Effects of Hydrogen Bonding on the Acidity of Uracil
Bibliographic record
Abstract
The present study uses density functional theory to investigate the effects of hydrogen bonding on the (N1) acidity of uracil. Uracil and uracil anion complexes with water, ammonia, and hydrogen fluoride at various uracil sites (O2(N3), O4(N3) and O4(C5)) are considered. The calculated geometries of the uracil anion complexes are significantly different from those of the (neutral) uracil counterparts, which leads to the significantly larger binding energies in the anionic complexes. The binding strength of each molecule to (neutral) uracil is largest at the O4(N3) position and at the O2(N3) position in the uracil (N1) anion. Our calculations reveal that hydrogen-bonding interactions with one molecule increase the (N1) acidity of uracil by up to approximately 50 kJ mol -1 and that the effect of two molecules is approximately equal to the sum of the individual effects. The acidity increase is largest when water and ammonia bind to the O4(C5) position and when hydrogen fluoride binds to the O2(N3) position. Our results lead to a greater fundamental understanding of hydrogen-bonding interactions involving uracil and have important implications for interactions in biological systems, such as those at the active site in uracil DNA glycosylase.
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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) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 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".