Elucidation of Fragmentation Mechanisms of Protonated Peptide Ions and Their Products: A Case Study on Glycylglycylglycine Using Density Functional Theory and Threshold Collision-Induced Dissociation
Bibliographic record
Abstract
The fragmentation mechanisms of protonated triglycine and its first-generation dissociation products have been investigated using a combination of density functional theory calculations and threshold collision-induced dissociation experiments. The activation barrier measured for the fragmentation of protonated triglycine to the b(2) ion and glycine is in good agreement with a calculated barrier at the B3LYP/6-31++G(d,p) level of theory reported earlier [Rodriquez, C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012]. The b(2) ion fragments to the a(2) ion via a transition state structure that is best described as acylium-like. Contrary to what is commonly assumed, the lowest energy structure of the a(2) ion is not an iminium ion, but a cyclic, protonated 4-imidazolidone. Furthermore, fragmentation of the b(2) to the a(1) ion proceeds not via a mechanism that results in HNCO and H(2)C=C=O as byproducts, as have been postulated, but via a transition state that contains an incipient a(1) ion and an incipient carbene. The fragmentation of a(2) to a(1) proceeds via a transition state structure that contains the a(1) ion, CO and an imine as incipient components.
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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 | 0.001 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".