Network of hydrogen bonds in Pro-Ala-Pro and Pro-Phe-Pro diamides: A first principles study of Ala→Phe point mutation in proline environment
Bibliographic record
Abstract
Intramolecular hydrogen bonding in the Pro-Ala-Pro and Pro-Phe-Pro tripeptides has been characterized using Bader's atoms in molecule (AIM) analyses of relevant electron density topologies. The properties of hydrogen bonds with corresponding ring strains were investigated. Good correlations along the decrease in electron densities at ring critical points were examined from five- to ten-membered hydrogen-bound ring sizes; seven-membered rings being the most energetically favored. AIM analysis confirms the logical conclusion that the molecule has to become very compact to form as many hydrogen bonds as possible. The relatively large hydrogen bond stabilization attributed to the pronounced network of interactions comes at the "energetic expense" of a relatively large internal repulsion due to the compactness of the structures. The net balanced result was a very modest increase in the zero point corrected conformation energy (DeltaE(ZPEC)). These findings aid in establishing hydrogen bonding rules in reductionist "bottoms-up" approaches to peptide and protein folding.
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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".