Theoretical volume profiles for conformational changes: Application to internal rotation of benzene ring in 1,12-dimethoxy-[12]-paracyclophane
Bibliographic record
Abstract
Identification of the transition state is an important step in the study of reaction kinetics and mechanisms. However, for non-rigid chemical systems where multiple viable reaction pathways may exist, enumeration of all possible transition states quickly becomes computationally expensive, if at all feasible. As an alternative approach, we recently proposed a methodology where the volumetric properties of a flexible reaction system are used to locate its transition state ensemble through a comparison of its theoretically determined volume profile and experimental activation volumes derived from high pressure kinetic data. In this work, we apply this method to internal rotation of the benzene ring in 1,12-dimethoxy-[12]-paracyclophane. For this system, the transition state ensemble was found to be the state with the lowest volume, where the benzene ring and the flexible methylene tether are coplanar. This result was verified by comparison with a Gibbs free energy profile obtained via umbrella sampling.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 | 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 | 0.001 | 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".