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

2. Sources of Experimental Data

Goldberg and Tewari (NIST) have searched the literature for experimental measurements of apparent equilibrium constants and enthalpies of biochemical reactions and have evaluated these data in a series of publications:

R.N. Goldberg; Y.B. Tewari, D. Bell, and K. Fazio, Thermodynamics of Enzyme-catalyzed Reactions: Part 1. Oxidoreductases, J. Phys. Chem. Ref. Data 22, 515 (1993).

R.N. Goldberg and Y.B. Tewari, Thermodynamics of Enzyme-catalyzed Reactions: Part 2. Transferases, J. Phys. Chem. Ref. Data 23, 547-617 (1994).

R.N. Goldberg and Y.B. Tewari, Thermodynamics of Enzyme-catalyzed Reactions: Part 3. Hydrolases, J. Phys. Chem. Ref. Data, 23, 1035-1103 (1994).

R.N. Goldberg and Y.B. Tewari, Thermodynamics of Enzyme-catalyzed Reactions: Part 4. Lyases, J. Phys. Chem. Ref. Data 24, 1669-1698 (1995).

R.N. Goldberg and Y.B. Tewari, Thermodynamics of Enzyme-catalyzed Reactions: Part 5. Isomerases and Ligases, J. Phys. Chem. Ref. Data 24, 1765-1801 (1995).

R.N. Goldberg, Thermodynamics of Enzyme-catalyzed Reactions: Part 6 - 1999 Update, J. Phys. Chem. Ref. Data 28, 931-965 (1999).

Goldberg has also put these references and an index on the web:
http://wwwbmcd.nist.gov:8080/enzyme/enzyme.html

Thus experimental values of apparent equilibrium constants are available on about 400 enzyme-catalyzed reactions involving about 1000 different reactants. Thus in principle, standard thermodynamic properties can be calculated for species of about 1000 reactants in biochemical reactions. There is an urgent need for more measurements of apparent equilibrium constants and heats of biochemical reactions.

The interpretation of the pH dependencies of apparent equilibrium constants depends on the pKs of acidic groups in reactants, and the following review contains pKs for sixty eight weak acids.

R.N. Goldberg, N. Kishore, and R.M. Lenner, Thermodynamic Quantities for the Ionization Reactions of Buffers, J. Phys. Ref. Data 31, 231-370 (2002).

Klotz (Northwestern U.) has compiled a large number of apparent equilibrium constants for protein-ligand equilibria.

I.M. Klotz, Ligand-Receptor Energetics, Wiley, Hoboken, NJ, 1997.

There are two sources of standard chemical thermodynamic properties of species in dilute aqueous solutions:

D.D. Wagman, W.H. Evans, V.B. Parker, R.H. Schumm, I. Halow, S.M. Bailey, K.L. Churney, and R.L. Nutall, The NBS Tables of Chemical Thermodynamic Properties, J. Phys. Chem. Ref. Data, 11, Suppl. 2 (1982).

J.D. Cox, D.D. Wagman, and V.A. Medvedev, CODATA Key Values for Thermodynamics, Hemisphere, Washington, D. C., 1989.

The NBS tables do not go beyond C₁ and C₂ species, but these tables do contain a number of species of biochemical interest. Tables like the NBS Tables provide the most efficient way of storing thermodynamic information on reactions because they can be used to calculate standard thermodynamic properties of reactions that have not been studied experimentally. The reason the NBS Tables do not go beyond C₂ is that chemical equilibrium and calorimetric measurements with larger organic molecules produce very complicated mixtures. Also reaction rates are often slow or essentially zero in aqueous solution at room temperature. Enzyme catalysis changes this situation completely. The current data base of transformed thermodynamic properties includes about 130 biochemical reactants, but work is required to increase this number, as described in the next section. On the basis of such a data base, the standard transformed thermodynamic properties of many other biochemical reactants can be estimated on the basis of structural similarities.

NIST provides a Chemistry WebBook with a variety of types of information useful in thermodynamics.
http://webbook.nist.gov/chemistry/

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