The formulation of chemical potentials and free energy changes in biochemical reactions
Bibliographic record
Abstract
In 1994, an IUBMB-IUPAC joint committee recommended a revised formulation for standard chemical potentials and reaction free energies motivated by the fact that, in biochemistry, the reactants and products often exist in multiple charge states depending on the pH and pMg of the solution environment. The recommendation involved both the use of (1) a mathematical transform with the intent to hold the pH constant, and (2) the formulation of reference chemical potentials of ionized isomeric species based on the log sum of the individual standard chemical potentials of each isomeric species. Recently, several reports including a 2020 IUPAC report have appeared that challenged the need for such summary formulations, arguing that the standard chemical potentials were sufficient with full accounting of each of the different charge state isomers involved in a biochemical reaction. This work critically evaluates both the use of thermodynamic transforms and the different chemical potential formulations. It is shown that (1) transforms are not necessary to hold the pH constant and (2) demonstrates that the two chemical potential formulations are not equivalent. Which formulation is appropriate depends on what species are measured experimentally or whether an assumption of equilibrium among the charge state isomers is reasonable and desirable.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.004 | 0.008 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.005 |
| Scholarly communication | 0.003 | 0.007 |
| Open science | 0.003 | 0.003 |
| Research integrity | 0.003 | 0.005 |
| Insufficient payload (model declined to judge) | 0.005 | 0.002 |
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 source (direct Gemma or distilled Codex), 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".