A thorough theoretical study of phase-transfer quaternary ammonium catalysts designed by the Maruoka group has been performed in an attempt to gain better understanding of the properties and catalytic behavior of the homo- and heterochiral forms of these systems. The conformationally flexible analogue is found to easily undergo interconversion from the homo- to the heterochiral form driven by the higher thermodynamic stability of the heterochiral isomer and resulting in alternation in catalytic behavior. Theoretical calculations of H-1 NMR spectra of the two isomers for different model systems are in good agreement with the experimental data, allowing us to conclude that the upfield shift of signals for the benzylic protons in the heterochiral form could be explained by an increase in the shielding effect of the aromatic parts of the system around these protons due to the conformational changes. By applying the automated transition state (TS) search procedure for the alkylation of glycine derivatives catalyzed by the homo-/heterochiral form of a conformationally rigid analogue, we were able to locate more than 40 configurations of the TS structures. In brief, the homochiral form was theoretically confirmed to catalyze the formation of the predominant R-product, while for the heterochiral form the catalytic activity is found to depend on two factors: (i) formation of a tight ion pair between the catalyst and the glycine derivative, which results in a decrease in the reaction rate, in agreement with the experimental data, and formation of only the R-product, and (ii) the possibility that the reaction occurs without the initial formation of the ion pair or after its dissociation, in which case the formation of an S-product is predominant. The combined effects of both factors would explain the lower reaction rate and the poor enantioselectivity observed experimentally for the heterochiral form.