Self-Assembling ADADA Helices Formed by Hydrogen Bonding
Bibliographic record
Abstract
A computational investigation of the electronic properties of an experimentally prepared ADADA helix indicates that the helix is held together with four strong hydrogen bonds as well as many other weak interactions. Determination of the electronic energy changes, as well as thermodynamic parameters, suggests that helix formation is a favorable process, driven by the formation of the hydrogen bonds. For instance, the unsubstituted helix has an electronic binding energy of -85.8 kJ/mol. Furthermore, the strength of binding can be tuned to some extent by the careful selection of substituents. The hydrogen bonds are strengthened when the pyridine ring (H-bond acceptor) is substituted with an electron-donating group such as an amine, while electron-withdrawing groups on the thiazine ring (H-bond donor) are preferred. The most significant enhancement in binding is achieved when the helix is constructed from monomers that consist of contiguous hydrogen-bond acceptors or donors. This so-called AAAAA-DDDDD helix exhibits a binding energy almost 4-fold greater than that of the unsubstituted ADADA helix at -335.4 kJ/mol, a dramatic improvement over the ADADA helix.
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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 | 0.001 | 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".