Skip to main content

Advertisement

SpringerLink
Log in

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

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14

Similar content being viewed by others

References

  1. Kasting J (1993) Earth’s early atmosphere. Science 259:920–926

    Article  CAS  Google Scholar 

  2. Orgel LE (1998) The origin of life – how long did it take? Orig Life Evol Biosph 28:91–96

    Article  CAS  Google Scholar 

  3. Oparin AI (1924) ProischogdenieZhizni. MoscovskyRobotschii.

    Google Scholar 

  4. Oparin AI (1965) Origin of life2nd edn. Dover Publication

  5. Miller SL (1953) A production of amino acids under possible primitive earth conditions. Science 117:2

    Article  Google Scholar 

  6. Miller SL (1955) Production of some organic compounds under possible primitive earth conditions. J Am Chem Soc 77:2351–2361

    Article  CAS  Google Scholar 

  7. Schwartz W (1967) Sidney W. Fox (Herausgeber), The origin of prebiological systems and of their molecular matrices. XX + 482 S., 110 Abb., 35 Tab, vol 7. Academic Press. $ 8. Z Allg Mikrobiol, New York, London 1965, pp 245–245

    Google Scholar 

  8. Cleaves II HJ, ScottAM HFC, Leszczynski J, Sahai N, Hazen R (2012) Mineral-organic interfacial processes: potential roles in the origins of life. Chem Soc Rev 41:5502–5525

    Article  CAS  Google Scholar 

  9. Haldane JBS (1929) The origin of life. Ration Annu 148:8

    Google Scholar 

  10. MillerSS UHC (1959) Organic coumpound synthesis on primitive earth. Science 130:7

    Article  Google Scholar 

  11. Parker ET, Cleaves HJ, Dworkin JP, Glavin DP, Callahan M, Aubrey A, Lazcano A, Bada JL (2011) Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. Proc Natl Acad Sci U S A 108:5526–5531

    Article  CAS  Google Scholar 

  12. Morowitz HJ (1999) A theory of biochemical organization, metabolic pathways, and evolution. Complexity 4:39–53

    Article  Google Scholar 

  13. QuayleJR FT (1978) Evolutionary aspects of autotrophy. Microbiol Rev 42:251–273

    Google Scholar 

  14. Eschenmoser A (2007) The search for the chemistry of life’s origin. Tetrahedron 63:12821–12844

    Article  CAS  Google Scholar 

  15. Wächtershäuser G (1990) Evolution of the first metabolic cycles. Proc Natl Acad Sci U S A 87:200–204

    Article  Google Scholar 

  16. Hartman H (1975) Speculations on the origin and evolution of metabolism. J Mol Evol 4:359–370

    Article  CAS  Google Scholar 

  17. McFadden BA (1973) Autotrophic CO2 assimilation and the evolution of ribulose diphosphate carboxylase. Bacteriol Rev 37:289–319

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Morowitz HJ, Kostelnik JD, Yang J, Cody GD (2000) The origin of intermediary metabolism. Proc Natl Acad Sci U S A 97:7704–7708

    Article  CAS  Google Scholar 

  19. Sagi VN, Punna V, Hu F, Meher G, Krishnamurthy R (2012) Exploratory experiments on the chemistry of the “Glyoxylate Scenario”: formation of ketosugars from dihydroxyfumarate. J Am Chem Soc 134:3577–3589

    Article  CAS  Google Scholar 

  20. Butch C, Cope ED, Pollet P, Gelbaum L, Krishnamurthy R, Liotta CL (2013) Production of tartrates by cyanide-mediated dimerization of glyoxylate: a potential abiotic pathway to the citric acid cycle. J Am Chem Soc 135:13440–13445

    Article  CAS  Google Scholar 

  21. Butch CJ, Wang J, Gu J, Vindas R, Crowe J, Pollet P, Gelbaum L, Leszczynski J, Krishnamurthy R, Liotta CL (2016) pH-controlled reaction divergence of decarboxylation versus fragmentation in reactions of dihydroxyfumarate with glyoxylate and formaldehyde: parallels to biological pathways. J Phys Org Chem 29:352–360

    Article  CAS  Google Scholar 

  22. Eschenmoser A (2007) On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycle. Chem Biodivers 4:554–573

    Article  CAS  Google Scholar 

  23. Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor Chem Accounts 120:215–241

    Article  CAS  Google Scholar 

  24. Ayala PY, Schlegel HB (1997) A combined method for determining reaction paths, minima, and TS geometries. J Chem Phys 107:375–384

  25. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2018) Gaussian 09, Revision E.01, Inc., Wallingford CT.

  26. MarvinView, ChemAxon. 2014, (6.3.0).

  27. Walker M, Harvey AJA, Sen A, Dessent CEH (2013) Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model system with dispersion and ionic hydrogen-bonding interactions. J Phys Chem A 117:12590–12600

    Article  CAS  Google Scholar 

  28. Hohenstein EG, Chill ST, Sherrill CD (2008) Assessment of the performance of the M05 − 2X and M06 − 2X exchange-correlation functionals for noncovalent interactions in biomolecules. J Chem Theory Comput 4:1996–2000

    Article  CAS  Google Scholar 

  29. Mennucci B (2012) Polarizable continuum model. Wiley Interdiscip Rev Comput Mol Sci 2:386–404

    CAS  Google Scholar 

  30. Fukui K (1981) The path of chemical reactions - the IRC approach. Acc Chem Res 14:363–368

    Article  CAS  Google Scholar 

Download references

Funding

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.

Author information

Authors and Affiliations

  1. Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA

    Mehedi Khan, Supratik Kar, Jing Wang & Jerzy Leszczynski

Authors
  1. Mehedi Khan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Supratik Kar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jerzy Leszczynski
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jerzy Leszczynski.

Additional information

This paper is dedicated to Professor Zdzislaw Latajka, on occasion of his 70th Birthday in recognition of his numerous vital research contributions.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This paper belongs to the Topical Collection Zdzislaw Latajka 70th Birthday Festschrift.

Electronic supplementary material

ESM 1

(DOCX 184 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Khan, M., Kar, S., Wang, J. et al. Theoretical study of formate, tartrate, tartronate, and glycolate production from 6-carbon trioxylate intermediate in the citric acid cycle. J Mol Model 25, 347 (2019). https://doi.org/10.1007/s00894-019-4240-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-019-4240-z

Keywords

Search

Navigation