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Abstract
We study the double proton transfer (DPT) tautomerization process in Guanine- Cytosine (GC) DNA base pairs. In particular, we investigate the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics study in the tight-binding density functional theory framework, and compare the reactivity of the GC dimer in the gas phase with that of the same dimer embedded in a small DNA structure. The impact of nuclear quantum effects is also evaluated using the Ring Polymer Molecular Dynamics. Results show that in the isolated dimer, the DPT occurs via a concerted mechanism, while in the model biological environment, it turns into a step-wise process going through an intermediate structure. One of the water molecules in the vicinity of the proton transfer sites plays an important role as it changes H-bond pattern during the DPT reaction.
Supplementary materials
Title
Supporting Information
Description
In the supporting information we report: (1) Details on DFTB benchmarking; (2) Details
of reaction dynamics and Umbrella sampling simulations; (3) Additional results in terms
of population decays, rate constants, distance distributions and direct dynamics trajetories
with 16 beads, 5 base pairs, smaller time step and crystallographic water molecules around
the isolated base pair. Details on the charge calculation procedure are also provided with
the corresponding results.
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