Molecular dynamics simulations of guest-host hydrogen bonding in structure I, II, and H clathrate hydrates
Bibliographic record
Abstract
The standard picture is that clathrate hydrates form when hydrophobic guest molecules are compressed with water under high pressure-low temperature conditions. In the ice-like hydrate framework, water molecules form molecule-sized cavities that encapsulate the guests and minimize water-hydrophobic guest interactions. This picture, however, must be modified by observations that many water soluble, hydrogen- bonding molecules form hydrates under relatively mild pressure-temperature conditions as well. Furthermore, these hydrates form with the same canonical structures as hydrophobic guests. We recently performed a series of molecular dynamics simulations, single crystal X-ray crystallographic structural determinations, and NMR relaxation time experiments to explicitly study the presence of hydrogen bonds between the guest and host in clathrate hydrates. Systems studied include binary structure H hydrates of tertbutylmethylether and pinacolone, the binary structure II hydrates of tetrahydrofuran, tetrahydropyran, tert-butylamine, 1-propanol, 2-propanol, and ethanol and structure I hydrates of ethanol. These guests form hydrogen bonds of varying stability and lifetime which affect the hydrate structure and the dynamics of both the water host and the guests. Spectroscopic signatures of the guest-host hydrogen bonding are briefly discussed.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".