12 variously transformed reference potentials for 320 compounds of biochemical interest in unit kJ/mol.

Approximately 1360 of each type of transform are listed in columns 3 - 14. The number 1360 > 320 because a chemical compound often has multiple entries. This reflects that there are multiple data sources, phases, protonation states or Mg complexation states for that compound.

Column 2 contains the familiar reference (standard at the physical chemical reference state) physical chemical reference potentials (i.e., with the chemical elements in their stable state at T=298.15 K [25 C, gases H2, N2, O2 at 1 bar, graphite, phosphorous, sulfur and magnesium solids] as reference) collected from thermodynamic tables in the literature (see https://10.15490/fairdomhub.1.datafile.8462.1).
Column 1 contains the entry number of the chemical compound, followed by a code name, its biochemical name, its electric charge, indication whether it is a chemical species or a blend of such species, and the phase it is in. H-blends are protonmers, which are protonation pseudoconformers, i.e., the collection of all forms of a chemical compound that differ in equilbrating protonation states at a concentration equal to the total concentration and a chemical potential equal to that of the most alkaline form. Mg-blends are the corresponding collections of the compounds only differing in equilibrated Mg2+-binding.

The transformations are of the Legendre type, but not always Legendre transformations proper. They are gauge shifts: they alter the reference state of the reference thermodynamic potentials: For each chemical element present at a non-zero stoichiometry in the chemical species, that number multiplied by the chemical potential of a biochemical precursor is subtracted. This shifts the reference state for that chemical element away from the chemical element in the physical chemical reference state (i.e., H2, O2, N2 at 1 bar, graphite for C, phosphorous, sulfur and Mg powder), to a more biochemical reference state.

The most biochemical reference state is called the 'metabolic reference state' (column 10 and 11). It uses as precursors H+ at pH=7, Mg2+ at pMg=3, 99.5 mole % water (PI=0.3M), I=0.15 M, 1 mM of phosphate, sulfate, bicarbonate and ammonium H-blends. It has the switches in header entries H8 - H16 all set to 1 to signify that the corresponding Legendre-like transformations have been put in place. If one or more of these switches are 0 rather than 1 this means that the corresponding Legendre-like transformation has not been effected.

The I switch effects a correction for an activity coefficient smaller than 1 due to ion clouding computed by using the Alberty (2006) version of the Debye-Hueckel theory. The mM switch corrects the reference potential so as to enable the expression of the concentration of the species of interest in Millimolar rather than Molar.

The H, I-transformed reference potential at pH=7.14 is the apparent reference chemical potential proposed by Alberty (e.g., Alberty _et al. _(2011)). Alberty reported for pH=7.142 and pMg=3.57 (and I=0.25 M), which are the concentration based pHc=7.00 and pMgc=3.00. The H, I, Mg, mM, O, P, N, S, C transformed reference potential is most suitable for _in vivo _biochemistry and has been recommended as such in https://doi.org/10.1111/febs.70415. It is given for both T= 298.15 K (data in bold face) and T=310.14 K.

The T transformation transforms to a Temperature of 310.15 K by using the enthalpy of formation of the compound of interest obtained from the literature (see https://10.15490/fairdomhub.1.datafile.8462.1).

Further details are in https://doi.org/10.1111/febs.70415

The raw source data are the reference chemical potentials (molar Gibbs energy of formation from the elements in their physical chemical reference state) in https://10.15490/fairdomhub.1.datafile.8462.1. In this file every compound is given a code for the literature source of its reference Gibbs energy of formation and of its enthalpy of formation. In that same file the code is referred to a literature reference.