Spin Densities Adenine

The adenine anion has a = 3.5 [22]. After electron capture, the negative charge of the adenine radical anion resides mainly on N1, N3, and N7 and therefore protonation likely occurs at one of these nitrogens. The results show that in single crystals examined at 10 K, that reduction of adenine leads to the N3 protonated adenine radical anion, Ade(N3 -I- H), with spin densities of ca. p(C2) = 0.41, p(C8) = 0.14, and p(N3) = 0.12 [42]. 

The adenine radical cation was observed in a single crystal of adenine hydrochloride hemihydrate [43]. In this crystal, the adenine is protonated at Nl. After electron loss, the molecule deprotonates at Nl, giving Ade(Nl -l-H, Nl-H). This produces a radical that is structurally equivalent to the cation of the neutral adenine molecule with spin density on C8 and N6 [p(C8) = 0.17 and p(N6) = 0.25]. The adenine radical cation is strongly acidic (pi a< 1) [22]. This strong driving force makes the reaction independent of environmental conditions. In single crystals of adenosine [42] and anhydrous deoxyadenosine [44], the N6 deprotonated cation [Ade(N6-H) ] is observed which is characterized by p(C8) = 0.16 and p(N6) = 0.42. The experimental isotropic hyperfine couplings are N6-H = 33.9 MHz and C8-H = 12.4 MHz. 

Several recent papers have reported Density Functional Theory (DFT) calculations on the primary oxidation and reduction products observed in irradiated single crystals of the common nucleobases thymine [53], cytosine [54], guanine [55], and adenine [56]. The theoretical calculations include estimates of spin densities and isotropic and anisotropic hyperfine couplings which can be compared with experimental results (obtained from detailed EPR/ENDOR experiments). 

In the section on model compounds there are discussions about thymine, cytosine and guanine nucleotides. To date there have been no detailed EPR/ENDOR experiments on an adenine nucleotide because of the inability to grow good single crystals. The structure of 5 -dAMP hexahydrate is known from a crystal structure study [113]. It would be very interesting to analyze the primary radiation induced products in 5 -dAMP at helium temperature to see if there is actually spin density on both the phosphate and the adenine base for the oxidation product as reported in the theoretical study by Hou et al. [104],... 

Figure 12.17 Three-dimensional spin densities for the planar adenine anion calculated using AMI. The spin density is localized away from the major structure and is similar to a dipole bound state.

A few years ago the calculation of spin densities and hyperfine couplings on even small molecules was a very challenging task. Colson et al. reported the spin densities, computed at the 6-31G //3-21G level, for the anions and cations of the four DNA bases. Their results correctly indicated the majors regions of spin density. For example, the major sites of spin density for the adenine reduction product were computed to be p(C2) = 0.71, p(C8) = 0.03, and p(N3) = 0.08. While these are the sites of spin density expected for an adenine reduction product, these results are not very close to the experimentally determined spin densities of p(C2) = 0.41, p(C8) = 0.14, and p(N3) = 0.12. The numbering scheme used here is as shown. 

GTP = 5 -guanosine triphosphate AE = Activating enzyme BAN = Backbone amide nitrogen BioB = Biotin synthase CD = Circular dichroism cyt = Cytochrome DFT = Density functional theory DMSO = Dimethylsulfoxide Dx = Desulforedoxin ENDOR = Electron-nuclear double resonance EPR = Electron paramagnetic resonance ESEEM = Electron-spin echo envelop modulation ETF = Electron transferring flavoprotein EXAFS = Extended x-ray absorption fine structure FAD = Flavin adenine dinucleotide Fd = Ferredoxin FMN = Flavin mononucleotide FNR = Fumarate-nitrate reduction FTIR =... 

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