Solved?: the reductive radiation chemistry of alanine

The structural changes throughout the entire reductive radiation-induced pathway of L-alpha-alanine are solved on an atomistic level with the aid of periodic DFT and nudged elastic band (NEB) simulations. This yields unprecedented information on the conformational changes taking place, including the protonation state of the carboxyl group in the "unstable'' and "stable'' alanine radicals and the internal transformation converting these two radical variants at temperatures above 220 K. The structures of all stable radicals were verified by calculating EPR properties and comparing those with experimental data. The variation of the energy throughout the full radiochemical process provides crucial insight into the reason why these structural changes and rearrangements occur. Starting from electron capture, the excess electron quickly localizes on the carbon of a carboxyl group, which pyramidalizes and receives a proton from the amino group of a neighboring alanine molecule, forming a first stable radical species (up to 150 K). In the temperature interval 150-220 K, this radical deaminates and deprotonates at the carboxyl group, the detached amino group undergoes inversion and its methyl group sustains an internal rotation. This yields the so-called "unstable alanine radical''. Above 220 K, triggered by the attachment of an additional proton on the detached amino group, the radical then undergoes an internal rotation in the reverse direction, giving rise to the "stable alanine radical'', which is the final stage in the reductive radiation-induced decay of alanine

Free Radical Formation in X-Irradiated Crystals of 2\u27-Deoxycytidine Hydrochloride. Electron Magnetic Resonance Studies at 10 k

Single crystals of deoxycytidine hydrochloride (CdR·HCl) have been X- irradiated at 10 K with doses up to about 150 kGy and studied using 24 GHz (K-band) EPR, ENDOR and FSE spectroscopy. In this system, the cytosine base is protonated at the N3 position. Nine different radicals were characterized and identified. Three of these are ascribed to three versions of the one- electron reduced species, probably differing in their protonation state. Radicals formed by net hydrogen addition to the cytosine C5 and C6 positions were observed at 10 K. The hydrogen-abstraction radical at the deoxyribose C1\u27 position most probably results from initial oxidation of the base. The remaining radical species are all localized to the sugar moiety, representing products formed by net hydrogen abstraction from three of the five available carbons of the deoxyribose sugar. The lack of base-centered oxidation products as well as the structures of the one-electron reduced species is rationalized by considering the specific proton donor-acceptor properties of this crystalline lattice in comparison with similar systems

Primary Reduction and Oxidation of Thymine Derivatives. ESR/ENDOR of Thymidine and 1-Methylthymine X-Irradiated at 10 K

Single crystals of thymidine and 1-methylthymine were X-irradiated at 10 K and studied by using K-band ESR, ENDOR, and FSE spectroscopy. In thymidine, six primary radicals were identified. The major species were the O4-protonated anion (TI), the radical formed by net H addition to the C6 position of the base (TII), the radical formed by net H abstraction from the methyl group (TIII), and the alkoxy radical (TVI). The two minority radicals were one formed by net H addition to the C5 position of the base (TIV) and one in which the unpaired spin was localized on the sugar moiety, thought to be a C1′ H abstraction radical (TV). A small, nonexchangeable coupling in radical TI was shown to be due to a coupling to the methyl group. Evidence is presented that the characteristics of this coupling tensor indicates the protonation state of the thymine anion radical. Upon annealing, the anion decayed at about 40 K with no detectable successor. The alkoxy radical decays in the same temperature range. In 1-methylthymine, three major radical species were identified. These were the O4 protonated anion radical (MTI), the radical formed by net H abstraction from the C5 methyl group (MTII), and the radical formed by net H addition to the C5 position of the base (MTIII). The protonation state of the anion was interpreted from the characteristics of a small coupling with the methyl group. The anion decayed at about 40 K with no detectable successor. The thymin-5-yl radical slowly grew in upon prolonged annealing above 250 K. In both crystals the protonated anion is the reduction product. Comparison of the O4 protonated product\u27s magnetic parameters with those of products thought to be thymine anions in other thymine systems in the solid state led to the proposal that all were similarly protonated. Finally, evidence is reviewed for reactions in which thymin-5-yl radicals may arise from the O4 protonated anions or other precursors

Radiation Damage to DNA Base Pairs. II. Paramagnetic Resonance Studies of 1-Methyluracil·9-Ethyladenine Complex Crystals X-Irradiated at 10 K

Single crystals of the co-crystalline complex of 1-methyl-uracil and 9- ethyladenine were X-irradiated and studied using EPR, ENDOR and FSE spectroscopic techniques at 10 K. All together seven radicals were identified, and experimental evidence for at least one more species, as well as for a very low population of radical pairs, is available. Oxidation and reduction products appear to be stabilized at both base constituents of the pair. Of the 1-methyluracil moiety, the product formed by net hydrogen abstraction from the methyl group was observed, together with the 1- methyluracil anion and the 1-methyluracil-5-yl radical. From the 9- ethyladenine moiety, the N3-protonated 9-ethyladenine anion is stabilized. In addition, the 9-ethyladenine cation as well as traces of the amino- deprotonated cation were observed, together with the C8-H hydrogen adduct. The presence of oxidation and reduction products in each of the two bases may indicate that negligible energy transfer takes place between them. This behavior is different from that observed in the similar pair of 1- methylthymine·9-methyladenine. There also seems to be minor proton exchange between the two stacks of molecules: Interbase protonation-deprotonation channeled through the hydrogen-bonding scheme seems to be almost completely suppressed

Electron Spin Resonance and Electron Nuclear Double Resonance Study of X-Irradiated Deoxyadenosine: Proton Transfer Behavior of Primary Ionic Radicals

A study of deoxyadenosine crystals (anhydrous form) after irradiation at 10 K found four base-centered radicals and one sugar-centered radical. Radical R1, thermally stable to about 100 K and photobleachable easily with white light, was the product of deprotonation at the amino group by the primary radical cation. Radical R2, also thermally stable to about 100 K, was the product of protonation at N3 of the primary radical anion. Radical R3, stable to about 170 K, was centered in the deoxyribose moiety and evidently was the result of net hydrogen abstraction from C4\u27. Radicals R4 and RS were the C2 and C8 H-addition products with couplings typical of those species. Both R4 and R5 were formed at 10 K and were stable at room temperature. The behavior of R1 in several systems provides additional evidence for significant involvement of the hydrogen-bonding environment in controlling the stabilization (or formation) of radicals resulting directly from ionization, as described previously (Radiat. Res. 131, 272-284, 1992). From comparison of amino-group hydrogen-bonding environments in which radicals with the structure of R1 were stabilized, we conclude that oxygen atoms as proton acceptors are important in permitting the charge and spin separation necessary for radical stabilization. In particular, oxygens of ROH structures seem most efficient by readily permitting a multi-proton shuffle through a mechanism amounting to proton exchange. The collective results show that stabilization of these products is unlikely unless the charge and spin can be separated by at least one intervening molecule

EPR and ENDOR Studies of X-Irradiated Single Crystals of Deoxycytidine 5′-Phosphate Monohydrate at 10 and 77 K

The EPR spectra of single crystals of deoxycytidine 5′-phosphate monohydrate (5′dCMP), X-irradiated at 10 K, exhibit signals from several distinct radical species. Analysis of the ENDOR spectra from two of these radicals indicates that these result from oxidation and reduction of the cytosine base. The reduced species exhibits hyperfine coupling to the C6-Hα proton, and an additional small exchangeable hyperfine coupling from the N3-H proton. No additional couplings that may be associated with protonation of the amino group have been observed. Since the native molecule is protonated at N3, it appears that reduction of the cytosine base does not result in any further protonation. The oxidized species exhibits hyperfine couplings to C5-Hα and C1′-Hß, and two small exchangeable couplings from the C4-NH2 protons. Since no hyperfine coupling to N3-H was observed, the oxidized species is believed to be the N3-H deprotonated cation. At high X-ray dose there is also evidence for both C5 and C6 H-addition radicals at 10 K. The fate of these radicals has been studied under controlled warming conditions. Attempts have been made to relate the fate of the low-temperature radicals with several radicals that have been detected previously at 77 K and at room temperature