The main screen in 3DNormalModes is shown in Figure 1. Whatever molecule has been selected occupies the major portion of the screen, and all of the functions of the program are readily available via mouse clicks.

Figure 1. The main screen from 3DNormalModes. Formaldehyde’s 1500 cm^-1 CH₂ scissoring normal mode has been selected.

A molecule is selected from a list of 28 compounds (Fig. 2), which may be sorted by name, chemical formula, or symmetry by clicking the appropriate word. Formaldehyde has already been selected, so 3DNormalModes displays a list of its normal-mode frequencies (Fig. 3) along with simplified IR and Raman spectra (Fig. 4).

Figure 2. A molecule is selected from a scrolling list, by name, chemical formula, or symmetry.

Figure 3. You can select the mode you want to animate from a scrolling list of frequencies or types of motion.

Figure 4. You can also select a mode to animate by clicking on one of the lines in the molecule’s IR or Raman spectrum.

A normal mode is selected by clicking on a frequency in the list, or on one of the lines in either the IR or Raman spectrum. This begins a 3-D animation of the selected normal mode. In Figure 1, the third normal mode (1500 cm^-1; CH₂ scissoring) has been selected for formaldehyde.

Figure 5 shows snapshots of the animation of this normal mode. Optional displacement vectors show the extent and direction of motion for each atom in the molecule. With sliding controls, you can stop and restart the animation, change its speed, and change how far the atoms are displaced. You can also rotate (Fig. 6), translate, and zoom (Fig. 7) a molecule to reach the best vantage point from which to view its motion.

Figure 5. This series of images from 3DNormalModes illustrates the animation of the CH2 scissoring normal mode (1500 cm^-1) of formaldehyde. The molecule has been rotated from its starting position (shown in Fig. 1) for a better view of the in-plane scissoring motion. -Optional displacement vectors have been added to show the extent and direction of motion of each atom.

Figure 6. You can rotate a molecule in 3-D space, by any angle around any axis.

Figure 7. Zoom out or zoom in from the standard view of a molecule.

In summary, with 3DNormalModes you can:

• Animate each normal mode in a 3-D environment.
• Rotate, translate, and zoom to any viewpoint.
• Adjust the speed of the animation.
• Display atom displacement vectors.
• Adjust the length of the displacements of the atoms.
• Display simplified IR and Raman spectra and from them select a fundamental frequency.
• View information about the selected molecule and normal mode.

3DNormalModes can be used as a self-paced learning tool, as well as a classroom presentation. Students will be able to learn how to use the program from the built-in help screens, and the extensive selection of molecules allows for a broad range of student assignments to be made.

3DNormalModes can be used in conjunction with Alkanes in Motion (also on ACC) to compare individual normal modes with the overall vibrational motion of atoms in alkane molecules, thereby providing students with excellent visualizations of molecular motion.

MolVib is a similar program for Mac OS previously published by JCE Software (4) and also included in this edition of ACC. MolVib has limited capabilities of manipulation of the molecule in a real 3-D environment and includes a much smaller number of molecules. However, MolVib does allow users to add new molecules, a feature that is not available in 3DNormalModes.

3DNormalModes requires Windows XP, 2000, ME, or 98. A 3-D accelerator such as DirectX 7.0 (recommended) or OpenGL is suggested, but not required.

Literature Cited

1. NIST Chemistry WebBook (accessed Aug 2003).
2. Computational Chemistry Comparison and Benchmark DataBase (accessed Aug 2003).
3. Hehre, W. J.; Radom, L.; Schleyer, P. V.; Pople, J. Ab Initio Molecular Orbital Theory; Wiley: New York, 1986.
4. Huber, D.; Wagner, P. MolVib 2.0; J. Chem. Educ. Software, 1995, 7C1.