Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains
Bibliographic record
Abstract
Cation–π interactions play important roles in molecular recognition and in the stability and function of proteins. However, accurate description of the structure and energetics of cation–π interactions presents a challenge to both additive and polarizable force fields, which are rarely designed to account for the complexation of charged groups with aromatic moieties. We calibrate the Drude polarizable force field for complexes of alkali metal ions (Li + , Na + , K + , Rb + , Cs + ), ammonium (NH 4 + ), tetramethylammonium (TMA + ), and tetraethylammonium (TEA + ) with aromatic amino acid side chain model compounds (benzene, toluene, 4‐methylphenol, 3‐methylindole) using high‐level ab initio quantum chemical properties of these complexes. Molecular dynamics simulations reveal that cation–π complexes of the hard and tightly coordinated Li + and Na + ions are not stable in water but that larger ions form stable complexes, with binding free energies ranging between −0.8 and −2.9 kcal/mol. Like in gas phase, all complexes at equilibrium adopt an “en‐face” complexation mode in water. The optimized Drude polarizable model provides an accurate description of the cation–π interactions involving small ions and proteins. © 2019 Wiley Periodicals, Inc.
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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".