A study of the hydration of deoxydinucleoside monophosphates containing thymine, uracil and its 5-halogen derivatives: Monte Carlo simulation

An extensive Monte Carlo simulation of hydration of various conformations o f the dinucleoside monophosphates (DNP), containing thymine, uracil and its 5-halogen derivatives has been performed. An anti-anti conformation is the most energetically stable one for each of the DNPs. In the majority of cas es the energy preference is determined by water-water interaction. For othe r dimers conformational energy is the most important factor, or both the fa ctors are of nearly equal importance. The introduction of the methyl group into the 5-position of uracil ring most noticeably influences the conformat ional energy and leads to the decrease of its stabilizing contribution to t he total interaction energy. The introduction of halogen atoms increases th e relative content of anti-syn and syn-anti conformations of DNPs as compar ed to the parent ones due to the formation of an energetically more favorab le water structure around these conformations. A correlation is observed be tween the Monte Carlo results for the halogenated DNPs and their experiment al photoproduct distribution. The data obtained demonstrates a sequence dep endence in the photochemistry of the halogenated dinucleoside monophosphate s.