A Theoretical‐Computational Study of Phosphodiester Bond Cleavage Kinetics as a Function of the Temperature

A theoretical-computational procedure, based on a hybrid quantum/classical approach, was to applied reconstruct the kinetics of the alkaline hydrolysis of a DNA model compound within a wide range of temperatures. The model provided meaningful details about the phosphodiester bond cleavage reaction. Finally, the good agreement with the available data shows the potential of our approach for studying such reactions.

Abstract

The hydrolysis of the phosphodiester bond is an important chemical reaction involved in several biological processes. Here, we study the cleavage of this bond by means of a theoretical-computational method in a model system, the dineopentyl phosphate. By such an approach, we reconstructed the kinetics and related thermodynamics of this chemical reaction along an isochore. In particular, we evaluated the kinetic constants of all the reaction steps within a wide range of temperatures, mostly corresponding to conditions where no experimental measures are available due to the extremely slow kinetics. Our results, in good agreement with the experimental data, show the robustness of our theoretical-computational methodology which can be easily extended to more complex systems.

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