JCE Software, 3C1: MolVib

MolVib: Visualizing Molecular Vibrations

Daniel Huber
Metrohm, Ltd. , CH-9100 Herisau, Switzerland

Note:
MolVib has been updated. Please see issue 7C, 1 for information about MolVib 2.0.

Have you ever had difficulty visualizing how a molecule vibrates? Would you like to be able to demonstrate molecular vibrations to your students using computer animation? MolVib allows you to display a vibrating molecule on your computer screen and view it from whatever position you choose.
To make MolVib perform its animation you need only choose one of several molecules already available in a menu. Once a molecule has been selected you can choose each normal vibrational mode from a menu. Modes may be selected individually and then animated, or they may be mixed to demonstrate the equivalence of degenerate vibrations. Animation speed can be varied in order to see the vibration more clearly, and the molecule can be rotated so that the vibration can be observed from different viewpoints. In some cases details of a three-dimensional vibration may not be clearly evident on the two-dimensional screen, and so provision has been made to show static amplitude vectors for each normal mode.
Center-of-mass and Eckhart (angular momentum) conditions are always fulfilled during the motion so that mass effects such as isotopic substitutions can be demonstrated. H₂O, HDO, and D₂O can easily be compared, for example. In addition to the graphic output you can obtain numeric results for each vibration. If you want to view vibrations of a molecule that is not in the menu, it is necessary to supply the number of atoms, their masses and Cartesian coordinates, the number of internal coordinates and their types (stretch, bend), the force constants for interactions between each pair of atoms, and a set of directions for drawing the static molecule on the screen. This information is stored in a disk file and can be recalled easily any time the vibrations of that molecule are to be examined.
MolVib can be used appropriately at several levels. For introductory students it provides a convenient way to illustrate how molecules vibrate and to show differences in vibrations when isotopic substitutions are made. The animation of the molecule can be compared to the vibrations of weights on a spring, the close correlation being quite evident. At a more advanced level it is possible to show that if a subsection of a molecule has a very different vibrational frequency from the frequencies in the rest of the molecule, that vibrational mode will survive even in the composite molecule; for example, comparison of CH₄ and CHT₃ (T = tritium) shows that the C-H stretch remains independent of the three C-T vibrations. For use in physical chemistry and other advanced courses it is possible to print eigenvalues and eigenvectors for a given vibrational problem, and these could be compared with results of students' calculations.
Hardware and Software Requirements
MolVib requires a Macintosh Plus, SE, Classic, SE/30, or any Mac II model. The program has been tested using versions 6.02 and 6.03 of the Macintosh system software and ought to be compatible with any version 6.x system. For those who wish to use the software for class presentations a large monitor or overhead projection panel for the Macintosh will be needed. Several such panels and monitors are available (1).
Literature Cited

Susskind, T. Y. J. Chem. Educ.: Soft. 1988 1A(1), 16-24.

First Published: February 1991
Citation: Huber, D. MolVib: Visualizing Molecular Vibrations J. Chem. Educ. Software 3C1
Keywords: Lecture Aid; Computer Room; High School; General; Analytical; Organic; Physical; Molecular vibration animations; Normal modes

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Last Updated: April 26, 2001
Created: December 4, 1996 Created by: J. L. Holmes
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© 1997 Division of Chemical Education, Inc., American Chemical Society. All rights reserved.



MolVib: Visualizing Molecular Vibrations
Daniel Huber Metrohm, Ltd. , CH-9100 Herisau, Switzerland

Note:	MolVib has been updated. Please see issue 7C, 1 for information about MolVib 2.0.

Have you ever had difficulty visualizing how a molecule vibrates? Would you like to be able to demonstrate molecular vibrations to your students using computer animation? MolVib allows you to display a vibrating molecule on your computer screen and view it from whatever position you choose. To make MolVib perform its animation you need only choose one of several molecules already available in a menu. Once a molecule has been selected you can choose each normal vibrational mode from a menu. Modes may be selected individually and then animated, or they may be mixed to demonstrate the equivalence of degenerate vibrations. Animation speed can be varied in order to see the vibration more clearly, and the molecule can be rotated so that the vibration can be observed from different viewpoints. In some cases details of a three-dimensional vibration may not be clearly evident on the two-dimensional screen, and so provision has been made to show static amplitude vectors for each normal mode. Center-of-mass and Eckhart (angular momentum) conditions are always fulfilled during the motion so that mass effects such as isotopic substitutions can be demonstrated. H₂O, HDO, and D₂O can easily be compared, for example. In addition to the graphic output you can obtain numeric results for each vibration. If you want to view vibrations of a molecule that is not in the menu, it is necessary to supply the number of atoms, their masses and Cartesian coordinates, the number of internal coordinates and their types (stretch, bend), the force constants for interactions between each pair of atoms, and a set of directions for drawing the static molecule on the screen. This information is stored in a disk file and can be recalled easily any time the vibrations of that molecule are to be examined. MolVib can be used appropriately at several levels. For introductory students it provides a convenient way to illustrate how molecules vibrate and to show differences in vibrations when isotopic substitutions are made. The animation of the molecule can be compared to the vibrations of weights on a spring, the close correlation being quite evident. At a more advanced level it is possible to show that if a subsection of a molecule has a very different vibrational frequency from the frequencies in the rest of the molecule, that vibrational mode will survive even in the composite molecule; for example, comparison of CH₄ and CHT₃ (T = tritium) shows that the C-H stretch remains independent of the three C-T vibrations. For use in physical chemistry and other advanced courses it is possible to print eigenvalues and eigenvectors for a given vibrational problem, and these could be compared with results of students' calculations. Hardware and Software Requirements MolVib requires a Macintosh Plus, SE, Classic, SE/30, or any Mac II model. The program has been tested using versions 6.02 and 6.03 of the Macintosh system software and ought to be compatible with any version 6.x system. For those who wish to use the software for class presentations a large monitor or overhead projection panel for the Macintosh will be needed. Several such panels and monitors are available (1). Literature Cited Susskind, T. Y. J. Chem. Educ.: Soft. 1988 1A(1), 16-24.


News \| Issues \| CD-ROM / Video \| Find It! \| Technical Support \| For Authors
JCE Online \| Journal \| Software \| Internet \| Happenings \| About JCE \| Contact JCE

Last Updated: April 26, 2001 Created: December 4, 1996	Created by: J. L. Holmes Comments to: jceonline@chem.wisc.edu

© 1997 Division of Chemical Education, Inc., American Chemical Society. All rights reserved.