Prediction of the Crystalline Structure of a Novel Polythiophene Using Molecular Dynamics Simulations

A novel polythiophene, poly(3-acetamido-undecanoic-succinimidyl-thiophene), has been synthesized and characterized by using IR, RMN, X-ray, DSC, and density measurements. Powder X-ray analysis shows that the polymer crystallizes in a distinct lamellar structure with a spacing of ∼23 Å. Fine details at large diffraction angles indicated the presence of a three-dimensional crystalline structure although the data were insufficient to resolve the exact form of this structure. DSC measurements showed two distinct melting peaks a few degrees apart, which are possibly linked to a liquid-crystal intermediate phase. In a second stage, molecular dynamics (MD) simulations have been used in an attempt to predict the crystal structure and to shed light on the double melting peak behavior. Based on the initial assumption that the polymer backbones are parallel and the aliphatic side chains are linear (all trans), three trial starting configurations have been generated, energy minimized, and then allowed to relax by using constant pressure-constant temperature MD. Two of these systems have been followed for over 1 ns of elapsed time. Although both of these latter systems maintain a linear ordering of the polymer backbones, one shows a low degree of order in the arrangement of the side chains, whereas the other shows a high degree of order. Comparisons are made between the properties of the two systems and model X-ray diffractograms are presented and compared with experimental data.