A series of new rotaxanes with axles different in length was prepared. Following the synthetic protocol utilizing a known anion template effect (Scheme 1), surprisingly low yields in the order of 2 - 5% were obtained (Scheme 3), which furthermore significantly depended on the nature of the stopper (Fig. 1). Variations in the synthetic procedures and computational results from Monte Carlo simulations allowed us to analyze the origin of these findings: The rotaxane wheel 3 acts as a noncovalently bound 'protecting group' for the stopper nucleophile. The protection of the nucleophilic phenolate O-atom depends much on the steric demands of the stoppers (see 2 vs. 10) which induce different conformations of the wheel. Based on this model. an improved synthetic scheme is suggested.