Cytosine Tautomer energy

Table VII contains the results of the CNDO/2 calculation158 on the energy of cytosine tautomers 2, 3 or 6 and of some derivatives. It can be seen that the calculated energy shifts are in agreement with the effect of substitution on the tautomeric equilibrium of cytosine discussed in Section II, B. Thus, a 5-fluoro substituent causes a small tautomeric shift toward forms 3 (dB i3F Cyt - di ,3t = 2.98 kcal/mole) or 6 (JB l8F Cyt — = 4.87 kcal/mole), while a 6-fluoro substituent...

Figure 7.10 Structures and relative energies (kcal mor ) of mono- and dihydrated cytosine tautomers 13a and 13b. ...

TABLE 7.12 Relative Energies (in kcal mol of Cytosine Tautomers (13a-h)... 

The tautomeric equilibria of cytosine tautomers are more complex. The relative energies of three of the most stable tautomeric forms are within 1 kcal mol . All of these tautomers have been detected experimentally and characterized by ir3 -33 and microwave spectroscopic study... 

Table 4 Relative Energies of Cytosine Tautomers (kcal mol ) Calculated with 6-31G(d,p) Basis Set in HF/6-3 lG(d,p) Reference Geometries ...

Some of the impetus for studying tautomeric equilibria in heterocycles arises because of the postulate that point mutations in genetic material may be introduced when a given base exists in a tautomeric form during replication [279, 305-307], Cytosine, in particular, has imino and hydroxy tautomers that are within 3 kcal/mol of the global minimum illustrated above (because of the very large number of possible tautomers for the purines and pyrimidines, only the lowest energy tautomers are presented). This analysis has been made based on a... 

At low enough temperatures vibrational fine structure of aromatic chromophores may be well resolved, especially if they are embedded in a suitable matrix such as argon or N2, which is deposited on a transparent surface at 15 K. This matrix isolation spectroscopy77166 may reveal differences in spectra of conformers or, as in Fig. 23-16, of tautomers. In the latter example the IR spectra of the well-known amino-oxo and amino-hydroxy tautomers of cytosine can both be seen in the matrix isolation IR spectrum. Figure 23-16 is an IR spectrum, but at low temperatures electronic absorption spectra may display sharp vibrational structure. For example, aromatic hydrocarbons dissolved in n-heptane or n-octane and frozen often have absorption spectra, and therefore fluorescence excitation spectra, which often consist of very narrow lines. A laser can be tuned to excite only one line in the absorption spectrum. For example, in the spectrum of the carcinogen ll-methylbenz(a)anthrene in frozen octane three major transitions arise because there are three different environments for the molecule. Excitation of these lines separately yields distinctly different emission spectra.77 Likewise, in complex mixtures of different hydrocarbons emission can be excited from each one at will and can be used for estimation of amounts. Other related methods of energy-... 

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. 

The tautomers of cytosine have also been examined with continuum solvation methods. Both Miertus-Scrocco-Tomasi (MST) and PCM computations predict that 13a is the lowest energy conformer in aqueous solution. This is consistent with the explicit water computations. Aqueous solvation, therefore, substantially alters the relative energies of the tautomers of cytosine. The canonical representation of cytosine 13a, the tautomer invoked in Watson-Crick base pairing, is in fact the most favorable tautomer in solution, but not in the gas phase. 

The positions of the absorption bands of thiocytosine and isothio-cytosine are given in Table XXXV together with the predicted values. The CNDO/2 calculation shows that tautomers 52 and 55 of thiocytosine have similar energies, and the tt-SCF MO Cl calculations for... 

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