Model Calculations of Radiation-Induced Damage in Thymine Derivatives

When the thymine base is oxidized, the resulting cation may deprotonate reversibly at N3, or irreversibly at >C5-CH₃. In all thymine derivatives studied so far in the solid state, there is always a significant concentration of a radical formed by net H-abstraction from the >C5-CH₃. DFT calculations on this allyl-like radical are in good agreement with the experimental results for both the isotropic and anisotropic hyperfine couplings. There is a tendency for the thymine cation to deprotonate at N3 in solution. Calculations on the N3 deprotonated thymine cation yield two structures, one planar radical with an unusually large N1-C2 bond length, and one nonplanar radical with the N3 more than 25° out of the molecular plane. Calculations show that the structure with the lowest energy is the allyl-like radical.     

Quinone sensitized electron transfer photooxidation of nucleic acids: chemistry of thymine and thymidine radical cations in aqueous solution

The 2-methyl-1,4-naphthoquinone (MQ) sensitized photooxidation of nucleic acid derivatives has been studied by laser flash photolysis and steady state methods. Thymine and thymidine, as well as other DNA model compounds, quench triplet MQ by electron transfer to give MQ radical anions and pyrimidine or purine radical cations. Although the pyrimidine radical cations cannot be directly observed by flash photolysis, the addition of N,N,N',N'-tetramethyl-1,4-phenylenediamine (TMPD) results in the formation of the TMPD radical cation via scavenging of the pyrimidine radical cation. The photooxidation products for thymine and thymidine are shown to result from subsequent chemical reactions of the radical cations in oxygenated aqueous solution. The quantum yield for substrate loss at limiting substrate concentrations is 0.38 for thymine and 0.66 for thymidine. The chemistry of the radical cations involves hydration by water leading to C(6)-OH adduct radicals of the pyrimidine and deprotonation from the N(1) position in thymine and the C(5) methyl group for thymidine. Superoxide ions produced via quenching of the quinone radical anion with oxygen appear to be involved in the formation of thymine and thymidine hydroperoxides and in the reaction with N(1)-thyminyl radicals to regenerate thymine. The effects of pH were examined in the range pH 5-8 in both the presence and absence of superoxide dismutase. Initial C(6)-OH thymine adducts are suggested to dehydrate to give N(1)-thyminyl radicals.     

Structures and energetics of the deprotonated adenine-uracil base pair, including proton-transferred systems

The B3LYP/DZP++ level of theory has been employed to investigate the structures and energetics of the deprotonated adenine-uracil base pairs, (AU-H)-. Formation of the lowest-energy structure, [A(N9)-U]- (which corresponds to deprotonation at the N9 atom of adenine), through electron attachment to the corresponding neutral is accompanied by proton transfer from the uracil N3 atom to the adenine N1 atom. The driving force for this proton transfer is a significant stabilization from the base pairing in the proton transferred form. Such proton transfer upon electron attachment is also observed for the [A(N6b)-U]- and [A(C2)-U]- anions. Electron attachment to the A-U(N3) radical causes strong lone pair repulsion between the adenine N1 and the uracil N3 atoms, driving the two bases apart. Similarly, lone pair repulsion in the anion A(N6a)-U causes the loss of coplanarity of the two base units. The computed adiabatic electron attachment energies for nine AU-H radicals range from 1.86 to 3.75 eV, implying that the corresponding (AU-H)- anions are strongly bound. Because of the large AEAs of the (AU-H) radicals, the C-H and N-H bond dissociation in the AU- base pair anions requires less energy than the neutral AU base pair. The computed C-H and N-H bond dissociation energies for the AU- anion (i.e., the AU base pair plus one electron) are in the range 1.0-3.2 eV, while those for neutral AU are 4.08 eV or higher.     

Single crystals of L-O-serine phosphate X-irradiated at low temperatures: EPR, ENDOR, EIE, and DFT studies

Single crystals of the phosphorylated amino acid L-O-serine phosphate were X-irradiated and studied at 10 K and at 77 K using EPR, ENDOR, and EIE techniques. Two radicals, R1(10 K) and R1(77 K), were detected and characterized as two different geometrical conformations of the protonated reduction product >CH-C(OH)(2). R1(10 K) is only observed after irradiation at 10 K, and upon heating to 40 K, R1(10 K) transforms rapidly and irreversibly into R1(77 K). The transition from R1(10 K) to R1(77 K) strongly increases the isotropic hyperfine coupling of the C-CH(beta) coupling (Delta = 32 MHz) and the major C-OH(beta) coupling (Delta = 47 MHz), in sharp contrast to the their much reduced anisotropic hyperfine couplings after the transition. An umbrella-like inversion of the carboxylic acid center, accompanied by minor geometrical adjustments, explains the changes of these observed isotropic and anisotropic couplings. DFT calculations were done on the reduced and protonated L-O-serine phosphate radical at the B3LYP/6-311+G(2df,p)//B3LYP/6-31+G(d) level of theory in order to support the experimental observations. Two different conformations of the anion radical, related by an inversion at the carboxylic center, could be found within the single molecule partial energy-optimization scheme. These two conformations reproduce the experimental hyperfine couplings from radicals R1(10 K) and R1(77 K). A third radical, radical R2, was observed experimentally at both 10 and 77 K and was shown to be due to the decarboxylated L-O-serine phosphate oxidation product, a conclusion fully supported from the DFT calculations. Upon thermal annealing from 77 to 295 K, radicals R1(77 K) and R2 disappeared and all three previously observed room-temperature radicals could be observed. No phosphate-centered radicals could be observed at any temperatures, indicating that the phosphate-ester bond break for one of the room-temperature radicals does not occur by dissociative electron capture at the phosphate group.     

Pulsed EPR and DFT characterization of radicals produced by photo-oxidation of zeaxanthin and violaxanthin on silica-alumina

Pulsed electron nuclear double resonance (ENDOR) and two-dimensional (2D)-hyperfine sublevel correlation spectroscopy (HYSCORE) studies in combination with density functional theory (DFT) calculations revealed that photo-oxidation of natural zeaxanthin (ex Lycium halimifolium) and violaxanthin (ex Viola tricolor) on silica-alumina produces the carotenoid radical cations (Car*+) and also the neutral carotenoid radicals (#Car*) as a result of proton loss (indicated by #) from the C4(4') methylene position or one of the methyl groups at position C5(5'), C9(9'), or C13(13'), except for violaxanthin where the epoxide at positions C5(5')-C6(6') raises the energy barrier for proton loss, and the neutral radicals #Car*(4) and #Car*(5) are not observed. DFT calculations predict the largest isotropic beta-methyl proton hyperfine couplings to be 8 to 10 MHz for Car*+, in agreement with previously reported hyperfine couplings for carotenoid pi-conjugated radicals with unpaired spin density delocalized over the whole molecule. Anisotropic alpha-proton hyperfine coupling tensors determined from the HYSCORE analysis were assigned on the basis of DFT calculations with the B3LYP exchange-correlation functional and found to arise not only from the carotenoid radical cation but also from carotenoid neutral radicals, in agreement with the analysis of the pulsed ENDOR data. The formation of the neutral radical of zeaxanthin should provide another effective nonphotochemical quencher of the excited state of chlorophyll for photoprotection in the presence of excess light.     

Q-band EPR and ENDOR of low temperature X-irradiated beta-D-fructose single crystals

Beta-D-fructose single crystals were in situ X-irradiated at 80 K and measured using electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques at Q-band (34 GHz) microwave frequencies. The measurements revealed the presence of at least four carbon-centered radicals stable at 80 K. By means of ENDOR angular variations in the three principal crystallographic planes, six proton hyperfine coupling tensors could be determined and were assigned to four different radicals by the aid of EIE. Two of the radicals exhibit only beta-proton hyperfine couplings and reveal almost identical EIE spectra. For the other two radicals, the major hyperfine splitting originates from a single alpha-proton hyperfine coupling and their EIE spectra were also quite similar. The similarity of the EIE spectra and hyperfine tensors led to the assumption that there are only two essentially different radical structures. The radical exhibiting only beta-proton hyperfine couplings was assigned to a C3 centered radical arising from H3 abstraction and the other radical suggested to be an open-ring species with a disrupted C2-C3 bond and a double C2-O2 bond. A possible formation mechanism for the latter open-ring radical is presented. By means of cluster density functional theory (DFT) calculations, the structures of the two radicals were determined and a fairly good agreement between the calculated and experimental hyperfine tensors was found.     

Combined electron magnetic resonance and density functional theory study of 10 K X-irradiated beta-D-fructose single crystals

Primary free radical formations in fructose single crystals X-irradiated at 10 K were investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three principal crystallographic planes and a fourth skewed plane allowed the unambiguous determination of five proton hyperfine coupling tensors. From the EIE studies, these hyperfine interactions were assigned to three different radicals, labeled T1, T1* and T2. For the T1 and T1* radicals, the close similarity in hyperfine coupling tensors suggests that they are due to the same type of radical stabilized in two slightly different geometrical conformations. Periodic density functional theory calculations were used to aid the identification of the structure of the radiation-induced radicals. For the T1/T1* radicals a C3 centered hydroxyalkyl radical model formed by a net H abstraction is proposed. The T2 radical is proposed to be a C5 centered hydroxyalkyl radical, formed by a net hydrogen abstraction. For both radicals, a very good agreement between calculated and experimental hyperfine coupling tensors was obtained.     

The guanine cation radical: investigation of deprotonation states by ESR and DFT

This work reports ESR studies that identify the favored site of deprotonation of the guanine cation radical (G*+) in an aqueous medium at 77 K. Using ESR and UV-visible spectroscopy, one-electron oxidized guanine is investigated in frozen aqueous D2O solutions of 2'-deoxyguanosine (dGuo) at low temperatures at various pHs at which the guanine cation radical, G*+ (pH 3-5), singly deprotonated species, G(-H)* (pH 7-9), and doubly deprotonated species, G(-2H)*- (pH > 11), are found. C-8-deuteration of dGuo to give 8-D-dGuo removes the major proton hyperfine coupling at C-8. This isolates the anisotropic nitrogen couplings for each of the three species and aids our analyses. These anisotropic nitrogen couplings were assigned to specific nitrogen sites by use of 15N-substituted derivatives at N1, N2, and N3 atoms in dGuo. Both ESR and UV-visible spectra are reported for each of the species: G*+, G(-H)*, and G(-2H)*-. The experimental anisotropic ESR hyperfine couplings are compared to those obtained from DFT calculations for the various tautomers of G(-H)*. Using the B3LYP/6-31G(d) method, the geometries and energies of G*+ and its singly deprotonated state in its two tautomeric forms, G(N1-H)* and G(N2-H)*, were investigated. In a nonhydrated state, G(N2-H)* is found to be more stable than G(N1-H)*, but on hydration with seven water molecules G(N1-H)* is found to be more stable than G(N2-H)*. The theoretically calculated hyperfine coupling constants (HFCCs) of G*+, G(N1-H)*, and G(-2H)*- match the experimentally observed HFCCs best on hydration with seven or more waters. For G(-2H)*-, the hyperfine coupling constant (HFCC) at the exocyclic nitrogen atom (N2) is especially sensitive to the number of hydrating water molecules; good agreement with experiment is not obtained until nine or 10 waters of hydration are included.     

EPR and ENDOR study of radiation-induced radical formation in purines: hypoxanthine hydrochloride monohydrate crystals X-irradiated at 10 K

Electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) study of hypoxanthine.HCl.H(2)O crystals irradiated at low temperatures (10 K) identified three radical species. In these crystals, the parent molecules exist in a cationic form with a proton at N7. R1 was the product of net hydrogen addition to N3 and exhibited alpha-proton hyperfine couplings to HC2, HN1, HC8, and HN3. The coupling to HC2 has an isotropic component smaller than usual, evidently an indication that the bonds to C2 are nonplanar. R2 was the product of net hydrogen loss from N7, equivalent to the one-electron oxidation product of neutral hypoxanthine, and exhibited alpha-proton hyperfine couplings to HC2 and HC8. Both couplings are characteristic of planar bonding arrangements at the centers of spin. R3 was provisionally identified as the product of net hydrogen addition to O6 and exhibited hyperfine alpha-proton couplings to HC8 and NH1. To identify the set of radicals, the experiments employed four crystal types: normal, deuterated only at NH positions, deuterated at HC8 and NH positions, and deuterated at HC8 only. The low-temperature data also showed clear evidence for H/D isotope effects in formation and/or stabilization of all radicals. To aid and support the identifications, the experimental results were compared to DFT calculations performed on a variety of radical structures plausible for the parent molecule and molecular packing within the crystal.     

The 2'-deoxyadenosine-5'-phosphate anion, the analogous radical, and the different hydrogen-abstracted radical anions: molecular structures and effects on DNA damage

The 2'-deoxyadenosine-5'-phosphate (5'-dAMP) anion and its related radicals have been studied by reliably calibrated theoretical approaches. This study reveals important physical characteristics of 5'-dAMP radical related processes. One-electron oxidation of the 5'-dAMP anion is found on both the phosphoryl group and the adenine base with electron detachment energies close to that of phosphate. Partial removal of electron density from the adenine fragment leads to an extended pi system which includes the amine group of the adenine. Although the radical-centered carbon increases the extent of bonding with its adjacent atoms, it usually weakens the chemical bonds between the atoms at the alpha- and beta-positions. This tendency should be important in predicting the reactivity of the sugar-based radicals. The overall stability sequence of the H-abstracted 5'-dAMP anionic radicals is consistent with the analogous results for the H-abstracted neutral radicals of the adenosine nucleoside: aliphatic radicals > aromatic radicals. The negatively charged phosphoryl group attached to atom C(5)' of the ribose does not change this energetic sequence. All the H-abstraction produced 5'-dAMP radical anions are distonic radical anions. Studies have shown that the charge-radical-separating feature of the distonic radical anions is biologically relevant. This result should be important in understanding the reactive properties of these H-abstraction-produced anion radicals.     

Pentazole-based energetic ionic liquids: a computational study

The structures of protonated pentazole cations (RN5H+), oxygen-containing anions such as N(NO2)2-, NO3-, and ClO4- and the corresponding ion pairs are investigated by ab initio quantum chemistry calculations. The stability of the pentazole cation is explored by examining the decomposition pathways of several monosubstituted cations (RN5H+) to yield N2 and the corresponding azidinium cation. The heats of formation of these cations, which are based on isodesmic (bond-type conserving) reactions, are calculated. The proton-transfer reaction from the cation to the anion is investigated.     

Lithium cation as radical-polymerization catalyst

Density-functional theory (DFT) and ab initio (QCISD and CBS-RAD) calculations suggest that complexation of "naked" lithium cations to olefins favors the addition of alkyl radicals to the double bond over abstraction of an allyllic hydrogen atom. Thus, "naked" lithium cations in nonpolar solvents can catalyze the radical polymerization of olefins by favoring the chain-lengthening reaction over the competing hydrogen-atom extraction, which is competitive in the absence of metal ions. One putative initiation reaction, addition of triplet dioxygen to the double bond, is thermoneutral and has a very low barrier when the oxygen molecule is complexed to a lithium cation. An alternative process, abstraction of an allyllic hydrogen atom to generate the allyl and hydroperoxy radicals, is also strongly favored by complexation of the oxygen to the lithium cation but is less favorable than addition. These results support Michl's recent interpretation of experimentally observed alkene polymerization in the presence of lithium salts of hydrophobic carborane anions.     

Structure of radicals from X-irradiated guanine derivatives: an experimental and computational study of sodium guanosine dihydrate single crystals

In sodium guanosine dihydrate single crystals, the guanine moiety is deprotonated at N1 due to growth from high-pH (>12) solutions. Electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) studies of crystals X-irradiated at 10 K detected evidence for three radical forms. Radical R1, characterized by two proton and two nitrogen hyperfine interactions, was identified as the product of net hydrogenation at N7 of the N1-deprotonated guanine unit. R1 exhibited an unusually distorted structure leading to net positive isotropic components of the hydrogen alpha-couplings. Radical R2, characterized by one proton and one nitrogen hyperfine coupling, was identified as the primary electron-loss product. This product is equivalent to that of deprotonation at N1 by the guanine cation and represents the first ENDOR characterization of that product. Radical R3, characterized by a single hydrogen hyperfine coupling, was identified as the product of net dehydrogenation at C1' of the ribose moiety. The identification of radicals R1-R3 was supported by density functional theory (DFT) calculations on several possible structures using the B3LYP/6-311G(2df,p)//6-31G(d,p) approach. Radical R4, detected after warming the crystals to room temperature, was identified as the well-known product of net hydrogenation of C8 of the (N1-deprotonated) guanine component. Radical R1, evidently formed by protonation of the primary electron addition product, was present as roughly 60% of the total radicals detected at 10 K. Radical R2 was present as roughly 27% of the total yield, and the concentration of R3 contributed the remaining 13%. R3 is evidently the product of one-electron oxidation followed by deprotonation; thus, the balance of oxidation and reduction products is approximately equal within experimental uncertainty.     

ESR Spectra of radicals produced by reduction of pyridine and pyrazine

Radicals produced by reaction of e^?_aq with pyridine, pyrazine, and pyrazinedicarboxylic acid have been studied by electron spin resonance using the in situ radiolysis steady-state ESR technique. The radical anions initially produced have been found to undergo rapid protonation on nitrogen to form pyridinyl and pyrazinyl radicals. The NH proton of pyridinyl radical does not dissociate even at pH 13.7. The radical from pyrazine has been observed only in the doubly protonated positively charged form in acid and neutral solutions, but no spectrum was observed in alkaline media. With 2,3-pyrazinedicarboxylic acid the doubly protonated radical has been observed at pH 4–8 and the singly protonated one at pH 11–12. The pK for this dissociation is 9.2. The hyperfine constants of the pyridinyl radical are compared with those obtained from INDO molecular orbital calculations.     

The initial stages of radiation damage in ionic liquids and ionic liquid-based extraction systems

Radical intermediates generated in radiolysis and photoionization of ionic liquids (ILs) composed of ammonium, phosphonium, pyrrolidinium, and imidazolium cations and bis(triflyl)amide, dicyanamide, and bis(oxalato)borate anions have been studied using magnetic resonance spectroscopy. Large yields of terminal and penultimate C-centered radicals are observed in the aliphatic chains of the phosphonium, ammonium, and pyrrolidinium cations, but not for imidazolium cation. This pattern is indicative of efficient deprotonation of a hole trapped on the parent cation (the radical dication) that competes with rapid electron transfer from a nearby anion. This charge transfer leads to the formation of stable N- or O-centered radicals; the dissociation of parent anions is a minor pathway. Addition of 10-40 wt % of trialkyl phosphate (a common extraction agent) has relatively little effect on the fragmentation of the ILs. The yield of the alkyl radical fragment generated by dissociative electron attachment to the trialkyl phosphate is <4% of the yield of the radical fragments derived from the IL solvent. The import of these observations for radiation stability of the prospective nuclear cycle extraction systems based upon the ILs is discussed.     

Structure and solvation of nitrobenzene and 1,4-dinitrobenzene radical anions

An INDO method extended to include a contribution from the solvent by means of an effective solvent field (INDO-ESF) and based on properly optimized geometries is applied to the nitrobenzene and 1,4-dinitrobenzene radical anions. The hyperfine couplings and their solvent sensitivities are reproduced within a planar structure of the radicals. The behaviour of¹⁴N and¹⁷O splittings in derivatives with twisted nitro groups is accounted for with no difficulty.     

Successive attachment of electrons to protonated Guanine: (G+H)* radicals and (G+H)- anions

The structures, energetics, and vibrational frequencies of nine hydrogenated 9H-keto-guanine radicals (G+H)(*) and closed-shell anions (G+H)(-) are predicted using the carefully calibrated (Chem. Rev. 2002, 102, 231) B3LYP density functional method in conjunction with a DZP++ basis set. These radical and anionic species come from consecutive electron attachment to the corresponding protonated (G+H)(+) cations in low pH environments. The (G+H)(+) cations are studied using the same level of theory. The proton affinity (PA) of guanine computed in this research (228.1 kcal/mol) is within 0.7 kcal/mol of the latest experiment value. The radicals range over 41 kcal/mol in relative energy, with radical r1, in which H is attached at the C8 site of guanine, having the lowest energy. The lowest energy anion is a2, derived by hydride ion attachment at the C2 site of guanine. No stable N2-site hydride should exist in the gas phase. Structure a9 was predicted to be dissociative in this research. The theoretical adiabatic electron affinities (AEA), vertical electron affinities, and vertical detachment energies were computed, with AEAs ranging from 0.07 to 3.12 eV for the nine radicals.     

Time-resolved FT-EPR study of photoreduction of duroquinone by triethylamine in methanol

Using time resolved Fourier transform EPR spectroscopy the photoreduction of duroquinone by triethylamine in methanol solution was investigated. It is found that the spin-polarized (CIDEP) duroquinone triplet deactivates by electron transfer from triethylamine generating duroquinone radical anion and amine radical cation, and by hydrogen transfer from the solvent generating durosemiquinone radical and hydroxymethyl radical, respectively. All radicals are observed at different conditions and are spin-polarized by triplet mechanism and partially by ST₀ radical pair mechanism. The time dependence of FT-EPR intensities of radical cation and radical anion on the amine concentration is investigated in the range of 1 to 100 mM triethylamine. The contribution of the triplet mechanism to the spin polarization of radicals changes with different triethylamine concentrations. The durosemiquinone radical is found to be transformed into duroquinone radical anion in the presence of triethylamine in the solution. CIDNP experiments indicate that the hydrogen back transfer between the durosemiquinone radical and hydroxymethyl radical pair has a significant influence on the time behaviour of duroquinone radical anion. The intensity of triethylamine radical cation is found to be decreased with the increase of triethylamine concentration, which is interpreted that the triethylamine radical cation is deprotonated by the amine. Based on the FT-EPR results, a new complete mechanism is proposed.     

Interplay of intrinsic and environmental effects on the magnetic properties of free radicals issuing from H-atom addition to cytosine.

Possible radical reaction products issuing from H-atom addition to cytosine have been characterized and analyzed by means of a comprehensive quantum mechanical approach including density functional computations (B3LYP), together with simulation of the solvent by the polarizable continuum model (PCM), and averaging of spectroscopic properties over the most important vibrational motions. The hyperfine couplings of the semirigid 5,6-dihydrocytos-6yl radical computed at the optimized geometry are in good agreement with their experimental counterparts. On the other hand, vibrational averaging is mandatory for obtaining an effectively planar structure for the 5,6-dihydrocytos-5yl radical with the consequent equivalence of beta-hydrogens. Finally, only proper consideration of environmental effects restores the agreement between computed and experimental couplings for the base anion protonated at N3.     

Multiple hydrogen bonds in cytosinium zoledronate trihydrate

The asymmetric unit of the title compound [systematic name: 4‐amino‐2‐oxo‐2,3‐dihydropyrimidin‐1‐ium 1‐hydroxy‐2‐(1H,3H‐imidazol‐3‐ium‐1‐yl)ethylidenediphosphonate trihydrate], C₄H₆N₃O⁺·C₅H₉N₂O₇P₂⁻·3H₂O, contains one cytosinium cation, one zoledronate anion and three water molecules. The zoledronate anion has a zwitterionic character, in which each phosphonate group is singly deprotonated and an imidazole N atom is protonated. Furthermore, proton transfer takes place from one of the phosphonic acid groups of the zoledronate anion to one of the N atoms of the cytosinium cation. The cytosinium cation forms a C(6) chain, while the zoledronate anion forms a rectangular‐shaped centrosymmetric dimer through N—H...O hydrogen bonds. The cations and anions are held together by N—H...O and O—H...O hydrogen bonds to form a one‐dimensional polymeric tape. The three water molecules play a crucial role in hydrogen bonding, resulting in a three‐dimensional hydrogen‐bonded network.