Solvation structure, thermodynamics, and conformational dependence of alanine dipeptide in aqueous solution analyzed with reference interaction site model theory
Bibliographic record
Abstract
With the CHARMM22 (Chemistry at Harvard Macromolecular Mechanics) all-atom nonbonded potential parameters for alanine dipeptide solute and the transferable intermolecular potential model water for the solvent, the reference interaction site model (RISM) integral equations with the hypernetted chain closure are solved to obtain all the atomic solvent–solute radial distribution functions. The solvation structures of alanine dipeptide in its seven conformations: C7eq, C7ax, C5, αR, β, αL and PII, in aqueous solution are analyzed at the atomic level in terms of the atomic solute–solvent radial distribution functions. At a temperature of T=298.15 K and bulk water density ρ=0.9970 g cm−3, the corresponding solvation free energies are calculated by using Singer and Chandler’s analytic solvation free energy formulation [Mol. Phys. 55, 621 (1985)]. Solvation energies, enthalpies, and entropies are also calculated in the RISM theory framework. The conformational dependence of solvation for alanine dipeptide in aqueous solution is analyzed. The solvation thermodynamcs for alanine dipeptide in aqueous solution are mainly controlled by the strong hydrophobic groups: CH3 and CH, which make alanine dipeptide show strong hydrophobicity. But the differences in the solvation thermodynamics for different alanine dipeptide conformers are controlled by the carbonyl groups and amide groups, which make alanine dipeptide show some hydrophilicity and exist in various conformations in aqueous solution. Solvation of alanine dipeptide in aqueous solution is determined by the competition among the molecular packing effects, intramolecular hydrogen bonds, and intermolecular hydrogen bonds. Due to the intramolecular hydrogen bonds in the two folded C7 conformations, the two most favorable conformations in gas phase become the least solvated in aqueous solution. Due to the intermolecular hydrogen bonds, C5, PII, αL, αR, and β become more solvated in aqueous solution.
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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".