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A polarizable environment, prominently the solvent, responds to electronicchanges in biomolecules rapidly. The knowledge of conformational relaxation ofthe biomolecule itself, however, may be scarce or missing. In this work, wedescribe in detail the structural changes in DNA undergoing electron transferbetween two adjacent nucleobases. We employ an approach based on averaging oftens to hundreds of thousands of nonequilibrium trajectories generated withmolecular dynamics simulation, and a reduction of dimensionality suitable forDNA. We show that the conformational response of the DNA proceeds along asingle collective coordinate that represents the relative orientation of twoconsecutive base pairs, namely, a combination of helical parameters shift andtilt. The structure of DNA relaxes on time scales reaching nanoseconds,contributing marginally to the relaxation of energies, which is dominated bythe modes of motion of the aqueous solvent. The concept of reaction pathaveraging (RPA), conveniently exploited in this context, makes it possible tofilter out any undesirable noise from the nonequilibrium data, and isapplicable to any chemical process in general.

Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer