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Journal of Molecular Modeling

, 25:347 | Cite as

Theoretical study of formate, tartrate, tartronate, and glycolate production from 6-carbon trioxylate intermediate in the citric acid cycle

  • Mehedi Khan
  • Supratik Kar
  • Jing Wang
  • Jerzy LeszczynskiEmail author
Original Paper
  • 38 Downloads
Part of the following topical collections:
  1. Zdzislaw Latajka 70th Birthday Festschrift

Abstract

Reaction pathways of side products (formate, glycolate, and tartronate) from dihydroxyfumarate (DHF) were theoretically investigated as DHF is an intermediate in the process of producing tartrates and oxalate from glyoxylate of the citric acid cycle. The proposed pathways for each reaction were mapped by density functional theory (DFT) calculations. The transitions states were confirmed by analyzing the vibrational frequency and the intrinsic reaction coordinate (IRC) theory. The corresponding reaction activation energy, enthalpy change, Gibb’s free energy change, and rate of reactions were calculated to get a clear picture of the whole reaction pathway. In the whole process, the decarboxylation reaction showed the highest energy barrier of 20–23 kcal/mol. Proton transfer and hydroxylation reactions were almost barrierless. As most of these reactions have very low energy barrier, our findings elucidate the high probability of those reactions under experimental conditions.

Keywords

Citric acid cycle DFT Formate Glycolate Tartrate Tartronate 

Notes

Funding information

This work was jointly supported by NSF and the NASA Astrobiology Program under the NSF Center for Chemical Evolution, CHE1004570. The computation time was provided by the Extreme Science and Engineering Discovery Environment (XSEDE) by National Science Foundation grant number OCI-1053575 and XSEDE award allocation number DMR110088 and by the Mississippi Center for Supercomputer Research.

Supplementary material

894_2019_4240_MOESM1_ESM.docx (185 kb)
ESM 1 (DOCX 184 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric SciencesJackson State UniversityJacksonUSA

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