Methylated uracil dimers: potential energy and free energy surfaces

Abstract

Theoretical analysis of the formation of 1-methyluracil, 3-methyluracil and 1,3-dimethyluracil dimers was performed. Stabilization energies of these dimers 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 the three dimers. Thermodynamic data were obtained with the rigid rotor–harmonic oscillator–ideal gas approximation. Furthermore, populations of various structures were determined by molecular dynamic simulations in the NVE microcanonical ensemble and numerical evaluation of the configuration integrals in the NVT canonical ensemble. The potential energy surfaces (PESs) and the free energy surfaces (FESs) of these dimers differ. The largest difference was found for the 1-methyluracil dimer where the global and first local minima on the PES and FES do not coincide.