An Investigation of the Structures of [(Glycine)(1‐Methyluracil)]M<sup>+</sup> Complexes (M=H, Li, Na, K) in the Gas Phase by IRMPD Spectroscopy and Theoretical Methods
Bibliographic record
Abstract
Abstract The presence of ions in the complexation of molecules can profoundly affect the structure, resulting in changes to functionality and stability. These non‐covalent interactions drive many biological processes both necessary and inimical and require extensive research to understand and predict their effects. Protonated and alkali metalated complexes of glycine (Gly) and 1‐methyluracil (1‐mUra) were studied using infrared multiphoton dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. The experimental and simulated vibrational spectra were compared to help elucidate the structure of each complex. The lowest energy structure for [(Gly)(1‐mUra)]H+ consists of amine protonated Gly bound to O4 of canonical 1‐mUra through a single ionic hydrogen bond with another, intraglycine ionic hydrogen bond between the protonated amine group and the carbonyl oxygen. For [(Gly)(1‐mUra)]Li+, [(Gly)(1‐mUra)]Na+ and [(Gly)(1‐mUra)]K+, the experimental spectra are most consistent with the metal cations binding in a trigonal planar geometry with 1‐mUra bound to the metal cation via the O4 carbonyl. In [(Gly)(1‐mUra)]Li+ and [(Gly)(1‐mUra)]Na+, the metal cation is bound to canonical Gly via the carbonyl oxygen and amine nitrogen, but in [(Gly)(1‐mUra)]K+, Gly is bound through both oxygens and contains an intraglycine hydrogen bond from the hydroxyl to the amine nitrogen. It was found that the B3LYP/6‐31+G(d,p) vibrational spectra are most consistent with the experimental spectra, but M062X was better than B3LYP at determining the lowest‐energy structures.
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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 | 0.000 |
| 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 | 0.001 | 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".