Adenine⋯2,4-difluorotoluene (modified base) pair: potential and free-energy surfaces: Non-empirical and empirical potential studies

Abstract

Ab initio calculations are described for bonded and stacked structures of adenine⋯2,4-difluorotoluene. Stabilization energies are determined with inclusion of correlation energy at the MP2/6-31G∗(0.25) level. Stacked structures of the pair are more stable than planar ones. The nucleic acid force field of Cornell et al. reproduces ab initio stabilization energies of planar and stacked structures well. The population of various structures of the pair, which is proportional to ΔG of base pair formation, was determined by long runs of molecular dynamics with the force field of Cornell et al. Potential- and free-energy surfaces are similar and, among 11 of the most populated dimer structures, there is no planar H-bonded structure.