Peptide models XXVII. An exploratory ab initio study on the 21<sup>st</sup> amino acid side-chain conformations of <i>N</i>-formyl-L-selenocysteinamide (For-L-Sec-NH<sub>2</sub>) and <i> N</i>-acetyl-L-selenocysteine-<i>N</i>-methylamide (Ac-L-Sec-NHMe) in their γ<sub>L</sub> backbone conformation
Bibliographic record
Abstract
Selenocysteine is expected to have 9 × 9 = 81 conformations [3 × 3 = 9 backbone: ψ (g + ,a,g - ) × ϕ (g + ,a,g - ) and 3 × 3 = 9 side-chain: χ 1 (g + ,a,g - ) × χ 2 (g + ,a,g - )]. In the present study, all the torsional modes of the side-chain (χ 1 : rotation about the C α -C β and χ 2 : rotation about the C β -Se bonds) were investigated in the relaxed γ L backbone [(ϕ,ψ); (g - ,g + )] conformation. Seven out of the nine expected minima were found at the RHF/3-21G level of theory for N-formyl-L-selenocysteinamide (For-L-Sec-NH 2 ) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe). The stabilization energy exerted by the -CH 2 -SeH side-chain has been compared with that of -CH 2 -SH and -CH 2 -OH. Relative energies of the various conformers were also obtained via single point calculations at the B3LYP/6-31G(d,p) level of theory. Topological analysis of the electron density has been performed by Bader's Atoms in Molecule (AIM) approach using the results. The structures were also optimized at the B3LYP/6-31+G(d,p) level of theory.Key words: selenocysteine side-chain conformations, ab initio MO study, Multidimensional Conformational Analysis (MDCA), Atoms in Molecules (AIM), Bader's electron density analysis.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| 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 | 0.002 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".