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.     

Methyl and silyl mesolytic dissociations in the radical cations and radical anions of but-1-ene,allylsilane, hexa-1,3-diene,and penta-2,4-dienylsilane. CAS-MCSCF and coupled cluster theoretical study

Methyl or silyl dissociation in the CH(2)=CHCH(2)-XH(3) (a-XH(3)(*)(+)) and CH(2)=CHCH=CHCH(2)-XH(3) (p-XH(3)(*) (+)) radical cations (X = C, Si) yields a(+) or p(+) and XH(3)(*). Similarly, the radical anions a-CH(3)(*) (-) and p-CH(3)(*) (-) give the pi-delocalized anion and CH(3)(*) preferentially. In contrast, a-SiH(3)(*) (-) and p-SiH(3)(*-) prefer to dissociate into the pi-delocalized radical and silide. All reactions are endoergic: by 43-50 kcal mol(-)(1) in the radical cations, and easier to some extent in the radical anions, that require 29-33 (X = C) and 13-14 kcal mol(-)(1) (X = Si). The fragmentation energy profiles do not present significant barriers for the backward process in the case of the radical cations. All radical anions exhibit an energy maximum along the dissociation pathway, but the barrier is lower than the dissociation limit. Fragmentation is "activated" more in the anions than in the cations with respect to homolysis in the corresponding neutrals (that requires 72-81 kcal mol(-)(1)). Wave function analysis indicates that the C-X bond cleavage in the hydrocarbon radical ions, although formally comparable to a homolytic process, is at variance with this model, due to the spin recoupling of one of the two C-X bond electrons with the originally unpaired electron. This is basically true also for the silyl-substituted radical anions, in which the initial more delocalized charge distribution might suggest some heterolytic character of the bond cleavage.     

Substituent and solvent effects on the beta-heterolysis reaction of beta-hydroxy arylethyl radicals

Time-resolved conversion of a series of beta-hydroxy arylethyl radicals with electron-donating and -withdrawing aromatic substituents to their corresponding styrene radical cation via heterolytic loss of the beta-hydroxy leaving group was examined with nanosecond laser flash photolysis. In all cases, the reaction was catalyzed by added perchloric acid. Radicals 2a-d reacted via a pre-equilibrium protonation mechanism in acidic 1,1,1,3,3,3-hexafluoroisopropanol (HFIP), and measuring rate constants for radical cation formation as a function of acid content allowed for the determination of absolute rate constants ranging from 3.6 x 10(6) to 3.8 x 10(7) s(-1) for the loss of water from the protonated beta-hydroxy arylethyl radicals 2a-d, as well as the acidity constants, pKa approximately 1.5 (in HFIP), for the protonated radicals. The 4-methoxy-substituted beta-hydroxy arylethyl radical 2e reacted by rate determining protonation in HFIP with a second-order rate constant of k(H+) = 7.8 x 10(8) M(-1) s(-1). However, in acetonitrile, 2,2,2-trifluoroethanol, and mixtures of these two solvents, 2e reacted by pre-equilibrium protonation, allowing for solvent effects on the rate constant for loss of water from the protonated radical 2e to be determined. With use of these data, substituent electronic effects on the kinetics of the beta-heterolysis reaction are discussed. Differences in the effect of solvent on the rate constant for loss of water from the protonated beta-hydroxy arylethyl radicals and other beta-substituted arylethyl radicals are also discussed.     

A mass spectrometry study of tirapazamine and its metabolites. insights into the mechanism of metabolic transformations and the characterization of reaction intermediates

Tandem mass spectrometry methods were used to study the sites of protonation and for identification of 3-amino-1,2,4-benzotriazine 1,4-dioxide (1, tirapazamine), and its metabolites (3-amino-1,2,4-benzotriazine 1-oxide (3), 3-amino-1,2,4-benzotriazine 4-oxide (4), 3-amino-1,2,4-benzotriazine (5), and a related isomer 3-amino-1,2,4-benzotriazine 2-oxide (6). Fragmentation pathways of 3 and 5 indicated the 4-N-atom as the most likely site of protonation. Among the N-oxides studied, the 4-oxide (4) showed the highest degree of protonation at the oxygen atom. The differences in collision-induced dissociation of isomeric protonated 1-, 2- and 4-oxides allowed for their identification by LC/MS/MS. Gas phase and liquid phase protonation of tirapazamine occurred exclusively at the oxygen in the 4-position. A loss of OH radical from these ions (2(+)) resulted in ionized 3. Neutralization-reionization mass spectrometry (NR MS) experiments demonstrated the stability of the neutral analogue of protonated tirapazamine in the gas phase in the micro s time-frame. A significant portion of the neutral tirapazamine radicals (2) dissociated by loss of hydroxyl radical during the NR MS event, which indicates that previously proposed mechanisms for redox-activated DNA damage are reasonable. The activation energy for loss of hydroxyl radical from activated tirapazamine (2) was estimated to be approximately 14 kcal mol(-1). Stable neutral analogues of [3 + H](+) and [5 + H](+) ions were also generated in the course of NR MS experiments. Structures of these radicals were assigned to the molecules having an extra hydrogen atom at one of the ring N-atoms. Quantum chemical calculations of protonated 1, 3, 4 and 5 and the corresponding neutrals were performed to assist in the interpretation of experimental results and to help identify their structures.     

Chemical radiation studies of 8-bromo-2'-deoxyinosine and 8-bromoinosine in aqueous solutions

The reactions of hydrated electrons (e(aq) (-)) with 8-bromo-2'-deoxyinosine (8) and 8-bromoinosine (12) have been investigated by radiolytic methods coupled with product studies and have been addressed computationally by means of BB1K-HMDFT calculations. Pulse radiolysis revealed that one-electron reductive cleavage of the C--Br bond gives the C8 radical 9 or 13 followed by a fast radical translocation to the sugar moiety. Selective generation of a C5' radical occurs in the 2'-deoxyribo derivative, whereas in the ribo analogue the reaction is partitioned between the C5' and C2' positions with similar rates. Both C5' radicals undergo cyclizations, 10-->11 and 14-->15, with rate constants of 1.4 x 10(5) and of 1.3 x 10(4) s(-1), respectively. The redox properties of radicals 10 and 11 have also been investigated. A synthetically useful photoreaction has also been developed as a one-pot procedure that allows the conversion of 8 to 5',8-cyclo-2'-deoxyinosine in a high yield and a diastereoisomeric ratio (5'R)/(5'S) of 4:1. The present results are compared with data previously obtained for 8-bromoadenine and 8-bromoguanine nucleosides. Theory suggests that the behavior of 8-bromopurine derivatives with respect to solvated electrons can be attributed to differences in the energy gap between the pi*- and sigma*-radical anions.     

Glycosidic bond cleavage of pyrimidine nucleosides by low-energy electrons: a theoretical rationale

DNA damage by attachment of low-energy secondary electrons is a very interesting and important mechanism. Electron capture and subsequent base release are thought to be the elementary steps of this mechanism. The process of the N1-glycosidic bond breaking of anion radicals of pyrimidine nucleosides, specifically the 2'-deoxyribothymidine (dT) and 2'-deoxyribocytidine (dC) anions, has been investigated theoretically at the B3LYP/DZP++ level of theory. The release of nucleobases by the attachment of low-energy electrons depends on the formation of a stable anion radical of the nucleoside. The lower bond-breaking activation energy and the higher vertical electron detachment energy for dT enables the heterolytic cleavage of the N1-glycosidic bond. However, with the higher bond-breaking activation energy and the lower vertical electron detachment energy for dC, the release of cytosine might be impractical when the incident electrons have high kinetic energy. Furthermore, the release of cytosine would have a quantum yield much lower than that of dT when the incident electrons have lower kinetic energy. This study also demonstrates the importance of the proton at O5' of 2'-deoxyribose in the base release process. Extending this investigation from dT to dC advances the insight into the mechanism of the N1-glycosidic bond-breaking process. The information from this extensive investigation should be valuable for further experimental studies of cytosine release in irradiated DNA.     

Model Calculations of Radiation-Induced Damage in 1-Methyluracil:9-Ethyladenine

Detailed EPR and ENDOR experiments on the cocrystalline complex of 1-methyluracil:9-Ethyladenine (MUEA) have revealed that the major radiation-induced products observed at 10 K on MU are: MUEA1, a radical formed by net hydrogen abstraction from the N1-CH₃ methyl group, MUEA2, the MU radical anion, and MUEA3, the C5 H-addition radical. The following four products were observed on the adenine moiety at 10 K, MUEA4, the N3 protonated adenine anion, MUEA5, the native adenine cation, MUEA6, the amino deprotonated adenine cation, and MUEA7, the C8 H-addition radical formed by net H-addition to C8 of the adenine base. The geometries, energetics, and hyperfine properties of all possible radicals of MU and EA, the native anions and cations, as well as radicals formed via net hydrogen atom abstraction (deprotonated cations) or addition (protonated anions) were investigated theoretically. All systems were optimized using the hybrid Hartree–Fock–density functional theory functional B3LYP, in conjunction with the 6-31G(d,p) basis set of Pople and co-workers. Calculations of the anisotropic hyperfine couplings for all the radicals observed in MUEA are presented and are shown to compare favorably with the experimentally measured hyperfine couplings. The calculated ionizations potentials indicate that EA would be the preferred oxidation site. In MUEA, both the adenine cation and its N4-deprotonated derivative were observed. The calculated electron affinities indicate that MU would be the preferred reduction site. In MUEA radical, MUEA2 is a uracil reduction product, however the protonation state of this radical could not be determined experimentally. Calculations suggest that MUEA2 is actually the C4=O protonated anion.     

The Protonated Guanine–Cytosine Base Pair

Protonated base pairs were recently implicated in the context of DNA proton transfer and charge migration. The effects of protonating different sites of the guanine–cytosine (GC) base pair are studied here by using the DZP++ B3LYP density functional method. Optimized structures for the protonated GC base pair are compared with those of parent GC and the neutral hydrogenated GC radical (GCH). Proton and hydrogen‐atom additions significantly disturb the structure of the GC base pair. However, the structural perturbations arising from protonation are often less than those arising from hydrogenation of GC. Protonation of the GC base pair causes significant strengthening of the interstrand hydrogen bonds and a concomitant increase in the base dissociation energies. The adiabatic ionization potentials (AIPs), vertical ionization potentials (VIPs), and proton affinities (PAs) for the different protonation sites of the GC base pair are predicted. The N7 site of guanine is the preferred site for protonation of the GC base pair.     

Ultrafast proton-coupled electron-transfer dynamics in pyrene-modified pyrimidine nucleosides: model studies towards an understanding of reductive electron transport in DNA.

5-(Pyren-1-yl)-2'-deoxyuridine (PydU) and 5-(Pyren-1-yl)-2'-deoxycytidine (PydC) were used as model nucleosides for DNA-mediated reductive electron transport (ET) in steady-state fluorescence and femtosecond time-resolved transient absorption spectroscopy studies. Excitation of the pyrene moiety in PydU and PydC leads to an intramolecular electron transfer that yields the pyrenyl radical cation and the corresponding pyrimidine radical anion (dU.- and dC.-. By comparing the excited state dynamics of PydC and PydU, we derived information about the energy difference between the two pyrimidine radical anion states. To determine the influence of protonation on the rates of photoinduced intramolecular ET, the spectroscopic investigations were performed in acetonitrile, MeCN, and in water at different pH values. The results show a significant difference in the basicity of the generated pyrimidine radical anions and imply an involvement of proton transfer during electron hopping in DNA. Our studies revealed that the radical anion dC.- is being protonated even in basic aqueous solution on a picosecond time scale (or faster). These results suggest that protonation of dC.- may also occur in DNA. In contrast, efficient ET in PydU could only be observed at low pH values (< 5). In conclusion, we propose--based on the free energy differences and the different basicities--that only dT.- but not dC.- can participate as an intermediate charge carrier for excess electron migration in DNA.     

Transient spectroscopy of ninhydrin

The photochemistry of ninhydrin in benzene and water was studied by laser flash photolysis and electron paramagnetic resonance. Its photochemistry was shown to be dependent on the solvent. In benzene, a triplet excited state was observed, which underwent hydrogen abstraction reactions or reduction to the radical anion. In water, the radical anion of ninhydrin was formed within the laser pulse (15 ns) at neutral pH, whereas the neutral ketyl radical was formed by protonation of the radical anion at low pH. A pKa of 0.77 was determined for the protonation equilibrium. The formation of hydrindantin is proposed to occur through the dimerization of the ketyl radical or the radical anion (or both). In addition, ninhydrin was shown to be a poor precursor for the photogeneration of hydroxyl radicals.     

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.     

15N CIDNP study of formation and decay of peroxynitric acid: evidence for formation of hydroxyl radicals

The reaction of nitrous acid with hydrogen peroxide leads to nitric acid as the only stable product. In the course of this reaction, peroxynitrous acid (ONOOH) and, in the presence of CO(2), a peroxynitrite-CO(2) adduct (ONOOCO(2)(-)) are intermediately formed. Both intermediates decompose to yield highly oxidizing radicals, which subsequently react with excess hydrogen peroxide to yield peroxynitric acid (O(2)NOOH) as a further intermediate. During these reactions, (15)N chemically induced dynamic nuclear polarization (CIDNP) effects are observed, the analysis of the pH dependency of which allows the elucidation of mechanistic details. The formation and decay of peroxynitric acid via free radicals NO(2)(*) and HOO(*) is demonstrated by the appearance of (15)N CIDNP leading to emission (E) in the (15)N NMR signal of O(2)NOOH during its formation and to enhanced absorption (A) during its decay reaction. Additionally, the (15)N NMR signal of the nitrate ion (NO(3)(-)) appears in emission at pH approximately 4.5. These observations are explained by proposing the intermediate formation of short-lived radical anions O(2)NOOH(*)(-) probably generated by electron transfer between peroxynitric acid and peroxynitrate anion, followed by decomposition of O(2)NOOH(*)(-) into NO(3)(-) and HO(*) and NO(2)(-) and HOO(*) radicals, respectively. The feasibility of such reactions is supported by quantum-chemical calculations at the CBS-Q level of theory including PCM solvation model corrections for aqueous solution. The release of free HO(*) radicals during decomposition of O(2)NOOH is supported by (13)C and (1)H NMR product studies of the reaction of preformed peroxynitric acid with [(13)C(2)]DMSO (to yield the typical "HO(*) products" methanesulfonic acid, methanol, and nitromethane) and by ESR spectroscopic detection of the HO(*) and CH(3)(*) radical adducts to the spin trap compound POBN in the absence and presence of isotopically labeled DMSO, respectively.     

Time-resolved FT EPR and optical spectroscopy study on photooxidation of aliphatic alpha-amino acids in aqueous solutions; electron transfer from amino vs carboxylate functional group

Using time-resolved Fourier transform electron paramagnetic resonance, FT EPR, and optical spectroscopy, the photooxidation of glycine, alpha-alanine, alpha-aminoisobutyric acid, and model compounds beta-alanine, methylamine and sodium acetate, by excited triplets of anthraquinone-2,6-disulfonate dianion was studied in aqueous solutions in the pH range 5-13. Anthraquinone radical trianions showing strong emissive spin-polarization (CIDEP) were formed, indicating fast electron transfer from the quenchers to the spin-polarized quinone triplet as the primary reaction. None of the primary radicals formed upon one-electron oxidation of quenchers could be detected at the nanosecond time scale of FT EPR measurements because of their very fast transformation into secondary products. The latter were identified to be decarboxylated alpha-aminoalkyl radicals for alpha-amino acids anions and zwitterions, beta-aminoalkyl radicals for beta-alanine zwitterions, and methyl radicals for acetate anions; corresponding aminyl radicals were the first EPR detectable products from beta-alanine anions and methylamine. Thus, anthraquinone-2,6-disulfonate triplet can take an electron from both NH(2)- and -CO(2)(-) functional groups forming aminium ((+*)NH(2)-) and acyloxyl (-CO(2)(*)) radicals, respectively. Aminium radicals derived from beta-alanine anions and CH(3)-NH(2) stabilize by deprotonation into aminyl radicals, whereas these derived from alpha-amino acids anions are known to suffer ultrafast decarboxylation (tau approximately 10 ps). Analysis of the polarization patterns revealed that decarboxylation from acyloxyl radicals are considerably slower (ns < tau < 0.1 micros). Therefore, in the case of alpha-amino acids, the isoelectronic structures NH(2)-CR(2)-CO(2)(*) and (+*)NH(2)-CR(2)-CO(2)(-) probably do not constitute resonance mesomeric forms of one and the same species and the decarboxylation of aminium radicals is not preceded by the intramolecular carboxylate to amino group electron transfer. Absolute triplet quenching rate constants at zero ionic strength were in the range of 2 x 10(8) to 2 x 10(9) M(-1) s(-1) for R-NH(2) and 2 x 10(7) to 10(8) M(-1) s(-1) for R-CO(2)(-) type of electron donors, reflecting in principle their standard reduction potentials. The strengths of acids: (+)NH(3)-(*)CH(2), (+)NH(3)-(*)C(CH(3))H, and (+)NH(3)-(*)C(CH(3))(2), pK(a) <4, >6, and >7, respectively, were found to be remarkably strongly dependent on alpha-C substitution. The conjugate bases of these alpha-aminoalkyl radicals reduce anthraquinone-2,6-disulfonate dianion ground state with k(sec) = 3 x 10(9) M(-1) s(-1).     

Activation of 3-amino-1,2,4-benzotriazine 1,4-dioxide antitumor agents to oxidizing species following their one-electron reduction

The mechanism by which a benzotriazine 1,4-dioxide class of anticancer drugs produce oxidizing radicals following their one-electron reduction has been investigated using tirapazamine (3-amino-1,2,4-benzotriazine 1,4-dioxide, 1) and its 6-methoxy (6), 7-dimethylamino (7), and 8-methyl (8) analogues. By measuring the changes in absorption with pH, we found that the radical anions undergo protonation with radical pK(r) values of 6.19 +/- 0.05, 6.10 +/- 0.03, 6.45 +/- 0.04, and 6.60 +/- 0.04, respectively. The one-electron reduced species underwent a first-order reaction, with increased rate constants from 112 +/- 23 s(-)(1) for 1 to 777 +/- 12 s(-)(1)(6), 1120 +/- 29 s(-)(1) (7), and 825 +/- 89 s(-)(1) (8) at pH 7. No overall change in conductance was observed following the one-electron reduction of 6, and 8 at pH 4.5, consistent with the protonation of the radical anions, but a loss in conductance was seen for one-electron reduced 7 because of further protonation of the initially formed radical. This is assigned to the protonation of the dimethylamino group of the radical species, which has a pK(a) of 8.8 +/- 0.3. All conductance changes take place on a time-scale shorter than those of the above first-order reactions, which are not associated with the formation or loss of charged species. The absorption spectra present at the end of the unimolecular reactions were found to be similar to those formed immediately upon the one-electron oxidation of the respective substituted 3-amino-1,2,4-benzotriazine 1-oxides, and it is suggested that common benzotriazinyl radicals are formed by both routes. All these intermediate radicals underwent dismutation to produce final spectra matched by equal contributions of the parent compound and their respective substituted 3-amino-1,2,4-benzotriazine 1-oxides. By establishing redox equilibria between the intermediate radicals formed on the one-electron oxidation of the respective 3-amino-1,2,4-benzotriazine 1-oxides of the compounds and reference compounds, we found the one-electron reduction potential of the oxidizing radicals to range from 0.94 to 1.31 V. The benzotriazinyl radical of tirapazamine was found to oxidize dGMP and 2-deoxyribose with rate constants of (1.4 +/- 0.2) x 10(8) M(-)(1) s(-)(1) and (3.7 +/- 0.5) x 10(6) M(-)(1) s(-)(1), respectively.     

Determination of N-NO bond dissociation energies of N-methyl-N-nitrosobenzenesulfonamides in acetonitrile and application in the mechanism analyses on NO transfer

The heterolytic and homolytic N-NO bond dissociation energies of seven substituted N-methyl-N-nitrosobenzenesulfonamides (abbreviated as G-MNBS, G = p-OCH(3), p-CH(3), p-H, p-Cl, p-Br, 2,5-2Cl, m-NO(2)) in acetonitrile solution were evaluated for the first time by using titration calorimetry and relative thermodynamic cycles according to Hess' law. The results show that the energetic scales of the heterolytic and homolytic N-NO bond dissociation energies of G-MNBS in acetonitrile solution cover the ranges from 44.3 to 49.5 and from 33.0 to 34.9 kcal/mol for the neutral G-MNBS, respectively, which indicates that N-methyl-N-nitrosobenzenesulfonamides are much easier to release a NO radical (NO(*)) than to release a NO cation (NO(+)). The estimation of the heterolytic and homolytic (N-NO)(-)(*) bond dissociation energies of the seven G-MNBS radical anions in acetonitrile solution gives the energetic ranges of -15.8 to -12.9 and -3.1 to 1.8 kcal/mol for the (N-NO)(-)(*) bond homolysis and heterolysis, respectively, which means that G-MNBS radical anions are very unstable at room temperature and able to spontaneously or easily release a NO radical or NO anion (NO(-)), but releasing a NO radical is easier than releasing NO anion. These determined N-NO bond dissociation energies of G-MNBS and their radical anions have been successfully used in the mechanism analyses of NO transfer from G-MNBS to 3,6-dibromocarbazole and the reactions of NO with the substituted N-methyl-benzenesulfonamide nitranions (G-MBSN(-)) in acetonitrile solution.     

Role of sequence and conformation on the photochemistry and the photophysics of A-T DNA dimers: an experimental and computational approach

The role of base sequence and conformation on the photochemistry and photophysics of thymidylyl (3'-5')-2'-deoxyadenosine sodium salt (TpdA) and 2-deoxyadenylyl (3'-5')-thymidine ammonium salt (dApT) was studied. To this end, nanosecond transient absorption at 266 nm, steady-state irradiation at 254 nm, and quantum chemical calculations were used. The transient absorption spectra show the solvated electron broad band in the visible region for each dinucleotide. In addition, low-intensity absorption bands are observed in the UV region, which are attributed to the deprotonated and protonated neutral radicals of adenine and thymine bases. Photoionization (PI) occurs by one- and two-photon pathways; the latter accounting for approximately 70% of the net PI yield. A diffusion-limited rate constant of 2.0 x 10(10) M(-1) s(-1) was obtained for the reaction of the neutral molecule with the photoejected electron in both sequences. The photodestruction yield, measured from the chromophore loss at 260 nm, decreases in the presence of well-known electron scavengers. This suggests the participation of base radical anions as one of the photodegradation pathways, which is higher in TpdA than in dApT. The intermediacy of a radical ion pair (charge separated state) between the adjacent adenine and thymine bases is proposed in the formation of the [2 + 2] cycloadduct intermediate. The [2 + 2] cycloadduct intermediate is known to be the precursor of the thymine-adenine eight-member ring photoproduct (TA*). Conformational constrains in the radical ion pair are suggested to explain the absence of the TA* photoproduct in dApT. This hypothesis is supported by semiempirical calculations performed on all relevant reactive intermediates proposed to participate in the mechanism of formation of TA*. Altogether, the results show that sequence and conformation profoundly influence the photochemistry and the photophysics of these DNA model systems.     

Mobile protons versus mobile radicals: Gas-phase unimolecular chemistry of radical cations of cysteine-containing peptides

A combination of electrospray ionization (ESI), multistage, and high-resolution mass spectrometry experiments are used to examine the gas-phase fragmentation reactions of radical cations of cysteine containing di- and tripeptides. Two different chemical methods were used to form initial populations of radical cations in which the radical sites were located at different positions: (1) sulfur-centered cysteinyl radicals via bond homolysis of protonated S-nitrosocysteine containing peptides; and (2) α-carbon backbone-centered radicals via Siu’s sequence of reactions (J. Am. Chem. Soc. 2008, 130, 7862). Comparison of the fragmentation reactions of these regiospecifically generated radicals suggests that hydrogen atom transfer (HAT) between the α C-H of adjacent residues and the cysteinyl radical can occur. In addition, using accurate mass measurements, deuterium labeling, and comparison with an authentic sample, a novel loss of part of the N-terminal cysteine residue was shown to give rise to the protonated, truncated N-formyl peptide (an even-electron x_n ion). DFT calculations were performed on the radical cation [GCG]^.+ to examine: the relative stabilities of isomers with different radical and protonation sites; the barriers associated with radical migration between four possible radical sites, [G.CG]⁺, [GC.G]⁺, [GCG.]⁺, and [GC(S.)G]⁺; and for dissociation from these sites to yield b₂-type ions.     

Rate and driving force for protonation of aryl radical anions in ethanol

Aryl radical anions created in liquid alcohols decay on the microsecond time scale by transfer of protons from the solvent. This paper reports a 4.5 decade range of rate constants for proton transfer from a single weak acid, ethanol, to a series of unsubstituted aryl radical anions, Ar-*. The rate constants correlate with free energy change, DeltaG(o), despite wide variations in the two factors that contribute to DeltaG(o): (a) the reduction potentials of the aryls and (b) the Ar-H* bond strengths in the product radicals. For aryl radical anions containing CH2OH substituents, such as 2,2'-biphenyldimethanol*- which is protonated with a rate constant of 3x10(9) s(-1), the faster rates do not fit well in the free energy correlation, suggesting a change in mechanism.     

Selective generation and reactivity of 5'-adenosinyl and 2'-adenosinyl radicals

The reaction of hydrated electrons (e(-)(aq) with 8-bromoadenosine 7 has been investigated by radiolytic methods coupled with product studies. Pulse radiolysis revealed that one-electron reductive cleavage of the C-Br bond gives the C8 radical 8 followed by a fast radical translocation to the sugar moiety. The reaction is partitioned between C5' and C2' positions in a 60:40 ratio leading to 5'-adenosinyl radical 9 and 2'-adenosinyl radical 11. This radical translocation from C8 to different sites of the sugar moiety has also been addressed computationally by means of DFT B3LYP calculations. In addition, ketone 21 was prepared and photolyzed providing an independent generation of C2' radical 11. Both C5' and C2' radicals undergo unimolecular reactions. Radical 9 attacks adenine with a rate constant of 1.0 x 10(4) s(-1) and gives the aromatic aminyl radical 10, whereas C2' radical 11 liberates adenine with a rate constant of 1.1 x 10(5) s(-1).     

Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes

A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ～10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT continuous, d[5'-G(3)A(5)T(5)C(3)-3'] > AT alternate, d[5'-G(3)(AT)(5)C(3)-3'] > GC-rich d[5'-A(3)G(5)C(5)T(3)-3']. (9) 3 binds to the AT-tract-containing DNA duplex (B* DNA, d[5'-G(3)A(5)T(5)C(3)-3']) with 1 order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5'-G(3)(AT)(5)C(3)-3']) and with almost 3 orders of magnitude higher affinity than a GC-rich DNA (A-form, d[5'-A(3)G(5)C(5)T(3)-3']).