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A theoretical framework for studying strong-field ionization of aligned molecules is presented, and alignment-dependent ionization yields are computed for CO2. Our calculations are in unprecedented agreement with recent experiments. We find that the ionization process is affected by intermediate resonance states, and the alignment-dependent ionization yields do not follow the electron density of the initial states. The theory explains the breakdown of semi-analytical theories, like the molecular tunneling theory and strong-field approximation, were excited electronic structure is neglected.

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