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We demonstrate a technique that uses high-order harmonic generation in molecules to probe nuclear dynamics and structural rearrangement on a subfemtosecond time scale. The chirped nature of the electron wavepacket produced by laser ionization in a strong field gives rise to a similar chirp in the photons emitted upon electron-ion recombination. Use of this chirp in the emitted light allows information about nuclear dynamics to be gained with 100-attosecond temporal resolution, from excitation by an 8-femtosecond pulse, in a single laser shot. Measurements on molecular hydrogen and deuterium agreed well with calculations of ultrafast nuclear dynamics in the H2+ molecule, confirming the validity of the method. We then measured harmonic spectra from CH4 and CD4 to demonstrate a few-femtosecond time scale for the onset of proton rearrangement in methane upon ionization.