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A thermodynamic atlas of carbon redox chemical space

Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel Segrè, Alán Aspuru-Guzik
doi: https://doi.org/10.1101/245811
Adrian Jinich
aDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge MA, 02138
bDivision of Infectious Diseases, Weill Department of Medicine, Weill-Cornell Medical College, NY, NY
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Benjamin Sanchez-Lengeling
aDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge MA, 02138
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Haniu Ren
aDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge MA, 02138
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Joshua E. Goldford
cBioinformatics Program and Biological Design Center, Boston University, Boston, MA 02215
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Elad Noor
dInstitute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland
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Jacob N. Sanders
eDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095
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Daniel Segrè
cBioinformatics Program and Biological Design Center, Boston University, Boston, MA 02215
fDepartment of Biology, Department of Biomedical Engineering, Department of Physics, Boston University, Boston, MA 02215
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Alán Aspuru-Guzik
gDepartment of Chemistry and Department of Computer Science, University of Toronto, ON, Canada
hVector Institute, Toronto, ON, Canada
iBiologically-Inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5S 1M1, Canada
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  • For correspondence: alan@aspuru.com
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Abstract

Redox biochemistry plays a key role in the transduction of chemical energy in living systems. However, the compounds observed in metabolic redox reactions are a minuscule fraction of chemical space. It is not clear whether compounds that ended up being selected as metabolites display specific properties that distinguish them from non-biological compounds. Here we introduce a systematic approach for comparing the chemical space of all possible redox states of linear-chain carbon molecules to the corresponding metabolites that appear in biology. Using cheminformatics and quantum chemistry, we analyze the physicochemical and thermodynamic properties of the biological and non-biological compounds. We find that, among all compounds, aldose sugars have the highest possible number of redox connections to other molecules. Metabolites are enriched in carboxylic acid functional groups and depleted of carbonyls, and have higher solubility than non-biological compounds. Upon constructing the energy landscape for the full chemical space as a function of pH and electron donor potential, we find that over a large range of conditions metabolites tend to have lower Gibbs energies than non-biological molecules. Finally, we generate Pourbaix phase diagrams that serve as a thermodynamic atlas to indicate which compounds are local and global energy minima in redox chemical space across a set of pH values and electron donor potentials. Our work yields insight into the physicochemical principles governing redox metabolism, and suggests that thermodynamic stability in aqueous environments may have played an important role in early metabolic processes.

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Posted May 21, 2019.
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A thermodynamic atlas of carbon redox chemical space
Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel Segrè, Alán Aspuru-Guzik
bioRxiv 245811; doi: https://doi.org/10.1101/245811
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A thermodynamic atlas of carbon redox chemical space
Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel Segrè, Alán Aspuru-Guzik
bioRxiv 245811; doi: https://doi.org/10.1101/245811

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