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We performed molecular dynamics simulations of the ammonia and methanol-based clathrate hydrates with the emphasis on characterizing hydrogen-bonding interactions of these guest molecules with the water lattice. Systems studied include structure II (sII) binary clathrate hydrates of tetrahydrofuran (THF) (large cage, L) + NH3 (small cage, S) and THF (L) + CH3OH (S), the structure I (sI) pure NH3 (L), pure CH3OH (L), the binary NH3 (L) + CH4 (S), and binary CH3OH (L) + CH4 (S) clathrate hydrates. We simulated these clathrate hydrates with the transferable intermolecular potential with four point changes (TIP4P) water potential and the TIP4P/ice water potential to determine the effect of the water potential on the predicted hydrogen bonding of the guest molecules. Simulations show that, despite strongly hydrogen bonding with the framework water molecules, clathrate hydrate phases with NH3 and CH3OH can be stable within temperatures ranges up to 240 K. Indeed, a limited number of thermodynamic integration free energy calculations show that both NH3 and CH3OH molecules give more stable guest-host configurations in the large sI clathrate hydrate cages than methane guests. Predictions of hydrogen bonding from simulations with the two different water potentials used can differ substantially. To study the effect of proton transfer from water to the basic NH3 guests, simulations were performed on a binary NH3 + CH4 sI clathrate hydrate where less than 10 % of the ammonia guests in the large cages were converted to NH4 + and a water molecule of the hydrate lattice in the same large cage was converted to OH-. The small percentage of proton transfer to ammonia guests in the large cages did not affect the stability of the resultant hydrate. The structural perturbations in the lattice that result from this proton transfer are characterized.Peer reviewed: YesNRC publication: Ye

Molecular Dynamics Simulations of Hydrogen Bonding in Clathrate Hydrates with Ammonia and Methanol Guest Molecules