Effect of guest size and conformation on crystal structure and stability of structure H clathrate hydrates: Experimental and molecular dynamics simulation studies

To better understand the effect of size and flexibility of large molecule guest substances (LMGSs) on crystal lattice structure and thermodynamic stability of structure H (sH) clathrate hydrates, we performed powder X-ray diffraction (PXRD) measurements and Parrinello-Rahman molecular dynamics (MD) simulations on six alkane and cycloalkane LMGS in the presence of methane help gas. We first quantitatively analyze the dependence of the experimental lattice constants and formation pressure on the average maximum length of the LMGS guests as determined by MD simulation. The PXRD results show that within a family of LMGSs with similar molecular structures molecules of optimum size give better stability of sH hydrate phase. The most stable hydrate in each class has larger lattice constants along the a-axis and smaller lattice constant along the c-axis. The lattice expansion/shrinkage is well reproduced in the MD simulations. From the MD simulations, we determine the changes in the conformation as a result of encapsulation and the tilt angle with respect to the long axis of the sH large cages of the LMGSs. The results indicate that the molecular shapes inside the sH large cages can significantly differ from those of the most stable molecular structure in the gas phase. In the case of flexible molecules, such as 2-methylbutane, the 1-4 dihedral angles and effective molecular sizes change upon encapsulation. Molecules with shorter length generally have larger tilt angles in the large cages; however, the effective width dimension of the LMGS also affects the tilt angle. Understanding the stability of sH hydrates of various LMGSs requires a consideration of guest molecule size, structural flexibility, and tilt angle in the cages. None of these quantities alone explain trends in the stability. During simulation trajectories, we observe changes in conformation in the LMGS molecules in the large cages. The effects of these different factors make a priori structural determinations of the large cages guests extremely complex.