DFT Calculations of Core−Electron Binding Energies of the Peptide Bond
Bibliographic record
Abstract
Although an efficient DFT method using the generalized transition-state model to calculate core−electron binding energies had been successfully applied to over 200 cases, with an average absolute deviation of only 0.21 eV from experiment, a new Δ E KS (PW86−PW91)/cc-pCVTZ model based on total Kohn−Sham energy difference was recently developed. Not only was the model error-free, but also the average absolute deviation for 32 cases studied was found to be 0.15 eV. In this study, we first confirm the excellent performance of such a Δ E KS approach with 46 new cases, with the result that the average absolute deviation from experiment for the 78 cases remains at 0.15 eV. With such consistent accuracy, this new method is applied to the peptide bond. The model molecules studied in this work include formamide, N -methylformamide, N, N -dimethylformamide, acetamide, N -methylacetamide, N, N -dimethylacetamide, and two model dipeptides, one cyclic and one acyclic. The difference in the computed nitrogen core−electron binding energy between the two model dipeptides is found to be 0.85 eV, several times our average absolute deviation. This may be of interest to other workers studying other aspects of the peptide bond.
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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 | 0.000 | 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 | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".