Application of molecular dynamics in determination of conformation change with temperature of poly(3-dodecylthiophene) in crystalline cell

Molecular simulation of the crystalline structure of poly(3-dodecylthiophene) (P3DDT) with a consideration of thermal agitation in the main chains and side chains using molecular dynamics and diffraction simulation software is carried out. The incorporation of molecular dynamics to take account of the thermal motions of flexible alkyl side chains and ring distortion of the conjugated main chains provides a capability to calculate the conformational change with varying temperature. The temperature for simulation ranges from −130 to 125 °C. As temperature increases, the alkyl side chain tends to lie on the plane of the nearly coplanar main chain, and the molecular arrangement in the unit cell has no obvious change. The portion of gauche conformation of alkyl side chains of P3DDT is found to increase from 10 to about 25% as the temperature increases from −130 to 125 °C. A transition of the z-averaged torsion angle of the main chains from 30 to 35° occurs in the temperature range from 55 to 85 °C, which is in good agreement with that of the thermochromism as determined from the UV-Vis spectra.