Cytosine monohydrate

Oxidation of cytosine produces a radical with sites of unpaired spin density at Nl, N3, and C5. The cytosine cation has a pKn<4 and in solution deprotonates at NH2 [22]. In the solid state, Sagstuen et al. [24] assigned the primary oxidation radical observed in cytosine monohydrate as the Nl deprotonated cation, Cyt(Nl—H) . It is known from the ENDOR... 

The previous section outlined the typical e loss and e gain products observed in the nucleic acid bases in the solid state. These studies can be applied to the study of the radiation chemistry of DNA. The relevance of the study of model systems is shown by considering the following remarkable observations. Years ago, Ehrenberg et al. showed the EPR spectra of the 5,6-dihydrothymine-5-yl radical observed in thymine, thymidine, and DNA. The spectra are nearly identical [46]. The reduction product observed in cytosine monohydrate is the N3 protonated anion. In solution, this reduction product gives rise to a 1.4-mT EPR doublet. The same feature is present in irradiated DNA at 77 K. Likewise, the result of e loss in guanine bases is characterized by a broad EPR singlet. The same feature is also evident in the EPR spectrum of DNA irradiated and observed at 77 K. 

Radical formation in a mixed crystal system of cytosine monohydrate doped with small amounts of thiocytosine (ca. 0.5%) was investigated on order to gain insight into hole transfer in a well-defined crystalline system.31 Also of interest was whether the protonation state of the thiocytosine radical(s) was the same as that of the cystosine radical(s). Crystals were X-irradiated (ca. 30 kGy) and ESR and ENDOR spectra recorded at ca. 15 K. After irradiation, many types of free radicals were formed. Among these, the low field resonance from a sulfur centered radical (42), with g-tensor (2.132, 2.004, 2.002), was clearly visible. Radical 42 constituted approximately 10% of the total cohort of radicals formed in the crystal and is apparently the only sulfur-centred radical observed in this experiment. Six weakly coupled protons were observed, two of which are shown... 

Summary. The studies of cytosine monohydrate doped with 2-thiocytosine find evidence for hole transfer from cytosine to thiocytosine. If transfer is considered to occur along only the a-stacked bases, 31 relatively large transfer distances are calculated. In more recent work, however, the authors suggests that the transfer is more likely to be 3-dimensional in character and, thus, the overall transfer distance is only a few bases at 15 K.33 The authors suggest the trapping of the hole on cytosine is accompanied by deprotonation which stabilizes the hole on this site and prevents further transfer and that hole transfer is competitive process with cytosine deprotonation. A hypothesis is put forward that the ill understood 3aH radical may originate with small amounts of 5-methylcytosine in the systems studied. 

Figure 17-9. B3LYP/6-311G" optimized structures of cytosine monohydrates (distances in A) (adapted from Ref. [56])...

Wetmore et al. also examined the oxidation product in cytosine [79], They computed spin densities p(Nl) = 0.29 and p(C5) = 0.49 for the N1 deproto-nated cation observed in cytosine monohydrate. These results are very close to the experimental results presented in Section 18.4.1.1 p(Nl) = 0.30 and p(C5) = 0.57. However, since their calculated C5-H isotropic hyperfine coupling (—31.5 MHz) is significantly different from the experimental value (—41.4 MHz), and their calculation predicts only a small N4 spin density, they reject the N1 deprotonated cation model. To see why this is not correct, one can invoke the litany of observations presented above from a radiation chemistry perspective. 

First of all the high spin density on C5 is indicative of an oxidation product. In order to be stably trapped, cations have to deprotonate. In cytosine monohydrate, this deprotonation can most easily occur at N1 or N4. Deprotonation at the amino group would give a radical species that would not fit the EPR/ENDOR data. Therefore the N1 deprotonated cation is the best model to represent the experimental data, and actually the best model from the calculations that Wetmore et al. performed [79], The disagreement Wetmore et al. report is with the C5-H isotropic hyperfine coupling. This is actually to be expected since the authors have not included the important effects of the hydrogen bonded network present in the single crystal in their calculations. 

A more complex variation of the structure is observed in cytosine monohydrate [CYTOSH], which was studied as the deuterated compound by neutron diffraction. It contains cyclic trimers linking -ND2, D20 and C=0 groups (Fig. 15.11b). 

In 5-fluoro cytosine monohydrate [BIRMEU] (Fig. 15.15), there are two symmetry-independent molecules which have almost identical hydrogen bonding. The... 

The configuration CC22 is observed in cytosine [CYTSIN01] cytosine monohydrate [CYTOSM11] thiocytosine [THCYTOIO] 5-bromocytosine-hemi-di-oxane solvate [BRCYTS]. 

BIRMEU. 5-Fluoro-cytosine monohydrate (C4H4FN30, H20). Louis T, Low JN, Ibllin P (1982) Cryst Struct Commun 11 1059... 

CADZAI. 1 -/3-D-5-Methylarabinosyl-cytosine monohydrate (C10H15N3O5, H20). Birnbaum GI, Gentry GA (1983) J Am Chem Soc 105 5398... 

CYTOSM11. Cytosine monohydrate (C4H5N30, H20). McClure RJ, Craven BM (1973) Acta Crystallogr, Sect B 29 1234... 

Table 6 Comparison of theoretical and experimental HFCCs (G) for the first major radical product assigned experimentally in irradiated cytosine monohydrate crystals [C(N3H)1. ...

Weber, H.-P., and Craven, B. M, Electrostatic properties of cytosine monohydrate from diffraction data. Acta Cryst. B46, 532-538 (1990). 

From studies of cytosine monohydrate single crystals irradiated at 10 K Sagstuen et al. concluded that the primary reduction product is the N3 protonated anion (Radical Rl). ENDOR experiments detected the C6-H hyperfine coupling, the N3-Hj, hyperfine coupling and one of the small couplings to the N4-H2 protons (see Table H)." ... 

Crystalline Cytosine Monohydrate , by Close et al, J Phys. Chem. B,... 

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