Alkyl-substituted 1,3-dioxolanes, including 4,5-dimethyl-2-pentan-3-yl-1,3-dioxolane (Fuel 1), 4,5-dimethyl-2-pentyl-1,3-dioxolane (Fuel 2), and 2-(heptan-3-yl)-4,5-dimethyl-1,3-dioxolane (Fuel 3), have been recently suggested as potential biodiesels. In this paper, we investigate the initial pyrolysis of the alkyl-substituted 1,3-dioxolanes at high temperatures using ReaxFF molecular dynamics (MD) simulations. We analyze the decomposition rate, reaction mechanism, and product distribution in the pyrolysis of the three alkyl 1,3-dioxlanes. The three fuels primarily decompose to 4,5-dimethyl-1,3-dioxolane radical and hydrocarbons derived from the alkyl side-chains. The further decomposition of 4,5-dimethyl-1,3-dioxolane radical primarily leads to 2-C4H8 and CO2 within a few decomposition steps. The hydrocarbon product distribution is significantly affected by the molecular structure of the alkyl side-chain, which would have a strong influence on the sooting tendency of these fuels. The ReaxFF simulations predict that the order of sooting tendency would be Fuel 3 > Fuel 1 > Fuel 2, which agrees with the measured sooting tendency trend. Based on the pyrolysis mechanism identified by ReaxFF, we propose a new alkyl dioxolane, 4-hexyl-5-methyl-1,3-dioxolane (Fuel 4), which might produce even less soot, by modifying the molecular structure of Fuel 2. Our ReaxFF simulation shows that Fuel 4 produce much less C4H8, an effective non-aromatic soot precursor, than Fuel 2. Moreover, more carbon atoms are bonded to each oxygen atom in Fuel 4 than Fuel 2, which would help reduce soot yield by removing more carbon atoms from the soot-producing pool of species. The major decomposition pathways identified in this work can be used to develop chemical kinetic models for 1,3-dioxolane based compounds, as biodiesel components, applicable to combustion engine simulations. We also demonstrate that the chemical kinetic insight offered by ReaxFF simulations can be used to design new fuel molecules with more desired properties.