Role of Aromacity, Ring Strain, and Stereochemistry of Selected Disulfides and Their Congeners in the Oxidative Linkage of DNA Strands at the Major Groove. A Computational Study
Bibliographic record
Abstract
Three aromatic disulfides and their two selected congeners were studied in order to see if they could be initiators or catalysts in a process that aims to tie together the two strands of a DNA double helix. Thermodynamic functions were calculated from first principle molecular computations on deoxyribose models and the disulfide congener. The gas reaction of one of the disulfides turned out to be the closest to the thermoneutral process. Solvation study caused a relatively minor energetic modification. The disulfides were subjected to docking studies, and the stabilities of the complexes obtained were further analyzed by molecular dynamics simulations. Only one of the two atropic disulfide enantiomers was the matching partner of the chiral DNA double helix, and therefore this remained in the major groove of the DNA. The other enantiomer dissociated from the major groove as it was incapable of forming a stable complex with the chiral double helix. A mechanistic scheme for the reaction has been investigated.
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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".