Fragmentation Reactions of a<sub>2</sub> Ions Derived From Deprotonated DipeptidesA Synergy Between Experiment and Theory
Bibliographic record
Abstract
The fragmentation reactions of a number of a 2 ions ([M−H−CO 2 ] - ) derived from dipeptides have been studied by energy-resolved mass spectrometry, isotopic labeling, and MS 3 experiments. The general reaction sequence leading eventually to a deprotonated amine, is shown to occur, a reaction sequence first proposed by Styles and O'Hair ( Rapid Commun. Mass Spectrom . 1998, 12, 809) from a study of the a 2 ion derived from glycylglycine. When an amidic hydrogen (R 2 = H) is present, the initial proton-transfer reaction 1 is nonreversible. However, when there is no amidic hydrogen, as in the a 2 ions derived from H−Ala−Pro−OH or H−Gly−Sar−OH, the initial proton-transfer reaction 1 becomes reversible, leading to the interchange of N-bonded and C-bonded hydrogens. Ab initio calculations at the MP2/6-31+G(d) level of the energies and interconversion pathways of anions derived by deprotonation of glycine N -methylamide show a barrier of 8 kcal mol -1 for reaction 1, with reaction 2 being 23.8 kcal mol -1 endothermic. When an amidic hydrogen (R 2 = H) is present, the amine-deprotonated species formed in reaction 1 abstracts a proton from the amide nitrogen to form the amide-deprotonated species, the most stable species on the potential energy surface. The system effectively becomes trapped in this low-energy well and exits upon activation by reactions 2 and 3 as observed when glycine N -methylamide is deprotonated directly. When no amidic hydrogen is present, this low-energy state does not exist, and reaction 1 becomes reversible, leading to the interchange of N-bonded and C-bonded hydrogens. In these cases, a significant population of the original a 2 ion is formed, which fragments by the reaction
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 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 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".