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Physical and Biophysical Chemistry Division (I)


Number: 2006-023-3-100

Title: Recommendations for nomenclature and databases for biochemical thermodynamics

Task Group
: Robert Alberty

Members: Athel Cornish-Bowden, Hal Dixon, Robert N. Goldberg, Gordon Hammes, Keith Tipton, and Hans V. Westerhoff

To revise IUPAC Recommendations for Nomenclature and Tables in Biochemical Thermodynamics 1994*. Update these recommendations and increase their usefulness by providing more about computers and databases that have been developed since 1994. Describe the connection between the thermodynamics of enzyme-catalyzed reactions and the kinetics of enzyme-catalyzed reactions that is provided by Haldane relations.

*Pure Appl. Chem. 66, 1641-1666 (1994) > link to issue content to access ful text

The concept of a transformed Gibbs energy G' that provides the criterion for spontaneous change and equilibrium at a specified pH was developed in 1992 (Alberty, Biophys. 42, 117-131 and 43, 239-254), and so it is quite remarkable that the IUPAC Recommendations were published in Pure Appl. Chem. 66, 1641-1666 (1994). They were reprinted in Eur. J. Biochem. 240, 1-14 (1996).

A lot has happened in the field since 1994, especially the use of computers and the publication of articles and putting databases on the web. A book titled 'Biochemical Thermodynamics: Applications of Mathematica (Wiley, Hoboken, NJ (2006), ISBN: 0-471-75798-5) that gives apparent equilibrium constants at 298.15 K, 0.25 M ionic strength, and pHs 5 to 9 for over 300 enzyme-catalyzed reactions was written by the Task Group Chair.

These Recommendations are to be published as IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN).

The Sections to be drafted include:

  1. Preamble
  2. Introduction
  3. Basic Thermodynamics
  4. Thermodynamics of Chemical Reactions
  5. Legendre Transform to Introduce the pH as an Independent Variable in Biochemical Thermodynamics
  6. Equations for the Standard Transformed Formation Properties of a Reactant
  7. Thermodynamics of Biochemical Reactions
  8. Stoichiometry
  9. Standard Apparent Reduction Potentials for Half Reactions of Enzyme-Catalyzed Reactions
  10. Building a Database
  11. Relations Between Biochemical Thermodynamics and Biochemical Kinetics
  12. Nomenclature
  13. References



Last update: 19 October 2006

<project announcement to be published in Chem. Int >


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