Ab Initio Molecular Dynamics Investigation of the Formyl Cation in the Superacid SbF5/HF

Superhalogen-based composite with strong acidity-a crossing point between two topics

Correlation between the acidity and the vertical electron detachment energy verifies the rationality of constructing superacid from superhalogen.

Carbon monoxide protonation in condensed phases and bonding to surface superacidic Brønsted centers

Using infrared (IR) spectroscopy and density functional theory (DFT) calculations, interaction of CO with the strongest known pure Brønsted carborane superacids, H(CHB₁₁Hal₁₁) (Hal = F, Cl), was studied.

When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration

In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.

Structure and Function of Vanadium Haloperoxidases

A quantum mechanics/molecular mechanics study of the resting state of the vanadium dependent chloroperoxidase from fungi Curvularia inaequalis and of the early intermediates of the halide oxidation is reported. The investigation of different protonation states indicates that the enzyme likely consists of an anionic H2VO4- vanadate moiety where one hydroxo group is in axial position. The calculations suggest that the hydrogen peroxide binding may not involve an initial protonation of the vanadate cofactor. A low free energy reactive path is found where the hydrogen peroxide directly attacks the axial hydroxo group, resulting in the formation of an hydrogen peroxide intermediate. This intermediate is promptly protonated to yield a peroxo species. The free energy barrier for the formation of the peroxo species does not depend significantly upon the protonation state of the cofactor. The most likely protonation states of the peroxo cofactor are neutral forms HVO2(O2) with a hydroxo group either H-bonded to Ser402 or coordinated to Arg360. The peroxo cofactor is also coordinated to an axial water molecule, which could be important for the stability of the peroxovanadate/His496 adduct. Our calculations strongly suggest that the halide oxidation may take place with the preliminary formation of a peroxovanadate/halogen adduct. Subsequently, the halogen reacts with the peroxo moiety yielding a hypohalogen vanadate. The most reactive protonation state of peroxovanadate is the neutral HVO2(O2) with the hydroxo group H-bonded to Ser402. The important role of Lys353 in determining the catalytic activity is also confirmed.

On the Quantum Nature of an Excess Proton in Liquid Hydrogen Fluoride

Liquid hydrogen fluoride consists of chains of hydrogen-bonded molecules. The nature of an excess proton in liquid HF, which is of interest not only for its own sake, but also in relation to super-acid chemistry and to its behavior in water, has been studied using computer simulations. The methodology employed is the density-functional-theory-based path-integral Car-Parrinello ab initio molecular dynamics. The excess proton, which formally exists as a H2F+ or a H2F2+ defect in an HF chain, is found to strongly perturb the chain to which it is attached. Moreover, due to large zero-point energy, the charge defect is largely delocalized over several HF molecules.

First-principles molecular dynamics investigation of the D-amino acid oxidative half-reaction catalyzed by the flavoenzyme D-amino acid oxidase

Large-scale Car-Parrinello molecular dynamics simulations of D-alanine oxidation catalyzed by the flavoenzyme D-amino acid oxidase have been carried out. A model of the enzyme active site was built by starting from the enzyme X-ray structure, and by testing different subsystems comprising different sets of aminoacyl residues. In this process, the stability of the enzyme-substrate complex was taken as a measure of the accuracy of the model. The activated transfer of the amino acid alpha-hydrogen from the substrate to the flavin N5 position was then induced by constraining a suitable transfer reaction coordinate, and the free energy profile of the reaction was calculated. The evolution of electronic and structural properties of both enzyme-bound substrate and flavin cofactor along the reaction path is consistent with a hydride-transfer mechanism. The calculated free energy barrier for this process (13 kcal/mol) is in excellent agreement with the activation energy value derived from the experimentally determined rate constant for the corresponding enzyme-catalyzed reaction. The electronic distribution of the reduced flavin shows that the transferred electrons tend to be centered near the C4a position rather than delocalized over the flavin pyrimidine ring. This feature is mechanistically relevant in that such an electronic distribution may promote the subsequent enzyme-catalyzed reduction of molecular oxygen to yield hydrogen peroxide via a postulated flavin 4a-peroxide intermediate. These results also show that a first-principles molecular dynamics approach is suitable to study the mechanism of complex enzymatic processes, provided that a smaller, yet reliable, subsystem of the enzyme can be identified, and special computational techniques are employed to enhance the sampling of the reactive event.