Rapid Estimation Of The Binding Energies Between Uracils And/or Thymines

Hydrogen bonds play an important role in nucleic-nucleic acid complexes. Therefore, it is necessary to put forward a method to rapidly evaluate the binding energies in hydrogen-bonded nucleic acid base complexes.An analytic potential energy function for hydrogen bonds has been established in our laboratory and has been successfully used to calculate the N-H...O=C and C-H...O=C hydrogen bond energies for a series of hydrogen-bonded peptides and nucleic acid bases. In this dissertation, we further apply this analytic potential energy function to some hydrogen-bonded nucleic acid base complexes. The analytic potential energy function is employed to calculate the binding energies. For all the21dimers, the analytic potential energy function yields the binding energies of the MP2/6-311++G(3df,2p) with BSSE correction within the error limits of0.50kcal/mol for13dimers,8complexes between0.5and0.76kcal/mol, the relative error is less than4.7%for these8dimers. The standard deviation is0.46kcal/mol for all the dimers. For all the72trimers, the analytic potential energy function yields the binding energies of the MP2/6-311++G(3df,2p) with BSSE correction within the error limits of0.50kcal/mol for59trimers,9complexes between0.5and0.85kcal/mol, and the remaining4complexes have the error ranging between1.0and2.15kcal/mol, the relative error is less than7%for these13trimers. The standard deviation is0.52kcal/mol for all the trimers. The analytic potential energy function yields the binding energies of the MP2/6-311++G(3df,2p) with BSSE correction within the error limits of0.50kcal/mol for all the3tetramers, the standard deviation is only0.20kcal/mol. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen-bonded base-base complexes quickly and accurately. In this paper, either uracil or thymine possesses three binding sites (Site1, Site2, and Site3) that can induce strong directional hydrogen bonding interaction. We find that the hydrogen bonds formed through Site1are the strongest, those formed through Site3are next, while those formed through Site2are the weakest.