Confidence limits in pulse dipolar EPR spectroscopy: estimates for individual measurements.

The distribution of inter-label distances obtained by electron paramagnetic resonance (EPR) pulse dipolar spectroscopies (PDS), such as DEER aka PELDOR, gives a valuable characterization of structure on the nanometer scale. The impact of random experimental noise on such experiments is examined for three independent methods for analysing PDS data: the model-free method with Tikhonov regularization, model-free with Mellin-transformation, and a model-based method. All three methods show negative bias for the mean distance and positive bias for the distribution width. Both biases grow with increasing noise levels. The estimated confidence bands and the uncertainties obtained from a single experimental measurement by the standard bootstrapping or χ2-surface scanning approaches are inconsistent and can exclude the true distance distribution. Yet, both approaches can provide quite valuable support for hypothesis testing in PDS studies.

Non-uniform sampling in pulse dipolar spectroscopy by EPR: the redistribution of noise and the optimization of data acquisition.

Pulse dipolar spectroscopy (PDS) in Electron Paramagnetic Resonance (EPR) is the method of choice for determining the distance distribution function for mono-, bi- or multi- spin-labeled macromolecules and nanostructures. PDS acquisition schemes conventionally use uniform sampling of the dipolar trace, but non-uniform sampling (NUS) schemes can decrease the total measurement time or increase the accuracy of the resulting distance distributions. NUS requires optimization of the data acquisition scheme, as well as changes in data processing algorithms to accommodate the non-uniformly sampled data. We investigate in silico the applicability of the NUS approach in PDS, considering its effect on random, truncation and sampling noise in the experimental data. Each type of noise in the time-domain data propagates differently and non-uniformly into the distance spectrum as errors in the distance distribution. NUS schemes seem to be a valid approach for increasing sensitivity and/or throughput in PDS by decreasing and redistributing noise in the distance spectrum so that it has less impact on the distance spectrum.

Improving B1 field homogeneity in dielectric tube resonators for EPR spectroscopy via controlled shaping of the dielectric insert.

We propose an approach for improving the homogeneity of microwave magnetic field amplitude in a dielectric tube resonator for electron paramagnetic resonance spectroscopy at X-band. The improvement is achieved by "shaping" (controllable variation of the outer diameter of a dielectric insert along its axial direction). Various shaping scenarios based on the principle of discrete solenoids and electromagnetic calculations have been considered. The dielectric insert having the most promising shape was manufactured from a bismuth germanate single crystal. The shaped insert increases the area at B1 > 0.9 B1max from 5.06 to 7.36 mm. Higher sensitivity and lower likelihood of quantitative errors have been achieved in pulse EPR experiments for "long" samples (whose length was comparable to that of the dielectric insert) in a shaped dielectric insert.

Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway.

Human apurinic/apyrimidinic (AP) endonuclease APE1 catalyses the hydrolysis of phosphodiester bonds on the 5' side of an AP-site (in the base excision repair pathway) and of some damaged nucleotides (in the nucleotide incision repair pathway). The range of substrate specificity includes structurally unrelated damaged nucleotides. Here, to examine the mechanism of broad substrate specificity of APE1, we performed pulsed electron-electron double resonance (PELDOR) spectroscopy and pre-steady-state kinetic analysis with Förster resonance energy transfer (FRET) detection of DNA conformational changes during DNA binding and lesion recognition. Equilibrium PELDOR and kinetic FRET data revealed that DNA binding by APE1 leads to noticeable damage-dependent bending of a DNA duplex. Molecular dynamics simulations showed that the damaged nucleotide is everted from the DNA helix and placed into the enzyme's binding pocket, which is formed by Asn-174, Asn-212, Asn-229, Ala-230, Phe-266 and Trp-280. Nevertheless, no damage-specific contacts were detected between these amino acid residues in the active site of the enzyme and model damaged substrates containing 1,N6-ethenoadenosine, α-adenosine, 5,6-dihydrouridine or F-site. These data suggest that the substrate specificity of APE1 is controlled by the ability of a damaged nucleotide to flip out from the DNA duplex in response to an enzyme-induced DNA distortion.

Analytical solution of the PELDOR inverse problem using the integral Mellin transform.

We describe a new model-free approach to solve the inverse problem in pulsed double electron-electron resonance (PELDOR, also known as DEER) spectroscopy and obtain the distance distribution function between two radicals from time-domain PELDOR data. The approach is based on analytical solutions of the Fredholm integral equations of the first kind using integral Mellin transforms to provide the distance distribution function directly. The approach appears to confine the noise in the computed distance distribution to short distances and does not introduce systematic distortions. Thus, the proposed analysis method can be a useful supplement to current methods to determine complicated distance distributions.

Extraction and coordination studies of a carbonyl-phosphine oxide scorpionate ligand with uranyl and lanthanide(III) nitrates: structural, spectroscopic and DFT characterization of the complexes.

Hybrid scorpionate ligand (OPPh2)2CHCH2C(O)Me (L) was synthesized and characterized by spectroscopic methods and X-ray diffraction. The selected coordination chemistry of L with UO2(NO3)2 and Ln(NO3)3 (Ln = La, Nd, Lu) has been evaluated. The isolated mono- and binuclear complexes, namely, [UO2(NO3)2L] (1), [{UO2(NO3)L}2(µ2-O2)]·EtOH (2), [La(NO3)3L2]·2.33MeCN (3), [Nd(NO3)3L2]·3MeCN (4), [Nd(NO3)2L2]+·(NO3)−·EtOH (5) and [Lu(NO3)3L2] (6) have been characterized by IR spectroscopy and elemental analysis. Single-crystal X-ray structures have been determined for complexes 1-5. Intramolecular intraligand π-stacking interactions between two phenyl fragments of the coordinated ligand(s) were observed in all complexes 1-5. The π-stacking interaction energy was estimated from Bader's AIM theory calculations performed at the DFT level. Solution properties have been examined using IR and multinuclear ((1)H, (13)C, and (31)P) NMR spectroscopy in CD3CN and CDCl3. Coordination modes of L vary with the coordination polyhedron of the metal and solvent nature showing many coordination modes: P(O),P(O), P(O),P(O),C(O), P(O),C(O), and P(O). Preliminary extraction studies of U(VI) and Ln(III) (Ln = La, Nd, Ho, Yb) from 3.75 M HNO3 into CHCl3 show that scorpionate L extracts f-block elements (especially uranium) better than its unmodified prototype (OPPh2)2CH2.

Difficulties in building radiation-generated three-spin systems using spin-labeled luminophores.

Aromatic compounds are well-known acceptors of primary radical ions that are formed under high-energy irradiation of nonpolar systems. Thus formed radical ion pairs recombine and produce magnetosensitive fluorescence, which helps study the short-lived radical ions. It was initially suggested that a simple introduction of a spin label into the original arene would allow an easy transition from two-spin to three-spin systems, retaining the experimental techniques available for radical pairs. However, it turned out that spin-labeled arenes often do not produce magnetosensitive fluorescence in the conditions of a conventional radiochemical experiment. To understand the effect of the introduced spin label, we synthesized a series of compounds with the general structure "stable 3-imidazoline radical-two-carbon bridge-naphthalene" as well as their diamagnetic analogues. By use of this set of acceptors, we determined the processes that ruin the observed signal and established their connection with the chemical structure of the compound. We found that the compounds with flexible (saturated) two-carbon bridges between the luminophore and the stable radical moieties exist in solution in folded conformation, which leads to suppression of luminescence from naphthalene due to efficient through-space exchange quenching of the excited state by the radical. Increasing the rigidity of the bridge by introducing the double bond drastically increases the reactivity of the extended pi-system. In these compounds, the energy released upon recombination is spent in radiationless processes of chemical transformations both at the stage of the radical ion and at the stage of the electronically excited molecule.