Hydrogen Atom Loss in Pyrimidine DNA Bases Induced by Low-Energy Electrons: Energetics Predicted by Theory
Bibliographic record
Abstract
In addition to inducing DNA strand breaks, low-energy electrons (LEEs) also have been shown to induce fragmentation of pyrimidine bases (uracil, thymine, and cytosine) in the gas and condensed phases. Loss of a hydrogen atom from a DNA base−electron adduct initiates chemical modification of the base, which can cause permanent damage to the base as well as to DNA. Thus, the energetics of hydrogen atom loss reactions from anionic bases is crucial to understanding the mechanism of LEE-induced damage to DNA and its component bases. Following our previous report on LEE interactions with uracil [ J. Phys. Chem . B 2004, 108, 5472−5476], in this work we investigate LEE interactions with thymine and cytosine. The adiabatic potential energy surface along each N−H or C−H bond is explored up to 3 Å at the DFT level. The changes in energy, enthalpy, and free energy (Δ E, Δ H, and Δ G ) for a complete separation of an H atom or a methyl (amino) group from the anionic base as well as bond dissociation energies of neutral bases are calculated at the CBS-Q level. The electron affinities of the DNA base thymine and cytosine and their H-deleted neutral fragments are also calculated. All N−H bonds are more susceptible to LEE-induced fragmentation than C−H bonds, with N 1 −H as the most vulnerable site. Since N 1 is the site of the glycosidic bond between the deoxyribose and the base in DNA, the vulnerable nature of this site toward bond rupture suggests that LEEs are likely to induce base release in DNA. Investigations along these lines are under way.
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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 | 0.001 | 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".