Thymine Tautomer energy

TABLE 7.17 Relative Energies (in Real mol ) of Thymine Tautomers (5a-my... 

However, the thymine tautomers, with lack of correlation between HOMA index and relative energies of the tautomers, are an instructive... 

Figure 3 Dependence of HOMA on relative energy, rei, for thymine tautomers. Group (a) blue (black In print versions) circles, (b) red (light gray in print versions) diamonds, and (c) crosses. HOMA, harmonic oscillator model of aromaticity. Reproduced by permission of The Royal Society of Chemistry from Stasyuk et al. (2014OBC6476).

Starting from the comparative study of the ionization constants of uracil itself as well as of its several methylated or ethylated derivatives (representing models of tautomeric forms), it may be seen (Table XVII) that uracil and uridine exist in aqueous solution in the diketo form 32. The pX values are not known for the model tautomers 27, 29, and 30, but these forms have been ruled out on the basis of UV studies. Recently the ionization constants of uracil, thymine, their derivatives and nucleotides were determined over the range 10-50°, and thermodynamic enthalpy, entropy, and free energy changes for protonation and depro-tonation of these compounds have been evaluated.93-95,332... 

Electron transmission spectroscopy results bB3LYP/D95V+(D) except for G which is estimated from trends CDFT (B3LYP/6-311+G(2df,p)) destimated from stable valence anion complexes, e.g.., U(Ar)- ebest estimates from DFT basis set dependence study (vide infra). Thymine from ref. [88], note these values are likely too positive by 0.15 eV fEstimate of keto tautomer from enol tautomer experimental value (—0.46eV) plus calculated difference in energy between keto and enol tautomers (0.28 eV) ref. [94],... 

In this section, we present the results of computational studies of the five nucleic acid bases cytosine 13, guanine 14, adenine 15, thymine 16, and uracil 17. The canonical structures, those that are involved in the Watson-Crick base pairing within DNA, are drawn below. Other tautomers for each base can be energetically competitive with the canonical structure, and these other tautomers are invoked in some models of DNA mutations and anomalous DNA structures. The ensuing discussion focuses on the relative energies of the tautomers, in both the gas and solution phases. Structural changes that accompany this phase change are also noted. 

From ETS experiments (Aflatooni et al. 1998), Aflatooni et al. showed that energies required to attach an electron into the lowest empty valence molecular orbitals of all the bases are positive. This means that all the bases have negative valence vertical electron affinity (<0). The vertically formed anions of pyrimidines bases (C, T, and U) were found to be more stable than the purines (G and A) by ca. 0.2 eV. The ETS spectra of U, T, C, G, and A are shown in O Fig. 34-7. The spectra in O Fig. 34-7 arise due to the occupation of the lowest empty 7t -MOs of the parent molecules by the electron. The vertical lines on the spectra (O Fig. 34-7) show the position of the vertical attachment energies. For guanine anion, the ETS (shown in O Fig. 34-7) was observed for its enol tautomer (for details see Aflatooni et al. [1998]). For each of these molecules, three VAEs, associated with the three lowest vacant tTi, tT2, and 7T3 MOs, were determined. The VAEs 0.22,1.58, and 3.83 eV for uracil 0.29,1.71, and 4.05 eV for thymine 0.32,1.53, and 4.50 eV for cytosine 0.54,1.36, and 2.17 eV for adenine and 0.46,1.37, and 2.36 eV for guanine(enol) tautomer were determined by ETS. 

Only the major tautomer predominates in the gas phase equilibria of uracil, thymine, and adenine. Such equilibria of guanine and cytosine are rather complex and involve the coexistence of three tautomeric forms close in energy. 

Nucleobases, such as cytosine, thymine, and uracil are the most important pyrimidine derivatives. In a recent gas-phase study [64], three low-energy tautomers were identified on the basis of CCSD(T)/cc-pVQZ energy calculations andMP2/6-311++G(2d,2p) estimation ofthe vibrational frequencies. The authors emphasize the importance of the high-level estimation of the frequencies and the related thermal correction in order to obtain rehable AG within a 0.7 kcal mol free energy range of the tautomers at T = 450 K. The lowest-free-energy structure is the canonical hydroxy-amine form of cytosine. 

Relative energies of 13 tautomers/conformers for each of thymine and uracil were determined at a high theoretical level in the gas-phase by Rejnek et al. [66]. 

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