Spontaneous pattern of linear molecules in strongly confined spaces

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In this work, we study the tight packing of short linear molecules in confined space by performing molecular dynamic simulations. The short chain-like molecules spontaneously arrange within single-walled carbon nanotubes (SWNTs) and exhibit a variety of chiral and achiral structures, depending on the pore size and molecule length. Simulation results show that the packing structures for these confined short linear molecules are controlled by the competition between positional order and orientational order. For linear molecules with short molecular length, such as the two-site Lennard-Jones molecules, the orientational order gradually decreases as temperature increases, and then the positional order begins to disappear. While for longer molecules, such as four-site Lennard-Jones molecules, the positional order decreases more rapidly than the orientational order as temperature increases. We also investigated the effect of molecular rigidity. For linear molecules with higher rigidity, part of packing structures may slowly rotate as a whole, and the rotation of packing arrangements is found to be induced by the preexisting defects.