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Alikeness in Motion
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Jade Hun Kim
Kongju National University, Kogjusi, Chungnam, Republic of Korea 314-701 |
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This program is included in both the General Chemistry Collection (SP-16) and the Advanced Chemistry Collection (SP-28).
To Order General Chemistry Collection |
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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 studentsÕ 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.
 The molecular motion of alkane molecules was calculated using the molecular dynamics simulation (2, 3) in HyperChem (4). 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., three hexane molecules) (Fig. 1) and one octadecane (Fig. 2) at a temperature of 600 K and is done using the MM+ method, based on the MM2 functional form, authored by Allinger (5).
 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. A time stamp was added to show the relative time of molecular motion. 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 CÐH 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. Previously, only rough and approximate movement of atoms vibrating, rotating, and translating could be shown. These animations depict the movement of molecules more realistically.
Hardware and Software Requirements
Acknowledgement These animations were produced with the support of the Yonam Foundation in the Republic of Korea.
Literature Cited
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Last Updated: July 19, 2001 Created: June 16, 1999 |
Created by: N. S. Gettys Comments to: jceonline@chem.wisc.edu |
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| © 1997 Division of Chemical Education, Inc., American Chemical Society. All rights reserved. | |