Molecular dynamics simulation of double proton transfer: adenine-thymine base pair

Molecular dynamics of proton transfer was simulated from normal (N) to tautomeric (T) form of the base pair (bp) adenine-thymine (A-T). The results for the model system, consisting of one A-T base pair in SPC/E water, was analysed in terms of its hydration properties, difference on free energy, conformational changes, and magnetic properties. It is suggested that during proton transfer the base pair remains on the same conformational state. The free energy of the protons transfer appears to be almost insensitive to the presence of water. The overall hydrophobicity of the A-T pairs is slightly modified by the proton transfer the N form being a little more hydrophobic. The behavior of the magnetic shielding suggests that a current is produced in the ring of the hydrogen bonds due to strong pi -electron delocalization in the amide-amidine complex.