Cytosine quantum mechanical studies

Cytosine as well as the other heterocyclic nucleic acid bases are quasiaromatic compounds, expected to be planar. The experimental evidence shows that this is not strictly so, but the deviations of the ring atoms of cytosine from planarity are, in general, small, and in most cases within the limits of the experimental accuracy. Oxygen and amino groups, and the atoms of substituents, when present, appear to deviate more from planarity. In all the quantum-mechanical studies the cytosine ring has been assumed to be planar. 

Cytosine was the first nucleobase whose radiationless decay was studied with quantum mechanical methods. Nevertheless, its first excited states are not so clearly separated as in uracil and thymine, and this causes complications in the computational studies of the photophysics. So, many computational studies have been reported to elucidate the mechanisms for radiationless decay to the ground state but, not always with the same conclusions. 

Up to now, quantum-mechanical methods have not been applied to the study of the vibrational spectra of cytosine (see Section V, however, for an interpretation of the hydrogen bond vibrational spectra of the quanine-cytosine base pair). 

Perakyla M. A model study of the enzyme-catalyzed cytosine methylation using ab initio quantum mechanical and density functional theory calculations pKa of the cytosine N3 in the intermediates and transition states of the reaction. J. Amer. Chem. Soc. 1998 120 12895-12902. 

Owing to importance of cytosine in biochemistry and significant effects of tautomeric interconversions on DNA mutations, the tautomerism in cytosine was extensively studied by quantum-mechanical calculations on various levels. In contrast to uracil, the dioxo tautomer of which is significantly more stable than the other tautomers, three tautomers of cytosine (201a-c) are reasonably close in energy, so the order of stability is essentially determined by the level of calculations. 

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