Initial Excited-State Structural Dynamics of Uracil from Resonance Raman Spectroscopy Are Different from Those of Thymine (5-Methyluracil)
Bibliographic record
Abstract
To explore the origin of the differences in UV photochemistry of uracil (RNA) and thymine (DNA) nucleobases, we have measured the UV resonance Raman spectra of uracil in aqueous solution at wavelengths throughout the lowest-energy absorption band and analyzed the resulting resonance Raman excitation profiles and absorption spectra using a time-dependent wave-packet formalism to obtain the initial excited-state structural changes. In contrast to thymine, which differs from uracil only by the presence of a methyl group at C(5), most of the resonance Raman intensity and resulting initial excited-state structural dynamics for uracil occur along in-plane hydrogen-bond angle deformation, ring stretching, and carbonyl vibrational modes. Weaker intensities and less significant structural dynamics are observed along the C=C stretching mode. These results suggest that the initial excited-state structural dynamics of uracil occur along a carbon pyramidalization coordinate. These dynamics are different from those of thymine, which distorts primarily along a C(5)=C(6) bond lengthening coordinate. These differences in initial excited-state structural dynamics can explain the different primary photoproducts observed for these two pyrimidine nucleobases.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".