Visualizing the Three-Dimensional Arrangement of Hydrogen Atoms in Organic Molecules by Coulomb Explosion Imaging
Bibliographic record
Abstract
Structure-sensitive methods based on femtosecond light or electron pulses are now making it possible to measure how molecular structures change during light-induced processes. Despite significant progress, high-fidelity imaging of nuclear positions remains a challenge even for relatively small molecular systems and, notably, regarding the positions of hydrogen atoms. As demonstrated in recent work, X-ray-induced Coulomb explosion imaging (CEI) may overcome this obstacle, as its sensitivity does not depend on the mass of the imaged atoms. The photoinduced ring opening of the heterocyclic molecule 2(5 H )-thiophenone has attracted recent interest. Here, we show that CEI offers a powerful route to imaging the peripheral H atoms in this molecule and thus, more generally, to tracking detailed nuclear motions (e.g., isomerizations) in organic molecules on ultrafast time scales. Specifically, we record momentum-space Coulomb explosion images that report on the three-dimensional positioning of all nuclei within the molecule, for instance, distinguishing H atoms in C–H bonds that lie within or are directed out of the plane defined by the heavy atoms. The prospect of imaging peripheral H atoms to probe photochemical dynamics is explored by coupling ab initio molecular dynamics with classical Coulomb explosion simulations, thereby differentiating potential photoproduct isomers, including those whose structures primarily differ in the position of the hydrogens.
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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 | 0.000 | 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) | 0.001 | 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".