Hybrid QM/MM calculations on the structure and electronic properties of hydrated RNA base pair

Structures of hydrated A-U base pair were investigated by using DFT and hybrid ONIOM methods in order to examine the efficacy of the ONIOM (QM:MM) approach in describing the structure of the hydrated RNA base pair. Comparison of these results reveals that the ONIOM (DFT:AMBER) approach, in which the nucleic acid base pair is treated quantum chemically by DFT and ambient water molecules treated by AMBER molecular mechanics, maintains the structures of the hydrated A-U base pair optimized by full DFT quantum chemical methods.