New Thermodynamics Table: standard metabolic energies

Version 1

The first sheet in this excel file is a Table that collects the standard Gibbs energies of formation (from the elements) of a large number of chemical species that are relevant for metabolism. It obtained these from a substantial number of sources, including Thauer et al and Alberty, as indicated at the bottom of the first sheet of the Table. Following Alberty, (2006) the Table also computes the further transformed Gibbs energies of formation, under the standard conditions also used by Alberty, i.e. T=298.15 K, pHc=7, pMgc=3, I=0.25 M. This involves Legendre transformations for pH and pMg, and also the computation of the apparenn Gibbs energies of formation of 'reactants' (totals of chemical species, such as ATP4-, HATP3-, H2ATP2-, MgATP2-).
It further calculates the standard metabolic energies of the metabolites, as defined in an upcoming paper by Westerhoff et al. (2023) entitled 'Thermodynamics in short for analyzing the living state'. This then involves a further Legendre transformation with the chemical potential of water. The resulting standard metabolic energies can then be used to calculate the metabolic energies of metabolites, by also using their total concentration, in millimolar. No computations of activity coefficients aare needed. The metabolic energies come with a new standard which is T=310.15 K (37 C), pH=7, pMg=3, I=0.15 M and osmolarity=0.35 M and is taken to be more valid for most intracellular biology. The standard metabolic energies are dependent on these conditions and the Table enables one to calcuate the standard values for other conditions, such as T=298.15 K (25 C). Other sheets in the excelfile calculate energies of a number reactions as examples.