Conformational dynamics of the dimethyl phosphate anion in solution

The conformational dynamics of the DNA phosphodiester linkage in solution is modeled by performing first principles molecular dynamics simulations of the dimethyl phosphate anion ((CH3O)2PO2− or DMP−) in water, in the presence of a sodium cation. We observe conformational changes in DMP− in solution, which are related to the approach of the sodium cation to the anionic oxygens of DMP−. These simulations demonstrate that the presence of a counterion may play a significant role in driving the transition between different conformers of DMP−.