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From UNIX to PC via X-Windows: Molecular Modeling for the General Chemistry Lab
Georgia State University Atlanta, GA 30303
Donald Pavia and Mark Wicholas Department of Chemistry, Western Washington University, Bellingham, WA 98225
The emphasis of molecular modeling in the undergraduate curriculum has generally been directed toward sophomore organic and higher-level chemistry instruction, especially when UNIX systems are used. When developing plans for incorporating molecular modeling into the curriculum, we decided to also include it in our first-year general chemistry course. Modeling would serve primarily as a visualization tool to augment the general chemistry coverage of bonding and structure. Our first thoughts were rather naive: we would set up a number of workstations and somehow get our general chemistry students, as many as 480 in one academic quarter, directly onto these machines at some time in a 1–2 week period during their weekly 3-hour lab. Further exploration of our options revealed that a better approach was to use PCs as dummy terminals for UNIX workstations. Described below are the hardware and software for this venture and the modeling experiment done by our students in general chemistry. Hardware and Software Our chemistry building has four general chemistry laboratories and a student computer laboratory where students have access to a combined total of approximately 70 computers. Each general chemistry laboratory has twelve stations to serve 24 students. A 386-PC with 8 MB RAM and Microsoft Windows for Workgroups is located at each station. We purchased five SGI Power Indigo2-XZ workstations and one SGI Indy, the latter being used as a file-sharing server. An X-Windows server program for Windows (Micro X-Win-32 by StarNet Communications) enables students to run molecular modeling software on the SGI workstations through the PC network. In normal operation two adjacent laboratories are scheduled simultaneously. The 24 PCs, functioning as dummy terminals, have the dedicated use of the 5 SGI workstations for the laboratory period with 4–5 PCs per workstation and 2 students per PC. The software used is Spartan by Wavefunction Inc. As a timesaving
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alternative to the establishment of individual accounts for approximately 800 general chemistry students, shared, read-only files, each with a prebuilt molecule, are used. The molecules are prebuilt using structural parameters from the literature when available or from ab-initio calculations with Spartan. Laboratory Experiment The 3-hour experiment attempts to illustrate the relationship between molecular geometry as predicted by the VSEPR model and valence bond theory. As a pre-laboratory take-home exercise, students are given a list of 23 species and asked to predict bond angles, geometry, and hybridization. Molecules and ions include NF3, SF 4, and NO2{, for example. In the laboratory students open the read-only files and, molecule by molecule, measure bond angles (and in some instances bond lengths) while comparing the predicted geometry (from the take-home assignment) with that shown on the monitor. Each pair of students is also given a molecular model set in the laboratory for simultaneously building the molecules and locating the lone pairs. The relay speed of ball-and stick images from SGI to PC is fast, a matter of but a few seconds. Translation, rotation, and sizing of molecules can be done instantaneously. The quality of image on the PC is reasonable but not as good as that seen on the SGI workstation. At the end of this exercise students have time to build and minimize more complicated molecules such as amino acids, or to observe models illustrating commonly recurring geometric forms such as tetrahedron (P4 ), chair (C6 H12), or chair plus tetrahedron (P4 O10). Having described what we do in general chemistry, the question remains: is downloading from UNIX to PC the best way to present “molecular modeling” in the first year course? We believe it is only an interim solution. There is clearly a need for low-cost instructional modeling software for general chemistry that can be accessed from a PC server.
Journal of Chemical Education • Vol. 74 No. 4 April 1997
