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)(2)PO2- 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-.