Spin Densities Guanine

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). 

Crystals of 2 -Deoxyguanosine 5 -Monophosphate Tetrahydrate Disodium Salt (5 -dGMP) have a neutral guanine base. In the solid-state, oxidation of 5 -dGMP at 10 K leads to deprotonation at the exocyclic nitrogen which is characterized by p(C8) = 0.175 and p(N2) = 0.33 [37], The same radical was detected in crystals of 3, 5 -cyclic guanosine 5 -monohydrate. In this second study, the N3 spin density was determined to be 0.31 [38], These two studies then provide a detailed description of the amino deprotonated guanine cation G(N2-H) ... 

Figure 18-12. Structure of the guanine cation with spin densities p(N2) = 0.168 and p(C8) = 0.182. (Reprinted with permission from ref. [36], J. Chem. Phys. (1985) American Physical Society.)...

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 12.15 Three-dimensional spin densities for the planar guanine anion calculated using AMI. The spin density is localized on the hydrogen bonding sites and is similar to a dipole bound state.

Figure 12.19 Three-dimensional spin densities for the GC anion keto cytosine calculated using AMI. READS(G/C) = 0.05. In this structure the guanine is in an excited state with an Ea of 0.3 eV, as compared to the global minimum with an Ea of 1.51 eV.

Figure 12.21 Three-dimensional spin densities for the GC(—3) anion keto cytosine anion calculated using AMI. As more electrons are added to the hydrogen-bonded base pair, the spin distribution is distributed to the guanine.

The earliest example of diabatization by FDE was given in Ref. [48]. This is shown in Fig. 4.1, where the spin densities for a pair of guanines are calculated. KS-DFT of the supersystem carried out with semilocal XC functionals fails in the prediction of the spin density. This is because the self-interaction error makes the spin density spread on both guanines against the prediction given by more accurate theoretical work [35] and experimental studies [99-101]. On the contrary, FDE localizes the charge on a guanine of choice. 

Fig. 4.1 Spin densities of a guanine-cytosine dimer radical cation, (GC)j. a KS-DFT supramole-cular calculation using PW91 functional, b FDE calculation considering two subsystems where the left side subsystems blue contour) is positively charged and c FDE calculation for four subsystems with one subsystems blue contour) is positively charged. The nucleobases structures and spin densities were taken from Ref. [48]...

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