Molecular Dynamics Study of Guest–Host Hydrogen Bonding in Ethylene Oxide, Trimethylene Oxide, and Formaldehyde Structure I Clathrate Hydrates
Bibliographic record
Abstract
Molecular dynamics simulations are used to study the guest–host hydrogen bonding and guest dynamics in the clathrate hydrate phases of trimethylene oxide (TMO), ethylene oxide (EO), and formaldehyde (FA) as polar guests. Two water models, the SPC/E and TIP4P/ice, were used in the simulations. Binary hydrates are constructed with these guests in the large 14-sided cages and methane placed in the small 12-sided cages of the structure sI clathrate hydrates. The results of these simulations are compared with the nonpolar guests with analogous structures, cyclobutane (CB), cyclopropane (CP), and ethane, respectively, for TMO, EO, and FA. These simulations show that oxygen atoms of the cyclic ethers and carbonyl oxygen of formaldehyde form hydrogen bonds to differing degrees with cage water hydrogen atoms. The TMO size is larger than that of the EO and FA molecules and the closer proximity of the atoms of this large guest to the cage water molecule enhances the probability of guest–host hydrogen bonding in the TMO clathrate. The TMO oxygen atom is tethered by a lattice water hydrogen atom by hydrogen bonding for longer times, which reduces the range of translational and rotational motions of the TMO guests in the cages compared to EO and FA. The effect of guest–host hydrogen bond formation is the insertion of Bjerrum L-defects in the clathrate water lattice. We consider guest dynamic properties such as velocity autocorrelation function (VACF) and orientational autocorrelation function (OACF) of the different guests in these hydrate phases and compare the hydrogen bonding and non-hydrogen bonding analogues. We discuss some other potential experimentally observable effects of the guest–host hydrogen bonding on the guest and water dynamics in the corresponding clathrate hydrates.
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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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| 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".