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Consequences of Covalent and Non-Covalent Interactions on Conformational Preferences and pi-Electron Delocalization for the Substrate (Pyruvate) and Inhibitor (Oxamate) of Lactate Dehydrogenase - DFT Studies

Raczyńska E. D., Hallmann M., Duczmal K.

Polish Journal of Chemistry

2008

Vol. 82, nr 5

1077-1090

Conformational preferences and pi-electron delocalization for the isolated substrate (pyruvate) and inhibitor (oxamate) of lactate dehydrogenase (LDH), their protonated forms, adducts with alkali metal cations, and complexes with imidazole and/or the guanidinium cation (models for His195 and Arg171 of the LDH pocket, respectively) have been investigated at the DFT(B3LYP)/6-31++G(d,p) level. Covalent and non covalent bonds in acids, adducts and complexes cause greater conformational changes for pyruvate than for oxamate. Delocalization of pi electrons for the OCO frag ments is similar for similar structures. For isolated anions, adducts and complexes, the HOMED(OCO) values are between 0.9 and 1.0. For protonated forms, the HOMED(OCO) val ues are re duced to 0.55-0.75. Delocalization of pi electrons for the CCO fragment in pyruvate and for the NCO fragment in oxamate in creases when the anions form covalent and non-covalent bonds with other ions and molecules. The HOMED(CCO) values vary from 0.1 to 0.5 forsigma-pi conjugated pyruvate, whereas the HOMED(NCO) values vary from 0.9 to 1.0 for n-pi conjugated oxamate.

Comparison of the Proton (H+) and Alkali Metal Ion (Li+, Na+ and K+) Binding Affinities of Pyruvate and Oxamate Anions in the Gas Phase. Quantum-Chemical Studies

Duczmal K., Hallmann M., Raczynska E., Gal F., Maria P.

Polish Journal of Chemistry

2007

Vol. 81, nr 5-6

1011-1020

Proton affinity (PA), lithium, sodium and potassium cation affinities (CA) in the gas phase were estimated by Gaussian-2 (G2), Möller-Plesset (MP2) methods and/or hybrid density functional theory calculations (B3LYP) for pyruvate and oxamate anions. Comparison of these affinities shows that the COO– groups of both anions have similar basicities. Differences between their calculated PAs as well as between their calculated CAs are not larger than 3 kcal mol–1. Somewhat larger differences are evidenced for the formations of the alkali metal complexes with the cation located between the oxygen atoms of the alfaC=O and COO– groups for which the lithium, sodium and potassium cation affinities are larger for oxamate than for pyruvate (by 40.5 kcal mol–1 at theG2 level and by 60.5 kcal mol–1 at the DFT(B3LYP)/6-31++G** level). This is a consequence of the chelate effect on the cation binding seen on the calculatedmost stable structures of the adducts.