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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 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, SF4, 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 (C6H12), or chair plus tetrahedron (P4O10).
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.
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