Solid-State Radiation Chemistry of DNA: The Bases

The long term goal of this program is to determine the fundamental rules needed to predict the type and yield of damage produced in DNA due to direct effects of ionizing radiation. The focus is on damage to the sugar-phosphate backbone, damage that would lead to strand breaks. Model systems have been chosen that permit various aspects of this problem to be investigated. The emphasis will be on single crystals of monosaccharides, nucleosides, and nucleotides but will also include some powder work on polynucleotides. In these model systems, free radical products and reactions are observed by electron spin resonance (ESR) and electron nuclear double resonance (ENDOR) techniques. The information thus gained is used in constructing rules that predict what primary free radicals are formed in single crystals of model compounds and the reactions stemming from the primary radicals. The formulation of a set of rules that work in model systems will represent a major advance toward formulating a set of rules that predict the direct damage in DNA itself. In a broader context this program is part of the effort to understand and predict the effects of exposure to ionizing radiation received at low dose rates over long periods of time. Assessment of low dose effects requires a basic understanding of the action of radiation at the molecular level. By contributing to that basic understanding, this program will help solve the problems of risk assessment under low dose conditions. 5 refs., 3 figs.

The secondary radiation-induced radicals in lithium formate monohydrate were studied using electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques complemented with periodic density functional theory (DFT) calculations. Single crystals of lithium formate monohydrate were X irradiated at 77 K and at room temperature. The main radicals present after irradiation at 77 K are the CO(2)(•-) radical (R1), the recently identified protonated electron-gain product, HCOOH(•-) (R2) (Krivokapić et al., Radiat Res 2014: 181:503-11), and a different geometrical conformation of this latter radical, a species that, up until now, has remained unidentified (R3). The successful quantum chemical modeling of R3 confirmed its structure and also provided a possible mechanism for its formation. After irradiation at 295 K, the crystals were investigated both shortly after irradiation and after storage for eight months at room temperature in ambient environments. After long-term storage the CO(2)(•-) radical had significantly decayed and the EPR spectra were dominated by two minority radicals. Both of these radicals are most likely formate-centered π-radicals, and based on the observed EPR parameters (g- and hyperfine coupling tensors) tentative candidates are the CO(•-) radical and the dimer formed by the CO(2)(•-) radical and a neighboring formate molecule yielding the radical (-)O(2)C·O·(•)CH·O(-).

Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) techniques were used to obtain structural information about the copper(II)-chelidamate complex. Well-resolved nitrogen ENDOR spectra could be recorded from solid solution samples by using selective excitation of spin packets. Evaluation of nuclear quadrupole and dipolar hyperfine interaction of the directly ligated nitrogen allowed for an identification of the bond direction to the copper ion within the eigen frame of the copper g-matrix. Invoking two-dimensional EPR techniques, additional hyperfine interaction with a "distant" nitrogen spin, identified as resulting from the solvent dimethylformamide (DMF), was observed. The experimental data are only consistent with formation of a stable pseudoplanar copper complex with single solvent ligation via its oxygen atom.

Chapter 2 Electron spin resonance

Different pulse Electron Paramagnetic Resonance (EPR) and Electron Nuclear DOuble Resonance (ENDOR) techniques are used to study the electronic and geometric structure of (tetraphenylporphyrinato)cobaltate(II) with pyridine as an axial ligand (cobaltous tetraphenylporphyrin(pyridine), CoTPP(py)). This complex is considered as a model for the heme group in deoxygenated hemoglobin and myoglobin. For the first time, the small hyperfine and nuclear quadrupole interactions of the porphyrin nitrogens of CoTPP(py) are determined using three-pulse electron spin−echo envelope modulation (ESEEM), hyperfine sublevel correlation (HYSCORE), and double nuclear coherence transfer (DONUT)−HYSCORE spectroscopy as well as Davies-ENDOR, and hyperfine correlated ENDOR (HYEND). The assignment of the different cross-peaks in the HYSCORE spectra is shown to be considerably facilitated by the DONUT−HYSCORE experiment. Furthermore, the hyperfine interactions of the surrounding protons are investigated by Davies- and Mims-ENDOR and HYSCORE spectroscopy at X- and S-band microwave frequencies. For the first time, the potential of proton HYSCORE spectroscopy at S-band is demonstrated. Assignment of the observed couplings is facilitated using deuterated pyridine as the axial ligand. The interactions with the ortho and meta protons of pyridine and with the protons of the porphyrin ligand are determined. From the Davies-ENDOR spectra of CoTPP(py) and CoTPP([15N]py), the hyperfine and nuclear quadrupole couplings of the pyridine nitrogen are evaluated. From the hyperfine and nuclear quadrupole parameters, structural (internuclear distances) and electronic information is derived. Comparisons are made with known EPR and ENDOR studies on a number of porphyrin systems with different metal ions. The similarities and differences are discussed in detail.

Electron paramagnetic resonance (EPR) experiments of light activated Ge, Sn and Pb impurities in wurtzite type CdSe crystals are presented. These2S1/2 centres exhibit a large hyperfine structure which shows a variation with temperature. 25 shells of neighbour nuclei are resolved for CdSe∶Sn by means of the Electron nuclear double resonance (ENDOR) technique. All shells belong to one of three distinct shell symmetries of the lattice thus confirming a high symmetry defect. Additional Sn respectively Ge related spectra are described and interpreted as complex centres correlated with lithium.

The distinct spin, optical, and coherence characteristics of solid-state spin defects in semiconductors have positioned them as potential qubits for quantum technologies. Both bulk and two-dimensional materials, with varying structural properties, can serve as crystalline hosts for color centers. In this study, we conduct a comparative analysis of the spin–optical, electron–nuclear, and relaxation properties of nitrogen-bound vacancy defects using electron paramagnetic resonance (EPR) and electron–nuclear double resonance (ENDOR) techniques. We examine key parameters of the spin Hamiltonian for the nitrogen vacancy (NV−) center in 4H-SiC: D = 1.3 GHz, Azz = 1.1 MHz, and CQ = 2.53 MHz, as well as for the boron vacancy (VB−) in hBN: D = 3.6 GHz, Azz = 85 MHz, and CQ = 2.11 MHz, and their dependence on the material matrix. The spin–spin relaxation times T2 (NV− center: 50 µs and VB−: 15 µs) are influenced by the local nuclear environment and spin diffusion while Rabi oscillation damping times depend on crystal size and the spatial distribution of microwave excitation. The ENDOR absorption width varies significantly among color centers due to differences in crystal structures. These findings underscore the importance of selecting an appropriate material platform for developing quantum registers based on high-spin color centers in quantum information systems.

Role of the Coordinating Histidine in Altering the Mixed Valency of Cu A: An Electron Nuclear Double Resonance-Electron Paramagnetic Resonance Investigation

Single crystals of cytidine have been x-irradiated and studied by electron nuclear double double resonance, electron nuclear double resonance, and electron spin resonance techniques at room temperature. One radical species was studied in detail and the results show anisotropic couplings of an unpaired electron to three hydrogen nuclei with the following principal values: a1, −66.3 MHz, −43.5 MHz, −20.7 MHz; a2, −68.9 MHz, −43.4 MHz, −20.3 MHz; a3, −37.2 MHz, −27.0 MHz, −13.6 MHz. The g tensor principal values are 2.0031, 2.0025, and 2,0021. These data indicate a radical formed in the ribose sugar group with spin density localized on C4′ and C5′.

Radicals trapped in a γ-irradiated single crystal of N-methylurea oxalic acid have been investigated using the techniques of electron spin resonance (ESR) and electron nuclear double resonance (ENDOR). Detailed ENDOR studies have been carried out on the two initially observed radicals. One of these radicals has been assigned to a protonated anion. Two protons, belonging to neighboring molecules, have been identified as transferred protons. The other radical is formed at the urea molecule by hydrogen abstraction from the methyl group. The observed completely transferred proton exhibits very small isotropic coupling. The third radical seen, only in aged crystals, after prolonged duration has been assigned to a R–ĊHOH type of radical. These results are compared to those from the urea oxalic acid systems.

Powders of β-tricalcium phosphate (β-TCP, Ca3PO4) doped with manganese (Mn2+) are comprehensively analyzed with electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) techniques. The modeling of the spectra permitted to calculate the values of zero-field splitting (B20 = −904 MHz; B40 = −1.41 MHz and B43 = 195.2 MHz) and explain the origin of the low-field hyperfine structures as the allowed spin transitions of fine structure. Three structurally inequivalent positions for Mn2+ in the β-TCP crystal lattice are identified and their g-factors and hyperfine constants are quantified. The obtained results can serve as fundamental background to the study of structurally disordered matrices with high spin (S ≥ 1) impurities which are important for catalytic systems.

Pulsed electron paramagnetic resonance at the microwave K(a) band (~30 GHz) was used to study the coordination of adenosine nucleotides to Mn(2+) at the active site of myosin ATPase and in solution. We have found that the electron spin echo (ESE) field sweep, electron-nuclear double resonance (ENDOR) and ESE envelope modulation (ESEEM) techniques are not sufficiently specific for reliable differentiation between the solvated and myosin-bound Mn·nucleotide complexes. Therefore, to directly detect binding of the Mn·nucleotide to myosin, we used nonhydrolizable nucleotide analogs, site-directed spin labeling, and pulsed electron-electron double resonance to detect spin probe-manganese dipolar interaction. We found that under substoichiometric conditions, both Mn·AMPPNP and Mn·ADP·AlF(4) form a complex with myosin, and Mn·ADP does not form such a complex. This correlates well with the biological dissociation of Mg·ADP from myosin after the hydrolysis of ATP. The analysis of (31)P ENDOR spectra reveals that in Mn·AMPPNP, Mn·ATP, and Mn·ADP at myosin or in solution, the nucleotide is coordinated to Mn(2+) by two phosphate groups, whereas in Mn·ADP·AlF(4), only one phosphate group is coordinated. The observation of two phosphates and one nitrogen in the coordination sphere of Mn·ADP in solution by ESEEM spectroscopy suggests that a significant population of Mn ions is coordinated by two ADP molecules, one of which is coordinated by phosphates, and the other one, by a nitrogen atom. The developed approach will be generally useful for monitoring the metal-protein binding when such binding does not provide reliable spectroscopic signatures.

Studies of membrane peptide interactions at the molecular level are important for understanding essential processes such as membrane disruption or fusion by membrane active peptides. In a previous study, we combined several electron paramagnetic resonance (EPR) techniques, particularly continuous wave (CW) EPR, electron spin echo envelope modulation (ESEEM), and double electron-electron resonance (DEER) with Monte Carlo (MC) simulations to probe the conformation, insertion depth, and orientation with respect to the membrane of the membrane active peptide melittin. Here, we combined these EPR techniques with cryogenic transmission electron microscopy (cryo-TEM) to examine the effect of the peptide/phospholipid (P/PL) molar ratio, in the range of 1:400 to 1:25, on the membrane shape, lipids packing, and peptide orientation and penetration. Large unilamellar vesicles (LUVs) of DPPC/PG (7:3 dipalmitoylphosphatidylcholine/egg phosphatidylglycerol) were used as model membranes. Spin-labeled peptides were used to probe the peptide behavior whereas spin-labeled phspholipids were used to examine the membrane properties. The cryo-TEM results showed that melittin causes vesicle rupture and fusion into new vesicles with ill-defined structures. This new state was investigated by the EPR methods. In terms of the peptide, CW EPR showed decreased mobility, and ESEEM revealed increased insertion depth as the P/PL ratio was raised. DEER measurements did not reveal specific aggregates of melittin, thus excluding the presence of stable, well-defined pore structures. In terms of membrane properties, the CW EPR reported reduced mobility in both polar head and alkyl chain regions with increasing P/PL. ESEEM measurements showed that, as the P/PL ratio increased, a small increase in water content in the PL headgroup region took place and no change was observed in the alkyl chains part close to the hydrophilic region. In terms of lipid local density, opposite behavior was observed for the polar head and alkyl chain regions with increasing P/PL; while the DPPC density increased in the polar head region, it decreased in the alkyl chain region. These results are consistent with disruption of the lipid order and segregation of the PL constituents of the membrane as a consequence of the melittin binding. This work further demonstrates the applicability and potential of pulse EPR techniques for the study of peptide-membrane interactions.

The dehydrated aluminum form of the metal−organic framework compound MIL-53 shows a temperature-driven phase transition with pronounced structural hysteresis as recently shown by neutron diffraction and scattering experiments (Liu et al. J. Am. Chem. Soc. 2008, 130, 11813). Thereby, the structure of the corner-sharing metal AlO4(OH)2 octahedra differs in terms of local symmetry for the dehydrated MIL-53(Al) material in its high- and low-temperature form with open or closed pore structure, respectively. In this work, some of the framework aluminum ions were exchanged by chromium(III) to introduce an electron spin resonance (ESR) active probe ion. The resulting material was investigated by means of ESR and electron nuclear double resonance (ENDOR) spectroscopy to verify the incorporation of chromium at the octahedral framework sites. In addition, variable-temperature ESR measurements were performed to analyze the temperature-dependent phase behavior of the doped MIL-53 material. The Cr(III) ions have an ele...

In this study, radiation effects on coffee beans have been investigated by Electron Spin Resonance (ESR) technique. ESR spectra of natural and irradiated samples at different doses between 0.5 Gy and 11 kGy by 60Co gamma source were recorded with X-band ESR spectrometer and, radiation dose, ESR microwave power and cavity temperature dependency of paramagnetic centers were investigated. At the results of dose- response and kinetic studies it was determined that the paramagnetic centers in coffee beans are stable, and sensitive to radiation. Thus, it is shown that the irradiated beans can be used for detection as radiation dosimeter in the investigated dose range.