Applied Sciences · 2020 · 21 citations · 44 references
Natural SciencesChemistryPhysicsComputational ChemistryPhysical ChemistryTheoretical ChemistryHydrate FormationHydrogen AtomMolecular DynamicsMolecular InteractionsMolecular SimulationMolecular ThermodynamicsActivation EnergyActivation Energy DeterminationArrhenius EquationClassical Molecular DynamicsEnergy Barrier AnalysisHydrate Cage OccupancyHydrate Structure TypeHydrate Thermodynamics
The inter-cage hopping in a type II clathrate hydrate with different numbers of H2 and D2 molecules, from 1 to 4 molecules per large cage, was studied using a classical molecular dynamics simulation at temperatures of 80 to 240 K. We present the results for the diffusion of these guest molecules (H2 or D2) at all of the different occupations and temperatures, and we also calculated the activation energy as the energy barrier for the diffusion using the Arrhenius equation. The average occupancy number over the simulation time showed that the structures with double and triple large-cage H2 occupancy appeared to be the most stable, while the small cages remained with only one guest molecule. A Markov model was also calculated based on the number of transitions between the different cage types.
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A smooth particle mesh Ewald method
Ulrich Essmann, L. Perera, Max L. Berkowitz et al. · The Journal of Chemical Physics · 1995 · 22.9K citations
GROMACS: Fast, flexible, and free
David van der Spoel, Erik Lindahl, Berk Hess et al. · Journal of Computational Chemistry · 2005 · 19.1K citations
Natural Sciences, Chemistry, Physics +17