance (PELDOR) data was experimentally studied. For biradicals with known distances between two spin labels, it is shown that refocused echo amplitude decreases with increasing the pumping pulse duration and decreasing the distance between spin labels. The effect becomes substantial when the pumping pulse duration is comparable or exceeds the inverse value of the dipole?Cdipole interaction between spin labels. This effect is essential for determination of distance distribution between labels in double-labeled molecules and for determination of the number of labels in clusters of spin-labeled molecules. PELDOR signal distortion was observed when the pumping pulse position in the time scale coincided with those of the detecting pulses. An approach of signal correction to eliminate this distortion is proposed.     

Conformational Properties of the Spin-Labeled Tylopeptin B and Heptaibin Peptaibiotics Based on PELDOR Spectroscopy Data

X-Band pulsed electron–electron double resonance (PELDOR) spectroscopy was used to investigate for the first time the magnetic dipole–dipole interaction between spin labels for frozen glassy methanol solutions at 77 K of double spin-labeled, medium-length peptaibiotics, namely, tylopeptin B and heptaibin. This study was conducted on tylopeptin labeled at positions 3 and 13 (T313) and heptaibin labeled at positions 2 and 14 (H214). PELDOR data analysis was carried out using the theory developed for short inter-spin distances. The distance distribution functions between spin labels for T313 (maximum at 1.76 nm, half-width of 0.07 nm) and H214 (maximum at 2.30 nm, half-width of 0.065 nm) were determined. It is found that the distance distribution function for peptide T313 has the Gaussian shape. The main part of the distance spectrum for H214 has Gaussian shape and additional less intensive broad lines are shifted to high distances range 2.5–3.5 nm. The upper limit of distance spectrum in this case corresponds approximately to the length of extended peptide molecule and the number of such configurations is low. Intramolecular distances between the labels at maxima observed allowed us to assign α-helical conformation to T313 and 3₁₀-helical structure to H214 in methanol solution.     

Low-Field, Time-Resolved Dynamic Nuclear Polarization with Field Cycling and High-Resolution NMR Detection

Dynamic nuclear polarization (DNP) effects in aqueous solutions of stable 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPOL) radicals were studied in a pulsed mode of pumping the electron paramagnetic resonance (EPR) transitions. Our fast field cycling setup allowed us to perform the EPR pumping at low magnetic fields and to detect the enhanced nuclear magnetic resonance signals at 7 T with high spectral resolution. Pumping was performed at two different frequencies, 300 MHz and 1.4 GHz, corresponding to magnetic fields around 10 and 48.6 mT, respectively. For both frequencies, the DNP enhancements were close to the limiting theoretical values of ?110 (¹⁴N TEMPOL) and ?165 (¹⁵N TEMPOL). Our pulsed experiments exploit coherent motion of the electronic spins in the radio-frequency field as seen by an oscillatory component in the dependence of the DNP effect on the radio-frequency pulse duration. The DNP enhancement was studied in detail as a function of the pulse length, duty cycle, delay between the pulses, and applied power. The analysis of the results shows that pulsed DNP experiments provide an opportunity to achieve enhancements of about ?110 with relatively low applied power as compared to the standard continuous-wave DNP experiments. An adequate theoretical approach to the problem under study is suggested.