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Density-functional study on the equilibria in the ThDP activation.

Eduardo J Delgado1, Joel B Alderete, Gonzalo A Jaña

  • 1Theoretical and Computational Chemistry Group (QTC), Physical Chemistry Department, Facultad de Ciencias Químicas, casilla 160-C, Universidad de Concepción, Concepción, Chile. edelgado@udec.cl

Journal of Molecular Modeling
|May 12, 2011
PubMed
Summary
This summary is machine-generated.

This study uses high-level density functional theory to explore thiamine diphosphate (ThDP) activation equilibria. It reveals all ionization and tautomeric states are accessible, with specific forms driving key catalytic steps.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Physical Chemistry

Background:

  • Thiamine diphosphate (ThDP) is a crucial cofactor in many metabolic enzymes.
  • Understanding ThDP activation mechanisms is vital for enzyme catalysis research.
  • Previous studies lacked comprehensive thermodynamic data for ThDP ionization and tautomerization.

Purpose of the Study:

  • To elucidate the ionization and tautomeric equilibria in ThDP activation.
  • To determine the role of medium polarity on ThDP's thermodynamic properties.
  • To provide the first theoretical thermodynamic data for ThDP internal equilibria.

Main Methods:

  • High-level density functional theory (DFT) calculations.
  • Utilized the X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p) level of theory.
  • Simulated reactions in both apolar (cyclohexane) and polar (water) media.

Main Results:

  • All ionization and tautomeric states of ThDP are accessible during the catalytic cycle.
  • The APH(+) form is essential for interconverting AP and IP tautomers.
  • Ylide generation occurs via the IP tautomer, with calculated ΔG° values enabling equilibrium constant determination.

Conclusions:

  • The study provides the first theoretical thermodynamic data for ThDP activation equilibria.
  • Medium polarity significantly influences ThDP's geometry and thermodynamics.
  • The findings clarify the catalytic initiation step involving thiazolium C2 atom ionization (pK(C2)).