Methylated uracil dimers: potential energy and free energy surfaces

Theoretical analysis of the formation of 1-methyluracil, 3-methyluracil and 1,3-dimethyluracil dimers was performed. Stabilization energies of these d imers were evaluated with the Cornell et al. force field (J. Am. Chem. Soc. , 1995, 117, 5179). In total 16, 13 and 15 energy minima were studied for t he three dimers. Thermodynamic data were obtained with the rigid rotor-harm onic oscillator-ideal gas approximation. Furthermore, populations of variou s structures were determined by molecular dynamic simulations in the NVE mi crocanonical ensemble and numerical evaluation of the configuration integra ls in the NVT canonical ensemble. The potential energy surfaces (PESs) and the free energy surfaces (FESs) of these dimers differ. The largest differe nce was found for the 1-methyluracil dimer where the global and first local minima on the PES and FES do not coincide.