An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy
Bibliographic record
Abstract
The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic-structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free-electron laser (FEL) and an electrospray-ion-trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6-311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the alpha-amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol(-1)) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side-chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the alpha-amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol(-1) higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760-1800 cm(-1) is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.
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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 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| 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".