Abstract (Expand)
Chemical potentials (molar Gibbs energies) are usually extrapolated to the remote physical–chemical reference state and then stored. Subsequent use under
in vivo
conditions requires a similarly … conditions requires a similarly substantial, reverse extrapolation, again with significant potential errors. In order to shrink both extrapolations drastically and thereby enhance both biological meaning and accuracy, we propose a transformation to a more biological reference state: pH = 7, pMg = 3, 99.5% water, with 1 m
m
each of the additional ‘precursors’ inorganic phosphate, sulfate, ammonium, and bicarbonate, and with twin temperatures 37 and 25 °C, ionic strength 0.15
m
and m
m
as concentration unit. These precursors substitute for reference compounds alien to biology such as H
2
at 1 bar, and solid graphite, sulfur, and phosphorus. The standard chemical potentials are herewith increased by the magnitudes of the chemical potentials of protons, Mg
2+
, water, and the four precursors, each multiplied by the number of corresponding atoms in the molecule. This defines standard ‘metabolic potentials’. We make these potentials findable and accessible as 1360 collated standard chemical potentials for 320 compounds of biochemical interest at the twin metabolic reference states. We do this for 3 reference pH's: We present the
metabolic reference state
as a convenient
anchor
, not a universal intracellular milieu. All datasets must continue to report the
actual
experimental state (
T
, pH, pMg,
I
, osmolarity, concentrations), yet aim at (also) reporting parameter values for this anchor state; we supply algorithms to transform between states. This preserves interoperability across diverse organelles, media and between enzymology and chemical engineering, while facilitating reuse.
Authors: Hans V. Westerhoff, Barbara M. Bakker, Andreas S. Bommarius, Maria Luz Cárdenas, Athel Cornish‐Bowden, Paul Fitzpatrick, Peter J. Halling, Vassily Hatzimanikatis, Carsten Kettner, Yanhua Liu, Andrew G. McDonald, Elad Noor, Jürgen Pleiss, Frank M. Raushel, Johann M. Rohwer, Santiago Schnell, Keith F. Tipton, Ming‐Daw Tsai, Urs von Stockar, Ulrike Wittig, Roland Wohlgemuth, John M. Woodley
Date Published: 5th Mar 2026
Publication Type: Journal Article
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