Project Details Chemical and Biochemical Thermodynamics Reunification

Project No.:
2017-021-2-100
Start Date:
25 October 2017
End Date:
Division Name:
Physical and Biophysical Chemistry Division
Division No.:
100

Objective

According to IUBMB-IUPAC joint commission on biochemical nomenclature (JCBN) on chemical and biochemical reactions, two categories of thermodynamics based on different concepts and different formalisms have been established: i) chemical thermodynamics that employs conventional thermodynamic potentials to deal with chemical reactions; ii) biochemical thermodynamics that employs Legendre-transformed thermodynamic potentials to deal with biochemical reactions based on the formalism proposed by Alberty [1]. We plan to show that the two worlds of chemical and biochemical thermodynamics, which so far have been treated separately, can be reunified within the same thermodynamic framework.

1) R. A. Alberty, A. Cornish-Bowden, R. N. Goldberg, G. G. Hammes, K. Tipton, and H. V. Westerhoff, Biophys. Chem., 155 (2011) 89-203; https://doi.org/10.1016/j.bpc.2011.03.007

Description

The thermodynamics of chemical reactions in which all species are explicitly considered with atoms and charge balanced is compared with the transformed thermodynamics generally used to treat biochemical reactions where atoms and charges are not balanced. The transformed thermodynamic quantities suggested by Alberty are obtained by execution of Legendre transformation of the usual thermodynamic potentials. The present analysis demonstrates that the transformed values for ΔG and Δcan be obtained directly without performing Legendre transformations by simply writing the chemical reactions with all the pseudoisomers explicitly included and charges balanced. The appropriate procedures for computing the stoichiometric coefficients for the pseudoisomers are fully explained by means of an example calculation for the biochemical ATP hydrolysis reaction. It is concluded that the analysis has reunited the “two separate worlds” of conventional thermodynamics and transformed thermodynamics. However, the issue of how to define thermodynamic functions goes beyond the fields of chemistry and biochemistry and includes chemical physics and other allied fields as well.

The publications containing the issues summarized above are the following:

Iotti S, Sabatini A, Vacca A, Chemical and biochemical thermodynamics: from ATP hydrolysis to a general reassessment. J. Phys. Chem. B (2010), 114: 1985–1993; doi.org/10.1021/jp903990j

Sabatini A, Vacca A , Iotti S , Balanced Biochemical Reactions: A New Approach to Unify Chemical and Biochemical Thermodynamics. PLoS ONE (2012), 7(1): e29529; doi.org/10.1371/journal.pone.0029529

Stefano Iotti, Lionel Raff, Antonio Sabatini. Chemical and biochemical thermodynamics: Is it time for a reunification? Biophysical Chemistry (2017) 221: 49–57; doi.org/10.1016/j.bpc.2016.10.004

Progress

Project announcement published in Chem Int Apr 2018, p. 38 <https://doi.org/10.1515/ci-2018-0216>

The Task Group met in Florence, Italy, on 23 May 2018; from left: Wiliiam Cannon, Antonio Sabatini, Marco Borsari, Stefano Iotti, and Lionel Raff

June 2018 update – The task group met in Florence on 23 May 2018 and set the work to ultimately deliver a IUPAC Recommendations to be published in Pure and Applied Chemistry and a dissemination follow-up to inform the Editors in Chief of the main scientific journals of the field about the new recommendations suggesting to adopt them as part of the instructions for authors.

The group reviewed a preliminary draft prepared by the task group chair and agreed on a workplan; specific tasks were assigned to each member as following:
Raff Lionel and William Cannon will amended the preliminary draft document adding the issues agreed by all members.
Antonio Sabatini, Stefano Iotti and Marco Borsari will revise the amended draft preparing the document which will be the basis for writing the final recommendations document to be proposed to the IUPAC Physical and Biophysical Chemistry Division.
Gerard Moss will be asked to take care of the preparation of the publication in Pure and Applied Chemistry based on the Recommendations document that will be prepared.
Marco Borsari and William Cannon will prepare a list of relevant Scientific Journals encompassing the issue of chemical and biochemical thermodynamics adopting a selection criteria of scientific quality (Impact Factor, H index, renowned in the field etc.).

March 2019 update – An update is published in Chemistry International 41(2), April 2019 and in more detailed in this document [PDF: ci.2019.41.2.34_project2017-021-2-100_online], presenting an analysis of both methods. Ultimately, through this project 2017-021-2-100, the task group plans to show that the use of these methods allows the two worlds of chemical and biochemical thermodynamics, which so far have been treated separately, to be reunified within the same thermodynamic framework.

Page last updated 28 March 2019