Paper Citing NAMD - Abstract
Peters, Baron; Zimmermann, Nils E. R.; Beckham, Gregg T.; Tester, Jefferson W.; Trout, Bernhardt L.
Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:17342-17350, DEC 24 2008
Increased interest in natural gas hydrate formation and decomposition, coupled with experimental difficulties in diffusion measurements, makes estimating transport properties in hydrates an important technological challenge. This research uses an equilibrium path sampling method for free energy calculations [Radhakrishnan, R.; Schlick, T. J. Chem. Phys. 2004, 121, 2436] with reactive flux and kinetic Monte Carlo simulations to estimate the methane diffusivity within a structure I gas hydrate crystal. The calculations support a water-vacancy assisted diffusion mechanism where methane hops from an occupied "donor" cage to an adjacent "acceptor" cage. For pathways between cages that are separated by five-membered water rings, the free energy landscape has a high barrier with a shallow well at the top. For pathways between cages that are separated by six-membered water rings, the free energy calculations show a lower barrier with no stable intermediate. Reactive flux simulations confirm that many reactive trajectories become trapped in the shallow intermediate at the top of the barrier leading to a small transmission coefficient for these paths. Stable intermediate configurations are identified as doubly occupied off-pathway cages and methane occupying the position of a water vacancy. Rate constants are computed and used to simulate self-diffusion with a kinetic Monte Carlo algorithm. Self-diffusion rates were much slower than the Einstein estimate because of lattice connectivity and methane's preference for large cages over small cages. Specifically, the fastest pathways for methane hopping are arranged in parallel (nonintersecting) channels, so methane must hop via a slow pathway to escape the channel. From a computational perspective, this paper demonstrates that equilibrium path sampling can compute free energies for a broader class of coordinates than umbrella sampling with molecular dynamics. From a technological perspective, this paper provides one estimate for an important transport property that has been difficult to measure. In a hydrate I crystal at 250 K with nearly all cages occupied by methane, we estimate D approximate to 7 x 10(-15) X m(2)/s where X is the fraction of unoccupied cages.
