The Applicability of the Kinetic Method for Measuring Relative Affinities of Macromolecules for Polyatomic Substrates
Bibliographic record
Abstract
This paper is a review of the kinetic method for the determination of thermochemical values for gas-phase molecules. In addition, we have explored the utility of the kinetic method to obtain meaningful relative binding energies of macromolecules for polyatomic substrates using a system comprising poly(methylmethacrylate) (PMMA) oligomers and doubly protonated diaminoalkanes. The major factors which determined the suitability of the kinetic method for this system were identified as (i) the structural arrangement of the parent ion complex, (ii) possible reverse activation barriers, and (iii) the evaluations of Δ(ΔS‡). Molecular mechanics/molecular dynamics (MM/MD) simulations, together with ion mobility spectrometry, suggests the parent ion complexes represent a relatively equal sharing of the substrate between two the PMMA oligomers within the complex and that the two PMMA oligomers interact almost exclusively with the substrate, and not with each other. MS/MS of the trimeric parent complexes resulted in one PMMA unit leaving as a neutral which suggests very limited coulombic repulsion (that would contribute to a reverse activation barrier). The drift times of PMMA-diaminoalkane complexes that were generated directly by ESI-MS or by dissociation of a trimeric PMMA-diaminoalkane-PMMA complex were found to be identical, and when combined with MM/MD simulations suggested that the product PMMA-diaminoalkane dication has the same conformation as it does when part of a trimeric complex. This is evidence for Δ(ΔS‡) ≃ Δ(ΔS) and using a statistical mechanics approach, Δ(ΔS) ≃ 0. The effective temperature variable in the kinetic method expression was found to decrease as a function of the size of the trimeric complex, suggesting that the population distribution of the dissociating ensemble of complexes narrows as size increases.
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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 | 0.003 | 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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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".