Geometry of cytosine

FIGURE 2.2 Optimized TS geometries of the cytosine alkylation reaction by o-QM, without and with water assistance. Bond lengths (in A) and activation Gibbs free energies (in kcal/mol) in the gas phase and in aqueous solution (in parentheses) at the B3LYP/6-311 +G(d,p)// B3LYP/6-31G(d) level of theory with respect to the reactants have been taken from Ref. [14]. 

FIGURE 27.4 Geometry of the stacking interaction between substituted benzenes and cytosine. (Reprinted from Mignon, P., Loverix, S., Steyaert, J., and Geerlings, P., Nucl. Acids Res., 33, 1779, 2005. With permission.)... 

What would be the geometry of the guanine-cytosine complex were there no hydrogen bonds or, more to the point, were chemists not to know about the benefits of hydrogen bonding More than likely, it would be a more closely-packed geometry, such as the following. 

For other CNDO/2 calculations on tautomeric stability of cytosine, see refs. 14, 152, 153. In all these calculations the same geometry of the ring has been used for different tautomers. 

To understand these highly interesting photophysical properties of nucleobases, we have carried out CIS and coupled cluster (CC) calculations of the potential energy profiles of cytosine and its derivatives at optimized CIS geometries [10]. The results indicate that the Sj S0 internal conversion occurs through a barrierless state switch from the initially excited 1 tttt state to a biradical state, which intersects... 

The anionic Watson-Crick guanine-cytosine base pair behaves in a different manner [75], Namely, out of several possible configurations, differing with the position of proton(s), the geometry with proton transferred from the N1 atom of guanine to the N3 atom of cytosine turned out to be the global minimum. This structure is more stable than the Watson-Crick anion by 2.9 (B3LYP) and... 

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