Protonation of guanine quartets and quartet stacks: insights from DFT studies
Bibliographic record
Abstract
Density functional theory methods have been used to investigate the effects of adding one to four protons to a one-plane guanine quartet (G4) and a two-plane guanine quartet stack (2G4). The singly protonated G4 complex prefers protonation at the Watson-Crick face of the O6 moiety. However, all multi-protonated G4 complexes favour protonation at the Hoogsteen face of the O6 centres. The proton affinities have also been calculated for the addition of one, two, three and four protons to the central oxygens of G4 and have been compared with those of monomeric guanine and other biochemically appropriate bases. These results suggest that a G4 might reasonably readily accept two protons. For the singly to quadruply protonated 2G4's, the added protons prefer to distribute over both planes with maximally two per plane. Furthermore, unlike the (G4-nH+) n>or= 2 complexes, protonation at the Watson-Crick faces of the O6 moieties is found to be preferred for all protonation states. In addition, (2G4-nH+) n=1-4 complexes were also obtained in which inter-plane hydrogen bonds were formed, effectively enabling the protons to 'sit between' planes.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 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 | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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 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".