Carsten Kettner

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About Carsten Kettner:

Project manager of STRENDA and MIRAGE @Beilstein-Institut

SEEK ID: https://fairdomhub.org/people/1205

Location: Germany

ORCID: https://orcid.org/0000-0002-8697-6842

Joined: 22nd Nov 2018

Expertise: Biochemistry, Project Management, electrophysiology

Tools: Data Management, standards, Databases

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FAIR Biocatalysis

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Projects: EnzymeML, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling

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Standardization of enzyme-catalyzed reaction modelling

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Programme: FAIR Biocatalysis

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Standardization of enzyme-catalyzed reaction measurement

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Programme: FAIR Biocatalysis

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Organisms: Not specified

EnzymeML

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Programme: FAIR Biocatalysis

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Beilstein Institut

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Country: Germany

City: Frankfurt/Main

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Transformed reference potentials

Thermodynamics, Book on Thermodynamics, and kinetics, Thermotables for biochemistry

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12 variously transformed reference potentials for 320 compounds of biochemical interest in unit kJ/mol.

Approximately 1360 of each type of transform are listed in columns 3 - 14. The number 1360 > 320 because a chemical compound often has multiple entries. This reflects that there are multiple data sources, phases, protonation states or Mg complexation states for that compound.

Column 2 contains the familiar reference (standard at the physical chemical reference state) physical chemical ...

Creators: Hans V. Westerhoff, Peter J. Halling, Johann Rohwer, Carsten Kettner, Yanhua Liu, Yanhua Liu, HVW collected physical chemical reference potentials from the literature and developed and carried out all transformations thereto writing an excel file. YL checked the values obtained from the literature. PJH and HVW developed the CNPS gauge shifts. PJH checked the methodology used as well as the naming of the compounds. JR developed a Python program to compute the transformed reference potentials and thereby checked the values obtained by HVW. (A limited number of errors was identified and eliminated in this manner).

Submitter: Hans V. Westerhoff

DOI: 10.15490/fairdomhub.1.datafile.9798.2

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Created: 3rd Jul 2026 at 20:59, Last updated: 8th Jul 2026 at 19:44

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Metabolic thermodynamics: pertinent reference state and energy potentials

Thermodynamics, Book on Thermodynamics, and kinetics, Thermotables for biochemistry

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Abstract (Expand)

Chemical potentials (molar Gibbs energies) are usually extrapolated to the remote physical–chemical reference state and then stored. Subsequent use under in vivo conditions requires a similarly … conditions requires a similarly substantial, reverse extrapolation, again with significant potential errors. In order to shrink both extrapolations drastically and thereby enhance both biological meaning and accuracy, we propose a transformation to a more biological reference state: pH = 7, pMg = 3, 99.5% water, with 1 m m each of the additional ‘precursors’ inorganic phosphate, sulfate, ammonium, and bicarbonate, and with twin temperatures 37 and 25 °C, ionic strength 0.15 m and m m as concentration unit. These precursors substitute for reference compounds alien to biology such as H 2 at 1 bar, and solid graphite, sulfur, and phosphorus. The standard chemical potentials are herewith increased by the magnitudes of the chemical potentials of protons, Mg 2+ , water, and the four precursors, each multiplied by the number of corresponding atoms in the molecule. This defines standard ‘metabolic potentials’. We make these potentials findable and accessible as 1360 collated standard chemical potentials for 320 compounds of biochemical interest at the twin metabolic reference states. We do this for 3 reference pH's: We present the metabolic reference state as a convenient anchor , not a universal intracellular milieu. All datasets must continue to report the actual experimental state ( T , pH, pMg, I , osmolarity, concentrations), yet aim at (also) reporting parameter values for this anchor state; we supply algorithms to transform between states. This preserves interoperability across diverse organelles, media and between enzymology and chemical engineering, while facilitating reuse.

Authors: Hans V. Westerhoff, Barbara M. Bakker, Andreas S. Bommarius, Maria Luz Cárdenas, Athel Cornish‐Bowden, Paul Fitzpatrick, Peter J. Halling, Vassily Hatzimanikatis, Carsten Kettner, Yanhua Liu, Andrew G. McDonald, Elad Noor, Jürgen Pleiss, Frank M. Raushel, Johann M. Rohwer, Santiago Schnell, Keith F. Tipton, Ming‐Daw Tsai, Urs von Stockar, Ulrike Wittig, Roland Wohlgemuth, John M. Woodley

Date Published: 5th Mar 2026

Publication Type: Journal Article

DOI: 10.1111/febs.70415

Citation: The FEBS Journal 293(11):3111-3126.

Created: 6th Jul 2026 at 20:37, Last updated: 6th Jul 2026 at 20:40

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