3D Normal Modes Shockwave: Three-Dimensional Perception of Molecular Normal Modes on the Web
Nickolas D. Charistos, C. A. Tsipis, and Michael P. Sigalas
Laboratory of Applied Quantum Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
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.
Figure 1. A screen from 3D Normal
Modes showing the BH2 twisting normal mode of diborane.
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.
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.
Young, P. R. Organic Chemistry Online, CD-ROM with Workbook, Brooks/Cole: San Diego, 1999.
Supplement
This application, along with supporting materials, is available in the JCE WebWare peer-reviewed collection of the JCE Digital Library Only @
JCEOnline.
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Citation
Charistos, Nickolas D.; Tsipis, C. A.; Sigalas, Michael P. J. Chem. Educ.2004 81 1231.
Keywords
Molecular Models*; Multimedia; Normal Modes*; Vibrational Spectra*
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