Uracil dimer:: Potential energy and free energy surfaces.: Ab initio beyond Hartree-Fock and empirical potential studies

The first complete theoretical analysis of the gas-phase formation of a nucleic acid base pair (uracil dimer) has been performed. The study is based on a combination of AMBER 4.1 empirical potential, correlated ab initio quantum chemical methods, computer simulations, and statistical thermodynamical methods. In total, 11 low-energy minima structures were located on the potential energy surface of the uracil dimer: seven of them are H-bonded, one is T-shaped, and three correspond to various stacked arrangements. The most stable structure is a H-bonded dimer with two N-1-H ... O-2 H-bonds, designated as HB4; it has an energy minimum of -15.9 kcal/mol at the MP2/6-31G*(0.25)//HF/6-31G** level of theory. T-shaped structure and stacked structures are less stable than H-bonded ones. Thermodynamic characteristics were obtained using the rigid rotor-harmonic oscillator-ideal gas (RR-HO-IG) approximation adopting the AMBER 4.1 and ab initio characteristics. Furthermore, the population of various structures was determined by computer simulations in the NVT canonical and NVE microcanonical ensembles. Results obtained from the RR-HO-IG approximation and the NVT ensemble are very similar and differ from the result of the NVE ensemble. The present analysis demonstrates that different gas-phase experimental techniques can be used for investigating different regions of the conformational space for nucleic acid base pairs. The fact that entropy is always significant and differs for H-bonded and stacked structures is of importance.