Two approaches to the concept of chemical species: Relations between potential energy and molecular shape
Bibliographic record
Abstract
Chemical species are usually defined in terms of the potential energy function. In this work we explore the relationships between this definition and an alternative one, based on the concept of molecular shape. The molecular shape is given a quantitative expression in the framework of the shape group method. The model representation chosen for the molecular surfaces is the continua of fused-sphere van der Waals surfaces. Simple molecular systems are considered, where the “chemical species” are represented by 1-dimensional potentials as torsional rotamers. It is shown that within well-defined ranges of atomic van der Waals radii and nuclear geometries, the identity of the molecular species, as defined by shape, remains invariant under torsional motions. The number and size of such invariance domains can, under certain conditions, follow closely the regions in configuration space where a rotamer is defined according to the minima and curvature of the potential energy function. These findings provide new tools for the study of the interplay between molecular shape and electronic energy, regarding the recognition of active conformations.
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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 | 0.003 | 0.008 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.001 | 0.011 |
| Scholarly communication | 0.004 | 0.011 |
| Open science | 0.003 | 0.004 |
| Research integrity | 0.003 | 0.004 |
| Insufficient payload (model declined to judge) | 0.005 | 0.001 |
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".