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Wavefunction, Inc.: Irvine, CA, 1998. 307 pp. ISBN 1-890661-06-6. $30.00.
This workbook is the latest in a series of "lab
manuals" designed to increase the presence of molecular modeling
and computational chemistry in undergraduate courses.
The authors have designed the workbook to differ from its
predecessors in two ways: the target audience is
introductory organic chemistry students, and a CD-ROM
containing files of molecules and data replaces the need for
expensive molecular modeling software. It also differs from its
predecessors in that the exercises in it are not really
molecular modeling experiments. Instead, students are introduced
to the field by viewing the results of computational work
stored on the CD-ROM.
The workbook is divided into 21 chapters, each of
which covers a topic encountered in introductory-level
organic chemistry. The sequence of chapters follows the sequence
of topics that instructors of introductory organic courses
might employ, allowing the workbook to be used with most
modern organic chemistry texts.
The heart of the workbook, though, is the
CD-ROM included with the book. It contains files of molecules
and their accompanying computational results as well as
Spartan View, a software package that allows these models
to be visualized. Although it does not allow actual
calculations to be performed, Spartan View permits the user to
rotate molecules, intermediates, and transition states and
retrieve "precalculated" values of bond and dihedral angles,
bond lengths, energies, dipole moments, charge, and
frequency of vibration. Spartan View also allows the user to
search molecules and intermediates for electron-rich or
electron-poor regions by showing electrostatic potential as well as
HOMOs and LUMOs. Some files allow for animation of reactions
or conformational changes. Note, however, that since the data
are just stored on the CD-ROM, not all the data are
available for all files. Although performing calculations is not
an option, Spartan View can be used to display models and
data obtained using Spartan or MacSpartan and stored on a
disk. In this way, student exercises can be customized by
the instructor or the instructor can prepare customized
examples for use in lecture.
Each chapter in the workbook contains a series of 3
to 17 exercises that use models and associated data
contained on the accompanying CD-ROM. The exercises are not
simply cookbook procedures in which the student is directed
how to solve a problem. Instead, the authors provide
background in a two-part tutorial and several essays that describe
the information that can be obtained through molecular
modeling, and then introduce a problem in organic chemistry that
can be addressed using molecular modeling. The student is
left to determine how best to obtain the requested data.
For example, an exercise in the chapter Acids & Bases directs
the student to determine the atomic charges and view the
electrostatic potential map of the conjugate bases of three organic
acids. The student is not, however, told which menu to
pull or button to push. At the end of the exercise, the student
is directed to compare the reactivity of the acids with the
data collected from Spartan View. The exercises are relatively
easy to complete after spending a few minutes with the
tutorials, and many require students to compare the results of
calculations with the reactivity of the molecules as discussed in
the traditional lecture portion of the course. In this sense,
the workbook provides a meaningful link between
molecular modeling exercises outside of class and activities in the
classroom.
While some exercises involve comparing the
energies of intermediates or transition states, others
are more like videos of processes. Instructors will find many of these to
be useful as visual aids in lecture. Mechanisms of Ring
Inversion, for example, allows the instructor to show the stepwise
ring flip of cyclohexane. Although some of the animations are
very similar to those contained on CD-ROMs that
sometimes accompany textbooks, the exercises in this workbook
allow for the retrieval of data such as the energies of the
various conformations cyclohexane. Not only can the student see
the stepwise conversion of one chair conformation into
another, but the changes in energy as the ring flip occurs are
available. Also, unlike many of the visualizations on the
CD-ROMs packaged with textbooks, these give the student control
over the orientation of the structures on the screen, allowing
views from numerous angles. The possibility of the
instructor's customizing the exercises adds to the appeal of this workbook.
In reviewing this book, I noted a couple of
problems. The energy of molecules is presented in hartrees or
atomic units (au). Although a factor is given for converting
these values into the more familiar kcal/mol or kJ/mol, wouldn't
it be easier to use these results if they were given in the units
that are more typically used in introductory organic
chemistry texts? Similarly, a number of exercises ask the student to
plot data that they have calculated in the exercise. However,
no routine for plotting the data is included with Spartan
View and students must go through the cumbersome process
of copying the values and preparing the plots using
another program or by hand. And, finally, in Tutorial B,
animations are introduced by showing "the
SN2 displacement of chloride in
tert-butyl chloride by bromide." Although the
animation shows an SN1 mechanism with the
C-Cl bond breaking before approach of the incoming bromide ion,
students who are new to organic mechanisms will be misled by
the erroneous description in the workbook.
Although instructors may want to carefully
consider whether to add an additional $30 to the already high cost
of required texts, this workbook provides a unique and
potentially valuable addition to the introductory organic
chemistry course. With many exercises involving the visualization
of electrostatic potentials and HOMOs and LUMOs, it
adds an increased presence of physical organic chemistry in
the introductory course. And, although the exercises are
not really molecular modeling, this workbook also provides a
low-cost introduction to the field without the considerable
cost of modeling software. If Spartan or MacSpartan is
already available in the department, the possible tie-in with
the workbook and the capability to project the results should
make this an attractive addition to any instructor's
repertoire of visualization tools for lecture. The Molecular
Modeling Workbook for Organic Chemistry is definitely worthy
of consideration by anyone interested in adding
molecular modeling to the organic course.
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