Calculation of Free Energy Profiles for Elementary Bimolecular Reactions by ab Initio Molecular Dynamics: Sampling Methods and Thermostat Considerations
Bibliographic record
Abstract
A study designed to refine the procedure for performing ab initio molecular dynamics calculations (AIMD) on chemical reactions is presented. Of key interest is the calculation of changes in free energy along the entire reaction path. Several simple elementary reactions are studied with the Car−Parrinello projector augmented-wave (CP−PAW) density-functional theory (DFT) methodology. The illustrative gas-phase bimolecular addition reactions are (i) a σ complexation of BH 3 + H 2 O → H 2 O·BH 3, (ii) the Diels−Alder reactions of butadiene with ethene, C 4 H 6 + C 2 H 4 → cyclohexene, 1,3-cyclopentadiene (CP) and ethene, CP + C 2 H 4 → norbornene, and the stereoselective reaction of 5-amino-CP with ethene, amino-CP + C 2 H 4 → amino-norbornene, (iii) the carbene cyclopropanation Cl 2 C + C 2 H 4 → Cl 2 C 3 H 4, and (iv) the dimerization of ketene. These reactions were used to test both the slow-growth and point-wise thermodynamic integration (STI and PTI) methods of phase-space sampling as well as the Nosé−Hoover and Andersen thermostats. It is found that the PTI technique is potentially superior to the slow-growth method in terms of computational expense and is at least as accurate. The Nosé−Hoover thermostat appears to be inadequate for most of the reactions modeled here, whereas the stochastic Andersen thermostat affords more accurate results.
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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".