Free Energy Profiles for the Identity S<sub>N</sub>2 Reactions Cl<sup>-</sup> + CH<sub>3</sub>Cl and NH<sub>3</sub> + H<sub>3</sub>BNH<sub>3</sub>: A Constraint <i>Ab Initio</i> Molecular Dynamics Study
Bibliographic record
Abstract
Density functional theory (DFT) together with Car-Parrinello ab initio molecular dynamics (CP-AIMD) simulation has been used to investigate the free energy profiles of two representative S N 2 reactions: (A) Cl - + CH 3 Cl → ClCH 3 + Cl -; (B) NH 3 + H 3 BNH 3 → H 3 NBH 3 + NH 3 . The free energy profiles along the reaction coordinates at 300 K and 600 K were determined directly by a pointwise thermodynamic integration (PTI) technique. Comparison between the well-known double-well potential energy profile (PEP) and the free energy profiles (FEP) has been made. The results show that, for reaction A, the double-well profile is maintained for the FEP at 300 K due to the stronger ion−dipole interaction between chloromethane and the chloride anion. In comparison with the PEP, the FEP has a higher central barrier and a more shallow well depth. However, at 600 K the double wells almost disappear on the FEP, whereas the central barrier increases further. For reaction B, the 300 K FEP also presents a higher central barrier peak and a more shallow well depth compared to the PEP. However, when the temperature increases to 600 K, a saddle shape FEP is obtained, which indicates that the reaction has changed mechanism from an associative S N 2 reaction to a dissociative S N 1 reaction. This change is driven by entropy.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.007 | 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".