The all-trans product is thermodynamically favored due to the reduced steric interference among the four substituents bonded to the cyclobutane.  These four large functional groups initially bonded cis to one another would result in a highly strained molecule, and this stereochemistry would increase its molecular energy (3) (Figure 1). However, the conformation of these pipercyclobutanamide heterodimers is inherently all-cis in nature, thus requiring a significant activation energy in order to overcome the strained bond orientations (4). When the activation energy can be overcome – due to the epimerization that occurs upon heating the mixture to 45 degrees Celsius – the trans product can be formed. This product, due to being much less sterically-hindered, is at a much lower energy state, allowing the reaction to proceed in a thermodynamically favorable direction towards the all-trans molecule.

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Figure 1