Intermolecular contributions, filtration effects and signal composition of SIFTER (single-frequency technique for refocusing)

To characterize structure and molecular order in the nanometre range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic resonance experiments. Here, for the single-frequency technique for refocusing dipolar couplings (SIFTER), the buildup of dipolar modulation signal and intermolecular contributions is analysed for a uniform random distribution of monoradicals and biradicals in frozen glassy solvent by using the product operator formalism for electron spin S = 1 / 2 . A dipolar oscillation artefact appearing at both ends of the SIFTER time trace is predicted, which originates from the weak coherence transfer between biradicals. The relative intensity of this artefact is predicted to be temperature independent but to increase with the spin concentration in the sample. Different compositions of the intermolecular background are predicted in the case of biradicals and in the case of monoradicals. Our theoretical account suggests that the appropriate procedure of extracting the intramolecular dipolar contribution (form factor) requires fitting and subtracting the unmodulated part, followed by division by an intermolecular background function that is different in shape. This scheme differs from the previously used heuristic background division approach. We compare our theoretical derivations to experimental SIFTER traces for nitroxide and trityl monoradicals and biradicals. Our analysis demonstrates a good qualitative match with the proposed theoretical description. The resulting perspectives for a quantitative analysis of SIFTER data are discussed.

Quantifying methyl tunneling induced (de)coherence of nitroxides in glassy ortho-terphenyl at low temperatures

The low-temperature Hahn echo decay signal of the pyrroline-based nitroxide H-mNOHex in ortho- terphenyl (OTP) shows two contributions on distinct time scales. Tunneling of the nitroxide’s methyl groups cause electron...

Ligand-specific conformational change drives interdomain allostery in Pin1

Pin1 is a two-domain cell regulator that isomerizes peptidyl-prolines. The catalytic domain (PPIase) and the other ligand-binding domain (WW) sample extended and compact conformations. Ligand binding changes the equilibrium of the interdomain conformations, but the conformational changes that lead to the altered domain sampling were unknown. Prior evidence has supported an interdomain allosteric mechanism. We recently introduced a magnetic resonance-based protocol that allowed us to determine the coupling of intra- and interdomain structural sampling in apo Pin1. Here, we describe ligand-specific conformational changes that occur upon binding of pCDC25c and FFpSPR. pCDC25c binding doubles the population of the extended states compared to the virtually identical populations of the apo and FFpSPR-bound forms. pCDC25c binding to the WW domain triggers conformational changes to propagate via the interdomain interface to the catalytic site, while FFpSPR binding displaces a helix in the PPIase that leads to repositioning of the PPIase catalytic loop.

Regularized dynamical decoupling noise spectroscopy - a decoherence descriptor for radicals in glassy matrices

Decoherence arises from a fluctuating spin environment, captured by its noise spectrum S(ω). Dynamical decoupling (DD) with n π pulses extends the dephasing time if the associated filter function attenuates S(ω). Inversely, DD noise spectroscopy (DDNS) reconstructs S(ω) from DD data by approximating the filters pass band by a δ-function. This restricts application to qubit-like spin systems with inherently long dephasing times and/or many applicable pulses. We introduce regularized DDNS to lift this limitation and thereby infer S(ω) from DD traces of paramagnetic centers in glassy o-terphenyl and water-glycerol matrices recorded with n ≤ 5. For nitroxide radicals at low temperatures, we utilize deuteration to identify distinct matrix- and spin center-induced spectral features. The former extends up to a matrix-specific cut-off frequency and characterizes nuclear spin diffusion. We demonstrate that rotational tunneling of intramolecular methyl groups drives the latter process, whereas at elevated temperatures S(ω) reflects the classical methyl group reorientation. Ultimately, S(ω) visualizes and quantifies variations in the electron spins couplings and thus reports on the underlying spin dynamics as a powerful decoherence descriptor.

Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance

Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.

Dynamical decoupling in water-glycerol glasses: a comparison of nitroxides, trityl radicals and gadolinium complexes

Our previous study on nitroxides in o-terphenyl (OTP) revealed two separable decoherence processes at low temperatures, best captured by the sum of two stretched exponentials (SSE) model. Dynamical decoupling (DD) extends both associated dephasing times linearly for 1 to 5 refocusing pulses [Soetbeer et al., Phys. Chem. Chem. Phys., 2018, 20, 1615]. Here we demonstrate an analogous DD behavior of water-soluble nitroxides in water-glycerol glass by using nitroxide and/or solvent deuteration for component assignment. Compared to the conventional Hahn experiment, we show that Carr-Purcell and Uhrig DD schemes are superior in resolving and identifying active dephasing mechanisms. Thereby, we observe a partial coherence loss to intramolecular nitroxide and trityl nuclei that can be alleviated, while the zero field splitting-induced losses for gadolinium labels cannot be refocused and contribute even at the central transition of this spin-7/2 system. Independent of the studied spin system, Uhrig DD leads to a characteristic convex dephasing envelope in both protonated water-glycerol and OTP glass, thus outperforming the Carr-Purcell scheme.

Non-uniform HYSCORE: Measurement, processing and analysis with Hyscorean

Non-uniform sampling (NUS) provides a considerable reduction of measurement time especially for multi-dimensional experiments. This comes at the cost of additional signal processing steps to reconstruct the complete signal from the experimental data points. Despite being routinely employed in NMR for many experiments, EPR applications have not benefited from NUS due to the lack of a straightforward implementation to perform NUS in common commercial spectrometers. In this work we present a novel method to perform NUS HYSCORE experiments on commercial Bruker EPR spectrometers, along with a benchmark of modern reconstruction methods, and new processing software tools for NUS HYSCORE signals. All of this comes in the form of a free-software package: Hyscorean. Experimental NUS spectra are measured and processed with this package using different reconstruction methods and compared to their uniform sampled counterparts, thereby showcasing the method's potential for EPR spectroscopy.

Conformation of bis-nitroxide polarizing agents by multi-frequency EPR spectroscopy

The chemical structure of polarizing agents critically determines the efficiency of dynamic nuclear polarization (DNP). For cross-effect DNP, biradicals are the polarizing agents of choice and the interaction and relative orientation of the two unpaired electrons should be optimal. Both parameters are affected by the molecular structure of the biradical in the frozen glassy matrix that is typically used for DNP/MAS NMR and likely differs from the structure observed with X-ray crystallography. We have determined the conformations of six bis-nitroxide polarizing agents, including the highly efficient AMUPol, in their DNP matrix with EPR spectroscopy at 9.7 GHz, 140 GHz, and 275 GHz. The multi-frequency approach in combination with an advanced fitting routine allows us to reliably extract the interaction and relative orientation of the nitroxide moieties. We compare the structures of six bis-nitroxides to their DNP performance at 500 MHz/330 GHz.

Artefact suppression in 5-pulse double electron electron resonance for distance distribution measurements

A 5-pulse version of the Double Electron Electron Resonance (DEER) experiment with Carr-Purcell delays and an additional pump pulse has been shown to significantly extend the experimentally accessible distance range in cases where nuclear spin diffusion dominates electron spin phase memory loss [Borbat et al., J. Phys. Chem. Lett., 2013, 4, 170]. We show that the sequence also prolongs coherence decay for spin labels in or near lipid bilayers, where this decay is mono-exponential. Compared to 4-pulse DEER, 5-pulse DEER suffers from additional artefacts that stem from pulse imperfection and excitation band overlap. Only some of these artefacts can be suppressed by phase cycling and the remaining ones have hindered widespread utilization of the method. Here, we report previously unknown additional artefact contributions stemming from overlap between the excitation bands of the microwave pulses that introduce additional dipolar evolution pathways. Experimental conditions are analyzed in detail that suppress these as well as the already known artefacts. Such suppression results in data that contain at most the partial excitation artefact, which can be deliberately shifted in time by a change in pulse timing without affecting the wanted contribution.

Dynamical decoupling of nitroxides in o-terphenyl: a study of temperature, deuteration and concentration effects

Distinct matrix- and molecule dependencies govern nitroxide decoherence in o-terphenyl at low temperatures, disclosing an optimal range for dynamical decoupling.

Marcus-type driving force correlations reveal the mechanism of proton-coupled electron transfer for phenols and [Ru(bpy)3]3+ in water at low pH

We examined PCET between a series of phenol derivatives and photogenerated [Ru(bpy)₃]³⁺ in low pH (≤4) water using the laser flash-quench technique.

Proton-coupled electron transfer (PCET) from tyrosine and other phenol derivatives in water is an important elementary reaction in chemistry and biology. We examined PCET between a series of phenol derivatives and photogenerated [Ru(bpy)₃]³⁺ in low pH (≤4) water using the laser flash-quench technique. From an analysis of the kinetic data using a Marcus-type free energy relationship, we propose that our model system follows a stepwise electron transfer-proton transfer (ETPT) pathway with a pH independent rate constant at low pH in water. This is in contrast to the concerted or proton-first (PTET) mechanisms that often dominate at higher pH and/or with buffers as primary proton acceptors. The stepwise mechanism remains competitive despite a significant change in the pK_a and redox potential of the phenols which leads to a span of rate constants from 1 × 10⁵ to 2 × 10⁹ M^–1 s^–1. These results support our previous studies which revealed separate mechanistic regions for PCET reactions and also assigned phenol oxidation by [Ru(bpy)₃]³⁺ at low pH to a stepwise PCET mechanism.