Temperature and Tautomeric Effects in High-Resolution Oxygen 1s X-ray Photoelectron Spectroscopy of Purines and Pyrimidines
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866910930524176384 |
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| author | Wei, Minrui Zuo, Junxiang Tian, Guangjun Hua, Weijie |
| author_facet | Wei, Minrui Zuo, Junxiang Tian, Guangjun Hua, Weijie |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2403_09109 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Temperature and Tautomeric Effects in High-Resolution Oxygen 1s X-ray Photoelectron Spectroscopy of Purines and Pyrimidines Wei, Minrui Zuo, Junxiang Tian, Guangjun Hua, Weijie Chemical Physics Atomic and Molecular Clusters Computational Physics Optics 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. |
| title | Temperature and Tautomeric Effects in High-Resolution Oxygen 1s X-ray Photoelectron Spectroscopy of Purines and Pyrimidines |
| topic | Chemical Physics Atomic and Molecular Clusters Computational Physics Optics |
| url | https://arxiv.org/abs/2403.09109 |