Reaction mechanism and isotope effects derived from centroid transition state theory in intramolecular proton transfer reactions
Bibliographic record
Abstract
In this article the tautomerization reaction of the enol form of malonaldehyde is used to investigate the magnitude and origin of changes in centroid transition state theory proton transfer reaction rate predictions caused by the quantum dispersion of heavy nuclei. Using an empirical valence bond method to construct the potential energy surface, it is found that quantization of the nuclear degrees of freedom of the carbon atoms significantly influences the centroid potential of mean force used to describe the proton transfer reaction. In contrast, an ab initio simulation carried out using a recently developed molecular mechanics based importance sampling method [J. Chem. Phys. 114, 6763 (2001)] in combination with an accurate density functional theory evaluation of the electronic energies shows a substantially smaller influence of the quantum nuclear degrees of freedom of the secondary atoms on the centroid potential of mean force. A detailed analysis of the different influence of quantization of the nuclear degrees of freedom of secondary atoms observed in the ab initio and empirical valence bond centroid potential of mean force was carried out. It is shown that for the empirical valence bond potential, a significant decrease of the centroid potential of mean force arises through the quantum tunneling of carbon atoms in the molecular backbone. Furthermore, it is demonstrated that in molecular mechanics potentials aimed to describe intramolecular proton transfer reactions, the functional form of the potential energy terms coupling the primary and secondary atom motions as the reaction proceeds as well as the mass of the primary particle can significantly influence the centroid transition state theory predictions of secondary kinetic isotope effects. Finally, the dependence of the reaction rate predictions and isotope effects on the choice of reaction coordinate is investigated and the validity of calculating kinetic isotope effects using the centroid transition state theory formalism is discussed.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".