Computational Study of the Deamination of 8-Oxoguanine
Bibliographic record
Abstract
Oxidation of guanine in DNA yields the nucleobase damage product 8-oxoguanine (8-oxoG), whose further oxidation gives other more stable products. In the present study, the mechanism for the deamination of 8-oxoG with H(2)O, 2H(2)O, H(2)O/OH(-), and 2H(2)O/OH(-) and for protonated 8-oxoG (8-oxoGH(+)) with H(2)O has been investigated using ab initio calculations. All structures were optimized at RHF/6-31G(d), MP2/6-31G(d), and B3LYP with the 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-31+G(d,p), and 6-31++G(d.p) basis sets. Energies were determined at the G3MP2 level of theory, and solvent calculations were performed using both the polarizable continuum model (PCM) and the solvation model on density (SMD). Intrinsic reaction coordinate calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and, in the final step, an intermediate that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with H(2)O/OH(-) was found to have an overall activation energy of 187, 176, and 156 kJ mol(-1) for the gas phase, PCM, and SMD, respectively, which are ∼50 kJ mol(-1) lower than with H(2)O only. These barriers can be compared to those for the reaction of 8-oxoGH(+) with H(2)O of 248 kJ mol(-1) in the gas phase and 238 kJ mol(-1) in aqueous solution (PCM). The lowest overall activation energies (G3MP2) are for the deamination of 8-oxoG with 2H(2)O/OH(-), 134 kJ mol(-1) in the gas phase and 129 kJ mol(-1) with PCM.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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".