Mass diffusion coefficients are critically related to the predictive capability of computational combustion modeling. To date, the most common approach used to determine the molecular transport of gases is the Boltzmann transport equation of the gas kinetic theory. The Chapman-Enskog (CE) solution of this transport equation, combined with Lennard-Jones potential parameters, suggests a simple analytical expression for computing self and mutual diffusion coefficients. This approach has been applied over a wide range of flame modeling conditions due to its minimal computational requirement, despite the fact that the theory was developed only for molecules that have a spherical structure. In this study, we computed the binary diffusion coefficients of linear alkanes using all-atom molecular dynamics simulations over the temperature range 500-1000 K. The effect of molecular configurations on diffusion coefficients was determined relating the radii of gyration of the molecules to their corresponding collision diameters. The comparison between diffusion coefficients determined with molecular dynamics and the values obtained from the CE theory shows significant discrepancies, especially for nonspherical molecules. This study reveals the inability of CE theory with spherical potentials to account for the effect of molecular shapes on diffusion coefficients.