Molecular dynamics of paraffins in the n-alkane/urea clathrate

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Abstract
Simulations of the molecular dynamics of n‐CNH2N+2 in the n‐alkane/urea clathrate have been performed for N=13,23,33, for a period of 1 ns. Parallel simulations were performed starting from conformations in which all CH2–CH2 bonds were in the trans conformation, and starting from a conformation in which one of the terminal CH2–CH2 bonds was in a gauche conformation. These simulations suggest less than 3% of the terminal CH2–CH2 bonds would be in a gauche state at equilibrium. The gauche content is much smaller at the CH2–CH2 bonds further removed from the ends of the chain. No significant differences are seen in the simulations performed with n‐alkanes with N=13,23,33. The mobility of the C–H bond vectors about the axis defined by the channel is greater at the ends than in the middle of the chain. The angular distribution is nearly randomized in 1 ns for the C–H vector in a methyl group, but a longer time scale would be required for randomization of this distribution for the C–H vector bonded to the central methylene group in C33H68.