Theoretical Study of Substituent Effects on the Gas-Phase Acidities of Benzoic and Phenylacetic Acids.

The relative gas-phase acidities of 25 ring-substituted benzoic and phenylacetic acids were theoretically determined with proton-transfer reactions. The energies and geometries of the acids and their corresponding anions, which were involved in the reactions, were calculated at the B3LYP/6-311+G(2d,p) level of theory. The obtained substituent effects were compared with each other and those of phenols. The acidities of the benzoic and phenylacetic acids were governed by three kinds of electronic effects (inductive, resonance, and saturation effects), which confirmed that the acidities were reflected in the nature of the benzoate and phenylacetate anions, respectively. Substituent effect analyses with an extended Yukawa-Tsuno equation, ${ - {\rm{\Delta }}E_X = \rho \left( {\sigma ^0 + r^ - {\rm{\Delta }}\bar \sigma _{\rm{R}}^ - + s{\rm{\Delta }}\bar \sigma _{\rm{S}} } \right)}$, gave excellent linear correlations for both anionic systems. The degrees of through-resonance and saturation effects in the phenylacetate anion, as reflected by the resultant r- and s values, were unexpectedly larger than those in the benzoate anion, which were mainly attributed to hyperconjugation and through-space interactions between the anionic moiety and the benzene π-electron system, respectively. The acidities of the benzoic acids (or stabilities of the benzoate anions) constituted a better system than the acidities of phenylacetic acids (or stabilities of the phenylacetate anions) for a standard of the normal substituent constants (σ0 ) for anions in the gas phase, in contrast to solution-phase results.

Molecular dynamics simulation study on stabilities and reactivities of NADH cytochrome B5 reductase.

Binding free energies between coenzyme (FAD and NADH) and the apoenzyme of NADH-cytochrome b5 reductase (b5R) were estimated by applying the continuum Poisson-Boltzmann (PB) model to structures sampled from molecular dynamics simulations in explicit water molecules. Important residues for the enzymatic catalysis were clarified using a computational alanine scanning method. The binding free energies calculated by applying an alanine scanning method can successfully reproduce the trends of the measured steady-state enzymatic activities kcatNADH/KmNADH. Significant decreases in the binding free energy are expected when one of the four residues Arg91, Lys110, Ser127, and Thr181 is mutated into Ala. According to the results of the molecular dynamics simulation, Thr181 is considered to be one of the key residues that helps NADH to approach the isoalloxazine in FAD. Finally, we have constructed very simplified model systems and carried out density functional theory calculations using B3LYP/LANL2DZ//ROHF(or RHF)/LANL2DZ level of theory in order to elucidate a realistic and feasible mechanism of the hydride-ion transfer from NADH to FAD affected by HEME(Fe3+) as an electron acceptor. Our calculated results suggest that the electron and/or hydride-ion transfer reaction from NADH to FAD can be accelerated in the presence of HEME(Fe3+).

Theoretical study of the electronic spectra of oxidized and reduced states of lumiflavin and its derivative.

Time-dependent density functional theory has been applied to investigate the electronic absorption spectrum of oxidized and reduced lumiflavin and its derivative, 8-NH(2)-lumiflavin. The calculations allow the authors to explain the origin of the difference in spectral features between oxidized and reduced states of lumiflavin. For the reduced lumiflavin, a reasonable assignment of the experimental spectrum has been made for the first time. Furthermore, the results obtained reveal that the NH(2) group plays a critical role in shaping the spectral features of 8-NH(2)-lumiflavin, and offer a reasonable explanation for the spectral changes upon substituting the NH(2) group for the CH(3) group of lumiflavin.