Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.

@article{Mori2013FreeenergyAO,
  title={Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.},
  author={Yoshiharu Mori and Yuko Okamoto},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  year={2013},
  volume={87 2},
  pages={
          023301
        }
}
  • Yoshiharu Mori, Y. Okamoto
  • Published 2 June 2012
  • Chemistry
  • Physical review. E, Statistical, nonlinear, and soft matter physics
A simulated tempering method, which is referred to as simulated-tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed to study the intramolecular proton transfer reaction of malonaldehyde in an aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be… 

Figures from this paper

Free energy surface for rotamers of cis-enol malonaldehyde in aqueous solution studied by molecular dynamics calculations
Two-dimensional free energy surfaces for four rotamers of cis-enol malonaldehyde in water have been investigated by umbrella sampling molecular dynamics (MD) calculations. Biasing potential used in
Quantum chemical replica-exchange umbrella sampling molecular dynamics simulations reveal the formation mechanism of iron phthalocyanine from iron and phthalonitrile.
TLDR
Analysis of the MD trajectories reveals a three-step FePc formation mechanism for the PN method, and a metastable structure very similar to FeP c but with a reactive nitrene unit was also identified that might explain the incomplete conversion of the reactants into FePC.
Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface.
TLDR
The combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches.
Density functional tight binding‐based free energy simulations in the DFTB+ program
TLDR
A new interface between the DFTB+ software package and the PLUMED library for performing DFT B‐based free energy calculations is reported and the performance of this interface is demonstrated for 3 archetypal rare‐event chemical reactions.
Protein structure predictions by enhanced conformational sampling methods
  • Y. Okamoto
  • Chemistry
    Biophysics and physicobiology
  • 2019
TLDR
Enhanced conformational sampling methods for protein structure predictions are reviewed and several generalized-ensemble algorithms such as multicanonical algorithm, replica-exchange method, etc. and parallel Monte Carlo or molecular dynamics method with genetic crossover are presented.
New QM/MM implementation of the DFTB3 method in the gromacs package
The approximate density‐functional tight‐binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package.
Efficient free energy calculations by combining two complementary tempering sampling methods.
TLDR
This work proposes an effective approach to combine temperature accelerated molecular dynamics (TAMD) with the integrated tempering sampling (ITS), a generalized ensemble sampling method, and shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.
A global reaction route mapping-based kinetic Monte Carlo algorithm.
TLDR
The GRRM-KMC method is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle, demonstrating that in both cases the method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.
...
...

References

SHOWING 1-10 OF 58 REFERENCES
Multistate Empirical Valence Bond Model for Proton Transport in Water
A multistate empirical valence bond (MS-EVB) model for describing proton transport in aqueous systems is presented. In this approach the electrostatic interaction of the solvent water molecules with
Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)
A very efficient scheme is presented to simulate proton transport by classical molecular dynamics simulation coupled with quantum mechanically derived proton hopping. Simulated proton transfer rates
A reactive molecular dynamics study of the thermal decomposition of perfluorodimethyl ether.
Classical reactive molecular dynamics (RMD) simulation is used to model the thermal decomposition of perfluorodimethyl ether (CF(3)OCF(3)), which is relevant as a simple molecule containing the
Multidimensional replica-exchange method for free-energy calculations
TLDR
A new simulation algorithm for free-energy calculations that greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.
Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides
A molecular dynamics (MD) method using the multicanonical algorithm, multicanonical MD, is proposed to enhance the efficiency of conformational sampling of peptides. Multicanonical MD is a constant
ReaxFF: A Reactive Force Field for Hydrocarbons
To make practical the molecular dynamics simulation of large scale reactive chemical systems (1000s of atoms), we developed ReaxFF, a force field for reactive systems. ReaxFF uses a general
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The
Generalized-ensemble algorithms for molecular simulations of biopolymers.
TLDR
Three new generalized-ensemble algorithms that combine the merits of the multicanonical algorithm, simulated tempering, and replica-exchange method are presented, which are tested with short peptide systems.
...
...