Many-Body Effects in Systems of Peptide Hydrogen-Bonded Networks and Their Contributions to Ligand Binding: A Comparison of the Performances of DFT and Polarizable Molecular Mechanics
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Bibliographic record
Abstract
We compute the stabilization energies of the complexes formed between formate or water and a linear array of n = 2−5 N -methylformamide (NMF) molecules. We perform density functional theory (DFT), ab initio SCF and MP2, and SIBFA molecular mechanics computations. A very significant amount of cooperativity is found by DFT in the formate--(NMF) n complexes, amounting to −17 kcal/mol with n = 5. The SIBFA computations with fixed internal geometries for the monomers recover up to 80% of the DFT values. Single-point SCF/MP2 computations at the SIBFA-optimized geometries give binding energies and cooperativities very close to the SIBFA values. Solvation effects as represented by a continuum reaction field procedure are found to affect cooperativity to a modest extent. The implications for oligopeptides are discussed.
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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) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 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 it