The RDF for chosen atoms on the cyclic guests with the lattice water oxygen atoms (OW) and hydrogen atoms (HW). For the ethers, the chosen atom is the ether oxygen (OS) and for cyclopentane, the atom is an arbitrarily chosen carbon atom. Due to attractive electrostatic interactions, the first peaks are spaced inwards compared to the peaks. The first peaks in the OS-HW and OS-OW RDF of THP give a strong indication of hydrogen bonding between the oxygen in this ether with the water.
Snapshots of a large sII clathrate cage with a THF guest molecule at 200 K. (a) A THF-water hydrogen bond is indicated with the light dashed line and the asterisk. The guest-induced -type Bjerrum defect formed between adjacent water molecules in the cage lattice is shown with the black dashed line. (b) The same configuration as part (a) seen from above. (c) A snapshot of the same sII clathrate large cage 0.25 ps after the configuration of part (a). The guest-host hydrogen bond has broken and the water molecule rotates back into position in the clathrate water lattice (shown with the ellipse), thus eliminating the -type defect. (d) The same configuration as part (c) seen from above.
A snapshot of the sII large cage with a THP molecule at 200 K. The guest-host hydrogen bond is shown with the light dashed line. In the case of the THP clathrate, the guest-host hydrogen bonds are long lived and the -type Bjerrum defects in the clathrate water lattice have a longer lifetime.
Guest-host hydrogen bond formation for a selected THF sII clathrate large cages from a simulation trajectories at 250 K (top) and 200 K (bottom). Configurations with a guest-host hydrogen bond are shown with a number 1 and configurations with no such bonding are shown with a 0. At the higher temperature, hydrogen bond formation occurs much more frequently. The lifetimes of the hydrogen bonds are short at both temperatures.
The van’t Hoff plot for the logarithm of the probability of the THF-water hydrogen bond formation as a function of the inverse temperature in the sII clathrate.
Calculated temperature dependence of the lattice vector for CP, THF, 1,3-dioxolane, THP, and -dioxane sII clathrates at ambient pressure. The magnitude of the lattice vector increases as the guest volumes become larger, but thermal expansivities of the clathrates are similar. Experimental data points for THF and THP clathrates are shown with the stars encased in circles and a square, respectively.
Pressure dependence of unit cell volume for CP, THF, and 1,3-dioxolane, THP, and -dioxane at 250 K.
The VACF for the chosen ring atoms at 200 K and ambient pressure for CP, THF, and 1,3-dioxolane. The VACFs become randomized more quickly for CP. The inset shows the details of the oscillations in the VACF at long times. The fast Fourier transform (FFT) of the VACF shows the distribution of periods of the oscillations.
The velocity autocorrelation function for the oxygen atoms for THP and -dioxane at 200 K and ambient pressure. The inset shows the details of the oscillations in the VACF at long times and the FFT of the VACF curve.
The reduced orientational (dipole-dipole) autocorrelation functions for CP, THF, -dioxane, and THP at 200 K and ambient pressure. The dipole-dipole autocorrelation function for THP at 150 K is also given.
Atomic point charges and LJ parameters for and selected atoms on guest molecules. The dipole moments of the guest molecules are also given. AMBER labels are used to specify atom types.
The isothermal compressibility of the sII clathrates at 250 K.
Biexponential decay parameters for the orientational autocorrelation functions for guests in the sII large cages.
Experimental guest reorientation activation energies (kJ/mol), the guest-host defect formation activation energies, and the water reorientation energies for sII clathrates THF, CP, and -dioxane. The water reorientation energy for hexagonal ice is given for comparison.
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