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 statist ical thermodynamical methods. In total, 11 low-energy minima structure s were located on the potential energy surface of the uracil dimer: se ven of them are H-bonded, one is T-shaped, and three correspond to var ious stacked arrangements. The most stable structure is a H-bonded dim er 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 o f theory. T-shaped structure and stacked structures are less stable th an H-bonded ones. Thermodynamic characteristics were obtained using th e rigid rotor-harmonic oscillator-ideal gas (RR-HO-IG) approximation a dopting the AMBER 4.1 and ab initio characteristics. Furthermore, the population of various structures was determined by computer simulation s in the NVT canonical and NVE microcanonical ensembles. Results obtai ned from the RR-HO-IG approximation and the NVT ensemble are very simi lar and differ from the result of the NVE ensemble. The present analys is demonstrates that different gas-phase experimental techniques can b e used for investigating different regions of the conformational space for nucleic acid base pairs. The fact that entropy is always signific ant and differs for H-bonded and stacked structures is of importance.