Vibration of Propane Molecules
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Vibration and rotation of propane molecules in the gas phase at 600 K are shown.

Translation of Propane Molecules
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Translation, vibration and rotation of propane molecules in the gas phase at 600 K are shown.

Vibration of Hexane Molecules
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Vibration and rotation of hexane molecules in the gas phase at 600 K are shown.

Translation of Hexane Molecules
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Translation, vibration and rotation of hexane molecules in the gas phase at 600 K are shown.

Vibration of Nonane Molecules at 600 K
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Vibration and rotation of nonane molecules in the gas phase at 600 K are shown.

Vibration of Nonane Molecules at 1200 K
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Vibration and rotation of nonane molecules in the gas phase at 1200 K are shown.

Translation of Nonane Molecules at 600 K
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Translation, vibration and rotation of nonane molecules in the gas phase at 600 K are shown.

Translation of Nonane Molecules at 1200 K
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Translation, vibration and rotation of nonane molecules in the gas phase at 1200 K are shown.

Vibration of Octadecane Molecules
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Vibration and rotation of octadecane molecules in the gas phase at 600 K are shown.

Translation of Octadecane Molecules
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Translation, vibration and rotation of octadecane molecules in the gas phase at 600 K, in addition to their vibration and rotation

Discussion
The motion of gas molecules is very complicated owing to the combination of translation, rotation, and vibration. Such motion is difficult to depict using static media, such as the printed page. Also, simple animations tend to focus on only one aspect of molecular motion (1). 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 hydrocarbon molecules in the gas phase. Four animations from the collection were published previously by JCE Software. These four animations consist of two animations each of propane and octadecane, one animation calculated to show translational motion, and one to show vibrational motion. (2)

The molecular motion of alkane molecules was calculated using the molecular dynamics simulation (3, 4) in HyperChem (5). The simulations were used to obtain the position of each atom of each molecule at each time step. Each simulated molecular system includes 18 carbons, (i.e., six propane, three hexane, two nonane, or one octadecane) at a temperature of 600 K and is done using the MM+ method, based on the MM2 functional form, authored by Allinger (6). Animations for nonane were also made at 1200 K for comparison to the motion at 600 K.

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. To show translational motion, a second animation captured at 25-femtosecond intervals was done. The individual frames were then compiled into a QuickTime animation.

Each animation contains 900 frames. The molecules are rendered using a CPK-model; the color of carbon is cyan and the color of hydrogen, white. The total real time of the one-femtosecond interval animation is 0.9 picoseconds; at the 25-femtosecond capture rate the animation is 22.5 picoseconds in duration.

These animations of hydrocarbon systems clearly and accurately show the motion of molecules in the gas phase. In the one-femtosecond interval animations, the vibration and rotation of C-H and alkyl groups can be clearly seen. The 25-femtosecond interval animations show translation in addition to vibration and rotation. In some cases they show the detailed motion of atoms in molecules after a collision between two molecules. For nonane, the animations at 600 K and 1200 K show the difference in molecular motion at different temperatures. Previously, only rough and approximate movement of atoms vibrating, rotating, and translating could be shown. These animations depict the movement of molecules more realistically.