Reply to the “Comment on 'Theoretical Study of Polaron Formation in Poly(G)–Poly(C) Cations'”
Bibliographic record
Abstract
A dhikary and Sevilla 1 have commented on our theoretical study of polaron formation in poly(G)Àpoly(C) cations. 2 Adhikary and Sevilla's comment 1 clarified the interpretation of their experiments on the ESR spectrum of DNA oligomers, which reveal the localization of the hole in contiguous G sequences in B-DNA oligomers.3 They also emphasized that their experimental results are supported by the theoretical calculations of Voityuk and Blancafort, 4,5 and Kumar and Sevilla.6,7 According to our ONIOM calculations, 2 the hole in the poly(G)Àpoly(C) radical cation is delocalized over several guanine residues.In the theoretical calculations of Blancafort and Voityuk, 5 the charge distributions in the π-stacked GAG and GTG single strand were investigated.Kumar and Sevilla's calculation 6 on the GÀC radical cation with 11 water molecules was performed for only one GÀC base pair, and the 11 water molecules were optimized to be nearly in the plane of GÀC pair.These calculations do not accurately represent the real situation in B-DNA.For example, the GC + 11H 2 O scheme 6 has an optimized geometry with two water molecules near the N 1 (C) and N 9 (G) atoms.This geometry is not feasible for B-DNA oligomers, because N 1 (C) and N 9 (G) are bonded with the sugarÀphosphate backbone, and water molecules cannot be placed near them.Due to the presence of the sugarÀphosphate backbone, these two water molecules must be neglected in the calculation of B-DNA.Furthermore, the neighboring water molecules must be neglected because they form a hydrogen-bonding network and do not form hydrogen bonds with the GÀC base pair.Therefore, only seven
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.007 | 0.032 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.004 | 0.007 |
| Scholarly communication | 0.003 | 0.005 |
| Open science | 0.008 | 0.004 |
| Research integrity | 0.045 | 0.050 |
| Insufficient payload (model declined to judge) | 0.009 | 0.009 |
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 source (direct Gemma or distilled Codex), 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".