Geobiochemistry of metabolism: Standard state thermodynamic properties of the citric acid cycle

Canovas, Peter A.; Shock, Everett L.

doi:10.1016/j.gca.2016.08.028

Cited by 14 publications

(19 citation statements)

References 132 publications

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“…In practice, we evaluate equilibrium constants for reactions in the citric acid cycle with equations, data, and parameters from Canovas and Shock (2016), together with a new set of parameters developed in this study for the DEW model. Activity products are calculated from compositional constraints from natural or laboratory systems.…”

Section: Thermodynamic Framework and Computational Methodsmentioning

confidence: 99%

“…One way to approach this goal is to determine energetic demands of biochemical pathways and cycles that are met in the deep biosphere by geochemical energy sources. In this chapter, we combine our standard state thermodynamic data for aqueous species involved in the citric acid cycle (Canovas & Shock, 2016) with estimates of their intercellular abundances to evaluate thermodynamic affinities for reactions within the citric acid cycle at elevated pressures and temperatures. We also evaluate new parameters for the same aqueous species consistent with the Deep Earth Water (DEW) model (Sverjensky, Harrison, et al, 2014), which allows us to extrapolate the energetics of the citric acid cycle into conditions of shallow subduction zones.…”

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confidence: 99%

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Energetics of the Citric Acid Cycle in the Deep Biosphere

Canovas

Shock

2020

Geophysical Monograph Series

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Constraints on the internal composition of microbial cells are used together with standard state thermodynamic data to evaluate energy demands associated with the citric acid cycle and its individual steps to explore geobiochemical processes in the deep subsurface biosphere. Two pressure-temperature ranges are considered: up to 200 °C and to ~2 kb with the revised Helgeson-Kirkham-Flowers equations of state, and up to 200 °C from 10 to 60 kilobars with the Deep Earth Water model. The former pressure-temperature ranges encompass conditions for known life in natural systems, and the latter push the upper pressures for life into those of subduction zones using guidance from laboratory experiments. The neutral solutes H 2 (aq) and CO 2 (aq) can diffuse freely across cell membranes and impose external conditions into the composition of microbial cells, and as a result there is a range of chemical affinities for citric acid cycle reactions that prevail throughout the deep subsurface biosphere. These ranges raise the possibility that the citric acid cycle releases energy when run in either the forward or reverse directions depending on the affinities involved. The results of this theoretical study support the notion that life may extend far deeper into subduction zones than is generally appreciated. 25 25.1. PHYSICAL CONDITIONS OF THE DEEP BIOSPHERE

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Section: Thermodynamic Framework and Computational Methodsmentioning

confidence: 99%

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confidence: 99%

Energetics of the Citric Acid Cycle in the Deep Biosphere

Canovas

Shock

2020

Geophysical Monograph Series

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“…Temperature dependence of standard Gibbs energies of steps of the citric acid cycle (Canovas and Shock, 2016) demo("TCA") logK to 150°C for formation of monovalent and divalent metal-glycinate complexes (Azadi et al, 2019) demo("glycinate") can be used extend the original calculations. For instance, the "Introduction to CHNOSZ" vignette shows how a calculation of ATP speciation described by Alberty (2003) can be enhanced by inclusion of the temperature dependence of standard Gibbs energies (LaRowe and Helgeson, 2006b).…”

Section: Description Locationmentioning

confidence: 99%

“…These and many other calculations are becoming more tractable through the expansion of thermodynamic databases to include more organic and biochemical species at greater ranges of temperature and pressure (Shock and Helgeson, 1990;Shock, 1995;Amend and Helgeson, 1997;Helgeson et al, 1998;Richard and Helgeson, 1998;Dick et al, 2006;LaRowe and Helgeson, 2006a,b;LaRowe and Dick, 2012;Kitadai, 2014;Canovas and Shock, 2016;Lowe et al, 2017;Azadi et al, 2019). However, there are limited choices of software packages for thermodynamic calculations and diagrams commonly used in hydrothermal geochemistry.…”

Section: Introductionmentioning

confidence: 99%

CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

Dick

2019

Front. Earth Sci.

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Thermodynamic calculations are an essential tool for many areas of geochemistry. Thermodynamics provides a framework for the quantitative description and prediction of the solubilities and relative stabilities of different minerals, metal transport in hydrothermal fluids, and geobiochemical reactions that drive microbial metabolism and contribute to the compositional variation of proteins. Accessible and up-to-date software and databases are important for the development and reproducible application of thermodynamic models. CHNOSZ is a free package for R that has been frequently updated since its first release in 2008. The package provides an integrated set of functions to calculate the standard molal thermodynamic properties and chemical affinities of reactions. It uses the graphical capabilities of R to produce high-quality chemical activity diagrams for aqueous species and predominance diagrams including Eh-pH (Pourbaix) and logf O 2-T diagrams. The extensive database utilizes the well-known revised Helgeson-Kirkham-Flowers (HKF) equations for aqueous species. Recent additions to the database include the Berman equations for minerals, the Deep Earth Water model, which extends the applicability of the HKF equations to higher pressures, and the Akinfiev-Diamond model for aqueous nonelectrolytes. The package comes with many types of documentation, including technical help pages with short code examples, longer code demos, and in-depth vignettes combining code, text and graphics, giving users a wide array of starting points for their own research. This paper provides a concise overview of the package and illustrates the new features using examples selected from the literature. Although the package does not provide a complete chemical speciation model, numerous examples from the package demonstrate the ease of reproducing selected published calculations and sometimes identifying issues with existing datasets and models.

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“…These pressures in the Earth are realised below the deepest part of the Earth's crust, or over 40 km depths. These efforts are now motivated to evaluate models of solution equilibrium developed by geochemists, which calculate solute activities and the equilibrium constants for a wide range of aqueous reactions [125][126][127][128][129][130][131][132]. The HKF model is among the most widely used ('HKF' from 'Helgeson, Kirkham and Flowers') and employs as one key variable the static dielectric constant of water at elevated temperatures and pressures [13,14,[34][35][36][37][38][39][40][41][42][120][121][122][123][124][125][126][127][128][129][130][131][132][133][134].…”

Section: Devices To Reach Gpa Pressures For Solution Nmrmentioning

confidence: 99%

17 O NMR as a Tool in Discrete Metal Oxide Cluster Chemistry

Ohlin

Casey

2018

Annual Reports on NMR Spectroscopy

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This chapter covers recent developments in 17 O NMR spectroscopy as applied to discrete metal oxide clusters, particularly in the context of their use as models in geochemistry and catalysis. Dynamic 17 O NMR methods based on the McConnell-Bloch equations are explored in depth, and recent advances are reviewed. High-pressure NMR methods are also discussed and reviewed, as are recent developments in the use of density functional theory in the computation of 17 O NMR shifts in polyoxometalates. The emphasis of the chapter is on the new developments that promise to reinvigorate 17 O NMR as a central tool in the study of aqueous chemical kinetics, with the most urgent challenges being understanding the rates of isotopic substitution into bridging oxygens in clusters.

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Geobiochemistry of metabolism: Standard state thermodynamic properties of the citric acid cycle

Cited by 14 publications

References 132 publications

Energetics of the Citric Acid Cycle in the Deep Biosphere

Energetics of the Citric Acid Cycle in the Deep Biosphere

CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

17 O NMR as a Tool in Discrete Metal Oxide Cluster Chemistry

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