In physical chemistry, Gibbs free energies and chemical potentials (not energies) are the descriptors for the energetics of compounds and processes. They integrate energy, entropy and volume-work. Changes in Gibbs energy and between chemical potentials equal the useful work at constant temperature and pressure. However, this systematics requires one to be explicit about the protonation, Mg-complexation and hydration states of the molecules, and to correct of activity coefficients differing from 1. Moreover the standard chemical potentials are defined for biologically irrelevant situations such as pH=pMg=0, concentrations of 1 Molar, hydrogen gas at 1 atmosphere and crystalline phosphorous. In addition, one must monitor the number of protons and Mg ions liberated or consumed by the reaction. Rather than a single ATP synthesis reaction, this methodology requires describing some 20 reaction variants, explicating the various protonation, Mg-complexation and hydration states of the three molecules involved. Indeed, multiple literature studies have presented highly complex ways of calculating the standard Gibbs energy of this highly important reaction, which then typically differed by 17 kJ/mol from its actual work potential.
We here present new ‘metabolic’ energies and potentials. These should replace the Gibbs free energy and the chemical potential for life processes and metabolites under in-vivo like conditions. We also present a new ‘Thermotable’, which contains the standard metabolic potentials for up to a thousand metabolites of interest to systems biology. The Thermotable enables the direct computation of standard (i.e., concentration-independent) reaction energies by simple subtraction. These are immediately relevant for the in vivo reference conditions of pH=7, pMg=3, ionic strength 0.15 M, and T=310 K, and concentrations of 1 mM. There is no need for correcting concentrations to activities. The new standard reaction energies are very good approximations towards the actual reaction energies, for when concentrations are unknown (yet on the order of 1 mM rather than 1 M).
The metabolic potentials given in the Thermotable are much better descriptors of the energetic potential of biochemicals than the chemical potentials were, because they are taken relative to a growth medium of biological significance, i.e., 1 mM of (total) bicarbonate, ammonium, phosphate, and sulfate, as well as liquid water, H+ at pH7, and Mg2+ at pMg3. This will be illustrated by plotting the metabolic energy landscape for travelling down major metabolic pathways. Whilst the maps of chemical potentials were rugged and irregular, the magnitudes of the potentials are realistic (in terms of numbers of ATP energies) and the new maps are smoothly down-hill except for steps up of about 50 kJ/mol where ATP energy is invested (and down where ATP is made). With the new metabolic energies, the calculation of free energy differences and equilibrium constants becomes facile, omitting the many usual points of confusion in calculating from standard chemical potentials.
The new thermodynamics will be useful for turning metabolic network maps into metabolic energy landscapes and for warning against perpetua mobilia proposed by Flux Balance Analysis.