Infrared Multiple Photon Dissociation Spectroscopy as Structural Confirmation for GlyGlyGlyH<sup>+</sup> and AlaAlaAlaH<sup>+</sup> in the Gas Phase. Evidence for Amide Oxygen as the Protonation Site
Bibliographic record
Abstract
Protonation sites in biological molecules are very important because they directly determine their structures, properties, and functions. The protonation sites and structures of the tripeptides of Gly and Ala have been investigated using infrared multiple photon dissociation (IRMPD) spectroscopy in combination with theoretical calculations. The experimental and calculated results indicate that two isomers coexist under the experimental conditions. Different protonation sites result in the different structures. If the excess proton is bound to the amino group, a cyclic structure is formed, in which the N-terminus and carbonyl oxygen of the C-terminus are linked by a strong hydrogen bond. In contrast, if the excess proton is bound to the amide carbonyl oxygen, a linear structure is formed in which a very strong hydrogen bond is formed, linking the two amide carbonyls. For the first time, IR spectroscopic evidence confirms that an amide oxygen may serve as the protonation site for peptides.
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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) | 0.000 | 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 | 0.001 | 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".