Pulsed EPR Dipolar Spectroscopy under the Breakdown of the High-Field Approximation: The High-Spin Iron(III) Case

Pulsed EPR dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling and thus the distance between electron-spin centers. To date, PDS measurements to metal centers were limited to ions that adhere to the high-field approximation. Here, the PDS methodology is extended to cases where the high-field approximation breaks down on the example of the high-spin Fe³⁺/nitroxide spin-pair. First, the theory developed by Maryasov et al. (Appl. Magn. Reson. 2006 , 30, 683–702) was adapted to derive equations for the dipolar coupling constant, which revealed that the dipolar spectrum does not only depend on the length and orientation of the interspin distance vector with respect to the applied magnetic field but also on its orientation to the effective g-tensor of the Fe³⁺ ion. Then, it is shown on a model system and a heme protein that a PDS method called relaxation-induced dipolar modulation enhancement (RIDME) is well-suited to measuring such spectra and that the experimentally obtained dipolar spectra are in full agreement with the derived equations. Finally, a RIDME data analysis procedure was developed, which facilitates the determination of distance and angular distributions from the RIDME data. Thus, this study enables the application of PDS to for example, the highly relevant class of high-spin Fe³⁺ heme proteins.     

EPR‐Based Approach for the Localization of Paramagnetic Metal Ions in Biomolecules

Metal ions play an important role in the catalysis and folding of proteins and oligonucleotides. Their localization within the three‐dimensional fold of such biomolecules is therefore an important goal in understanding structure–function relationships. A trilateration approach for the localization of metal ions by means of long‐range distance measurements based on electron paramagnetic resonance (EPR) is introduced. The approach is tested on the Cu²⁺ center of azurin, and factors affecting the precision of the method are discussed.     

Ragnar Frisch and interior-point methods

The distinguished econometrician Ragnar Frisch (1895–1973) also played an important role in optimization theory. In fact, he was a pioneer of interior-point methods. This note reconsiders his contribution, relating it to history and modern developments.     

Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

Pore-Scale Level Set Simulations of Capillary-Controlled Displacement with Adaptive Mesh Refinement

Transport in Porous Media - Multiphase flow simulations on imaged porous rock structures require numerical methods that are accurate and robust when applied on complex geometries. A key element in...     

Synthesis and Rearrangement of P‐Nitroxyl‐Substituted PIII and PV Phosphanes: A Combined Experimental and Theoretical Case Study

Low‐temperature generation of P‐nitroxyl phosphane 2 (Ph₂POTEMP), which was obtained by the reaction of Ph₂PH ( 1 ) with two equivalents of TEMPO, is presented. Upon warming, phosphane 2 decomposed to give P‐nitroxyl phosphane P‐oxide 3 (Ph₂P(O)OTEMP) as one of the final products. This facile synthetic protocol also enabled access to P‐sulfide and P‐borane derivatives 7 and 13 , respectively, by using Ph₂P(S)H ( 6 ) or Ph₂P(BH₃)H ( 11 ) and TEMPO. Phosphane sulfide 7 revealed a rearrangement to phosphane oxide 8 (Ph₂P(O)STEMP) in CDCl₃ at ambient temperature, whereas in THF, thermal decomposition of sulfide 7 yielded salt 10 ([TEMP‐H₂][Ph₂P(S)O]). As well as EPR and detailed NMR kinetic studies, indepth theoretical studies provided an insight into the reaction pathways and spin‐density distributions of the reactive intermediates.     

EPR on Medically Relevant NO Adsorbed to Zn-LTA

For medical purposes, materials are required that store and target specifically deliver exogenous nitric oxide (NO). Partially zinc-exchanged Na-LTA (Linde type A) zeolite (Zn-LTA) has high potential in this respect due to its non-toxicity and adsorption capacity for NO. In contrast to NO adsorbed to LTA zeolites prepared for catalytic purposes, lower dehydration temperature prior to NO adsorption is used to achieve a balance between production cost and high activity. In order to study the interaction of NO with the metal sites in the samples prepared under these medical conditions, continuous-wave X-band electron paramagnetic resonance has been applied. In contrast to Na-LTA with only one weakly interacting NO monomer, three different monomers, having stronger interaction to the metal sites than in Na-LTA, were observed in Zn-LTA. To improve the storage capacity of Zn-LTA, higher dehydration temperatures would be necessary.     

Local Thermodynamic Description of Isothermal Single-Phase Flow in Simple Porous Media

Transport in Porous Media - Darcy’s law for porous media transport is given a new local thermodynamic basis in terms of the grand potential of confined fluids. The local effective pressure...     

Relaxation oscillations in spruce–budworm interactions

We review and complement the study of the mathematical properties of the predator–prey dynamical system for spruce–budworm interactions studied in Ludwig et al. [D. Ludwig, D. Jones, C.S. Holling, Qualitative analysis of insect outbreak systems: the spruce budworm and forest, Journal of Animal Ecology 47 (1978), 315–332]. We use the singular perturbation method to identify parameter regimes which permit relaxation oscillations. The leading order contribution to the period of these oscillations is computed by means of this method and compared with the outcome of direct numerical simulations.     

SLIM: A Short‐Linked,Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements

The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site‐directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in‐cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide‐functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm , and shows high stability against reduction. Using this label, the guanine‐nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.