A DFT-based QM-MM approach designed for the treatment of large molecular systems: application to chorismate mutase

Article Abstract:

A density functional theory (DFT) hybrid quantum mechanical/molecular mechanical (QM-MM) implementation developed for simulations of reactions in complex environments is presented. The catalytic activity achieved by chorismate mutase relative to the uncatalyzed reaction in solution is attributed to both a minor destabilization of the substrate molecule by compression and a major electrostatic stabilization of the transition state, which reduce the activation energy of the reaction.

United States, Analysis, Density functionals, Density functional theory, Molecular systematics

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An MD/QM study of the chorismate mutase-catalyzed Claisen rearrangement reaction

Article Abstract:

The calculation of the reaction path for the rearrangement of chorismate to prephenate, catalyzed by chorismate mutase using ab initio quantum chemistry is presented. The results of the electronic activation energies calculation for both enzyme conformations studied are found lower than the reaction barrier obtained experimentally.

Chemical reactions

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The Claisen rearrangements of an unusual in chorismate mutase

Article Abstract:

The molecular dynamics (MD) and quantum chemical (QM) methodology is used to calculate reaction path for an unusual substrate of chorismate mutase. It was found that the calculated reaction paths for an unusual substrate of chorismate mutase are completely comparable with the native chorismate.

Molecular dynamics

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