Transformed thermodynamic properties, biochemical

Explains the distinction between biochemical and chemical equations, and the calculation and meaning of transformed thermodynamic properties for ATP and other phosphorylated compounds. 

Tables of Standard Transformed Thermodynamic Properties at 298.15 K for Biochemical Reactants at Specified pH and Ionic Strength... 

When the pH is specified, we enter into a whole new world of thermodynamics because there is a complete set of new thermodynamic properties, called transformed properties, new fundamental equations, new Maxwell equations, new Gibbs-Helmholtz equations, and a new Gibbs-Duhem equation. These new equations are similar to those in chemical thermodynamics, which were discussed in the preceding chapter, but they deal with properties of reactants (sums of species) rather than species. The fundamental equations for transformed thermodynamic potentials include additional terms for hydrogen ions, and perhaps metal ions. The transformed thermodynamic properties of reactants in biochemical reactions are connected with the thermodynamic properties of species in chemical reactions by equations given here. 

The relationships between the thermodynamic properties of chemical reactions and the transformed thermodynamic properties of biochemical reactions have been treated in several reviews (Alberty, 1993a, 1994c, 1997b, 2001 e). Recommendations for Nomenclature and Tables in Biochemical Thermodynamics from an IUPAC-IUBMB Committee were published in 1994 and republished in 1996. This report is available on the Web http llwww.chem.qmw.ac.uhlimbmbl thermodl. 

R. A. Alberty, Calculation of transformed thermodynamic properties of biochemical reactants at specified dpH and pMg, Biophys. Chem. 43.239-254 (1992). 

As shown by the Maxwell relations in equations 3.4-12 to 3.4-16, all the other thermodynamic properties of a biochemical reactant can be calculated by taking partial derivatives of the function of T, pH, and ionic strength for Af G,- °. This is illustrated by calculating the other standard transformed thermodynamic properties of inorganic phosphate. 

Two-dimensional Plots of Transformed Thermodynamic Properties of Biochemical Reactions... 

R. A. Alberty, Effect of temperature on the standard transformed thermodynamic properties of biochemical reactions with emphasis on the Maxwell equations, J. Phys. Chem. 107 B, 3631-3635 (2003). (Supporting Information is available.)... 

Chapters 3-5 have described the calculation of various transformed thermodynamic properties of biochemical reactants and reactions from standard thermodynamic properties of species, but they have not discussed how these species properties were determined. Of course, some species properties came directly out of the National Bureau of Standard Tables (1) and CODATA Tables (2). One way to calculate standard thermodynamic properties of species not in the tables of chemical thermodynamic properties is to express the apparent equilibrium constant K in terms of the equilibrium constant K of a reference chemical reaction, that is a reference reaction written in terms of species, and binding polynomials of reactants, as described in Chapter 2. In order to do this the piiTs of the reactants in the pH range of interest must be known, and if metal ions are bound, the dissociation constants of the metal ion complexes must also be known. For the hydrolysis of adenosine triphosphate to adenosine diphosphate, the apparent equilibrium constant is given by... 

We have seen that calculating species properties from experimental values of K and A // ° is more complicated than calculating K and Ar ° from species values. Thermodynamic calculations can be made by alternate paths, and so there is more than one way to calculate species properties from experimental properties. This chapter emphasizes the concept of the inverse Legendre transform discussed by Callen (8). Biochemical reaction systems are described by transformed thermodynamic properties, and the inverse transform given in equation 6.2-1 provides the transformation from experimental reactant properties to calculated species properties. In this ehapter we first considered calculations of species properties at 298.15 K from measurements of K and Ar ° at 298.15 K. Then we considered the more difficult problem of calculating Af G°(298.15 K) and Af //°(298.15 K) from Ar G "(313.15 K) and Ar H (313.15 K). The programs developed here make it possible to go from Ar G and Ar H (F.pH,/) to Af G (298.15 K,/=0) and Af H (298.15 K,/=0) in one step. 

The Appendix contains a copy of the Mathematica notebook BasicBiochemDataS.nb, Tables of Transformed Thermodynamic Properties, the Glossary of Names of Reactants, the Glossary of Symbols for Thermodynamic Properties, a List of Mathematica programs, and Sources of Biochemical Thermodynamic Information on the Web. The Mathematica package BasicBiochemData3.m, which is also available at... 

The field of theoretical molecular sciences ranges from fundamental physical questions relevant to the molecular concept, through the statics and dynamics of isolated molecules, aggregates and materials, molecular properties and interactions, and the role of molecules in the biological sciences. Therefore, it involves the physical basis for geometric and electronic structure, states of aggregation, physical and chemical transformations, thermodynamic and kinetic properties, as well as unusual properties such as extreme flexibility or strong relativistic or quantum-field effects, extreme conditions such as intense radiation fields or interaction with the continuum, and the specificity of biochemical reactions. 

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... 

The calculation of Af G° and Af H° of species from experimental data on apparent equilibrium constants and transformed enthalpies of reaction is described in R. A. Alberty, Thermodynamics of Biochemical Reactions, Wiley, Hoboken, NJ (2003) and a number of places in the literature. That is not discussed here because this package is oriented toward the derivation of mathematical functions to calculate thermodynamic properties at specified T, pH, and ionic strength. There are two types of biochemical reactants in the database ... 

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