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

7. Use of Mathematica^®

It is convenient to have thermodynamic data in computer-readable form because the calculation of transformed thermodynamic properties is complicated. Mathematica^® is very well suited to these calculations because of its symbolic operations, plotting and table making. Akers and Goldberg published an article on performing calculations on biochemical reactions in the Mathematica Journal, which is available on the web in computer-readable form.

D.L. Akers and R.N. Goldberg; "BioEqCalc: A package for performing equilibrium calculations on biochemical reactions," Mathematica J., 8, 86-113 (2001).

http://www.mathematica-journal.com/issue/v8i1/

In this article they show how to input a chemical equation and obtain the corresponding stoichiometric matrix.

The database BasicBiochemData2 mentioned above contains about 20 programs in computer-readable form. A second package at MathSource at the same address provides programs that are useful in treating the thermodynamics of protein-ligand binding.

R.A. Alberty, ProteinLigandProg (2003) l

http://www.mathsource.com/cgi-bin/msitem?0211-622

Recent publications of RAA are given in the following URL:
http://web.mit.edu/chemistry/www/faculty/alberty

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