C-H•••carboxylate oxygen hydrogen bonding in substrate activation by acyl-CoA dehydrogenases:: Synergy between the H-bonds

Several model systems for the a-carbonyl proton abstraction reaction were studied at the DFT level to examine the role of hydrogen bonding interactions in the enzyme catalytic activity of acyl-CoA dehydrogenase. Each system contains the thioester portion of acyl-CoA (CH3CH2(C=O)SCH3) a weakly basic -COOcircle minus representing Glu376. H-donor molecules (methanol and methylformamide) with zero, one or two H-donors bound to the carbonyl oxygen of the thioester correspond to the Glu376 and FAD side-chains. Five transition structures (TS-2(a), TS-2(b), TS-2(d) TS-2(a*). and TS-2(b*)) for the a-proton abstraction step and their corresponding ground state minima have been fully optimized at the B3LYP/6-31+G(d,p) level of theory. Classical activation energy barriers of 5.8, 10.4, 7.7, 9.9, and 12.3 kcaUmol have been calculated for these model systems, respectively. ChelpG. NBO charge distribution analysis in conjunction with the structural properties of the transition structures suggest their enolate-like character and the "normal" character of hydrogen bonds to the carbonyl oxygen. These energetic consequences are discussed in terms of a synergistic interplay between charge-augmented (ionic) and neutral ("normal") H-bonds. These interactions serve to disperse this negative charge not only in the ground state but also in the TS, thereby strengthening the internal H-bonds along the entire reaction coordinate. An additional unanticipated insight, with the identification of a strong ionic C-H...carboxylate-oxygen H-bond along the reaction coordinate provides an activating influence for the a-proton abstraction. The ionic C-H...(OOC)-O-circle minus H-bond identified here would not only orient the general base prior to proton abstraction, but also transfers electron density to the developing enolate anion along the reaction coordinate. This strengthens the H-bonds to the thioester carbonyl oxygen that prove so critical in the acidification of the a-proton and lowers the energy of the transition state for enolization. The correlation between the reaction endothermicity. barrier height and location of the transition state along the reaction coordinate is consistent with the classical Hammond postulate. Solvent modeling performed with the COSMO//B3LYP/6-31+G(d,p) method confirms the important role of desolvation of the carboxylate anion prior to the a-proton abstraction step.