Secondary Structure Dependence and Hydration Effect of the Infrared Intensity of the Amide II Mode of Peptide Chains
Bibliographic record
Abstract
Every vibrational mode to be used as a marker of the structural, dynamical, and/or interaction properties demands our good understanding of the relations between those properties and the spectral features. The present study is devoted to elucidating the effects of secondary structure variations and hydration on the infrared (IR) intensity of the amide II mode of peptide chains. It is shown that the IR intensity is significantly enhanced for the C5 (fully extended planar β-strand) conformation because of the interpeptide charge flux through the H···O interaction of the C5 ring, and there is a small cooperative effect giving rise to a larger enhancement for a consecutive C5 conformation. In contrast, the IR intensity is reduced for the α-helix conformation because of the partially canceling polarization effect of the hydrogen-bond accepting O atom in the N-H···O═C hydrogen bond and the absence of the interpeptide charge flux. With regard to the hydration effect, it is found that the IR intensity enhancement/reduction depends critically on the angular position of the hydrating water molecule, and is related to the presence/absence of the intermolecular charge flux and the polarization effect. It is suggested that, both for the secondary structure dependence and for the hydration effect, the geometrical relation between the vibrating N-H bond and the H···O interaction (of the C5 ring and/or the hydrogen bond) is an essential factor determining the enhancement/reduction of the IR intensity of the amide II mode.
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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".