#106 Gibbs free energy of reaction

[Anonymous]

Hi Nick,

here's another wish by Wolf (wolfram.liebermeister@gmail.com):

I see that SBO has "SBO:0000583 - standard Gibbs energy of reaction", which is defined based on the assumption of compounds being in standard concentrations.

I would like to have a "Gibbs energy of reaction", which would be defined for ANY compound concentrations. The symbol would be Delta G (without the little circle).

Moreover, the same quantity, but with a negative sign, is also called "Reaction affinity"; perhaps it would be worthwhile to define this one as well, because with this sign, it's more practical to work with. A synonym (but used only by few people) is "Thermodynamic driving force".

Both new entries could be under "SBO:0000581 - Gibbs free energy change"

Another thought regarding Gibbs energies: in calculations, one often considers a given pH value; under that condition, normally one does not use the Gibbs energies as such, but "transformed Gibbs energies" (denoted by a little prime); see e.g.
http://www.ncbi.nlm.nih.gov/pubmed/9578607. It would be good if SBO could differentiate between normal and transformed Gibbs energies. This would mean doubling all entries under "SBO:0000581 - Gibbs free energy change"

Thank you!

Best, Wolf

[Nick Juty]

Thanks to Wolfram for his extensive feedback (offline) in refining these terms. I have now added the following structure:
Gibbs free energy (SBO:0000580)
--| Gibbs free energy change (SBO:0000581)
--|--| standard Gibbs free energy of formation (SBO:0000582)
--|--| standard Gibbs free energy of reaction (SBO:0000583)
--|--| Gibbs free energy of reaction new (SBO:0000617)
--|--| reaction affinity new (SBO:0000618)
--| Transformed Gibbs free energy change new (SBO:0000619)
--|--| transformed standard Gibbs free energy of reaction new (SBO:0000620)
--|--| transformed standard Gibbs free energy of formation new (SBO:0000621)
--|--| transformed Gibbs free energy of reaction new (SBO:0000622)

Suggestions for further improvement appreciated as always.
Thanks for the requests.