Small Molecule X‐ray Crystal Structures at a Crossroads
Bibliographic record
Abstract
Abstract Refinement of ‘small molecule’ crystal structures from X‐ray diffraction benefits from advances in methods derived from quantum crystallography. After outlining some pertinent principles and reasons for needed improvements in the theoretical structure model, the author′s experience in implementing Hirshfeld Atom Refinement using the NoSpherA2 option in the popular Olex2 crystallographic GUI is outlined. The method allows the placement of hydrogen atoms with accuracy comparable to neutron diffraction. Moreover, the average precisions of bonds involving light atoms is found to improve in most cases, with the degree of improvement correlating strongly with the overall quality of the diffraction data and the refinement model. A suggested workflow for HAR with NoSpherA2 is provided. A call is made for wide‐spread adoption, along with a community‐wide development of ‘standard protocols for the use of aspherical form factors in chemical crystallography’.
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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) | 0.004 | 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".