  Purines and pyrimidines, crucial building blocks in biological systems, have
attracted significant interest across molecular physics, biochemistry,
pharmacology, and chemistry. Extensive spectroscopies have been employed for
characterization, while the temperature and potential tautomeric effects can
complicate the interpretation of underlying physics and chemistry. Here, we
conducted first-principles simulations to analyze the vibrationally-resolved
O1s X-ray photoelectron spectra of 6 common biomolecules at different
temperatures, comprising 3 purine (xanthine, caffeine, and hypoxanthine) and 3
pyrimidine (thymine, 5F-uracil, and uracil) derivatives, and the tautomeric
effect of hypoxanthine at varying temperatures. Using both time-independent
(TI) and time-dependent (TD) methods under the Franck-Condon approximation, we
obtained theoretical spectra that exhibited excellent agreement with
experiments. Our analysis of these systems, all featuring carbonyl oxygens,
unveiled distinctive characteristics of oxygen in N-CO-N (O2) compared to that
within a N-CO-C structure (O1), showcasing higher O1s binding energy and total
vibrational reorganization energy. We observed small differences in the
zero-point vibration energies between the core-ionized and ground states,
indicating a weak Duschinsky rotation effect. We consistently found that O1s
ionization resulted in elongation of the O*=C bond length. The TI method
facilitated the assignment of experimental spectra to different atoms or
tautomers, where the atom-specific vibronic profiles of all 6 molecules
exhibited similarity, with the 0-2 transitions dominating. TD enabled a more
comprehensive exploration of the temperature effect, and the tautomeric effect
of hypoxanthine by incorporating the Boltzmann population ratios of tautomers.
We observed significant temperature dependence in the vibronic features present
in these spectra.
