Starting from detailed experimental studies of reaction kinetics, catalyst deactivation, and reactor flow conditions, mathematical models describing the dynamic reactor performance in zeolite catalyzed hydrocarbon transformations in packed beds have been developed. By using a sequential calculation procedure that involved changes in reactor models, solvers, and optimizers, kinetic parameters were regressed for two promising catalysts. Utilizing the estimated parameters and the developed kinetic and flow models, the skeletal isomerization of n-butene was accurately modeled. A proper description of adsorption and deactivation was shown to be as important as the kinetic formulation itself in obtaining good fits to the experimental results. Separable kinetics and deactivation functions were used. Relating the activity of the catalysts to the fraction of noncoked zeolite surface predicted the measured specific surface area to within 5-10%, indicating that reaction takes place throughout the whole catalyst pellet. Structure effects were observed in the estimated composite kinetic parameters. Protonated cyclopropane branching was much easier over H-FER, whereas n-butene codimerization with isobutene was significantly more facile over H-TON. Similar composite activation energies for the beta-scission steps were obtained for both zeolites. The estimated reaction enthalpies for the oligomerization-cracking surface reaction were substantially lower than the thermodynamically calculated heats of reaction for the corresponding gas phase reactions, suggesting that olefin addition proceeds via the stepwise oligornerization mechanism.