Such motion is difficult to depict using static media, such as the printed page. So, to improve students' understanding of molecular motion, Alkanes in Motion, a collection of clip animations generated from molecular dynamics calculations, was produced. It depicts the molecular motion of hydrocarbons in the gas phase. Four animations from the collection are presented here. These four animations consist of two animations each of hexane and octadecane, one animation calculated to show translational motion and one to show vibrational motion.
Frame fro the animation of octadecane.
Click figure to view video of an alkane in motion. The simulations were used to obtain the position of each atom of each molecule at each time step. The time increment of each molecular dynamics calculation was one femtosecond. The graphical display of the results of these calculations was then captured at periodic intervals. To accurately depict vibrational motion, animations were done capturing a frame each femtosecond.