Interaction and transport of representative (un)saturated hydrocarbon molecules involved in the proposed reaction network of n-butene isomerization in zeolites FER, TON, and AEL have been studied by classic molecular modeling calculations. Docking of the guest molecules into the zeolite frameworks revealed that isomers up to eight carbon atoms can be located inside the pores without significant conformational restraints. FER and AEL zeolites showed higher stabilization compared with TON zeolites for di- and tribranched octanes proposed as intermediates for selective bimolecular mechanisms. Simulated diffusion profiles of such highly branched molecules showed large diffusion barriers, confirming their low uptake found in previous adsorption studies. Docking and diffusion calculations with coke precursors, such as benzene, naphthalene, and biphenyl, revealed that condensed ring structures are unlikely to be formed inside of the zeolite channels investigated.