Ligand Close Packing, Molecular Compactness, the Methyl Tilt, Molecular Conformations, and a New Model for the Anomeric Effect
Bibliographic record
Abstract
All the atoms in a molecule attract each other until they reach their equilibrium positions at which point the repulsive forces between the atoms just balance the attractive forces and there are no resultant forces acting on any of the atoms in the molecule. Thus, we can consider that in the equilibrium geometry the atoms in a molecule are arranged as compactly as possible. This is the basis of the ligand close packing (LCP) model according to which three or four monatomic ligands X, such as F, Cl or O (formally =O or O(-)) pack as closely as possible around a small central atom such as a boron or carbon atom giving a truly close-packed equilateral triangular AX(3) molecule or a tetrahedral AX(4) molecules. Such monatomic ligands can, to a good approximation, be described as having a spherical shape with a single ligand radius r(X). In contrast, ligands with donor atoms with lone pairs such as the oxygen atom in an OX group have a less symmetrical electron density requiring two ligand radii, r(O(lp)) in the lone pair direction, and r(O(b)) in the bonding direction, where r(O(lp)) < r(O(b)) for an approximate description. On this basis we propose an explanation for the "methyl tilt", in methanol and many related molecules, and in conjunction with the concept of compactness, a model for explaining the relative energies of the conformations of molecules containing OH and OMe ligands, including molecules that exhibit the anomeric effect. We compare our model for the anomeric effect with the widely accepted "hyperconjugation" model. We also discuss the relationship between the concept of compactness and the concept of hardness.
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 | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".