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Formation and Structure of Radicals from D-Ribose and 2-Deoxy- D-Ribose by Reactions with SO 4 Radicals in Aqueous Solution

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Formation and Structure of Radicals from D-Ribose and 2-Deoxy- D-Ribose by Reactions with SO 4 Radicals in Aqueous Solution Formation and Structure of Radicals from D-Ribose and 2-Deoxy- D-ribose by Reactions with SO 4 Radicals in Aqueous Solution. An in-situ Electron Spin Resonance Study Janko N. Herak Faculty of Pharmacy and Biochemistry, The University of Zagreb, Zagreb. Croatia, Yugoslavia Günter Behrens Max-Planck-Institut für Strahlenchemie. D-4330 Mülheim a.d. Ruhr, Bundesrepublik Deutschland Z. Naturforsch. 41c, 1062 — 1068 (1986); received January 31, 1986 Free Radicals, Deoxy-D-ribose, D-Ribose, Conformational Kinetics, Electron Spin Resonance ESR spectroscopy has been used to analyse the conformation of the radicals produced by the reaction of SOj with D-ribose (1),and 2-deoxy-D-ribose (6 ),at pH 1.3-5. From ribose three different types of radicals formed by H abstraction at C-l, C-2 and C-3 followed by a regio- selective a,ß-water elimination have been identified: the 2-deoxy-ribonolacton-2-yl (3), the 1-deoxy-pentopyranos-2-ulos-l-yl (4). and the 4-deoxy-pentopyranos-3-ulos-4-yl (2). Using deoxyribose two radicals of similar type, formed by H abstraction at C-3 and C-4 followed by water elimination, have been observed: the 2,4-dideoxy-3-ulos-4-yl (7) and the 2,3-dideoxy-4- ulos-3-yl (8). In addition, from both sugars an a-hydroxyalkyl radical has been identified based in part on the timing of their conformational motions: the ribos-3-yl (5) (the precursor of 2) and the 2-deoxy-ribos-l-yl (9), respectively. For radical 5 the rate constant k(e) for the water elimination and hence transformation into radical 2 was estimated. From the analysis of selective line broadening the frequencies of conformational changes of radicals 2 and 7 have been estimated. For 7 the frequencies of exchange of the two methylene groups were found to differ by more than 3 orders of magnitude. Introduction In the present paper we report the ESR analysis of Considerable attention has been payed to the the — CH—CO— type radicals produced from d - study of radical reactions of carbohydrates [1—7], ribose and 2-deoxy-D-ribose. From the ESR parame­ Part of the reason for this lies in the importance of ters of the spectra we deduced the site of the un­ such reactions in radiation chemistry of nucleic acids paired electron, from which we can deduce the struc­ and their constituents [8—10]. In most ESR studies ture of the precursor radical and the direction of the of simple sugars the radicals were produced in the water elimination reaction. In cases where two dif­ reaction of these compounds with OH, generated ferent reactions of this type from the same precursor type from Tim and H 20 2 in a three-way mixing system in compete, we can conclude from the of the keto- an ESR cavity [1, 3-5]. In some of these studies it conjugated radical (ulosyl type) observed, which of has been shown [3,5], that the attack of the hydroxyl the two reactions is the preferred one. The regio- radicals in the sugars is rather unselective. In the selectivity of such processes is explained in terms of acidic solutions the a,ß-dihydroxy substituted radi­ the stability of the transition states of some of these cals originally formed by H-abstraction are transform­ radicals. From the line width analysis the rates of interconversions of conformation of some radicals ed into carbonyl-conjugated radicals, R 2C -C O —, by elimination of water. Although it has been stated have been estimated. that such radical rearrangements take place also in d - ribose and deoxy-D-ribose [1, 5], no detailed spec­ Experimental troscopic analysis of the carbonyl-conjugated radi­ cals, —CH—CO —, has been reported except for one The SO 4 radicals generated by photolysis of per- oxodisulfate, S 20 ^_, were used for abstraction of radical derived from D-ribose [1]. H atoms from the substrates. To an aqueous solution Reprint requests to Dr. G. Behrens. of ca. 10-2 mol ■ dm-'" of substrate and 3x10"' Verlag der Zeitschrift für Naturforschung. D-7400 Tübingen mol-dm -3 of K 2S20 8, about 3 x 10 -2 mol • dm -3 of 0341 - 0382/86/1100 -1062 $01.30/0 acetone was added to sensitize the photolytic cleav- J. N. Herak and G. Behrens • Radicals from Ribose and Deoxyribose 1063 age of S 2Og_ [8, 11]. The radicals were studied in situ Results with ESR spectroscopy at ca. 9.5 GHz and constant D-Ribose temperatures, e.g. 4 °C. The arrangement was de­ scribed elsewhere [11, 12]. The photolysis was con­ Using D-ribose at pH ~ 4, a complex spectrum, ducted at continuous flow using a 1 kW super­ depicted in Fig. 1, was obtained. A closer inspection pressure mercury arc focussed at a flat cell made of shows that there are at least four radicals present, fused Suprasil quartz plates. The cell was designed in each with a different g factor. At pH 1.3 three of our laboratory especially for the use with lossy water them were still observable. The two sets of the prom­ samples, even those of high conductivity. With this inent double doublets together with two similar sets arrangement the production rate of SO 4 radicals was of lines on the low-field side (not shown) belong to a about 1.5 x 10 -4 mol-dm~ 3-s_1. The samples were single radical species. The separation between the deaerated by continuously bubbling argon through two sets, one at the low- and the other at the high- the solution before flowing it through the cell. field side, is 6.86 mT. Since such separation is too D-Ribose and 2-deoxy-D-ribose (Sigma) and K 2S20 8 large to be a doublet H-splitting, we conclude that (Merck) were used without further purification. there must be some much broader resonances in the f t t t 5 Fig. 1. High-field part of ESR spectra of D-ribose at pH 4.0 (a), and at pH 1.3 (b). Below are the simulated spectra of radicals 2, 3 and 4, respectively. For simulations the line widths of 0.010, 0.014 and 0.006 mT were used, respectively. For the two inner groups of lines of radical 2 the width of 0.028 mT is used. The centres of the spectra are marked by c. The four arrows indicate the lines corresponding to radical 5. The insert depicts the broadened lines ((J)) of radical 2 measured at three-fold modulation amplitude and microwave power, and pH adjusted to 1.7. Some extra lines (x) have not been assigned. 1064 J. N. Herak and G. Behrens • Radicals from Ribose and Deoxyribose middle part of the spectrum, hardly to observe under scopic parameters are assigned to radical 2 because the high resolution conditions applied. The situation of the similarity with the ESR parameters of the is very similar to that first observed for the vinyl analogous radical derived from xylose [5]. radical [13] or even more similar to the l,4-dioxan-2- The couplings of the y-H at C-2 (0.272 mT) and of yl radical [14]. It is reasonable to assume that the the 6-proton at C-l (0.029 mT) on the other side of separation of 6.86 mT corresponds to the sum of two the carbonyl group are slightly larger than the related ß-proton splittings, the average being 3.43 mT. The couplings in similar open-chain radicals, e.g.: other parameters are 1.762, 0.272 and 0.029 mT and CH2-CO-CH2-CH2-CH2-OH [8]. g = 2.0044. The simulated spectrum, calculated with The second spectrum consisting of broad doublets these parameters is also shown in Fig. 1. For simula­ at pH 4, further split in smaller doublets (0.035 mT) tion the width of 0.010 mT for the lines belonging to at pH 1.3 is characterized by a(aH) = 2.020 mT. the outer four groups, and 0.028 mT for the inner a(ßH) = 4.040 mT, fl(yH) = 0.085, a(6H) = groups of lines are used. The simulated spectrum fits 0.035 mT and g = 2.0034. The spectrum is assigned the measured one nicely. The broader inner lines are to radical 3, mainly on the basis of its g factor, which too broad to be clearly observed at moderate resolu­ is typical for the ester type radicals (viz. tion used in Fig. la and lb. However, they are seen R '—CH—CO—O — R") [16]. The lines are sharper at better when higher microwave power and larger pH 1.3 than at pH 4, because the frequency of the modulation amplitude were applied (see lines protonation — deprotonation exchange at a ß-hy- marked (f) in Fig. lb). The broadening of these lines droxyl group (e.g. at C-3) is faster at lower pH [12], is brought about by the exchange of two non-equiva­ The large splitting of the ß-proton indicates this pro­ lent protons at “intermediate rates”, see Discus­ ton to be axial. Radical 3 is formed by H abstrac­ sion. tion at C-l and followed by water elimination. This In aqueous solution D-ribose is known to be pre­ radical has already been observed and identified [1], dominantly in the pyranose form. Of the four differ­ In the present study we obtain much higher resolu­ ent conformers in equilibrium in water conformer 1 tion and more precise spectroscopic parameters. is the most abundant one [15], The above spectro­ The eight distinct groups of well resolved lines (in Fig.
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