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Formation thermodynamics is examined for two different types of point defects which interrupt conjugation in polydiacetylene crystals: bond‐alternation and orbital‐flip defects. While bond‐alternation defects in these polymers are analogous to previously investigated radical pair defects in the polyenes, much lower equilibrium concentrations are expected in the polydiacetylenes than in the polyenes. For polydiacetylenes with small substituent groups or high‐energy side‐group packing, orbital‐flip defects provide a more plausible rationale for explaining observed thermochromism and carrier trapping effects in photoconductivity. During the formation of this type of defect, a π orbital at each of the two neighboring sp2 carbon atoms is rotated by 90°, so that the rotated π orbitals become conjugated with the out‐of‐plane orbitals neighboring sp carbon atoms. Thereby the system of overlapping π orbitals is interrupted without substantially decreasing the electronic stabilization energy. With an intramolecular strain energy increase of only about 2.6 kcal/mole, the polymer chain can return to lattice register within one monomer unit of the defect center. Since the electronic stabilization energy change is even smaller (about 0.2 kcal/mole), the major contribution to defect formation energy arises from the side‐group rotations.