Computer-simulation studies of β-quinol clathrate with various gases. Molecular interactions and crystal structure

Abstract

The crystal structure of β-quinol clathrate was investigated by empirical force-field calculations using two sets of potential functions—AMBER and CVFF. The crystal was approximated by the fragments containing 3402 and 15 750 quinol atoms. It was shown that the AMBER potentials are more precise when describing the experimental data on structure of β-quinol clathrate. The bond stretching, valence angle and out-of-plane bendings, dihedral torsion, van der Waals and electrostatic interactions, and hydrogen bonding were taken into account in the potential energy U. The contribution of each of these energies to the formation of structure was estimated. The energy U was minimized with respect to the independent coordinates of the lattice, unit-cell parameters, and both translation and orientation parameters of included molecules. The equilibrium states of encaged guest molecules, β-quinol lattice structure, and energy of clathrate formation were determined for 27 encaged guest molecules. It was shown that the β-quinol lattice can contract as well as expand depending on the type of an encaged molecule. The distribution of charges around the cage favors the positively charged atoms of the molecule to be located in the center of a cage, in contrast with those negatively charged which occupy the sites in the vicinity of peripheral hydroxyl hexagons. The electrostatic component of guest–guest interaction strongly affects the equilibrium position of guest molecules with large dipole moment. Quantitative estimates of various structural and energetic characteristics for β-quinol clathrate prove to be in good agreement with experimental data.

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

“…In 1 the center of the cavity is electropositive, and the potential increases along the cavity in the direction of the threefold axis, which suggests that electronegative regions of molecules situated in the cavity would point in these directions, for example, towards the hexagon of hydrogen‐bonded HQ molecules. This is in fact the case for the nitrogen atom of the cyano group at one end of the acetonitrile molecule, and this placement of electronegative groups was also suggested by Zubkus et al 37. In the perpendicular direction away from the center of the cavity, the electrostatic potential drops further, but due to steric hindrance the guest molecules in 1 cannot point in that direction.…”

Experimental Determination of Phase Equilibria and Occupancies for CO2, CH4, and N2 Hydroquinone Clathrates

“…This observation could result from the difference in dipole−dipole interactions between the guest and the β HQ lattice. 23,30−32 For Ar−HQ and N 2 −HQ clathrate, it is worth noting that dipole− dipole forces are absent, 29,33 while these forces are likely to be present for CO 2 and CH 4 HQ clathrates coupled to possible guest−guest interactions. 33 Regarding the values of clathrate occupancy in Table 2 and the plots shown in Figure 7, the occupancy decreases with temperature for the three systems studied, in good agreement with observations and simulations results reported previously in the literature.…”

“…23,30−32 For Ar−HQ and N 2 −HQ clathrate, it is worth noting that dipole− dipole forces are absent, 29,33 while these forces are likely to be present for CO 2 and CH 4 HQ clathrates coupled to possible guest−guest interactions. 33 Regarding the values of clathrate occupancy in Table 2 and the plots shown in Figure 7, the occupancy decreases with temperature for the three systems studied, in good agreement with observations and simulations results reported previously in the literature. [19][20][21]24,28 The occupancies for the CH 4 −HQ and N 2 −HQ clathrates are found very close each other in the range of temperature investigated in this work.…”

“…Similarly to the Ar–HQ system, HQ clathrates formed with N 2 are obtained with a higher pressure than for CO 2 and CH 4 . This observation could result from the difference in dipole–dipole interactions between the guest and the β-HQ lattice. ,− For Ar–HQ and N 2 –HQ clathrate, it is worth noting that dipole–dipole forces are absent, , while these forces are likely to be present for CO 2 and CH 4 HQ clathrates coupled to possible guest–guest interactions …”

Clathrate hydrates in the system H2O–Ar at pressures and temperatures up to 30 kbar and 140 °C

“…2 Clathrate hydrates have been extensively investigated experimentally 3,4 and by using computer simulations. 5,6 Recent studies include the crystal structure 7,8 and the thermodynamic stability 9,10 of clathrate hydrates.…”