The effect of urea on aqueous hydrophobic contact-pair interactions
Bibliographic record
Abstract
Urea is perhaps the most common denaturant used for studying proteins. However the mechanism of denaturation is still not well understood. Recent theoretical work suggests that van der Waals interactions between urea and non-polar amino acid residues are a major contributor to the protein denaturation process. However, there are few experimental data measuring the effect of urea on hydrophobic interactions. In this work we have determined how the addition of urea to the aqueous solvent affects the contact-pair formed between alkyl and phenyl groups in model compounds: the data indicate that for solutes having a radius smaller than 2.87 Å cavity formation energetics dominate, therefore the addition of urea promotes the formation of hydrophobic contact pairs; while for larger solutes, van der Waals interactions have the largest magnitude, causing urea to disrupt the formation of contact pairs. The influence of urea on hydrophobic interactions is shown to be continuous in the 1-8 M concentration range and is well-correlated with the predictions of scaled particle theory. This demonstrates that the effect of urea on hydrophobic contact pairs can be explained by the changes observed in the solvent packing density, without having to invoke changes in the hydrogen bonding network of water.
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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 | 0.000 |
| 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) | 0.000 | 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".