3D Normal Modes is a Web application for
interactive visualization and three-dimensional
perception of the normal modes of molecular
vibration, suitable for undergraduate students
in chemistry. The application uses the Macromedia
Shockwave plug-in (1) and
has been designed and developed especially
for the Web. It has a simple graphical user
interface and requires a download of only 120
KB, allowing it to be used even with low bandwidth
Internet connections. Its performance is comparable
to a desktop application.
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Figure 1. A screen from 3D Normal
Modes showing the BH2 twisting
normal mode of diborane.
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With 3D Normal Modes students and instructors
can:
- Animate a normal mode of a selected molecule
in a virtual 3D environment.
- Freely rotate and zoom in or out on the
molecule so that the vibration can be observed
from any viewpoint.
- Adjust the speed of the animation to see
the motion clearly.
- Display the atom displacement vectors for
the animated normal mode.
- Display the simplified IR and Raman spectra
of the selected molecule and select a fundamental
frequency.
- View information about the selected molecule
and normal mode.
3D Normal Modes can be used as a self-paced learning
tool for students, as well as a presentation
tool for chemistry instructors.
3D Normal Modes illustrates molecular vibrations
and properties of normal modes of vibration
in a highly interactive, three-dimensional,
virtual environment that encourages students
to manipulate the vibrating molecule. 3D Normal
Modes includes a database of the experimental
fundamental frequencies and the corresponding
normal modes of the 28 inorganic and organic
molecules (2). The
normal modes have been calculated by ab initio
HF/3-21G calculations (3, 4).
A number of other computer-based tools for
teaching vibrational spectroscopy have been
developed and published. The Chemistry Hypermedia
Project (5) incorporates
interactive spectroscopy and interpretation
into a multimedia presentation. Some Java-based
applets and applications use Internet browser
plug-ins (6, 7, 8)
and feature the interactive display and manipulation
of spectra, linking the spectra to molecular
displays. The IR-Tutor software developed at
Columbia University (9) has
a point-and-click interface that students use
to select an IR peak to see an animation of
the associated vibration; however, the vibrational
animation itself is not interactive. The Organic
Chemistry OnLine Tutorial (10) includes
a set of Java-driven spectroscopy problems,
with interactive menus that have static spectral
displays.
Literature Cited
- Macromedia
Shockwave Download (accessed May 2004).
- NIST
Chemistry WebBook (accessed May 2004).
- NIST
Computational Chemistry Comparison and
Benchmark DataBase (accessed May 2004).
- Hehre, W. J.; Radom, L.; Schleyer, P. v.
R.; Pople, J. A. Ab Initio Molecular
Orbital Theory; Wiley: New York, 1986.
- Tissue, B. M. Spectroscopy 1995, 10, 19; J.
Chem. Educ. 1996, 73, 65.
- Casher, O.; Chandramohan, G. K.; Hargreaves,
M. J.; Leach, C.; Murray-Rust, P.; Sayle,
R.; Rzepa, H. S.; Whitaker, B. J. J.
Chem. Soc., Perkin Trans. 1995, 2, 7.
- Rzepa, H. S.; Murray-Rust, P.; Whitaker,
B. J. J. Chem. Inf. Comput. Sci. 1998, 38, 976.
- Lathi, P. M.; Motyka, E. J.; Lancashire,
R. J. J.
Chem. Educ. 2000, 77, 649.
- Columiba
University Undergraduate Chemistry Multimedia
Projects (accessed May 2004).
- Young, P. R. Organic Chemistry Online,
CD-ROM with Workbook, Brooks/Cole: San Diego,
1999
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