Molecular dynamics simulations are reported on the structure and dynamics of 𝑛-decane and 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We have also analysed trajectory to obtain diffusivity and velocity autocorrelation function (VACF). Surprisingly, the diffusivity of 3-methylpentane which is having larger cross-section perpendicular to the long molecular axis is higher than 𝑛-decane at 300 K. Activation energies have been obtained from simulations performed at 200 K, 300 K, 350 K, 400 K and 450 K in the NVE ensemble. These results can be understood in terms of the previously known levitation effect. Arrhenious plot has higher value of slope for 𝑛-decane (5.9 kJ/mol) than 3-methylpentane (3.7 kJ/mol) in agreement with the prediction of levitation effect.