A study of the lowest excited dimer (excimer) singlet state of the DNA base cytosine was performed with fully optimized geometry (near the cis‐syn form) using a slightly modified version of MOPAC6 (AM1 hamiltonian) and 112 excited configurations involving an active space consisting of the four highest occupied and the two lowest empty MO of the dimer. A binding energy of 3 kcal/mol for the excimer state is demonstrated, and the excimer fluorescence is predicted to be shifted 150 nm to longer wavelengths relative to that of the monomer fluorescence. The excimer geometry has the planes nonparallel (40–45° interplanar angle) and distorted, with the C5‐C6 bonds showing quite close contact (2.4 Å). Excitation is found to be more localized in the region of the C5‐C6 bond than expected from the monomer wavefunction. No stable excimer was found if the planes were constrained to be planar, nor if the triplet state was selected. The results suggest that the excimer geometry found in this study may be a precursor to the cis‐syn cyclobutane photodimer.

Theoretical modeling of initial steps of the photodimerization mechanism of uracil, 5-methyl-and 5-halogen derivatives was performed. The interaction energy of bases in stacked dimers in the ground and lowest excited states was calculated as a function of the distance between the base planes and of the rotation angles within the perturbation theory for the extended Hückel treatment. The existence of excimer and exciplex region on the potential surface of the excited state was revealed. The excimer (exciplex) geometry has the planes nonparallel with more close contact of the C5-C6 bonds as compared to the ground state of dimers. The results provide new information useful for understanding the photodimerization mechanism of bases and testifies that the singlet excimer state can be a precursor of the photodimerization reaction.

An extensive computer simulation of nucleic acid bases and Watson-Crick base pairs in a water cluster and DMSO cluster is performed by the Monte Carlo method. It is demonstrated that the unfavorable energetics of pair formation in a water cluster is determined by the significant destabilizing contribution of solvent to the energy of complex formation. It is shown that the formation of coplanar base pairs in a DMSO cluster is favorable. The DMSO cluster stabilizes A-U and A-T base pairs and the insignificant destabilization of the G-C base pair by a DMSO cluster is much less than the stabilization which occurs due to the attraction between bases.