Carbonyl groups (C=O) play crucial roles in the photophysics and photochemistry of biological systems. O1s x-ray photoelectron spectroscopy allows for targeted investigation of the C=O group, and the coupling between C=O vibration and O1s ionization is reflected in the fine structures. To elucidate its characteristic vibronic features, systematic Franck–Condon simulations were conducted for six common biomolecules, including three purines (xanthine, caffeine, and hypoxanthine) and three pyrimidines (thymine, 5F-uracil, and uracil). The complexity of simulation for these biomolecules lies in accounting for temperature effects and potential tautomeric variations. We combined the time-dependent and time-independent methods to efficiently account for the temperature effects and to provide explicit assignments, respectively. For hypoxanthine, the tautomeric effect was considered by incorporating the Boltzmann population ratios of two tautomers. The simulations demonstrated good agreement with experimental spectra, enabling differentiation of two types of carbonyl oxygens with subtle local structural differences, positioned between two nitrogens (O1) or between one carbon and one nitrogen (O2). The analysis provided insights into the coupling between C=O vibration and O1s ionization, consistently showing an elongation of the C=O bond length (by 0.08–0.09 Å) upon O1s ionization.
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