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M O Calculations of Some Thymine Radicals at the in D O Level

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M O Calculations of Some Thymine Radicals at the in D O Level M O Calculations of Some Thymine Radicals at the I N D O Level E. Westhof Institut für Biophysik und physikalische Biochemie, Universität Regensburg and M. van Rooten Laboratoire de Chimie Biologique, Universite Libre de Bruxelles, Rhode St-Genese (Z. Naturforsch. 31c, 371— 376 [1976]; received January 30/March 12, 1976) MO, INDO, Thymine, Free Radicals The results of MO IND O calculations of some thymine radicals are presented. These include as well as the hydrogen addition radicals the hydroxyl addition radicals to C5 and to C6 of the C5 = C6 double bond of the thymine molecule. The radicals resulting from hydrogen abstraction from the methyl group and from the nitrogen N1 are also studied. Except for radicals where the main spin density is localized on nitrogen atoms, the agreement between experimental and theoreti­ cal couplings is satisfactory. 1. Introduction fine splitting constants in several thymine radicals. These include the H- and OH-addition radicals to Our knowledge about the structure of the radicals C5 and to C6 of the C5 = C6 double bond of thy­ produced by ionizing radiation in biological mole­ mine. The radicals resulting from H-abstraction cules is essentially based on electron spin resonance from the methyl group and from the nitrogen N l (ESR) studies. Analysis of ESR spectry yields ex­ are analysed in detail together with the cation perimental hyperfine splitting constants which can radical. Next to the anion radical and the radical be correlated to spin density distributions. The iden­ of H-addition at C6 of the thymine ring, Gregoli tification of the radicals is usually only possible et al. 1 isolated two other species. One could be when working on single crystals. However, single identified as the radical of OH-addition at C-6 of crystals have two main drawbacks. First, quantitative thymine on the basis of experimental data and of measurements or reaction kinetics are difficult or preliminary results of our calculations. No positive even impossible to make. An secondly, some radio- identification of the fourth radical could, however, chemically important radicals, like OH-addition be made. W e present evidence that this radical is radicals, have never been observed in such systems. the neutral radical resulting from hydrogen abstrac­ In fact, mainly H-addition radicals have been ob­ tion from the methyl group of the thymine molecule. served in single crystals. On the other hand, the study of frozen solutions permits to observe such 2. Method of Calculations radicals and their reaction kinetics. However, since the ESR spectra obtained from such samples are The molecular orbital calculations of the spin den­ powder patterns, the identification of the radicals sity distribution were done at the INDO level. The produced may be difficult or inconclusive. There­ INDO program used was the QCPE program n° fore, the need for calculations of spin density distri­ 1412. The atomic coordinates necessary for the butions together with theoretical reconstructions of INDO calculations were obtained either from crystal- powder spectra is increased. lographic data or by using the QCPE program n° Very recently, the formation of radicals in y-ir­ 1362. The proportionality constants relating the radiated frozen aqueous solutions of deoxythymi- spin densities to the isotropic hyperfine splittings dine-5,-monophosphate has been quantitatively were those of Pople and Beveridge 3. The anisotropic studied by Gregoli and coworkers1. In connection hyperfine splittings of the nitrogen nuclei of some with this work, we present the calculations of hyper- radicals have also been calculated. The radicals cal­ culated are ^-radicals — the diagonal elements of Requests for reprints should be sent to Dr. E. Westhof, the spin density matrix (2px , 2px) and (2py , 2py) Institut für Biophysik und physikalische Biochemie, Fach­ are only some percent of (2pz , 2pz) — and, there­ bereich Biologie, Universität Regensburg, Postfach 397, D-8400 Regensburg. fore the in-plane components of the spin density 372 E. Westhof and M. van Rooten • IND O of Thymine Radicals matrix were neglected. The hyperfine splitting ob­ Table I. Theoretical coupling constants for radicals 1 and 2 as calculated by INDO, together with experimental values tained with the magnetic field parallel to the ;r-orbi- (all values in gauss). tal is given by A = alS0 + 2 6aniso • I n the molecular Radical H(C 6) H(C5) H (C H S) plane, the coupling is A = a;s0 — 6aniso . The propor­ tionality constant for 6anjS0 was calculated with Sla­ Radical 1 35.0 * 22.1 ter orbitals — since the INDO method uses such or­ C - N : 1.40 Ä C - C : 1.50 A * bitals — and was found to be equal to 13.6 G. The Experimental 37.0-40.5 19.3-21.3 calculations were performed on a CDC 6500 at the (7, 8 ) Brussels Free Universities Computer Center. Radical 2 39.2 -1 7 .6 < 1.0 C - C : 1.50 Ä Experimental 44.0 -1 7 .4 * 3. Addition Radicals (9) The configuration of the molecules generally changes upon radical formation. INDO energy 0 0 minimization to obtain the optimum configuration should consequently be applied. However, with such procedures, the agreement between experimental and theoretical couplings is not particularly good. A more pragmatical method has been preferred. This consists in determining the lengths of the bonds be­ Radical 1 Radical 2 tween the H-addition site and the rest of the molecule which give best fit between experimental and theo­ retical couplings of some experimentally well-known of the methyl group in radical 1 can be reproduced radicals. These were the H-addition radicals of by the equation: benzene4 and imidazole5. The method has already o h ( G ) = B0 + B2' cos2 0 been applied in cases of the H-addition radicals some pyrimidines 6 and purines 13. A ll the radicals with Z?0= 1 .5 G and B 2 = 4< 1.2G. Since the methyl were calculated planar with the methylene protons group is freely rotating, the values for the methyl symmetrically disposed about the molecular plane. group in Table I are given in the form B 0 + 1/2 B 2 . The molecular dimensions were taken from the The experimental coupling constants of radical 1 crystallographic data 22,23. For radical 1, the dis­ depend on its environment and its range of varia­ tance between C5 and N1 was taken from the crystal tion is given in Table I. Radical 2 has been positive­ structure and new coordinates for C6 were cal­ ly identified in a single crystal of 5,6-dihydro-thy- culated with C6 —N1 equal to 1.40 Ä and C5 — C6 mine9. The agreement between experimental and equal to 1.50 Ä. For radical 2, it is the distance theoretical coupling constants is good. The tendency between C4 and C6 which was kept identical to the of the /ö-proton of radical 2 to be larger than that distance observed in the crystal and new coordinates of radical 1 is reproduced. In pyrimidines with un­ for C5 and the atoms bonded to it were calculated substituted C5 = C6 double bond, the inverse is ob­ with C4 — C5 and C5 — C6 equal to 1.50 Ä. served: H-addition radicals at C5 have smaller /5-proton coupling constants than H-addition radicals 3.1. H-addition radicals at C6 6’ 10. The results obtained for the radical resulting 3.2. OH-addition radicals from H-addition of C6 (radical 1) and giving rise to the famous octet re s o n a n c e 8 are presented in In these radicals, two other structural parameters Table I together with those obtained for the radical have to be determined. These are the C — 0 bond resulting from H-addition at C5 (radical 2 ). length and the orientation of the hydroxyl proton. In The rotation barrier for the methyl group was the crystal structure of cis-thymine glycoln , the calculated to be less than 0.5 kcal-mol-1 in radical C —O bond lengths are measured to be 1.418 and 1 and less than 3.0 kcal’ mol-1 in radical 2. The 1.430 Ä. The calculations were done with 1.40 and calculated /5-proton hyperfine coupling constants 1.43 Ä. The orientation of the hydroxyl proton was E. Westhof and M. van Rooten • IND O of Thymine Radicals 373 varied. The extrema of the hydroxyl proton coupling protons are identical to those in the H-addition were obtained for the cis and trans orientations. radical at C6 whereas the coupling of the ^-proton When looking down the C — 0 bond, the orientation at C6 is calculated to be smaller than that of the is called cis if the 0 — H bond is parallel to the methylene protons in the H-addition radical at C6. C5 — C6 bond (the C5 — C4 bond) in the C6-addi- The coupling caused by the hydroxyl proton varies tion radical (the C5-addition radical) and trans if with its orientation and is maximum in the cis orien­ antiparallel. At intermediate orientations, the hy­ tation. With the OH bond length equal to 0.97 Ä it droxyl proton is comprised between these extrema. is at most 5.0 G. Despite the too large value for the The results for radicals 3 and 4 with the bond proton bonded to C6 in radical 3, the calculations lengths for C —0 equal to 1.43 Ä and for 0 —H give satisfactory agreement with the experimental equal to 0.97 Ä are presented in Table II. couplings. Concerning the couplings due to nitrogen nuclei, one may add the following. In radicals 1 and 3, only Table II.
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