Contents

1. Introduction

2. Sources of Experimental Data

3. Calculation of Standard Thermodynamic Properties of Species from Apparent Equilibrium Constants and Heats of Biochemical Reactions

4. Calculation of Standard Transformed Thermodynamic Properties of Reactants and Reactions at Specified pH

5. Further Transformed Thermodynamic Properties

6. Maxwell Relations

7. Use of Mathematica®

8. Statistical Mechanics of Systems of Biochemical Reactions

9. Names of Enzymes

10. Acknowledgement

4. Calculation of Standard Transformed Thermodynamic Properties of Reactants and Reactions at Specified pH

The most efficient way to store thermodynamic information on biochemical reactions is to store ∆_fGº and ∆_fHº of the species in each reactant, as described in the preceding section. The program calcdGmat has been written to derive the function of pH and ionic strength that yields ∆_fG’º for a biochemical reactant (sum of species) at 298.15 K from the matrix of species properties. The program calcdHmat does the same thing for ∆_fH’º. The assignment operation can be used to calculate values of ∆_fG’º and ∆_fH’º for a reactant at any desired pH and ionic strength. These functions can also be used to make tables and plots.

Since the name of a reactant can represent the corresponding function of pH and ionic strength, the program calctrGerx can be used to calculate ∆_rG’º and ∆_r H’º for a biochemical reaction by simply typing it in. The program calckprime can be used to calculate apparent equilibrium constants. The program calcNHrx can be used to calculate the change in the binding of hydrogen ions in a reaction. Standard apparent reduction potentials for half reactions at various pHs and ionic strengths can be calculated using the program calcappredpot. If ∆_fHº values for all the species in a reactant are known, calcdGHT can be used to calculated standard thermodynamic properties at other temperatures. The ability to derive the function of temperature, pH, and ionic strength for ∆_fG’º and ∆_rG’’º is especially important because all the other thermodynamic properties can be calculated by taking partial derivatives of this function. This is discussed in Section 6.

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