Carbonate Radical Anion Research Articles

Hydration Leads to Efficient Reactions of the Carbonate Radical Anion with Hydrogen Chloride in the Gas Phase.

The carbonate radical anion CO3•- is a key intermediate in tropospheric anion chemistry. Despite its radical character, only a small number of reactions have been reported in the literature. Here we investigate the gas-phase reactions of CO3•- and CO3•-(H2O) with HCl under ultrahigh vacuum conditions. Bare CO3•- forms OHCl•- with a rate constant of 4.2 × 10-12 cm3 s-1, which corresponds to an efficiency of only 0.4%. Hydration accelerates the reaction, and ligand exchange of H2O against HCl proceeds with a rate of 2.7 × 10-10 cm3 s-1. Quantum chemical calculations reveal that OHCl•- is best described as an OH• hydrogen bonded to Cl-, while the ligand exchange product is Cl-(HCO3•). Under tropospheric conditions, where CO3•-(H2O) is the dominant species, Cl-(HCO3•) is efficiently formed. These reactions must be included in models of tropospheric anion chemistry.

Bicarbonate and Alkyl Carbonate Radicals: Structural Integrity and Reactions with Lipid Components.

The elusive neutral bicarbonate radical and the carbonate radical anion form an acid/conjugate base pair. We now report experimental studies for a model of bicarbonate radical, namely, methyl carbonate (methoxycarbonyloxyl) radical, complemented by DFT computations at the CAM-B3LYP level applied to the bicarbonate radical itself. Methyl carbonate radicals were generated by UV irradiation of oxime carbonate precursors. Kinetic EPR was employed to measure rate constants and Arrhenius parameters for their dissociation to CO2 and methoxyl radicals. With oleate and cholesterol lipid components, methyl carbonate radicals preferentially added to their double bonds; with linoleate and linolenate substrates, abstraction of the bis-allylic H atoms competed with addition. This contrasts with the behavior of ROS such as hydroxyl radicals that selectively abstract allylic and/or bis-allylic H atoms. The thermodynamic and activation parameters for bicarbonate radical dissociation, obtained from DFT computations, predicted it would indeed have substantial lifetime in gas and nonpolar solvents. The acidity of bicarbonate radicals was also examined by DFT methods. A noteworthy linear relationship was discovered between the known pKa's of strong acids and the computed numbers of microsolvating water molecules needed to bring about their ionization. DFT computations with bicarbonate radicals, solvated with up to eight water molecules, predicted that only five water molecules were needed to bring about its complete ionization. On comparing with the correlation, this indicated a pKa of about -2 units. This marks the bicarbonate radical as the strongest known carboxylic acid.

Ornaments in radiation treatment of cultural heritage: Color and UV–vis spectral changes in irradiated nacres

Cultural heritage objects that are radiation treated in order to stop their biodegradation often contain ornamenting materials that cannot be removed. Radiation may produce unwanted changes to such materials. Nacre is a common ornamenting material so this is an attempt to assess the impact of gamma-radiation on its optical properties. Two types of nacre (yellow and white) were obtained from a museum and subjected to different absorbed doses of Co-60 gamma irradiation under the same conditions. The radiation induced changes of nacres color were investigated with fiber optic reflectance spectroscopy (FORS). Colorimetry in CIE Lab space revealed that in both nacres the lightness shifted to darker grey hues at high doses while the color component's (red, green, yellow and blue) behavior depended on the nacre type. Observable changes occurred at doses much above the dose range needed for radiation treatment of cultural heritage objects that are often ornamented with nacre.In UV–vis reflectance spectra of samples irradiated to high doses carbonate radical anion absorption appeared.

Efficacy and site specificity of hydrogen abstraction from DNA 2-deoxyribose by carbonate radicals

The carbonate radical anion CO3•− is a potent reactive oxygen species (ROS) produced in vivo through enzymatic one-electron oxidation of bicarbonate or, mostly, via the reaction of CO2 with peroxynitrite. Due to the vitally essential role of the carbon dioxide/bicarbonate buffer system in regulation of physiological pH, CO3•− is arguably one of the most important ROS in biological systems. So far, the studies of reactions of CO3•− with DNA have been focused on the pathways initiated by oxidation of guanines in DNA. In this study, low-molecular products of attack of CO3•− on the sugar–phosphate backbone in vitro were analyzed by reversed phase HPLC. The selectivity of damage in double-stranded DNA (dsDNA) was found to follow the same pattern C4′ > C1′ > C5′ for both CO3•− and the hydroxyl radical, though the relative contribution of the C1′ damage induced by CO3•− is substantially higher. In single-stranded DNA (ssDNA) oxidation at C1′ by CO3•− prevails over all other sugar damages. An approximately 2000-fold preference for 8-oxoguanine (8oxoG) formation over sugar damage found in our study identifies CO3•− primarily as a one-electron oxidant with fairly low reactivity toward the sugar–phosphate backbone.

Pulse radiolysis and ultra-high-performance liquid chromatography/high-resolution mass spectrometry studies on the reactions of the carbonate radical with vitamin B12 derivatives.

The reactions of the carbonate radical anion (CO3 (.) (-) ) with vitamin B12 derivatives were studied by pulse radiolysis. The carbonate radical anion directly oxidizes the metal center of cob(II)alamin quantitively to give hydroxycobalamin, with a bimolecular rate constant of 2.0×10(9) M(-1) s(-1) . The reaction of CO3 (.) (-) with hydroxycobalamin proceeds in two steps. The second-order rate constant for the first reaction is 4.3×10(8) M(-1) s(-1) . The rate of the second reaction is independent of the hydroxycobalamin concentration and is approximately 3.0×10(3) s(-1) . Evidence for formation of corrinoid complexes differing from cobalamin by the abstraction of two or four hydrogen atoms from the corrin macrocycle and lactone ring formation has been obtained by ultra-high-performance liquid chromatography/high-resolution mass spectrometry (UHPLC/HRMS). A mechanism is proposed in which abstraction of a hydrogen atom by CO3 (.) (-) from a carbon atom not involved in the π conjugation system of the corrin occurs in the first step, resulting in formation of a Co(III) C-centered radical that undergoes rapid intramolecular electron transfer to form the corresponding Co(II) carbocation complex for about 50 % of these complexes. Subsequent competing pathways lead to formation of corrinoid complexes with two fewer hydrogen atoms and lactone derivatives of B12 . Our results demonstrate the potential of UHPLC combined with HRMS in the separation and identification of tetrapyrrole macrocycles with minor modifications from their parent molecule.

Reactivity of hypotaurine and cysteine sulfinic acid toward carbonate radical anion and nitrogen dioxide as explored by the peroxidase activity of Cu,Zn superoxide dismutase and by pulse radiolysis

Hypotaurine and cysteine sulfinic acid are known to be readily oxidized to the respective sulfonates, taurine and cysteic acid, by several oxidative agents that may be present in biological systems. In this work, the relevance of both the carbonate anion and nitrogen dioxide radicals in the oxidation of hypotaurine and cysteine sulfinic acid has been explored by the peroxidase activity of Cu,Zn superoxide dismutase (SOD) and by pulse radiolysis. The extent of sulfinate oxidation induced by the system SOD/H2O2 in the presence of bicarbonate (CO3•– generation), or nitrite (•NO2 generation) has been evaluated. Hypotaurine is efficiently oxidized by the carbonate radical anion generated by the peroxidase activity of Cu,Zn SOD. Pulse radiolysis studies have shown that the carbonate radical anion reacts with hypotaurine more rapidly (k = 1.1 × 109 M−1s−1) than nitrogen dioxide (k = 1.6 × 107 M−1s−1). Regarding cysteine sulfinic acid, it is less reactive with the carbonate radical anion (k = 5.5 × 107 M−1s−1) than hypotaurine. It has also been observed that the one-electron transfer oxidation of both sulfinates by the radicals is accompanied by the generation of transient sulfonyl radicals (RSO2•). Considering that the carbonate radical anion could be formed in vivo at high level from bicarbonate, this radical can be included in the oxidants capable of performing the last metabolic step of taurine biosynthesis. Moreover, the protective effect exerted by hypotaurine and cysteine sulfinate on the carbonate radical anion-mediated tyrosine dimerization indicates that both sulfinates have scavenging activity towards the carbonate radical anion. However, the formation of transient reactive intermediates during sulfinate oxidation by carbonate anion and nitrogen dioxide radical may at the same time promote oxidative reactions.

The Mechanisms and Physiological Relevance of Glycocalyx Degradation in Hepatic Ischemia/Reperfusion Injury

Hepatic ischemia/reperfusion (I/R) injury is an inevitable side effect of major liver surgery that can culminate in liver failure. The bulk of I/R-induced liver injury results from an overproduction of reactive oxygen and nitrogen species (ROS/RNS), which inflict both parenchymal and microcirculatory damage. A structure that is particularly prone to oxidative attack and modification is the glycocalyx (GCX), a meshwork of proteoglycans and glycosaminoglycans (GAGs) that covers the lumenal endothelial surface and safeguards microvascular homeostasis. ROS/RNS-mediated degradation of the GCX may exacerbate I/R injury by, for example, inducing vasoconstriction, facilitating leukocyte adherence, and directly activating innate immune cells. Preliminary experiments revealed that hepatic sinusoids contain a functional GCX that is damaged during murine hepatic I/R and major liver surgery in patients. There are three ROS that mediate GCX degradation: hydroxyl radicals, carbonate radical anions, and hypochlorous acid (HOCl). HOCl converts GAGs in the GCX to GAG chloramides that become site-specific targets for oxidizing and reducing species and are more efficiently fragmented than the parent molecules. In addition to ROS/RNS, the GAG-degrading enzyme heparanase acts at the endothelial surface to shed the GCX. The GCX seems to be degraded during major liver surgery, but the underlying cause remains ill-defined. The relative contribution of the different ROS and RNS intermediates to GCX degradation in vivo, the immunogenic potential of the shed GCX fragments, and the role of heparanase in liver I/R injury all warrant further investigation.

Formation of spiroiminodihydantoin due to the reaction between 8-oxoguanine and carbonate radical anion: A quantum computational study

Reaction of 8-oxoguanine (8OG) with carbonate radical anion (CO3·−) producing spiroiminodihydantoin has been investigated using density functional theory. Geometries of reactant complex, intermediate complexes, product complexes and transition states were optimized at the B3LYP/6-31G(d,p) level of theory in gas phase which was followed by single point energy calculations employing the B3LYP, M06-2X and WB97XD functionals along with the AUG-cc-pVDZ basis set in gas phase and aqueous media. Solvent effect was treated employing the integral equation formalism of the polarizable continuum model. Possible roles of aeration, stirring and photoirradiation of reaction media which are performed in experimental studies have been explained.

PP02 - Effects of hypotaurine on carbonate radical anion and nitrogen dioxide radical generated by peroxidase activity of Cu,Zn-superoxide dismutase

PP02 - Effects of hypotaurine on carbonate radical anion and nitrogen dioxide radical generated by peroxidase activity of Cu,Zn-superoxide dismutase

One-electron oxidation and reduction of glycosaminoglycan chloramides: A kinetic study

Hypochlorous acid and its acid–base counterpart, hypochlorite ions, produced under inflammatory conditions, may produce chloramides of glycosaminoglycans, these being significant components of the extracellular matrix (ECM). This may occur through the binding of myeloperoxidase directly to the glycosaminoglycans. The N–Cl group in the chloramides is a potential selective target for both reducing and oxidizing radicals, leading possibly to more efficient and damaging fragmentation of these biopolymers relative to the parent glycosaminoglycans. In this study, the fast reaction techniques of pulse radiolysis and nanosecond laser flash photolysis have been used to generate both oxidizing and reducing radicals to react with the chloramides of hyaluronan (HACl) and heparin (HepCl). The strong reducing formate radicals and hydrated electrons were found to react rapidly with both HACl and HepCl with rate constants of 1–1.7×108 and 0.7–1.2×108M−1s−1 for formate radicals and 2.2×109 and 7.2×108M−1s−1 for hydrated electrons, respectively. The spectral characteristics of the products of these reactions were identical and were consistent with initial attack at the N–Cl groups, followed by elimination of chloride ions to produce nitrogen-centered radicals, which rearrange subsequently and rapidly to produce C-2 radicals on the glucosamine moiety, supporting an earlier EPR study by M.D. Rees et al. (J. Am. Chem. Soc.125: 13719–13733; 2003). The oxidizing hydroxyl radicals also reacted rapidly with HACl and HepCl with rate constants of 2.2×108 and 1.6×108M−1s−1, with no evidence from these data for any degree of selective attack on the N–Cl group relative to the N–H groups and other sites of attack. The carbonate anion radicals were much slower with HACl and HepCl than hydroxyl radicals (1.0×105 and 8.0×104M−1s−1, respectively) but significantly faster than with the parent molecules (3.5×104 and 5.0×104M−1s−1, respectively). These findings suggest that these potential in vivo radicals may react in a site-specific manner with the N–Cl group in the glycosaminoglycan chloramides of the ECM, possibly to produce more efficient fragmentation. This is the first study therefore to conclusively demonstrate that reducing radicals react rapidly with glycosaminoglycan chloramides in a site-specific attack at the N–Cl group, probably to produce a 100% efficient biopolymer fragmentation process. Although less reactive, carbonate radicals, which may be produced in vivo via reactions of peroxynitrite with serum levels of carbon dioxide, also appear to react in a highly site-specific manner at the N–Cl group. It is not yet known if such site-specific attacks by this important in vivo species lead to a more efficient fragmentation of the biopolymers than would be expected for attack by the stronger oxidizing species, the hydroxyl radical. It is clear, however, that the N–Cl group formed under inflammatory conditions in the extracellular matrix does present a more likely target for both reactive oxygen species and reducing species than the N–H groups in the parent glycosaminoglycans.

Cerium oxide nanoparticles accelerate the decay of peroxynitrite (ONOO−)

Cerium oxide nanoparticles (CeO2 NPs) have been shown to possess a substantial oxygen storage capacity via the interchangeable surface reduction and oxidation of cerium atoms, cycling between the Ce(4+) and Ce(3+) redox states. It has been well established in many studies that depending on their reactivity and surface chemistry, CeO2 NPs can effectively convert both reactive oxygen species (superoxide, O2 (•-), and hydrogen peroxide) into more inert species and scavenge reactive nitrogen species (RNS)(nitric oxide, •NO), both in vitro and in vivo. Since much of damage attributed to •NO and O2 (•-) is actually the result of oxidation or nitration by peroxynitrite or its breakdown products and due to the multiple species that these nanoparticles target in vivo, it was logical to test their interaction with the highly reactive molecule peroxynitrite (ONOO(-)). Here, we report that CeO2 NPs significantly accelerated the decay of ONOO(-) by three independent methods. Additionally, our data suggest the ability of CeO2 NPs to interact with ONOO(-) is independent of the Ce(3+)/Ce(4+) ratio on the surface of the CeO2 NPs. The accelerated decay was not observed when reactions were carried out in an inert gas (argon), suggesting strongly that the decay of peroxynitrite is being accelerated due to a reaction of CeNPs with the carbonate radical anion. These results suggest that one of the protective effects of CeO2 NPs during RNS is likely due to reduction in peroxynitrite or its reactive breakdown products.

Photochemical decomposition of perfluorooctanoic acids in aqueous carbonate solution with UV irradiation

Perfluorooctanoic acid (PFOA) is a persisted organic pollutant and a common contaminant in wastewater because of its widespread occurrence in the environment and its ability to bioaccumulate. Recent studies indicate that PFOA is toxic and carcinogenic to animals such as rats, fishes, monkeys, and even humans. In this study, PFOA was decomposed in water using carbonate radical anions (CO3-) under 254nm UV irradiation at 400W. CO3- is a strong oxidizing and selective radical, however it works efficiently in decomposing PFOA solution. In this study, the results showed that PFOA was decomposed 100% after 12h by using a combination of UV irradiation and CO3-, while under only UV irradiation, 52.1% of PFOA was decomposed. In addition, the decomposition of PFOA with CO3- under UV irradiation was more favorable in a slightly alkaline (pH=8.8) solution and sodium hydrogen carbonate (NaHCO3) 40mM. Moreover, the intermediates included the shorter-chain perfluorinated carboxylic acids and fluorine ions.

Bicarbonate-dependent, carbonate radical anion-driven tocopherol-mediated human LDL peroxidation: an in vitro and in vivo study

We have here investigated possible occurrence of bicarbonate-dependent, carbonate radical anion (CO3•−)-driven tocopherol-mediated human LDL peroxidation (TMP) in vitro and in vivo. CO3•−, generated in vitro by the SOD1/H2O2/bicarbonate system, readily promoted TMP, which was dependent on α-tocopherol and bicarbonate concentrations, and was inhibited by the CO3•− scavenger ethanol; moreover, TMP induced in vitro by the SOD1/H2O2/bicarbonate system occurred in the presence of α-tocopherol that typically underwent slow oxidative consumption. In the in vivo clinical setting, we showed that, compared to controls, hypertensive patients with diuretic-induced metabolic alkalosis and heightened blood bicarbonate concentration had lipid hydroperoxide burden and decreased α-tocopherol content in the LDL fraction, with direct significant correlation between the LDL levels of α-tocopherol and those of lipid hydroperoxides; remarkably, after resolution of metabolic alkalosis, together with normalization of blood bicarbonate concentration, the LDL content of lipid hydroperoxides was decreased and that of α-tocopherol augmented significantly. These findings suggest bicarbonate-dependent, CO3•−-driven LDL TMP in vivo. In conclusion, the present study highlights the occurrence of bicarbonate-dependent, CO3•−-driven human LDL TMP, the role of which in pathological conditions such as atherosclerosis warrants, however, further investigation.

Carbonate radical anion as an efficient reactive oxygen species: Its reaction with guanyl radical and formation of 8-oxoguanine

Mechanisms of reactions of four different tautomers (G(-H1)·, G(-H2a)·, G(-H2b)· and G(-H9)·) of guanyl radical with carbonate radical anion (CO3.−) producing the mutagenic product 8-oxoguanine (8-oxoG) have been investigated theoretically using density functional theory and second order Møller–Plesset perturbation (MP2) theory. Geometries of reactant, intermediate and product complexes and those of transition states were optimized in gas phase. Solvent effect of aqueous media was treated by including eight specific water molecules in a hydration cell during optimization and single point energy calculations employing the polarizable continuum model. It is found that the specific water molecules catalyze proton transfer involving the different sites of the guanyl radical during the reaction. Possible roles of aeration, stirring and photoirradiation of reaction media which are employed to facilitate the reaction in experimental studies are explained. The carbonate radical anion is found to be a very effective reactive oxygen species.

Kinetics of the oxidation of reduced Cu,Zn-superoxide dismutase by peroxymonocarbonate

Kinetic evidence is reported for the role of the peroxymonocarbonate, HOOCO2−, as an oxidant for reduced Cu,Zn-superoxide dismutase-Cu(I) (SOD1) during the peroxidase activity of the enzyme. The formation of this reactive oxygen species results from the equilibrium between hydrogen peroxide and bicarbonate. Recently, peroxymonocarbonate has been proposed to be a key substrate for reduced SOD1 and has been shown to oxidize SOD1-Cu(I) to SOD1-Cu(II) much faster than H2O2. We have reinvestigated the kinetics of the reaction between SOD1-Cu(I) and HOOCO2− by using conventional stopped-flow spectrophotometry and obtained a second-order rate constant of k=1600±100M−1s−1 for SOD1-Cu(I) oxidation by HOOCO2−. Our results demonstrate that peroxymonocarbonate oxidizes SOD1-Cu(I) to SOD1-Cu(II) and is in turn reduced to the carbonate anion radical. It is proposed that the dissociation of His61 from the active site Cu(I) in SOD-Cu(I) contributes to this chemistry by facilitating the binding of larger anions, such as peroxymonocarbonate.

Reactions of Singly-Reduced Ethylene Carbonate in Lithium Battery Electrolytes: A Molecular Dynamics Simulation Study Using the ReaxFF

We have conducted quantum chemistry calculations and gas- and solution-phase reactive molecular dynamics simulation studies of reactions involving the ethylene carbonate (EC) radical anion EC(-) using the reactive force field ReaxFF. Our studies reveal that the substantial barrier for transition from the closed (cyclic) form, denoted c-EC(-), of the radical anion to the linear (open) form, denoted o-EC(-), results in a relatively long lifetime of the c-EC(-) allowing this compound to react with other singly reduced alkyl carbonates. Using ReaxFF, we systematically investigate the fate of both c-EC(-) and o-EC(-) in the gas phase and EC solution. In the gas phase and EC solutions with a relatively low concentration of Li(+)/x-EC(-) (where x = o or c), radical termination reactions between radical pairs to form either dilithium butylene dicarbonate (CH(2)CH(2)OCO(2)Li)(2) (by reacting two Li(+)/o-EC(-)) or ester-carbonate compound (by reacting Li(+)/o-EC(-) with Li(+)/c-EC(-)) are observed. At higher concentrations of Li(+)/x-EC(-) in solution, we observe the formation of diradicals which subsequently lead to formation of longer alkyl carbonates oligomers through reaction with other radicals or, in some cases, formation of (CH(2)OCO(2)Li)(2) through elimination of C(2)H(4). We conclude that the local ionic concentration is important in determining the fate of x-EC(-) and that the reaction of c-EC(-) with o-EC(-) may compete with the formation of various alkyl carbonates from o-EC(-)/o-EC(-) reactions.

Structural, energetic and dynamic properties of guanine(C8)–thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair

The one-electron oxidation of guanine in DNA by carbonate radical anions, a decomposition product of peroxynitrosocarbonate which is associated with the inflammatory response, can lead to the formation of intrastrand cross-links between guanine and thymine bases [Crean et al. (Oxidation of single-stranded oligonucleotides by carbonate radical anions: generating intrastrand cross-links between guanine and thymine bases separated by cytosines. Nucleic Acids Res. 2008; 36: 742–755.)]. These involve covalent bonds between the C8 positions of guanine (G*) and N3 of thymine (T*) in 5′-d(…G*pT*…) and 5′-d(…G*pCpT*…) sequence contexts. We have performed nucleotide excision repair (NER) experiments in human HeLa cell extracts which show that the G*CT* intrastrand cross-link is excised with approximately four times greater efficiency than the G*T* cross-link embedded in 135-mer DNA duplexes. In addition, thermal melting studies reveal that both lesions significantly destabilize duplex DNA, and that the destabilization induced by the G*CT* cross-link is considerably greater. Consistent with this difference in NER, our computations show that both lesions dynamically distort and destabilize duplex DNA. They disturb Watson–Crick base-pairing and base-stacking interactions, and cause untwisting and minor groove opening. These structural perturbations are much more pronounced in the G*CT* than in the G*T* cross-link. Our combined experimental and computational studies provide structural and thermodynamic understanding of the features of the damaged duplexes that produce the most robust NER response.

Solvent exposure associated with single abasic sites alters the base sequence dependence of oxidation of guanine in DNA in GG sequence contexts.

The effect of exposure of guanine in double-stranded oligonucleotides to aqueous solvent during oxidation by one-electron oxidants was investigated by introducing single synthetic tetrahydrofuran-type abasic sites (Ab) either adjacent to or opposite tandem GG sequences. The selective oxidation of guanine was initiated by photoexcitation of the aromatic sensitizers riboflavin and a pyrene derivative, and by the relatively small negatively charged carbonate radical anion. The relative rates of oxidation of the 5'- and 3' side G in runs of 5'⋅⋅⋅GG⋅⋅⋅ (evaluated by standard hot alkali treatment of the damaged DNA strand followed by high resolution gel electrophoresis of the cleavage fragments) are markedly affected by adjacent abasic sites either on the same or opposite strand. For example, in fully double-stranded DNA or one with an Ab adjacent to the 5'-G, the 5'-G/3'-G damage ratio is ≥4, but is inverted (<1.0) with the Ab adjacent to the 3'-G. These striking effects of Ab are attributed to the preferential localization of the "hole" on the most solvent-exposed guanine regardless of the size, charge, or reduction potential of the oxidizing species.

Quantum theoretical study of mechanism of the reaction between guanine radical cation and carbonate radical anion: Formation of 8‐oxoguanine

AbstractThe reaction between guanine radical cation (G+·) and carbonate radical anion (CO3−·) producing the mutagenic product 8‐oxoguanine that has been observed experimentally was investigated using density functional and second‐order Møller–Plesset perturbation (MP2) theories. The structures of reactant, intermediate, and product complexes as well as those of the transition states were fully optimized at the B3LYP/6‐31G**, B3LYP/AUG‐cc‐pVDZ, and BHandHLYP/AUG‐cc‐pVDZ levels of density functional theory in gas phase. Single point energy calculations were performed at the MP2/AUG‐cc‐pVDZ level using the BHandHLYP/AUG‐cc‐pVDZ level gas‐phase optimized geometries. To obtain the equivalent solvent that would approximately represent the complex medium used in the experimental study, bulk solvent effect on the stability of the reactant complex was studied by single point energy calculations in various solvent media (toluene, chlorobenzene, dichloroethane, acetone dimethylsulfoxide, and water) using the polarizable continuum model. Thus, chlorobenzene was found to represent the experimental medium fairly closely. The calculated Gibbs free barrier and released energies show that the reaction under consideration would occur efficiently. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Generation of Guanine–Thymidine Cross-Links in DNA by Peroxynitrite/Carbon Dioxide

Nitrosoperoxycarbonate derived from the combination of carbon dioxide and peroxynitrite is an important chemical mediator of inflammation. In aqueous solutions, it rapidly decomposes to the reactive species CO(3)(•-) and (•)NO(2) radicals that are known to initiate the selective oxidation and nitration of guanine in DNA. We have previously demonstrated that the reactions of carbonate radical anions with guanine in 2'-deoxyoligoribonucleotides generate a previously unknown intrastrand cross-linked guanine-thymine product G*-T* with a covalent bond between the C8 (G*) and the thymine N3 (T*) atoms (Crean Nucleic Acids Res. 2008, 36, 742-755). In this work, we demonstrate that G*-T* cross-linked products are also formed when peroxynitrite (0.1 mM) reacts with native DNA in aqueous solutions (pH 7.5-7.7) containing 25 mM carbon dioxide/bicarbonate, in addition to the well-known nitration/oxidation products of guanine such as 8-nitroguanine (8-nitro-G), 5-guanidino-4-nitroimidazole (NIm), 8-oxo-7,8-dehydroguanine (8-oxo-G), and spiroiminodihydantoin (Sp). The yields of these products, after enzymatic digestion with P1 nuclease and alkaline phosphatase to the nucleotide level and reversed phase HPLC separation, were compared with those obtained with the uniformly, isotopically labeled (15)N,(13)C-labeled 2'-deoxy oligoribonucleotides 5'-dGpT and 5'-dGpCpT. The d(G*pT*) and d(G*-T*) cross-linked products derived from the di- and trioligonucleotides, respectively, were used as standards for identifying the analogous lesions in calf thymus DNA by isotope dilution LC-MS/MS methods in the selected reaction monitoring mode. The NIm and 8-nitro-G are the major products formed (∼0.05% each), and lesser amounts of 8-oxo-G (∼0.02%) and d(G*pT*) and d(G*-T*) enzymatic digestion products (∼0.002% each) were found. It is shown that the formation of d(G*pT*) enzyme digestion product can arise only from intrastrand cross-links, whereas d(G*-T*) can arise from both interstrand and intrastrand cross-linked products.