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.