Ab initio molecular orbital investigations of the [2+2] electrocyclization of 3-substituted pentadienyl cations, where the substituents are BH 2, AlH 2, OH, SH, NH 2, PH 2, or H, show significant substituent effects on the ground state conformations, transition structures, and energies of activation. Locating the transition structure for the cyclization of the PH 2-substituted system was particularly trouble-some due to the tendency of the phosphorus group to undergo inversion. The AVS Chemistry Viewer, a data flow environment-based application for the analysis, visualization, and animation of molecular modeling results, proved useful in mapping the potential energy hypersurface and understanding the transition structures for this system.