Ammoniated Complexes of Uracil and Transition Metal Ions: Structures of [M(Ura-H)(Ura)(NH<sub>3</sub>)]<sup>+</sup>by IRMPD Spectroscopy and Computational Methods (M = Fe, Co, Ni, Cu, Zn, Cd)
Bibliographic record
Abstract
The structures of deprotonated d-block metal dication bound uracil dimers, solvated by a single ammonia molecule, were explored in the gas phase using infrared multiple photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance-mass spectrometer. The IRMPD spectra were then compared with computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31+G(d,p) basis set for all atoms, with the exception of Cd, for which the LANL2DZ basis set with relativistic core potentials was used. The calculations were then repeated using the def2-TZVPP basis set on all atoms and were compared to the first set of calculations. The lowest-energy structures are those in which one uracil is deprotonated at the N3 position and, aside from the Cu complex, the intact uracil is a tautomer in which the N3 hydrogen is at the O4 carbonyl oxygen. The metal displays a tetradentate interaction to the uracil moieties, with the exception of Cu, which is tridentate, and the ammonia molecule is bound directly to the metal center. In the Cu complex, a square planar geometry is observed about the metal center, consistent with Jahn-Teller distortions commonly observed in Cu(II) complexes, and the intact uracil assumes its canonical tautomer. All other metal cation complexes are five-coordinate, square pyramidal complexes, with the intact uracil adopting a tautomer in which the N3 hydrogen is on O4. The IRMPD spectroscopic data are consistent with the computed infrared spectra for the lowest-energy structures in all cases.
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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) | 0.001 | 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".