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.     

EPR and ENDOR study of radiation-induced radical formation in purines: sodium inosine crystals X-irradiated at 10 K

X-irradiated single crystals of sodium inosine (Na(+)*Inosine(-)*2.5H(2)O), in which the hypoxanthine base is present as the N1-deprotonated anion, were investigated using K-band (24 GHz) electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques at 10 K. At least five different radicals were present immediately after irradiation at 10 K. R1, which decayed upon warming the crystals to 50 K, was identified as the electron-loss product of the parent N1-deprotonated hypoxanthine base. Hyperfine couplings to HC8 and HC2 were fully characterized with ENDOR spectroscopy, and the identification was supported by DFT calculations. R2, which also decayed on warming to 50 K, exhibited nearly equal couplings to HC2 and HC8. Taken in combination with an extensive set of DFT calculations, the experimental results indicate that R2 is the (doubly negative) product of electron-gain by the initially anionic N1-deprotonated hypoxanthine parent. R3, which exhibited hyperfine coupling only to HC8 could not be identified. R4, which persisted on annealing to 260 K, exhibited one large alpha-proton hyperfine coupling which was fully characterized by ENDOR. Based on DFT calculations and the experimental data, R4 was identified as the product of net H-abstraction from C5'. The remaining HC5' was the source of the measured alpha-proton coupling. R5, present at low temperature and the only observable radical after warming the crystals to room temperature, was identified as the C8-H addition radical. The alpha-coupling to HC2 and beta-couplings to the pair of C8 methlyene protons were fully characterized by ENDOR.     

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.     

Free radical conformations and conversions in X-irradiated single crystals of L-cysteic acid by electron magnetic resonance and density functional theory studies

Single crystals of L-cysteic acid monohydrate were X-irradiated and studied at 295 K using EPR, ENDOR, and EIE techniques. Three spectroscopically different radicals were observed. These were a deamination radical reduction product (R1), and two oxidation products formed by hydrogen abstraction (radicals R2, R3). R2 and R3 were shown to exhibit the same chemical structure while exhibiting very different geometrical conformations. Cluster DFT calculations at the 6-31G(d,p) level of theory supported the experimental observations for radicals R1 and R2. It was not possible to simulate the R3 radical in any attempted cluster; hence, for this purpose a single molecule approach was used. The precursor radicals for R1, R2, and R3, identified in the low-temperature work on L-cysteic acid monohydrate by Box and Budzinski, were also investigated using DFT calculations. The experimentally determined EPR parameters for the low-temperature decarboxylated cation could only be reproduced correctly within the cluster when the carboxyl group remained in the proximity of the radical. Only one of the two observed low-temperature carboxyl anions (stable at 4 and 48 K) could be successfully simulated by the DFT calculations. Evidence is presented in support of the conclusions that the carboxyl reduction product already is protonated at 4 K and that the irreversible conversion between the two reduction products is brought forward by an umbrella-type inversion of the carboxyl group.     

Regulation of one-electron oxidation rate of guanine by base pairing with cytosine derivatives

Effects of base pairing on the one-electron oxidation rate of guanine derivatives, guanine, 8-bromoguanine, and 8-oxo-7,8-dihydroguanine have been studied. The one-electron oxidation rate of guanine derivatives was determined by triplet-quenching experiments, using N,N'-dibutylnaphthaldiimide (NDI) in the triplet excited state (3NDI*) and fullerene (C(60)) in the triplet excited state ((3)C(60*)) as oxidants. In all three guanine derivatives studied here, acceleration of the one-electron oxidation was observed upon hydrogen bonding with cytosine, which demonstrates lowering of the oxidation potential of guanine derivatives by base pairing with cytosine. When a methyl or bromo group was introduced to the C5 position of cytosine, acceleration or suppression of the one-electron oxidation relative to the guanine:cytosine base pair was observed, respectively. The results demonstrate that the one-electron oxidation rate of guanine in DNA can be regulated by introducing a substituent on base pairing cytosine.     

Oxidizing intermediates from the sterically hindered iron salen complexes related to the oxygen activation by nonheme iron enzymes

Oxidizing intermediates are generated from nonheme iron(III) complexes to investigate the electronic structure and the reactivity, in comparison with the oxoiron(IV) porphyrin pi-cation radical (compound I) as a heme enzyme model. Sterically hindered iron salen complexes, bearing a fifth ligand Cl (1), OH(2) (2), OEt (3), and OH (4), are oxidized both electrochemically and chemically. Stepwise one-electron oxidation of 1 and 2 generates iron(III)-mono- and diphenoxyl radicals, as revealed by detailed spectroscopic investigations, including UV-vis, EPR, M?ssbauer, resonance Raman, and ESIMS spectroscopies. In contrast to the oxoiron(IV) formation from the hydroxoiron(III) porphyrin upon one-electron oxidation, the hydroxo complex 4 does not generate oxoiron(IV) species. Reaction of 2 with mCPBA also results in the formation of the iron(III)-phenoxyl radical. One-electron oxidation of 3 leads to oxidative degradation of the fifth EtO ligand to liberate acetaldehyde even at 203 K. The iron(III)-phenoxyl radical shows high reactivity for alcoxide on iron(III) but exhibits virtually no reactivity for alcohols including even benzyl alcohol without a base to remove an alcohol proton. This study explains unique properties of mononuclear nonheme enzymes with Tyr residues and also the poor epoxidation activity of Fe salen compared to Mn and Cr salen compounds.     

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.     

EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level

Quantum mechanics/molecular mechanics (QM/MM) methods, employing density functional theory (DFT), have been used to compute the electron paramagnetic resonance (EPR) parameters of tryptophan and tyrosyl radical intermediates involved in the catalytic cycle of Pleurotus eryngii versatile peroxidase (VP) and its W164Y variant, respectively. These radicals have been previously experimentally detected and characterized both in the two-electron and one-electron activated forms of the enzymes. In this work, the well-studied W164 radical in VP has been chosen for calibration purposes because its spectroscopic properties have been extensively studied by multifrequency EPR and ENDOR spectroscopies. Using a B3LYP/CHARMM procedure, appropriately accounting for electrostatic, such as hydrogen bonding, and steric environmental interactions, a good agreement between the calculated and measured EPR parameters for both radicals has been achieved; g-tensors, hyperfine coupling constants (hfcc) and Mulliken spin densities have been correlated to changes in geometries, hydrogen bond networks and electrostatic environment, with the aim of understanding the influence of the protein surroundings on EPR properties. In addition, the present calculations demonstrate, for VP, the formation of a neutral tryptophan radical, hydrogen bonded to the nearby E243, via a stepwise electron and proton transfer with earlier involvement of a short-lived tryptophan cationic species. Instead, for W164Y, the QM/MM dynamics simulation shows that the tyrosine oxidation proceeds via a concerted electron and proton transfer and is accompanied by a significant reorganization of residues and water molecules surrounding the tyrosyl radical.     

Identification of primary free radicals in trehalose dihydrate single crystals X-irradiated at 10 K

Primary free radical formation in trehalose dihydrate single crystals X-irradiated at 10 K was investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques. The ENDOR results allowed the unambiguous determination of six proton hyperfine coupling (HFC) tensors. Using the EIE technique, these HF interactions were assigned to three different radicals, labeled R1, R2 and R3. The anisotropy of the EPR and EIE spectra indicated that R1 and R2 are alkyl radicals (i.e. carbon-centered) and R3 is an alkoxy radical (i.e. oxygen-centered). The EPR data also revealed the presence of an additional alkoxy radical species, labeled R4. Molecular modeling using periodic Density Functional Theory (DFT) calculations for simulating experimental data suggests that R1 and R2 are the hydrogen-abstracted alkyl species centered at C5' and C5, respectively, while the alkoxy radicals R3 and R4 have the unpaired electron localized mainly at O2 and O4'. Interestingly, the DFT study on R4 demonstrates that the trapping of a transferred proton can significantly influence the conformation of a deprotonated cation. Comparison of these results with those obtained from sucrose single crystals X-irradiated at 10 K indicates that the carbon situated next to the ring oxygen and connected to the CH(2)OH hydroxymethyl group is a better radical trapping site than other positions.     

A new coordination mode of the photometric reagent glyoxalbis(2-hydroxyanil) (H2gbha): bis-bidentate bridging by gbha2- in the redox series [(mu-gbha)[Ru(acac)2]2]n (n = -2, -1, 0, +1, +2), including a radical-bridged diruthenium(III) and a Ru(III)/Ru(IV) intermediate

The bis-bidentate bridging function of gbha2- with N,O-/N,O- coordination was observed for the first time in the complex (mu-gbha)[Ru(III)(acac)2]2 (1). Density functional theory calculations of 1 yield a triplet ground state with a large (deltaE > 6000 cm(-1)) singlet-triplet gap. Intermolecular antiferromagnetic coupling was observed (J approximately -5.3 cm(-1)) for the solid. Complex 1 undergoes two one-electron reduction and two one-electron oxidation steps; the five redox forms [(mu-gbha)[Ru(acac)2]2]n (n = -2, -1, 0, +1, +2) were characterized by UV-vis-NIR spectroelectrochemistry (NIR = near infrared). The paramagnetic intermediates were also investigated by electron paramagnetic resonance (EPR) spectroscopy. The monoanion with a comproportionation constant K(c) of 2.7 x 10(8) does not exhibit an NIR band for a Ru(III)/Ru(II) mixed-valent situation; it is best described as a 1,4-diazabutadiene radical anion containing ligand gbha*3-, which binds two ruthenium(III) centers. A Ru(III)-type EPR spectrum with g1 = 2.27, g2 = 2.21, and g3 = 1.73 is observed as a result of antiferromagnetic coupling between one Ru(III) and the ligand radical. The EPR-active monocation (K(c) = 1.7 x 10(6)) exhibits a broad (deltanu(1/2) = 2600 cm(-1)) intervalence charge-transfer band at 1800 nm, indicating a valence-averaged (Ru3.5)2 formulation (class III) with a tendency toward class II (borderline situation).     

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.     

Spectroscopic properties of tyrosyl radicals in dipeptides

Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes, including prostaglandin H synthase, galactose oxidase, ribonucleotide reductase, and photosystem II. Magnetic resonance and vibrational spectroscopy provide methods with which to study the structures of redox-active amino acids in proteins. In this report, ultraviolet photolysis was used to generate tyrosyl radicals from polycrystalline tyrosinate or dipeptides, and the structure of the radical was investigated with EPR and reaction-induced FT-IR spectroscopy at 77 K. Photolysis at 77 K is expected to generate a neutral tyrosyl radical through oxidation of the aromatic ring. EPR and FT-IR results obtained from (13)C-labeled tyrosine were consistent with that expectation. Surprisingly, labeling of the tyrosyl amino group with (15)N also resulted in isotope-shifted bands in the photolysis spectrum. The force constant of a NH deformation mode increased when the tyrosyl radical was generated. These data suggest an interaction between the pi system of the tyrosyl radical and the amino group. In spectra acquired from the dipeptides, evidence for a sequence-dependent interaction between the tyrosyl radical and the amide bond of the dipeptide was also obtained. We postulate that perturbation of the amino or the amide/imide groups may occur through a spin polarization mechanism, which is indirectly detected as a change in NH force constant. This conclusion is supported by density functional calculations, which suggest a conformationally sensitive delocalization of spin density onto the amino and carboxylate groups of the tyrosyl radical. These experiments provide a step toward a detailed spectral interpretation for protein-based tyrosyl radicals.     

Free radical products in X-irradiated Rochelle salt: low temperature ENDOR and DFT studies

Single crystals of Rochelle salt, [⁻OOC-CHOH-CHOH-COO⁻, Na⁺, K⁺]·4H₂O, X-irradiated at 10 K, have been examined using EPR, ENDOR and EIE spectroscopic techniques to characterize the radiation induced radicals stable at that temperature and their reactions upon warming. The one-electron gain product was observed and from the hyperfine interaction with a β-proton it was unambiguously centered at the C₄ position of the tartrate moiety. An additional nearly isotropic hyperfine structure of about 21 MHz was tentatively assigned to interaction with a sodium ion exhibiting a close contact to O₃ in the crystal. Evidence was obtained that the one-electron reduced radical had become protonated at one of the C₄ bonded carboxyl oxygens, most probably O₄. No evidence for the corresponding C₁-centered reduction product was found. Two resonance lines (R2, A1) were shown by EIE to belong to a species formed by decarboxylation at C₃, a secondary oxidation product. Two other resonance lines (K1, K2) were assigned to two varieties of another decarboxylation radical, centered at C₂, distinguished by differences in the potassium ion coordination. Furthermore, one other resonance line (A2) was tentatively ascribed to a third decarboxylation radical, centered at the opposite end of the tartrate moiety. The precursor of these products, that is, the one-electron loss product, was not observed after X-irradiation at 10 K. Thermally induced free radical reactions followed by EPR in the temperature range of 12-119 K indicate that a water molecule or a hydroxyl ion is eliminated from the one-electron reduction product radical and that a C₃-centered radical is formed. The reduction and oxidation reaction pathways of hydroxy acid derivatives are discussed.     

Targeted oxidase reactivity with a new redox-active ligand incorporating N2O2 donor atoms. Complexes of Cu(II), Ni(II), Pd(II), Fe(III), and V(V)

The coordination chemistry of the tetradentate ligand N,N'-bis(2-hydroxy-3,5-di-tert-butylphenyl)-2,2'-diaminobiphenyl H(4)L has been studied with the copper(II), nickel(II), palladium(II), iron(III), and vanadium(V) ions. The ligand is non-innocent in the sense that it is readily oxidized in the presence of air to its o-iminobenzosemiquinonato (L(**))(2-) radical form. The crystal structures of the diradical compounds, [Cu(II)(L(**))] 1, [Ni(II)(L(**))] 2, [Pd(II)(L(**))] 3, the monoradical high-spin compound [Fe(III)(HL(*))Cl] 4, and the di(mu-methoxo)divanadium(V) compound [L(2)V(2)(mu-OCH(3))(2)] 5 without a radical have been determined by X-ray crystallography at 100 K. The biphenyl backbone of the ligand induces a tetrahedral distortion of the metal(II) geometry in 1, 2, and 3 having a N(2)O(2) coordination environment. The dihedral angles between the metal planes are 35.5 degrees for 1, 30.8 degrees for 2, and 22.2 degrees for 3. Variable-temperature (2-290 K) magnetic susceptibility measurements together with Mossbauer and electron paramagnetic resonance (EPR) spectroscopy establish the electronic structures of the complexes. Electrochemical cyclic voltammetric measurements indicate four one-electron reversible redox processes of the ligand for 1, 2, and 3. Complex 1 is found to catalyze the aerial oxidation of benzylalcohol to benzaldehyde, thus modeling the catalytic function of the copper-containing enzyme Galactose Oxidase (GO). Kinetic measurements in conjunction with EPR and UV-vis spectroscopic studies have been used to decipher the catalytic oxidation process. A ligand-derived redox activity has been proposed as a mechanism in which complex 1 disproportionates in a basic medium to generate the catalytically active species. An "on-off" mechanism of the radicals without apparent participation of the metal center is invoked for the catalytic process, whose intimate mechanism thus differs from that of the enzyme Galactose Oxidase.     

Effect of hydrogen bonding on the photo-oxidation of DNA

The one-electron oxidation of DNA has been extensively studied as it leads to the formation of oxidative lesions that cause carcinogenesis and aging. In this paper, experimental results specifically addressing the effect of hydrogen bonding on the one-electron oxidation rate of nucleosides are presented. To separate the hydrogen bonding from the π-stacking effect, experiments were performed in dichloromethane, in which base-pair formation is possible at the monomer level. The effect of base pairing of guanine with cytosine on the rate constant of the electron transfer from guanine to electron acceptor molecules in the triplet excited state was investigated, and a selective enhancement of the electron transfer was observed for the guanine:cytosine base pair. By introducing a methyl or bromo group to the C5 position of cytosine, acceleration or suppression, respectively, of the one-electron oxidation relative to the guanine:cytosine base pair was observed. The results demonstrate that the one-electron oxidation rate of guanine in DNA can be regulated by introducing a substituent on the base-pairing cytosine.     

An EPR, ENDOR and EIE study of gamma-irradiated poly (lactide-co-glycolide) polymers

Gamma radiation of poly (lactide-co-glycolide) raw polymers and processed microspheres under vacuum and at 77 K results in the formation of a series of free radicals. The resulting powder electron paramagnetic resonance (EPR) spectrum contains a distribution of several different radicals, depending on the annealing temperature, and is therefore difficult to interpret. By utilising the selectivity of the electron nuclear DOuble resonance (ENDOR) and associated ENDOR induced EPR (EIE) techniques, a more direct approach for the deconvolution of the EPR spectrum can be achieved. Using this approach, the radiolytically induced CH3 *CHC(O)R- chain scission radical was identified at 120 K by simulation of the EIE spectrum. At elevated temperatures (250 K), this radical decays considerably and the more stable radicals -O*CHC(O)-, CH3 *C(OR)C(O)- and CH3 *C(OH)C(O)- predominate. This work demonstrates the utility of the EIE approach to supplement and aid the interpretation of powder EPR spectra of radicals in a polymer matrix.     

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.     

Structure of radicals from X-irradiated guanine derivatives. 2. An experimental and computational study of 9-ethylguanine single crystals

An EPR (electron paramagnetic resonance) and ENDOR (electron-nuclear double resonance) study of 9-ethylguanine crystals X-irradiated at 10 K detected evidence for three radical forms. Radical R1, characterized by three proton and two nitrogen hyperfine interactions, was identified as the product of net hydrogenation at N7 of the guanine unit. R1, which evidently formed by protonation of the primary electron addition product, exhibited an unusually distorted structure leading to net positive isotropic components of the alpha-coupling to the hydrogen attached to C8 of the guanine unit. Radical R2, characterized by two nitrogen and three proton hyperfine couplings, was identified as the primary electron loss product, *G+. Distinguishing between *G+ and its N1-deprotonated product is difficult because their couplings are so similar, and density functional theory (DFT) calculations were indispensable for doing so. The results for R2 provide the most complete ENDOR characterization of *G+ presented so far. Radical R3 exhibited a narrow EPR pattern but could not be identified. The identification of radicals R1 and R2 was supported by DFT calculations using the B3LYP/6-311+G(2df,p)//6-31+G(d,p) approach. Radical R4, detected after irradiation of the crystals at room temperature, was identified as the well-known product of net hydrogenation at C8 of the guanine component. Spectra from the room temperature irradiation contained evidence for R5, an additional radical that could not be identified. Radical concentrations from the low temperature irradiation were estimated as follows: R1, 20%; R2, 65%; R3, 15%.     

DNA mediated charge transport: characterization of a DNA radical localized at an artificial nucleic acid base

DNA assemblies containing 4-methylindole incorporated as an artificial base provide a chemically well-defined system in which to explore the oxidative charge transport process in DNA. Using this artificial base, we have combined transient absorption and EPR spectroscopies as well as biochemical methods to test experimentally current mechanisms for DNA charge transport. The 4-methylindole radical cation intermediate has been identified using both EPR and transient absorption spectroscopies in oxidative flash-quench studies using a dipyridophenazine complex of ruthenium as the intercalating oxidant. The 4-methylindole radical cation intermediate is particularly amenable to study given its strong absorptivity at 600 nm and EPR signal measured at 77 K with g = 2.0065. Both transient absorption and EPR spectroscopies show that the 4-methylindole is well incorporated in the duplex; the data also indicate no evidence of guanine radicals, given the low oxidation potential of 4-methylindole relative to the nucleic acid bases. Biochemical studies further support the irreversible oxidation of the indole moiety and allow the determination of yields of irreversible product formation. The construction of these assemblies containing 4-methylindole as an artificial base is also applied in examining long-range charge transport mediated by the DNA base pair stack as a function of intervening distance and sequence. The rate of formation of the indole radical cation is >/=10(7) s(-)(1) for different assemblies with the ruthenium positioned 17-37 A away from the methylindole and with intervening A-T base pairs primarily composing the bridge. In these assemblies, methylindole radical formation at a distance is essentially coincident with quenching of the ruthenium excited state to form the Ru(III) oxidant; charge transport is not rate limiting over this distance regime. The measurements here of rates of radical cation formation establish that a model of G-hopping and AT-tunneling is not sufficient to account for DNA charge transport. Instead, these data are viewed mechanistically as charge transport through the DNA duplex primarily through hopping among well stacked domains of the helix defined by DNA sequence and dynamics.     

EPR, ENDOR, and DFT study of free radicals in L-lysine·HCl·2H2O single crystals X-irradiated at 298 K

With K-band EPR (Electron Paramagnetic Resonance), ENDOR (Electron-Nuclear DOuble Resonance), and EIE (ENDOR-induced EPR) techniques, three free radicals (RI-RIII) in L-lysine hydrochloride dihydrate single crystals X-irradiated at 298 K were detected at 298 K, and six radicals (R1, R1', R2-R5) were detected if the temperature was lowered to 66 K from 298 K. R1 and RI dominated the central portion of the EPR at 66 and 298 K, respectively, and were identified as main chain deamination radicals, (-)OOC?H(CH(2))(4)(NH(3))(+). R1' was identified as a main chain deamination radical with the different configuration from R1 at 66 K, and it probably formed during cooling the temperature from 298 to 66 K. The configurations of R1, R1', and RI were analyzed with their coupling tensors. R2 and R3 each contain one α- and four β-proton couplings and have very similar EIEs at three crystallographic axes. The two-layer ONIOM calculations (at B3LYP/6-31G(d,p):PM3) support that R2 and R3 are from different radicals: dehydrogenation at C4, (-)OOCCH(NH(3))(+)CH(2)?H(CH(2))(2)(NH(3))(+), and dehydrogenation at C5, (-)OOCCH(NH(3))(+)(CH(2))(2)?HCH(2)(NH(3))(+), respectively. The comparisons of the coupling tensors indicated that R2 (66 K) is the same radical as RII (298 K), and R3 is the same as RIII. Thus, RII and RIII also are the radicals of C4 and C5 dehydrogenation. R4 and R5 are minority radicals and were observed only when temperature was lowered to 66 K. R4 and R5 were only tentatively assigned as the side chain deamination radical, (-)OOCCH (NH(3))(+)(CH(2))(3)?H(2), and the radical dehydrogenation at C3, (-)OOCCH(NH(3))(+)?H(CH(2))(3)(NH(3))(+), respectively, although the evidence was indirect. From simulation of the EPR (B//a, 66 K), the concentrations of R1, R1', and R2-R5 were estimated as: R1, 50%; R1', 11%; R2, 14%; R3, 16%; R4, 6%; R5, 3%.