Gibbs energies biochemical thermodynamics

Considerable use has been made of the thermodynamic perturbation and thermodynamic integration methods in biochemical modelling, calculating the relative Gibbs energies of binding of inhibitors of biological macromolecules (e.g. proteins) with the aid of suitable thermodynamic cycles. Some applications to materials are described by Alfe et al. [11]. 

Statistical mechanics is often thought of as a way to predict the thermodynamic properties of molecules from their microscopic properties, but statistical mechnics is more than that because it provides a complementary way of looking at thermodynamics. The transformed Gibbs energy G for a biochemical reaction system at specified pH is given by... 

Chapters 1 and 2 dealt with species properties. But in this chapter we have found that when the pH is specified, it is necessary to use a Legendre transform to define a transformed Gibbs energy G of a system and that this automatically brings in a transformed enthalpy H and transformed entropy S. In fact we have entered a whole new world of thermodynamics where attention is focussed on reactants, which are sums of species, rather than on species. This world of biochemical... 

In studying the thermodynamics of systems of biochemical reactions it is desirable to obtain a global view. One way to do that is to assume that coenzymes are in steady states because they are involved in so many different reactions. When coenzyme concentrations are specified, a further transformed Gibbs energy G can be defined by (7,8,9)... 

Note that there is considerable scatter in the results, which is an indication of the difficulty in obtaining accurate thermodynamic data for some biochemical reactions. It is also interesting to notice that the results for the equilibrium constants, Gibbs energies of reaction, and heats of reaction are all affected by pH. This is typical of reactions involving compounds that can ionize, as discussed earlier and will be considered in greater detail in Chapter 15. ... 

Keywords Aqueous systems bibliography biochemical systems enthalpy data entropy data equilibrium data excess properties Gibbs energy data heat capacHy data partial molar properties review articles thermochemistry thermodynamics. 

A discussion Is given of standard states appropriate to biochemical thermodynamics. Tabulated are Gibbs energies of hydrolysis of esters of acetic acid and related compounds, of thiol esters, amides, phosphates, and of glycolysis (and of decarboxylation). 

This ratio represents the kinetic control over the proportions of products and is a common feature of biochemical reactions where an enzyme facilitates a specific pathway—one with a low activation energy—favoring the formation of a desired product. If a reaction is allowed to reach equilibrium, then the proportion of products is determined by thermodynamic rather than kinetic factors, and the ratio of concentrations is controlled by considerations of the standard Gibbs energies of all the reactants and products. 

Standard Transformed Gibbs Energy of Formation for Important Biochemical Species Thermodynamic Quantities for the Ionization Reactions of Buffers in Water Biological Buffers... 

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