Molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation-X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towards high kinetic energies, resulting from a particular C-O bond stretch in the pp* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the np* state.

Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a 'molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

High harmonic spectra show that laser-induced strong field ionization of water has a significant contribution from an inner-valence orbital. Our experiment uses the ratio of H2O and D2O high harmonic yields to isolate the characteristic nuclear motion of the molecular ionic states. The nuclear motion initiated via ionization of the highest occupied molecular orbital (HOMO) is small and is expected to lead to similar harmonic yields for the two isotopes. In contrast, ionization of the second least bound orbital (HOMO-1) exhibits itself via a strong bending motion which creates a significant isotope effect. We elaborate on this interpretation by simulating strong field ionization and high harmonic generation from the water isotopes using the time-dependent Schrödinger equation. We expect that this isotope marking scheme for probing excited ionic states in strong field processes can be generalized to other molecules.