Temperature-dependent estimation of Gibbs energies using an updated group contribution method

Abstract

AbstractReaction equilibrium constants determine the mass action ratios necessary to drive flux through metabolic pathways. Group contribution methods offer a way to estimate reaction equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group contribution method with: 1) additional curated thermodynamic data used in fitting; and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermo-dynamic data, including reaction equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropies change of formation of compounds, and proton and metal ion binding constants. We further estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated necessary parameters, including standard entropy change of formation (ΔfS∘) and standard entropy change of reaction (ΔrS∘), using a model based on molecular properties. The median absolute errors in estimating ΔfS∘ and ΔrS∘ were 0.010 kJ/K/mol and 0.018 kJ/K/mol, respectively. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal ion concentrations. These results support the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions.