Dephasing of electron spin echoes for nitroxyl radicals in glassy solvents by non-methyl and methyl protons

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.

Perspectives of shaped pulses for EPR spectroscopy

This article describes current uses of shaped pulses, generated by an arbitrary waveform generator, in the field of EPR spectroscopy. We show applications of sech/tanh and WURST pulses to dipolar spectroscopy, including new pulse schemes and procedures, and discuss the more general concept of optimum-control-based pulses for applications in EPR spectroscopy. The article also describes a procedure to correct for experimental imperfections, mostly introduced by the microwave resonator, and discusses further potential applications and limitations of such pulses.

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.

Tuning the spin coherence time of Cu(II)-(bis)oxamato and Cu(II)-(bis)oxamidato complexes by advanced ESR pulse protocols

We have investigated with the pulsed ESR technique at X- and Q-band frequencies the coherence and relaxation of Cu spins S = 1/2 in single crystals of diamagnetically diluted mononuclear [n-Bu4N]2[Cu(opba)] (1%) in the host lattice of [n-Bu4N]2[Ni(opba)] (99%, opba = o-phenylenebis(oxamato)) and of diamagnetically diluted mononuclear [n-Bu4N]2[Cu(opbon-Pr2)] (1%) in the host lattice of [n-Bu4N]2[Ni(opbon-Pr2)] (99%, opbon-Pr2 = o-phenylenebis(N(propyl)oxamidato)). For that we have measured the electron spin dephasing time Tm at different temperatures with the two-pulse primary echo and with the special Carr-Purcell-Meiboom-Gill (CPMG) multiple microwave pulse sequence. Application of the CPMG protocol has led to a substantial increase of the spin coherence lifetime in both complexes as compared to the primary echo results. It shows the efficiency of the suppression of the electron spin decoherence channel in the studied complexes arising due to spectral diffusion induced by a random modulation of the hyperfine interaction with the nuclear spins. We argue that this method can be used as a test for the relevance of the spectral diffusion for the electron spin decoherence. Our results have revealed a prominent role of the opba4- and opbon-Pr24- ligands for the dephasing of the Cu spins. The presence of additional 14N nuclei and protons in [Cu(opbon-Pr2)]2- as compared to [Cu(opba)]2- yields significantly shorter Tm times. Such a detrimental effect of the opbon-Pr24- ligands has to be considered when discussing a potential application of the Cu(II)-(bis)oxamato and Cu(II)-(bis)oxamidato complexes as building blocks of more complex molecular structures in prototype spintronic devices. Furthermore, in our work we propose an improved CPMG pulse protocol that enables elimination of unwanted echoes that inevitably appear in the case of inhomogeneously broadened ESR spectra due to the selective excitation of electron spins.

Electron spin relaxation of a boron-containing heterocyclic radical

Preparation of the stable boron-containing heterocyclic phenanthrenedione radical, (C₆F₅)₂B(O₂C₁₄H₈), by frustrated Lewis pair chemistry has been reported recently. Electron paramagnetic resonance measurements of this radical were made at X-band in toluene:dichloromethane (9:1) from 10 to 293K, in toluene from 180 to 293K and at Q-band at 80K. In well-deoxygenated 0.1mM toluene solution at room temperature hyperfine splittings from ¹¹B, four pairs of ¹H, and 5 pairs of ¹⁹F contribute to an EPR spectrum with many resolved lines. Observed hyperfine couplings were assigned based on DFT calculations and account for all of the fluorines and protons in the molecule. Rigid lattice g values are g_x=2.0053, g_y=2.0044, and g_z=2.0028. Near the melting point of the solvent 1/T_m is enhanced due to motional averaging of g and A anisotropy. Increasing motion above the melting point enhances 1/T₁ due to contributions from tumbling-dependent processes. The overall temperature dependence of 1/T₁ from 10 to 293K was modeled with the sum of contributions of a process that is linear in T, a Raman process, spin rotation, and modulation of g anisotropy by molecular tumbling. The EPR measurements are consistent with the description of this compound as a substituted aromatic radical, with relatively small spin density on the boron.

Reliable nanometre-range distance distributions from 5-pulse double electron electron resonance

The partial excitation artefact in 5-pulse DEER data can be eliminated by experimental time shifting and signal processing.

Long Coherence Times in Nuclear Spin-Free Vanadyl Qubits

Quantum information processing (QIP) offers the potential to create new frontiers in fields ranging from quantum biology to cryptography. Two key figures of merit for electronic spin qubits, the smallest units of QIP, are the coherence time (T₂), the lifetime of the qubit, and the spin-lattice relaxation time (T₁), the thermally defined upper limit of T₂. To achieve QIP, processable qubits with long coherence times are required. Recent studies on (Ph₄P-d₂₀)₂[V(C₈S₈)₃], a vanadium-based qubit, demonstrate that millisecond T₂ times are achievable in transition metal complexes with nuclear spin-free environments. Applying these principles to vanadyl complexes offers a route to combine the previously established surface compatibility of the flatter vanadyl structures with a long T₂. Toward those ends, we investigated a series of four qubits, (Ph₄P)₂[VO(C₈S₈)₂] (1), (Ph₄P)₂[VO(β-C₃S₅)₂] (2), (Ph₄P)₂[VO(α-C₃S₅)₂] (3), and (Ph₄P)₂[VO(C₃S₄O)₂] (4), by pulsed electron paramagnetic resonance (EPR) spectroscopy and compared the performance of these species with our recently reported set of vanadium tris(dithiolene) complexes. Crucially we demonstrate that solutions of 1-4 in SO₂, a uniquely polar nuclear spin-free solvent, reveal T₂ values of up to 152(6) μs, comparable to the best molecular qubit candidates. Upon transitioning to vanadyl species from the tris(dithiolene) analogues, we observe a remarkable order of magnitude increase in T₁, attributed to stronger solute-solvent interactions with the polar vanadium-oxo moiety. Simultaneously, we detect a small decrease in T₂ for the vanadyl analogues relative to the tris(dithiolene) complexes. We attribute this decrease to the absence of one nuclear spin-free ligand, which served to shield the vanadium centers against solvent nuclear spins. Our results highlight new design principles for long T₁ and T₂ times by demonstrating the efficacy of ligand-based tuning of solute-solvent interactions.

Dynamics of 4-oxo-TEMPO-d16-(15)N nitroxide-propylene glycol system studied by ESR and ESE in liquid and glassy state in temperature range 10-295K

ESR spectra and electron spin relaxation of nitroxide radical in 4-oxo-TEMPO-d16-(15)N in propylene glycol were studied at X-band in the temperature range 10-295K. The spin-lattice relaxation in the liquid viscous state determined from the resonance line shape is governed by three mechanisms occurring during isotropic molecular reorientations. In the glassy state below 200K the spin-lattice relaxation, phase relaxation and electron spin echo envelope modulations (ESEEM) were studied by pulse spin echo technique using 2-pulse and 3-pulse induced signals. Electron spin-lattice relaxation is governed by a single non-phonon relaxation process produced by localized oscillators of energy 76cm(-1). Electron spin dephasing is dominated by a molecular motion producing a resonance-type peak in the temperature dependence of the dephasing rate around 120K. The origin of the peak is discussed and a simple method for the peak shape analysis is proposed, which gives the activation energy of a thermally activated motion Ea=7.8kJ/mol and correlation time τ0=10(-8)s. The spin echo amplitude is strongly modulated and FT spectrum contains a doublet of lines centered around the (2)D nuclei Zeeman frequency. The splitting into the doublet is discussed as due to a weak hyperfine coupling of nitroxide unpaired electron with deuterium of reorienting CD3 groups.

Room-temperature electron spin relaxation of nitroxides immobilized in trehalose: Effect of substituents adjacent to NO-group

Trehalose has been recently promoted as efficient immobilizer of biomolecules for room-temperature EPR studies, including distance measurements between attached nitroxide spin labels. Generally, the structure of nitroxide influences the electron spin relaxation times, being crucial parameters for room-temperature pulse EPR measurements. Therefore, in this work we investigated a series of nitroxides with different substituents adjacent to NO-moiety including spirocyclohexane, spirocyclopentane, tetraethyl and tetramethyl groups. Electron spin relaxation times (T1, Tm) of these radicals immobilized in trehalose were measured at room temperature at X- and Q-bands (9/34GHz). In addition, a comparison was made with the corresponding relaxation times in nitroxide-labeled DNA immobilized in trehalose. In all cases phase memory times Tm were close to 700ns and did not essentially depend on structure of substituents. Comparison of temperature dependences of Tm at T=80-300K shows that the benefit of spirocyclohexane substituents well-known at medium temperatures (∼100-180K) becomes negligible at 300K. Therefore, unless there are specific interactions between spin labels and biomolecules, the room-temperature value of Tm in trehalose is weakly dependent on the structure of substituents adjacent to NO-moiety of nitroxide. The issues of specific interactions and stability of nitroxide labels in biological media might be more important for room temperature pulsed dipolar EPR than differences in intrinsic spin relaxation of radicals.

Tailoring of Polarizing Agents in the bTurea Series for Cross-Effect Dynamic Nuclear Polarization in Aqueous Media

A series of 18 nitroxide biradicals derived from bTurea has been prepared, and their enhancement factors ɛ ((1)H) in cross-effect dynamic nuclear polarization (CE DNP) NMR experiments at 9.4 and 14.1 T and 100 K in a DNP-optimized glycerol/water matrix ("DNP juice") have been studied. We observe that ɛ ((1)H) is strongly correlated with the substituents on the polarizing agents, and its trend is discussed in terms of different molecular parameters: solubility, average e-e distance, relative orientation of the nitroxide moieties, and electron spin relaxation times. We show that too short an e-e distance or too long a T1e can dramatically limit ɛ ((1)H). Our study also shows that the molecular structure of AMUPol is not optimal and its ɛ ((1)H) could be further improved through stronger interaction with the glassy matrix and a better orientation of the TEMPO moieties. A new AMUPol derivative introduced here provides a better ɛ ((1)H) than AMUPol itself (by a factor of ca. 1.2).

Room-temperature distance measurements of immobilized spin-labeled protein by DEER/PELDOR

Nitroxide spin labels are used for double electron-electron resonance (DEER) measurements of distances between sites in biomolecules. Rotation of gem-dimethyls in commonly used nitroxides causes spin echo dephasing times (Tm) to be too short to perform DEER measurements at temperatures between ∼80 and 295 K, even in immobilized samples. A spirocyclohexyl spin label has been prepared that has longer Tm between 80 and 295 K in immobilized samples than conventional labels. Two of the spirocyclohexyl labels were attached to sites on T4 lysozyme introduced by site-directed spin labeling. Interspin distances up to ∼4 nm were measured by DEER at temperatures up to 160 K in water/glycerol glasses. In a glassy trehalose matrix the Tm for the doubly labeled T4 lysozyme was long enough to measure an interspin distance of 3.2 nm at 295 K, which could not be measured for the same protein labeled with the conventional 1-oxyl-2,2,5,5-tetramethyl-3-pyrroline-3-(methyl)methanethio-sulfonate label.

Temperature dependence of cross-effect dynamic nuclear polarization in rotating solids: advantages of elevated temperatures

DNP on proteins at 200 K.

Rational design of dinitroxide biradicals for efficient cross-effect dynamic nuclear polarization

A series of 37 dinitroxide biradicals have been prepared and their performance studied as polarizing agents in cross-effect DNP NMR experiments at 9.4 T and 100 K in 1,1,2,2-tetrachloroethane (TCE). We observe that in this regime the DNP performance is strongly correlated with the substituents on the polarizing agents, and electron and nuclear spin relaxation times, with longer relaxation times leading to better enhancements. We also observe that deuteration of the radicals generally leads to better DNP enhancement but with longer build-up time. One of the new radicals introduced here provides the best performance obtained so far under these conditions.

Gd(III) complexes for electron-electron dipolar spectroscopy: Effects of deuteration, pH and zero field splitting

Spectral parameters of Gd(III) complexes are intimately linked to the performance of the Gd(III)-nitroxide or Gd(III)-Gd(III) double electron-electron resonance (DEER or PELDOR) techniques, as well as to that of relaxation induced dipolar modulation enhancement (RIDME) spectroscopy with Gd(III) ions. These techniques are of interest for applications in structural biology, since they can selectively detect site-to-site distances in biomolecules or biomolecular complexes in the nanometer range. Here we report relaxation properties, echo detected EPR spectra, as well as the magnitude of the echo reduction effect in Gd(III)-nitroxide DEER for a series of Gadolinium(III) complexes with chelating agents derived from tetraazacyclododecane. We observed that solvent deuteration does not only lengthen the relaxation times of Gd(III) centers but also weakens the DEER echo reduction effect. Both of these phenomena lead to an improved signal-to-noise ratios or, alternatively, longer accessible distance range in pulse EPR measurements. The presented data enrich the knowledge on paramagnetic Gd(III) chelate complexes in frozen solutions, and can help optimize the experimental conditions for most types of the pulse measurements of the electron-electron dipolar interactions.

Efficient Dynamic Nuclear Polarization at 800 MHz/527 GHz with Trityl-Nitroxide Biradicals

Cross-effect (CE) dynamic nuclear polarization (DNP) is a rapidly developing technique that enhances the signal intensities in magic-angle spinning (MAS) NMR spectra. We report CE DNP experiments at 211, 600, and 800 MHz using a new series of biradical polarizing agents referred to as TEMTriPols, in which a nitroxide (TEMPO) and a trityl radical are chemically tethered. The TEMTriPol molecule with the optimal performance yields a record (1) H NMR signal enhancement of 65 at 800 MHz at a concentration of 10 mM in a glycerol/water solvent matrix. The CE DNP enhancement for the TEMTriPol biradicals does not decrease as the magnetic field is increased in the manner usually observed for bis-nitroxides. Instead, the relatively strong exchange interaction between the trityl and nitroxide moieties determines the magnetic field at which the optimum enhancement is observed.

Electron spin coherence near room temperature in magnetic quantum dots

We report on an example of confined magnetic ions with long spin coherence near room temperature. This was achieved by confining single Mn²⁺ spins in colloidal semiconductor quantum dots (QDs) and by dispersing the QDs in a proton-spin free matrix. The controlled suppression of Mn–Mn interactions and minimization of Mn–nuclear spin dipolar interactions result in unprecedentedly long phase memory (T_M ~ 8 μs) and spin–lattice relaxation (T₁ ~ 10 ms) time constants for Mn²⁺ ions at T = 4.5 K, and in electron spin coherence observable near room temperature (T_M ~ 1 μs).

Is solid-state NMR enhanced by dynamic nuclear polarization?

The recent trend of high-field (~5-20 T), low-temperature (~100 K) ssNMR combined with dynamic nuclear polarization (DNP) under magic angle spinning (MAS) conditions is analyzed. A brief overview of the current theory of hyperpolarization for so-called MAS-DNP experiments is given, along with various reasons why the DNP-enhancement, the ratio of the NMR signal intensities obtained in the presence and absence of microwave irradiation suitable for hyperpolarization, should not be used alone to gauge the value of performing MAS-DNP experiments relative to conventional ssNMR. This is demonstrated through a dissection of the current conditions required for MAS-DNP with particular attention to resulting absolute sensitivities and spectral resolution. Consequently, sample preparation methods specifically avoiding the surplus of glass-forming solvents so as to improve the absolute sensitivity and resolution are discussed, as are samples that are intrinsically pertinent for MAS-DNP studies (high surface area, amorphous, and porous). Owing to their pertinence, examples of recent applications on these types of samples where chemically-relevant information has been obtained that would have been impossible without the sensitivity increases bestowed by MAS-DNP are also detailed. Additionally, a promising further implementation for MAS-DNP is exampled, whereby the sensitivity improvements shown for (correlation) spectroscopy of nuclei at low natural isotopic abundance, facilitate internuclear distance measurements, especially for long distances (absence of dipolar truncation). Finally, we give some speculative perspectives for MAS-DNP.

An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids

The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements.

The spatial effect of protein deuteration on nitroxide spin-label relaxation: implications for EPR distance measurement

Pulsed electron-electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron paramagnetic resonance enables measurement on small quantities of bio-macromolecules, however short relaxation times impose a limit on the sensitivity and size of distances that can be measured using this technique. The persistence of the electron spin-echo, in the PELDOR experiment, is one of the most crucial limitations to distance measurement. At a temperature of around 50 K one of the predominant factors affecting persistence of an echo, and as such, the sensitivity and measurable distance between spin labels, is the electron spin echo dephasing time (Tm). It has become normal practice to use deuterated solvents to extend Tm and recently it has been demonstrated that deuteration of the underlying protein significantly extends Tm. Here we examine the spatial effect of segmental deuteration of the underlying protein, and also explore the concentration and temperature dependence of highly deuterated systems.

Zero field splitting fluctuations induced phase relaxation of Gd3+ in frozen solutions at cryogenic temperatures

Distance measurements using double electron-electron resonance (DEER) and Gd(3+) chelates for spin labels (GdSL) have been shown to be an attractive alternative to nitroxide spin labels at W-band (95GHz). The maximal distance that can be accessed by DEER measurements and the sensitivity of such measurements strongly depends on the phase relaxation of Gd(3+) chelates in frozen, glassy solutions. In this work, we explore the phase relaxation of Gd(3+)-DOTA as a representative of GdSL in temperature and concentration ranges typically used for W-band DEER measurements. We observed that in addition to the usual mechanisms of phase relaxation known for nitroxide based spin labels, GdSL are subjected to an additional phase relaxation mechanism that features an increase in the relaxation rate from the center to the periphery of the EPR spectrum. Since the EPR spectrum of GdSL is the sum of subspectra of the individual EPR transitions, we attribute this field dependence to transition dependent phase relaxation. Using simulations of the EPR spectra and its decomposition into the individual transition subspectra, we isolated the phase relaxation of each transition and found that its rate increases with |ms|. We suggest that this mechanism is due to transient zero field splitting (tZFS), where its magnitude and correlation time are scaled down and distributed as compared with similar situations in liquids. This tZFS induced phase relaxation mechanism becomes dominant (or at least significant) when all other well-known phase relaxation mechanisms, such as spectral diffusion caused by nuclear spin diffusion, instantaneous and electron spin spectral diffusion, are significantly suppressed by matrix deuteration and low concentration, and when the temperature is sufficiently low to disable spin lattice interaction as a source of phase relaxation.

ESR study of interfacial hydration layers of polypeptides in water-filled nanochannels and in vitrified bulk solvents

There is considerable evidence for the essential role of surface water in protein function and structure. However, it is unclear to what extent the hydration water and protein are coupled and interact with each other. Here, we show by ESR experiments (cw, DEER, ESEEM, and ESE techniques) with spin-labeling and nanoconfinement techniques that the vitrified hydration layers can be evidently recognized in the ESR spectra, providing nanoscale understanding for the biological interfacial water. Two peptides of different secondary structures and lengths are studied in vitrified bulk solvents and in water-filled nanochannels of different pore diameter (6.1∼7.6 nm). The existence of surface hydration and bulk shells are demonstrated. Water in the immediate vicinity of the nitroxide label (within the van der Waals contacts, ∼0.35 nm) at the water-peptide interface is verified to be non-crystalline at 50 K, and the water accessibility changes little with the nanochannel dimension. Nevertheless, this water accessibility for the nanochannel cases is only half the value for the bulk solvent, even though the peptide structures remain largely the same as those immersed in the bulk solvents. On the other hand, the hydration density in the range of ∼2 nm from the nitroxide spin increases substantially with decreasing pore size, as the density for the largest pore size (7.6 nm) is comparable to that for the bulk solvent. The results demonstrate that while the peptides are confined but structurally unaltered in the nanochannels, their surrounding water exhibits density heterogeneity along the peptide surface normal. The causes and implications, especially those involving the interactions between the first hydration water and peptides, of these observations are discussed. Spin-label ESR techniques are proven useful for studying the structure and influences of interfacial hydration.

Improved Sensitivity for Long-Distance Measurements in Biomolecules: Five-Pulse Double Electron-Electron Resonance

We describe significantly improved long-distance measurements in biomolecules by use of the new multipulse double electron-electron spin resonance (DEER) illustrated with the example of a five-pulse DEER sequence. In this sequence, an extra pulse at the pump frequency is used compared with standard four-pulse DEER. The position of the extra pulse is fixed relative to the three pulses of the detection sequence. This significantly reduces the effect of nuclear spin-diffusion on the electron-spin phase relaxation, thereby enabling longer dipolar evolution times that are required to measure longer distances. Using spin-labeled T4 lysozyme at a concentration less than 50 μM, as an example, we show that the evolution time increases by a factor of 1.8 in protonated solution and 1.4 in deuterated solution to 8 and 12 μs, respectively, with the potential to increase them further. This enables a significant increase in the measurable distances, improved distance resolution, or both.

The world as viewed by and with unpaired electrons

Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models.

Distance measurements across randomly distributed nitroxide probes from the temperature dependence of the electron spin phase memory time at 240 GHz

At 8.5 T, the polarization of an ensemble of electron spins is essentially 100% at 2 K, and decreases to 30% at 20 K. The strong temperature dependence of the electron spin polarization between 2 and 20 K leads to the phenomenon of spin bath quenching: temporal fluctuations of the dipolar magnetic fields associated with the energy-conserving spin "flip-flop" process are quenched as the temperature of the spin bath is lowered to the point of nearly complete spin polarization. This work uses pulsed electron paramagnetic resonance (EPR) at 240 GHz to investigate the effects of spin bath quenching on the phase memory times (T(M)) of randomly-distributed ensembles of nitroxide molecules below 20 K at 8.5 T. For a given electron spin concentration, a characteristic, dipolar flip-flop rate (W) is extracted by fitting the temperature dependence of T(M) to a simple model of decoherence driven by the spin flip-flop process. In frozen solutions of 4-Amino-TEMPO, a stable nitroxide radical in a deuterated water-glass, a calibration is used to quantify average spin-spin distances as large as r=6.6 nm from the dipolar flip-flop rate. For longer distances, nuclear spin fluctuations, which are not frozen out, begin to dominate over the electron spin flip-flop processes, placing an effective ceiling on this method for nitroxide molecules. For a bulk solution with a three-dimensional distribution of nitroxide molecules at concentration n, we find W∝n∝1/r(3), which is consistent with magnetic dipolar spin interactions. Alternatively, we observe W∝n(32) for nitroxides tethered to a quasi two-dimensional surface of large (Ø∼200 nm), unilamellar, lipid vesicles, demonstrating that the quantification of spin bath quenching can also be used to discern the geometry of molecular assembly or organization.

Chemical engineering of molecular qubits

We show that the electron spin phase memory time, the most important property of a molecular nanomagnet from the perspective of quantum information processing, can be improved dramatically by chemically engineering the molecular structure to optimize the environment of the spin. We vary systematically each structural component of the class of antiferromagnetic Cr(7)Ni rings to identify the sources of decoherence. The optimal structure exhibits a phase memory time exceeding 15  μs.

A spirocyclohexyl nitroxide amino acid spin label for pulsed EPR spectroscopy distance measurements

Site-directed spin labeling and EPR spectroscopy offer accurate, sensitive tools for the characterization of structure and function of macromolecules and their assemblies. A new rigid spin label, spirocyclohexyl nitroxide alpha-amino acid and its N-(9-fluorenylmethoxycarbonyl) derivative, have been synthesized, which exhibit slow enough spin-echo dephasing to permit accurate distance measurements by pulsed EPR spectroscopy at temperatures up to 125 K in 1:1 water/glycerol and at higher temperatures in matrices with higher glass transition temperatures. Distance measurements in the liquid nitrogen temperature range are less expensive than those that require liquid helium, which will greatly facilitate applications of pulsed EPR spectroscopy to the study of structure and conformation of peptides and proteins.

Pulsed EPR determination of water accessibility to spin-labeled amino acid residues in LHCIIb

Membrane proteins reside in a structured environment in which some of their residues are accessible to water, some are in contact with alkyl chains of lipid molecules, and some are buried in the protein. Water accessibility of residues may change during folding or function-related structural dynamics. Several techniques based on the combination of pulsed electron paramagnetic resonance (EPR) with site-directed spin labeling can be used to quantify such water accessibility. Accessibility parameters for different residues in major plant light-harvesting complex IIb are determined by electron spin echo envelope modulation spectroscopy in the presence of deuterated water, deuterium contrast in transversal relaxation rates, analysis of longitudinal relaxation rates, and line shape analysis of electron-spin-echo-detected EPR spectra as well as by the conventional techniques of measuring the maximum hyperfine splitting and progressive saturation in continuous-wave EPR. Systematic comparison of these parameters allows for a more detailed characterization of the environment of the spin-labeled residues. These techniques are applicable independently of protein size and require approximately 10-20 nmol of singly spin-labeled protein per sample. For a residue close to the N-terminus, in a domain unresolved in the existing x-ray structures of light-harvesting complex IIb, all methods indicate high water accessibility.

Relaxation rates for spirocyclohexyl nitroxyl radicals are suitable for interspin distance measurements at temperatures up to about 125 K

Between 65 and 175 K, nitroxyl radicals with spirocyclohexyl groups at the 2- and 6-positions of the piperidine ring exhibit spin echo dephasing rates that are slower than for nitroxyl radicals with 2,5-gem-dimethyl or 2,6-gem-dimethyl substituents that are currently used as spin labels, and are slow enough to permit DEER measurements at temperatures up to about 125 K for spin labels with analogous ring structures.

Electron-electron distances in spin-labeled low-spin metmyoglobin variants by relaxation enhancement

Thirteen single-cysteine variants of myoglobin were prepared by overexpression of apoprotein, spin labeling, and reconstitution with hemin. This procedure resulted in a protein with fewer hemichrome impurities than was obtained by an overexpression of holo-protein followed by spin labeling. Coordination of cyanide to the met heme formed low-spin complexes. Iron-nitroxyl interspin distances in the range of 17-30 A were determined by saturation recovery measurements of the enhancement of the nitroxyl spin lattice relaxation rates between approximately 30-140 K, and by spin-echo measurements of the enhancement of spin-spin relaxation rates at 10-30 K. Interspin distances were also calculated, using the molecular modeling program Insight II (Accelrys, San Diego, CA). For most variants, distances determined from the temperature dependence of spin-echo intensities at a pulse spacing of 200 ns agree with distances measured by saturation recovery and calculated with Insight II within about an angstrom, which is within experimental uncertainties. Measurements of interspin distances via spin-spin relaxation enhancement have the advantages that maximum effects are observed for slower metal relaxation rates than are required for spin-lattice relaxation enhancement, and the impact diminishes as r(-3) instead of r(-6), as with spin-lattice relaxation enhancement, which permits measurements at longer distances.

Impact of electron-electron spin interaction on electron spin relaxation of nitroxide diradicals and tetraradical in glassy solvents between 10 and 300 k

To determine the impact of electron-electron spin-spin interactions on electron spin relaxation rates, 1/T1 and 1/Tm were measured for nitroxide monoradical, diradical, and tetraradical derivatives of 1,3-alternate calix[4]arenes, for two pegylated high-spin nitroxide diradicals, and for an azine-linked nitroxide diradical. The synthesis and characterization by SQUID (superconducting quantum interference device) magnetometry of one of the high-spin diradicals, in which nitroxides are conformationally constrained to be coplanar with the m-phenylene unit, is reported. The interspin distances ranged from about 5-9 A, and the magnitude of the exchange interaction ranged from >150 to >0.1 K. 1/T1 and 1/Tm were measured by long-pulse saturation recovery, three-pulse inversion recovery, and two-pulse echo decay at X-band (9.5 GHz) and Q-band (35 GHz). For a diradical with interspin distance about 9 A, relaxation rates were only slightly faster than for a monoradical with analogous structure. For interspin distances of about 5-6 A, relaxation rates in glassy solvents up to 300 K increased in the order monoradical < diradical < tetraradical. Modulation of electron-electron interaction enhanced relaxation via the direct, Raman, and local mode processes. The largest differences in 1/T1 were observed below 10 K, where the direct process dominates. For the three diradicals with comparable magnitude of dipolar interaction, 1/Tm and 1/T1 were faster for the molecules with more flexible structures. Relaxation rates were faster in the less rigid low-polarity sucrose octaacetate glass than in the more rigid 4:1 toluene/chloroform or in hydrogen-bonded glycerol glasses, which highlights the impact of motion on relaxation.

Electron spin relaxation enhancement measurements of interspin distances in human, porcine, and Rhodobacter electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO)

Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a membrane-bound electron transfer protein that links primary flavoprotein dehydrogenases with the main respiratory chain. Human, porcine, and Rhodobacter sphaeroides ETF-QO each contain a single [4Fe-4S](2+,1+) cluster and one equivalent of FAD, which are diamagnetic in the isolated enzyme and become paramagnetic on reduction with the enzymatic electron donor or with dithionite. The anionic flavin semiquinone can be reduced further to diamagnetic hydroquinone. The redox potentials for the three redox couples are so similar that it is not possible to poise the proteins in a state where both the [4Fe-4S](+) cluster and the flavoquinone are fully in the paramagnetic form. Inversion recovery was used to measure the electron spin-lattice relaxation rates for the [4Fe-4S](+) between 8 and 18K and for semiquinone between 25 and 65K. At higher temperatures the spin-lattice relaxation rates for the [4Fe-4S](+) were calculated from the temperature-dependent contributions to the continuous wave linewidths. Although mixtures of the redox states are present, it was possible to analyze the enhancement of the electron spin relaxation of the FAD semiquinone signal due to dipolar interaction with the more rapidly relaxing [4Fe-4S](+) and obtain point-dipole interspin distances of 18.6+/-1A for the three proteins. The point-dipole distances are within experimental uncertainty of the value calculated based on the crystal structure of porcine ETF-QO when spin delocalization is taken into account. The results demonstrate that electron spin relaxation enhancement can be used to measure distances in redox poised proteins even when several redox states are present.

Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe

This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron-electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes.

Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance

The biological function of protein, DNA, and RNA molecules often depends on relative movements of domains with dimensions of a few nanometers. This length scale can be accessed by distance measurements between spin labels if pulsed electron paramagnetic resonance (EPR) techniques such as electron-electron double resonance (ELDOR) and double-quantum EPR are used. The approach does not require crystalline samples and is well suited to biomacromolecules with an intrinsic flexibility as distributions of distances can be measured. Furthermore, oligomerization or complexation of biomacromolecules can also be studied, even if it is incomplete. The sensitivity of the technique and the reliability of the measured distance distribution depend on careful optimization of the experimental conditions and procedures for data analysis. Interpretation of spin-to-spin distance distributions in terms of the structure of the biomacromolecules furthermore requires a model for the conformational distribution of the spin labels.

Measuring distances by pulsed dipolar ESR spectroscopy: spin-labeled histidine kinases

Applications of dipolar ESR spectroscopy to structural biology are rapidly expanding, and it has become a useful method that is aimed at resolving protein structure and functional mechanisms. The method of pulsed dipolar ESR spectroscopy (PDS) is outlined in the first half of the chapter, and it illustrates the simplicity and potential of this developing technology with applications to various biological systems. A more detailed description is presented of the implementation of PDS to reconstruct the ternary structure of a large dimeric protein complex from Thermotoga maritima, formed by the histidine kinase CheA and the coupling protein CheW. This protein complex is a building block of an extensive array composed of coupled supramolecular structures assembled from CheA/CheW proteins and transmembrane signaling chemoreceptors, which make up a sensor that is key to controlling the motility in bacterial chemotaxis. The reconstruction of the CheA/CheW complex has employed several techniques, including X-ray crystallography and pulsed ESR. Emphasis is on the role of PDS, which is part of a larger effort to reconstruct the entire signaling complex, including chemoreceptor, by means of PDS structural mapping. In order to precisely establish the mode of coupling of CheW to CheA and to globally map the complex, approximately 70 distances have already been determined and processed into molecular coordinates by readily available methods of distance geometry constraints.

Electron spin relaxation of copper(II) complexes in glassy solution between 10 and 120 K

The temperature dependence, between 10 and 120 K, of electron spin-lattice relaxation at X-band was analyzed for a series of eight pyrrolate-imine complexes and for ten other copper(II) complexes with varying ligands and geometry including copper-containing prion octarepeat domain and S100 type proteins. The geometry of the CuN4 coordination sphere for pyrrolate-imine complexes with R=H, methyl, n-butyl, diphenylmethyl, benzyl, 2-adamantyl, 1-adamantyl, and tert-butyl has been shown to range from planar to pseudo-tetrahedral. The fit to the recovery curves was better for a distribution of values of T1 than for a single time constant. Distributions of relaxation times may be characteristic of Cu(II) in glassy solution. Long-pulse saturation recovery and inversion recovery measurements were performed. The temperature dependence of spin-lattice relaxation rates was analyzed in terms of contributions from the direct process, the Raman process, and local modes. It was necessary to include more than one process to fit the experimental data. There was a small contribution from the direct process at low temperature. The Raman process was the dominant contribution to relaxation between about 20 and 60 K. Debye temperatures were between 80 and 120 K. For samples with similar Debye temperatures the coefficient of the Raman process tended to increase as gz increased, as expected if modulation of spin-orbit coupling is a major factor in relaxation rates. Above about 60 K local modes with energies in the range of 260-360 K (180-250 cm-1) dominated the relaxation. For molecules with similar geometry, relaxation rates were faster for more flexible molecules than for more rigid ones. Relaxation rates for the copper protein samples were similar to rates for small molecules with comparable coordination spheres. At each temperature studied the range of relaxation rates was less than an order of magnitude. The spread was smaller between 20 and 60 K where the Raman process dominates, than at higher temperatures where local modes dominate the relaxation. Spin echo dephasing time constants, Tm, were calculated from two-pulse spin echo decays. Near 10 K Tm was dominated by proton spins in the surroundings. As temperature was increased motion and spin-lattice relaxation made increasing contributions to Tm. Near 100 K spin-lattice relaxation dominated Tm.

Molecular dynamics of nitroxides in glasses as studied by multi-frequency EPR

Pulsed multi-frequency EPR was used to investigate orientational molecular motion of the nitroxide spin probe (Fremy's salt) in glycerol glass near the glass transition temperature. By measuring echo-detected EPR spectra at different pulse separation times at resonance frequencies of 3, 9.5, 95 and 180 GHz, we were able to discriminate between different relaxation mechanisms and characterize the timescale of molecular reorientations (10(-7)-10(-10) s). We found that near the glass transition temperature, the orientation-dependent transverse relaxation is dominated by fast reorientational fluctuations, which may be overlapped with fast modulations of the canonical g-matrix values. The data was interpreted using a new simulation program for the orientation-dependent transverse relaxation rate 1/T2 of nitroxides based on different models for the molecular motion. The validity of the different models was assessed by comparing least-square fits of the simulated relaxation behaviour to the experimental data.

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

Electron spin relaxation times for four triarylmethyl (trityl) radicals at room temperature were measured by long-pulse saturation recovery, inversion recovery, and electron spin echo at 250 MHz, 1.5, 3.1, and 9.2 GHz in mixtures of water and glycerol. At 250 MHz T(1) is shorter than at X-band and more strongly dependent on viscosity. The enhanced relaxation at 250 MHz is attributed to modulation of electron-proton dipolar coupling by tumbling of the trityl radicals at rates that are comparable to the reciprocal of the resonance frequency. Deuteration of the solvent was used to distinguish relaxation due to solvent protons from the relaxation due to intra-molecular electron-proton interactions at 250 MHz. For trityl-CD(3), which contains no protons, modulation of dipolar interaction with solvent protons dominates T(1). For proton-containing radicals the relative importance of modulation of intra- and inter-molecular proton interactions varies with solution viscosity. The viscosity and frequency dependence of T(1) was modeled based on dipolar interaction with a defined number of protons at specified distances from the unpaired electron. At each of the frequencies examined T(2) decreases with increasing viscosity consistent with contributions from T(1) and from incomplete motional averaging of anisotropic hyperfine interaction.