Biomimetic Cleavage of RNA Models Promoted by a Dinuclear Zn(II) Complex in Ethanol. Greater than 30 kcal/mol Stabilization of the Transition State for Cleavage of a Phosphate Diester
Bibliographic record
Abstract
The cleavage of a series of seven substituted aryl 2-hydroxypropyl phosphates (1a-g) promoted by a dinuclear Zn(II) complex (3:Zn(II)2:(-OCH2CH3)) was investigated in ethanol at pH 9.0 +/- 0.2 and 25 degrees C. The kinetics for appearance of the product phenols follow very strong saturation behavior for all substrates where the dissociation constant of the bound complex has an upper limit of Km = 3 x 10(-7) M and the k(cat)(max corr.) values (corrected for triflate inhibition) range from 168 to 3 s(-1). A partial s(s)pH/log k(cat)(max corr). profile for the 3:Zn(II)2:(-OCH2CH3)-catalyzed reaction of le (3-methoxyphenyl 2-hydroxypropyl phosphate) is bell-shaped, plateauing from 7.9-10, and is fit to a two kinetically important ionizations having s(s)pKa values of 7.22 and 10.9. The Brønsted plot of log (k(cat)(max corr.)) vs. the s(s)pKa values for the phenols shows a break at about 14.3 with two beta(lg), values of -1.12 and 0.0. This is analyzed in terms of a change in rate limiting step from cleavage of the phosphate to a conformational change where the binding of the phosphate changes from one P-O- ----Zn(II) interaction to a Zn(II)----O-P-O---Zn(II) double activation. An energetics calculation comparing the ethoxide promoted cleavage of 1a-g with the 3:Zn(ll)2:(-OEt) promoted reaction indicates that the complex, 3:Zn(II)2, stabilizes the ethoxide plus substrate transition state for the cleavage of 1a-g by between 33 and 36 kcal/mol. The origins of the large stabilization are discussed in terms of the effect of the medium on the various rate and equilibrium constants involved.
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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 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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".