Quantum chemical approach to estimating the thermodynamics of metabolic reactions.
Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA.
Adrian
A
Jinich
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA.
Dmitrij
D
Rappoport
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA.
Ian
I
Dunn
Lab. Chimie et Physique Quantiques, CNRS-Université de Toulouse, Toulouse, France.
Benjamin
B
Sanchez-Lengeling
Department of Chemistry, Princeton University, Princeton, NJ.
Roberto
R
Olivares-Amaya
Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
Elad
E
Noor
Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
Arren Bar
AB
Even
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA.
Alán
A
Aspuru-Guzik
D016208:Databases, Factual; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D053858:Metabolic Networks and Pathways; D008956:Models, Chemical; D011789:Quantum Theory; D055672:Static Electricity; D013816:Thermodynamics