A complete biomimetic iron-sulfur cubane redox series.

Synthetic iron-sulfur cubanes are models for biological cofactors, which are essential to delineate oxidation states in the more complex enzymatic systems. However, a complete series of [Fe4S4]n complexes spanning all redox states accessible by 1-electron transformations of the individual iron atoms (n = 0-4+) has never been prepared, deterring the methodical comparison of structure and spectroscopic signature. Here, we demonstrate that the use of a bulky arylthiolate ligand promoting the encapsulation of alkali-metal cations in the vicinity of the cubane enables the synthesis of such a series. Characterization by EPR, 57Fe Mössbauer spectroscopy, UV-visible electronic absorption, variable-temperature X-ray diffraction analysis, and cyclic voltammetry reveals key trends for the geometry of the Fe4S4 core as well as for the Mössbauer isomer shift, which both correlate systematically with oxidation state. Furthermore, we confirm the S = 4 electronic ground state of the most reduced member of the series, [Fe4S4]0, and provide electrochemical evidence that it is accessible within 0.82 V from the [Fe4S4]2+ state, highlighting its relevance as a mimic of the nitrogenase iron protein cluster.

Ensemble structure of the N-terminal domain (1-267) of FUS in a biomolecular condensate.

Solutions of some proteins phase separate into a condensed state of high protein concentration and a dispersed state of low concentration. Such behavior is observed in living cells for a number of RNA-binding proteins that feature intrinsically disordered domains. It is relevant for cell function via the formation of membraneless organelles and transcriptional condensates. On a basic level, the process can be studied in vitro on protein domains that are necessary and sufficient for liquid-liquid phase separation (LLPS). We have performed distance distribution measurements by electron paramagnetic resonance for 13 sections in an N-terminal domain (NTD) construct of the protein fused in sarcoma (FUS), consisting of the QGSY-rich domain and the RGG1 domain, in the denatured, dispersed, and condensed state. Using 10 distance distribution restraints for ensemble modeling and three such restraints for model validation, we have found that FUS NTD behaves as a random-coil polymer under good-solvent conditions in both the dispersed and condensed state. Conformation distribution in the biomolecular condensate is virtually indistinguishable from the one in an unrestrained ensemble, with the latter one being based on only residue-specific Ramachandran angle distributions. Over its whole length, FUS NTD is slightly more compact in the condensed than in the dispersed state, which is in line with the theory for random coils in good solvent proposed by de Gennes, Daoud, and Jannink. The estimated concentration in the condensate exceeds the overlap concentration resulting from this theory. The QGSY-rich domain is slightly more extended, slightly more hydrated, and has slightly higher propensity for LLPS than the RGG1 domain. Our results support previous suggestions that LLPS of FUS is driven by multiple transient nonspecific hydrogen bonding and π-sp2 interactions.

Pulsed dynamic nuclear polarization: a comprehensive Floquet description.

Dynamic nuclear polarization (DNP) experiments using microwave (mw) pulse sequences are one approach to transfer the larger polarization on the electron spin to nuclear spins of interest. How the result of such experiments depends on the external magnetic field and the excitation power is part of an ongoing debate and of paramount importance for applications that require high chemical-shift resolution. To date numerical simulations using operator-based Floquet theory have been used to predict and explain experimental data. However, such numerical simulations provide only limited insight into parameters relevant for efficient polarization transfer, such as transition amplitudes or resonance offsets. Here we present an alternative method to describe pulsed DNP experiments by using matrix-based Floquet theory. This approach leads to analytical expressions for the transition amplitudes and resonance offsets. We validate the method by comparing computations by these analytical expressions to their numerical counterparts and to experimental results for the XiX, TOP and TPPM DNP sequences. Our results explain the experimental data and are in very good agreement with the numerical simulations. The analytical expressions allow for the discussion of the scaling behaviour of pulsed DNP experiments with respect to the external magnetic field. We find that the transition amplitudes scale inversely with the external magnetic field.

Exploring tunneling ESEEM beyond methyl groups in nitroxides at low temperatures.

Tunneling of methyl rotors coupled to an electron spin causes magnetic field independent electron spin echo envelope modulation (ESEEM) at low temperatures. For nitroxides containing alkyl substituents, we observe this effect as a contribution at the beginning of the Hahn echo decay signal occurring on a faster time scale than the matrix-induced decoherence. The tunneling ESEEM contribution includes information on the local environment of the methyl rotors, which manifests as a distribution of rotation barriers P(V3) when measuring the paramagnetic species in a glassy matrix. Here, we investigate the differences in tunneling behaviour of geminal methyl and ethyl group rotors in nitroxides while exploring different levels of theory in our previously introduced methyl quantum rotor (MQR) model. Moreover, we extend the MQR model to analyze the tunneling ESEEM originating from two different rotor types coupled to the same electron spin. We find that ethyl groups in nitroxides give rise to stronger tunneling ESEEM contributions than methyl groups because the difference between hyperfine couplings of their methyl protons better matches the tunneling frequency. The methyl rotors of both ethyl and propyl groups exhibit distributions at lower rotation barriers compared to geminal methyl groups. This is in good agreement with density functional theory (DFT) calculations of their rotation barriers and showcases that conformational flexibility impacts the hindrance of rotation. Using Monte-Carlo based fitting in combination with an identifiability analysis of the MQR model parameter space, we extract rotation barrier distributions for the individual rotor types in mixed-rotor nitroxides as well as identify which rotors dominate the observed tunneling contribution in the Hahn echo decay signal.

Geometry and electronic structure of Yb(III)[CH(SiMe3)2]3 from EPR and solid-state NMR augmented by computations.

Characterization of paramagnetic compounds, in particular regarding the detailed conformation and electronic structure, remains a challenge, and - still today it often relies solely on the use of X-ray crystallography, thus limiting the access to electronic structure information. This is particularly true for lanthanide elements that are often associated with peculiar structural and electronic features in relation to their partially filled f-shell. Here, we develop a methodology based on the combined use of state-of-the-art magnetic resonance spectroscopies (EPR and solid-state NMR) and computational approaches as well as magnetic susceptibility measurements to determine the electronic structure and geometry of a paramagnetic Yb(III) alkyl complex, Yb(III)[CH(SiMe3)2]3, a prototypical example, which contains notable structural features according to X-ray crystallography. Each of these techniques revealed specific information about the geometry and electronic structure of the complex. Taken together, both EPR and NMR, augmented by quantum chemical calculations, provide a detailed and complementary understanding of such paramagnetic compounds. In particular, the EPR and NMR signatures point to the presence of three-centre-two-electron Yb-γ-Me-ß-Si secondary metal-ligand interactions in this otherwise tri-coordinate metal complex, similarly to its diamagnetic Lu analogues. The electronic structure of Yb(III) can be described as a single 4f13 configuration, while an unusually large crystal-field splitting results in a thermally isolated ground Kramers doublet. Furthermore, the computational data indicate that the Yb-carbon bond contains some π-character, reminiscent of the so-called α-H agostic interaction.

Structural insights into α-synuclein monomer-fibril interactions.

Protein aggregation into amyloid fibrils is associated with multiple neurodegenerative diseases, including Parkinson's disease. Kinetic data and biophysical characterization have shown that the secondary nucleation pathway highly accelerates aggregation via the absorption of monomeric protein on the surface of amyloid fibrils. Here, we used NMR and electron paramagnetic resonance spectroscopy to investigate the interaction of monomeric α-synuclein (α-Syn) with its fibrillar form. We demonstrate that α-Syn monomers interact transiently via their positively charged N terminus with the negatively charged flexible C-terminal ends of the fibrils. These intermolecular interactions reduce intramolecular contacts in monomeric α-Syn, yielding further unfolding of the partially collapsed intrinsically disordered states of α-Syn along with a possible increase in the local concentration of soluble α-Syn and alignment of individual monomers on the fibril surface. Our data indicate that intramolecular unfolding critically contributes to the aggregation kinetics of α-Syn during secondary nucleation.

Current Developments in Operando Electron Paramagnetic Resonance Spectroscopy.

Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for in situ/operando tracking of catalytic reactions that involve paramagnetic species either as a catalyst (e.g. transition metal ions or defects), reaction intermediates (radicals) or poisoning agents such as coke. This article provides a summary of recent experimental examples and developments in resonator design as well as detection schemes that were carried out in our group. Opportunities for applying this technique are illustrated by examples, including studies of transition metal exchanged zeolites and metal-free zeolites as well as metal oxide catalysts. The inherent limitations of EPR applied at high temperatures are discussed, as well as strategies in reducing or lifting these restrictions are evaluated and ideas for future improvements and methodologies are discussed.

Active Sites in Cr(III)-Based Ethylene Polymerization Catalysts from Machine-Learning-Supported XAS and EPR Spectroscopy.

The ethylene polymerization Phillips catalyst has been employed for decades and is central to the polymer industry. While Cr(III) alkyl species are proposed to be the propagating sites, there is so far no direct experimental evidence for such proposal. In this work, by coupling Surface organometallic chemistry, EPR spectroscopy, and machine learning-supported XAS studies, we have studied the electronic structure of well-defined silica-supported Cr(III) alkyls and identified the presence of several surface species in high and low-spin states, associated with different coordination environments. Notably, low-spin Cr(III) sites are shown to participate in ethylene polymerization, indicating that similar Cr(III) alkyl species could be involved in the related Phillips catalyst.

NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation.

Many RNA-binding proteins undergo liquid-liquid phase separation, which underlies the formation of membraneless organelles, such as stress granules and P-bodies. Studies of the molecular mechanism of phase separation in vitro are hampered by the coalescence and sedimentation of organelle-sized droplets interacting with glass surfaces. Here, we demonstrate that liquid droplets of fused in sarcoma (FUS)-a protein found in cytoplasmic aggregates of amyotrophic lateral sclerosis and frontotemporal dementia patients-can be stabilized in vitro using an agarose hydrogel that acts as a cytoskeleton mimic. This allows their spectroscopic characterization by liquid-phase NMR and electron paramagnetic resonance spectroscopy. Protein signals from both dispersed and condensed phases can be observed simultaneously, and their respective proportions can be quantified precisely. Furthermore, the agarose hydrogel acts as a cryoprotectant during shock-freezing, which facilitates pulsed electron paramagnetic resonance measurements at cryogenic temperatures. Surprisingly, double electron-electron resonance measurements revealed a compaction of FUS in the condensed phase.

Nickel(I)-Phenolate Complexes: The Key to Well-Defined Ni(I) Species.

Phosphine-stabilized monovalent nickel complexes play an important role in catalysis, either as catalytically active species or as decomposition products. Most routes to access these complexes are highly ligand specific or rely on strong reducing agents. Our group recently disclosed a path to access nickel(I)-phenolate complexes from bis(1,5-cyclooctadiene)nickel(0) (Ni(cod)2). Herein, we demonstrate this protocol's broad applicability by ligating a wide range of mono- and bidentate phosphine ligands. We further show the versatility of the phenolate fragment as a precursor to nickel(I)-alkyl or aryl species, which are relevant to Ni catalysis or synthetically useful nickel(I)-chloride and hydride complexes. We also demonstrate that the chloride complex can be synthesized in a one-pot procedure starting from Ni(cod)2 in good yield, making this protocol a valuable alternative to current procedures. Single-crystal X-ray diffraction, IR, and EPR (or NMR) spectroscopy were employed to characterize all of the synthesized nickel complexes.

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 spin echo envelope modulation (ESEEM) on a faster time scale compared to the slower matrix-induced decoherence contribution arising from nuclear pair ESEEM. Here we introduce the methyl quantum rotor (MQR) model that describes tunneling ESEEM originating from multiple methyl rotors coupled to the same electron spin. By formulating the MQR model based on a rotation barrier distribution P(V3), we account for the different local environments in a glassy matrix. Using this framework, we determine the methyl groups' rotation barrier distribution from experimental Hahn echo decay/two-pulse ESEEM data by a non-linear fitting approach. The inferred distributions are in good agreement with density functional theory (DFT) calculations of the methyl groups' rotation barriers in the low-temperature regime where tunneling constitutes the dominant methyl proton exchange process. In addition to comparing our results with previous decoherence studies performed on the same spin system, we experimentally confirm the characteristic properties of methyl tunneling by demonstrating that P(V3) is magnetic field independent and predominantly temperature independent between 10 and 50 K. This confirms the assignment of the fast Hahn echo decay contribution to methyl tunneling, showcasing how pulsed EPR sequences can coherently probe this quantum phenomenon for commonly employed nitroxide spin-labels.

Probing Methyl Group Tunneling in [(CH3)2NH2][Zn(HCOO)3] Hybrid Perovskite Using Co2+ EPR.

At low temperature, methyl groups act as hindered quantum rotors exhibiting rotational quantum tunneling, which is highly sensitive to a local methyl group environment. Recently, we observed this effect using pulsed electron paramagnetic resonance (EPR) in two dimethylammonium-containing hybrid perovskites doped with paramagnetic Mn2+ ions. Here, we investigate the feasibility of using an alternative fast-relaxing Co2+ paramagnetic center to study the methyl group tunneling, and, as a model compound, we use dimethylammonium zinc formate [(CH3)2NH2][Zn(HCOO)3] hybrid perovskite. Our multifrequency (X-, Q- and W-band) EPR experiments reveal a high-spin state of the incorporated Co2+ center, which exhibits fast spin-lattice relaxation and electron spin decoherence. Our pulsed EPR experiments reveal magnetic field independent electron spin echo envelope modulation (ESEEM) signals, which are assigned to the methyl group tunneling. We use density operator simulations to extract the tunnel frequency of 1.84 MHz from the experimental data, which is then used to calculate the rotational barrier of the methyl groups. We compare our results with the previously reported Mn2+ case showing that our approach can detect very small changes in the local methyl group environment in hybrid perovskites and related materials.

Methane Oxidation over Cu2+ /[CuOH]+ Pairs and Site-Specific Kinetics in Copper Mordenite Revealed by Operando Electron Paramagnetic Resonance and UV/Visible Spectroscopy.

Cu-exchanged mordenite (MOR) is a promising material for partial CH4 oxidation. The structural diversity of Cu species within MOR makes it difficult to identify the active Cu sites and to determine their redox and kinetic properties. In this study, the Cu speciation in Cu-MOR materials with different Cu loadings has been determined using operando electron paramagnetic resonance (EPR) and operando ultraviolet-visible (UV/Vis) spectroscopy as well as in situ photoluminescence (PL) and Fourier-transform infrared (FTIR) spectroscopy. A novel pathway for CH4 oxidation involving paired [CuOH]+ and bare Cu2+ species has been identified. The reduction of bare Cu2+ ions facilitated by adjacent [CuOH]+ demonstrates that the frequently reported assumption of redox-inert Cu2+ centers does not generally apply. The measured site-specific reaction kinetics show that dimeric Cu species exhibit a faster reaction rate and a higher apparent activation energy than monomeric Cu2+ active sites highlighting their difference in the CH4 oxidation potential.

Exceptionally Stable Dimers and Trimers of Au25 Clusters Linked with a Bidentate Dithiol: Synthesis, Structure and Chirality Study.

A bidentate chiral dithiol (diBINAS) is utilised to bridge Au25 nanoclusters to form oligomers. Separation by size allows the isolation of fractions that are stable thanks to the bidentate nature of the linker. The structure of the products is elucidated by small-angle X-ray scattering and calculated using density functional theory. Additional structural details are studied by diffusion-ordered nuclear magnetic resonance spectroscopy, transmission electron microscopy and matrix-assisted laser desorption/ionization time of flight mass spectrometry. Significant changes in the optical properties are analysed by UV/Vis and fluorescence spectroscopies, with the latter demonstrating a strong emission enhancement. Furthermore, the emergent chiral characteristics are studied by circular dichroism. Due to the geometry constraints of the nanocluster assemblies, diBINAS can be regarded as a templating molecule, taking a step towards the directed self-assembly of metal clusters.

A Robust and Efficient Propane Dehydrogenation Catalyst from Unexpectedly Segregated Pt2Mn Nanoparticles.

The increasing demand for short chain olefins like propene for plastics production and the availability of shale gas make the development of highly performing propane dehydrogenation (PDH) catalysts, robust toward industrially applied harsh regeneration conditions, a highly important field of research. A combination of surface organometallic chemistry and thermolytic molecular precursor approach was used to prepare a nanometric, bimetallic Pt-Mn material (3 wt % Pt, 1.3 wt % Mn) supported on silica via consecutive grafting of a Mn and Pt precursor on surface OH groups present on the support surface, followed by a treatment under a H2 flow at high temperature. The material exhibits a 70% fraction of the overall Mn as MnII single sites on the support surface; the remaining Mn is incorporated in segregated Pt2Mn nanoparticles. The material shows great performance in PDH reaction with a low deactivation rate. In particular, it shows outstanding robustness during repeated regeneration cycles, with conversion and selectivity stabilizing at ca. 37 and 98%, respectively. Notably, a material with a lower Pt loading of only 0.05 wt % shows an outstanding catalytic performance─initial productivity of 4523 gC3H6/gPt h and an extremely low kd of 0.003 h-1 under a partial pressure of H2, which are among the highest reported productivities. A combined in situ X-ray absorption spectroscopy, scanning transmission electron microscopy, electron paramagnetic resonance, and metadynamics at the density functional theory level study could show that the strong interaction between the MnII-decorated support and the unexpectedly segregated Pt2Mn particles is most likely responsible for the outstanding performance of the investigated materials.

Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.

The accurate cleavage of pre-micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA-induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here, we solved the solution structure of the two N-terminal dsRNA binding domains (dsRBDs) of TRBP in complex with a functionally asymmetric siRNA using NMR, EPR, and single-molecule spectroscopy. We find that siRNA recognition by the dsRBDs is not sequence-specific but rather depends on the RNA shape. The two dsRBDs can swap their binding sites, giving rise to two equally populated, pseudo-symmetrical complexes, showing that TRBP is not a primary sensor of siRNA asymmetry. Using our structure to model a Dicer-TRBP-siRNA ternary complex, we show that TRBP's dsRBDs and Dicer's RNase III domains bind a canonical 19 base pair siRNA on opposite sides, supporting a mechanism whereby TRBP influences Dicer-mediated cleavage accuracy by binding the dsRNA region of the pre-miRNA during Dicer cleavage.

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

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

Dipolar pathways in dipolar EPR spectroscopy.

Dipolar electron paramagnetic resonance (EPR) experiments such as double electron-electron resonance (DEER) measure distributions of nanometer-scale distances between unpaired electrons, which provide valuable information for structural characterization of proteins and other macromolecular systems. To determine these distributions from the experimental signal, it is critical to employ an accurate model of the signal. For dilute samples of doubly spin-labeled molecules, the signal is a product of an intramolecular and an intermolecular contribution. We present a general model based on dipolar pathways valid for dipolar EPR experiments with spin-1/2 labels. Our results show that the intramolecular contribution consists of a sum and the intermolecular contribution consists of a product over individual dipolar pathway contributions. We examine several commonly used dipolar EPR experiments in terms of dipolar pathways and show experimental results confirming the theoretical predictions. This multi-pathway model makes it possible to analyze a wide range of dipolar EPR experiments within a single theoretical framework.

Dipolar pathways in multi-spin and multi-dimensional dipolar EPR spectroscopy.

Dipolar electron paramagnetic resonance (EPR) experiments, such as double electron-electron resonance (DEER), measure distributions of nanometer-scale distances between unpaired electrons, which provide valuable information for structural characterization of proteins and other macromolecular systems. We present an extension to our previously published general model based on dipolar pathways valid for multi-dimensional dipolar EPR experiments with more than two spin-1/2 labels. We examine the 4-pulse DEER and TRIER experiments in terms of dipolar pathways and show experimental results confirming the theoretical predictions. This extension to the dipolar pathways model allows the analysis of previously challenging datasets and the extraction of multivariate distance distributions.

Cu2+-Induced self-assembly and amyloid formation of a cyclic D,L-α-peptide: structure and function.

In a wide spectrum of neurodegenerative diseases, self-assembly of pathogenic proteins to cytotoxic intermediates is accelerated by the presence of metal ions such as Cu2+. Only low concentrations of these early transient oligomeric intermediates are present in a mixture of species during fibril formation, and hence information on the extent of structuring of these oligomers is still largely unknown. Here, we investigate dimers as the first intermediates in the Cu2+-driven aggregation of a cyclic D,L-α-peptide architecture. The unique structural and functional properties of this model system recapitulate the self-assembling properties of amyloidogenic proteins including ß-sheet conformation and cross-interaction with pathogenic amyloids. We show that a histidine-rich cyclic D,L-α-octapeptide binds Cu2+ with high affinity and selectivity to generate amyloid-like cross-ß-sheet structures. By taking advantage of backbone amide methylation to arrest the self-assembly at the dimeric stage, we obtain structural information and characterize the degree of local order for the dimer. We found that, while catalytic amounts of Cu2+ promote aggregation of the peptide to fibrillar structures, higher concentrations dose-dependently reduce fibrillization and lead to formation of spherical particles, showing self-assembly to different polymorphs. For the initial self-assembly step to the dimers, we found that Cu2+ is coordinated on average by two histidines, similar to self-assembled peptides, indicating that a similar binding interface is perpetuated during Cu2+-driven oligomerization. The dimer itself is found in heterogeneous conformations that undergo dynamic exchange, leading to the formation of different polymorphs at the initial stage of the aggregation process.