Adiabatic electron affinities (AEAs) for the DNA and RNA bases are predicted by using a range of density functionals with a double-zeta plus polarization plus diffuse (DZP++) basis set in an effort to bracket the true EAs. Although the AEAs exhibit moderate fluctuations with respect to the choice of functional, systematic trends show that the covalent uracil (U) and thymine (T) anions are bound by 0.05-0.25 eV while the adenine (A) anion is clearly unbound. The computed AEAs for cytosine (C) and guanine (G) oscillate between small positive and negative values for the three most reliable functional combinations (BP86, B3LYP, and BLYP), and it remains unclear if either covalent anion is bound. AEAs with B3LYP/TZ2P++ single points are 0.19 (U), 0.16 (T), 0.07 (G), -0.02 (C), and -0.17 eV (A). Favorable comparisons are made to experimental estimates extrapolated from photoelectron spectra data for the complexes of the nucleobases with water. However, experimental values scaled from liquid-phase reduction potentials are shown to overestimate the AEAs by as much as 1.5 eV. Because the uracil and thymine covalent EAs are in energy ranges near those of their dipole-bound counterparts, preparation and precise experimental measurement of the thermodynamically stable covalent anions may prove challenging.
The adiabatic electron affinity (AEA) for the Watson-Crick guanine-cytosine (GC) DNA base pair is predicted using a range of density functional methods with double- and triple-zeta plus polarization plus diffuse (DZP++ and TZ2P++) basis sets in an effort to bracket the true electron affinity. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chem.Rev. 2002, 102, 231). Optimized structures for GC and the GC anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for sodium guanylyl-3',5'-cytidine nonahydrate, GpC.9H(2)O. Structural distortions and natural population (NPA) charge distributions of the GC anion indicate that the unpaired electron is localized primarily on the cytosine moiety. Unlike treatments using second-order perturbation theory (MP2), density functional theory consistently predicts a substantial positive adiabatic electron affinity for the GC pair (e.g., TZ2P++/B3LYP: +0.48 eV). The stabilization of C(-) via three hydrogen bonds to guanine is sufficient to facilitate adiabatic binding of an electron to GC and is also consistent with the positive experimental electron affinities obtained by photoelectron spectroscopy of cytosine anions incrementally microsolvated with water molecules. The pairing (dissociation) energy for GC(-) (35.6 kcal/mol) is determined with inclusion of electron correlation and shows the anion to have greater thermodynamic stability; the pairing energy for neutral GC (TZ2P++/B3LYP 23.9 kcal/mol) compares favorably to previous MP2/6-31G (23.4 kcal/mol) results and a debated experiment (21.0 kcal/mol).
The adiabatic electron affinity (AEA) for the Watson−Crick adenine−thymine (AT) DNA base pair is predicted and contrasted to that of guanine−cytosine (GC) with a range of density functional methods with double- and triple-ζ plus polarization plus diffuse (DZP++ and TZ2P++) basis sets. An estimate of the true AEA is provided using a bracketing method that has been calibrated against a comprehensive tabulation of experimental electron affinities [Rienstra-Kiracofe, J. C.; Tschumper, G. S.; Schaefer, H. F.; Nandi, S.; Ellison, G. B. Chem. Rev. 2002, 102, 10163]. Optimized structures for AT and the AT anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for the related sodium adenylyl-3‘,5‘-uridine hexahydrate, ApU·6H2O. In contrast to the angular distortions (to nonplanarity) occurring in GC upon anion formation, the angular distortions for the AT anion are slight. However, in an analogous fashion to the GC anion, major changes in the AT anion hydrogen bond distances, from 0.27 to 0.32 Å, are predicted relative to neutral AT. Natural population analysis (NPA) charge distributions are also seen to shift. Those of the AT anion also indicate that the unpaired electron is localized on the pyrimidine (thymine). Density functional theory consistently predicts a substantial positive adiabatic electron affinity for the AT pair (e.g., TZ2P++/B3LYP: +0.31 eV). This contrasts to second-order perturbation theory (MP2) treatments which predict unbound base pair anions. Despite the greater AEA of isolated T relative to C (+0.15 vs −0.02 eV), the AEA of the AT pair is slightly smaller than that of GC (0.31 vs 0.48 eV). This difference is attributed to the weaker solvating capacity of A (A·T-) relative to G (G·C-). The pairing (dissociation to A + T-) energy of AT- is determined to be 14.8 kcal/mol. This value is slightly greater than previous estimates for neutral AT from theory (12.4 kcal/mol) and experiment (13.0 kcal/mol).
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