Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations
Kiyoshi Yagi, Shingo Ito, Yuji Sugita
Abstract
with B3LYP-D3 in the QM/MM calculation is in agreement with the experimental results. The impact of conformational sampling in PMF calculations and the level of electronic structure calculations (DFTB vs B3LYP-D3) suggests reliable computational protocols for enzymatic reactions without high computational costs.
Topics & Concepts
QM/MMEnergy (signal processing)String (physics)QuantumInterface (matter)Computer scienceChemistryMolecular dynamicsPhysicsComputational chemistryQuantum mechanicsMoleculeGibbs isothermProtein Structure and DynamicsPhotosynthetic Processes and MechanismsSpectroscopy and Quantum Chemical Studies