A kinetic study of dimethyl sulfoxide reductase based on density functional theory
Bibliographic record
Abstract
We present a density functional theory study on the oxygen atom transfer (OAT) reaction of dimethyl sulfoxide (DMSO) with model complexes resembling a functional synthetic analogue of the molybdoenzyme DMSO reductase. The good agreement between our calculated Gibbs free energy profile and data derived from experimental kinetic parameters supports the reaction mechanisms of the oxygen atom transfer proposed in this study. When the mechanism involves the formation of a DMSO-bound intermediate, the calculations on the free energy surface provide valuable information that explains the origin of the apparent contradiction between the experimental findings and previous theoretical calculations with respect to the rate-limiting step of the reaction mechanism. The enzymatic mechanism of the OAT reaction is more complex than the mechanism of any synthetic analogue, mainly due to the formation of an enzyme-substrate adduct prior to the appearance of the substrate-bound intermediate. This study also presents a possible mechanism for the formation of such an adduct and the subsequent oxygen atom transfer. The mechanism involves a proton transfer to and from the substrate.
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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 | 0.001 | 0.001 |
| 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.009 | 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".