Information Textbooks Media Resources

Interdisciplinary Learning with Computational Chemistry:

A Collaboration between Chemistry and Geology
Kenny B. Lipkowitz,* Mehran Jalaie, Daniel Robertson
Department of Chemistry, Indiana University-Purdue University at Indianapolis (IUPUI), Indianapolis, IN 46202-3274;
*lipkowitz@chem.iupui.edu
Andrew Barth
Department of Geology, Indiana University-Purdue University at Indianapolis (IUPUI), Indianapolis, IN 46202

Chemistry is often touted as the central science (1).

While this claim may be true, in part because many scientists
in other disciplines are now beginning to focus their studies
at a molecular level (a domain that has traditionally belonged
to chemists), such a proclamation rings somewhat hollow
particularly in the area of chemical education. In fact, a
perusal of this Journal reveals that, with the exception of
biochemistry (a subset of chemistry), relatively few papers,
pedagogical or otherwise, are directed to other disciplines
with, perhaps, the exception of forensics or art restoration.
Why is it that so few chemical educators attempt to reach
out to other disciplines, especially in these times when so
many scientists and educators in those other disciplines have
a desire to carry out their research and to begin teaching from
an atomic and molecular level? One reason is that it takes a
lot of work to learn about another discipline and, so, the
momentum required to get started can be enormous. Another
reason for our lack of reaching out from chemistry to other
areas of education is that many subdisciplines in chemistry
are not really geared for such an adventure. Perhaps if there
were more overlap between the subdisciplines of chemistry and
disciplines outside of chemistry we would be more willing as
a group to make the connection.
Computational chemistry is inherently a multidisciplinary area of study that transcends the traditional barriers
separating biology, chemistry, physics, and mathematics.
Accordingly, computational chemistry is a perfect tool for
making the interconnections between chemistry and other
sciences. In this paper we describe how we have integrated
computational chemistry into a mineralogy course taught by
our geology department.
The Departments
At IUPUI the chemistry department offers a variety
of degree options including an ACS-certified B.S. degree; the
geology department offers B.S. and B.A. degrees. The
chemistry department (17 faculty) neither has a geochemist
on its staff nor does anyone carry out research in geological
or environmental sciences. The geology department (10
faculty) has no faculty members with a degree in chemistry.
While the chemistry department does not require its students
to take a course in geology, geology students are required to
take two semesters of freshman chemistry to prepare them
for courses in geochemistry, mineralogy, and petrology. The
chemistry department has already integrated computational
chemistry into its curriculum, in part from the efforts of two

Mailing address: 402 North Blackford Street, Indianapolis,

IN 46202.

684

of the coauthors of this paper (26 ). The geology department makes some use of computing for statistics and word
processing, for classes on the Internet, for map making,
and in some instances for running and manipulating data
from instrumentation, but no compuational chemistry existed before this collaboration began.
The geochemistry course taught at this institution is not
typical of what might be found in a chemistry department
or even in most geology departments where the emphasis is
on chemistry. Rather, the course offered here focuses on global
and environmental aspects of geochemistry, foregoing the
atomic-scale view of things. A more appropriate course for
our collaboration thus became Mineralogy 221, a sophomorelevel course required of all geology students. The book used
in that course is Manual of Mineralogy by Klein and Hurlbut,
in its 21st printing (7).
Our institution is fairly well endowed when it comes to
technology because we have instituted a technology fee. The
school of science maintains several student clusters containing
PC and Macintosh computers and the chemistry department
uses those machines for molecular modeling, especially for
organic chemistry classes and their associated labs. We also
maintain a high-end research laboratory that is used for
departmental research activities but also for upper-division
computational chemistry projects in our curriculum. This is
the facility we use for the mineralogy classes simply because
it is configured for in-lab tutorials and also because it has
the equipment and software we need (see below).
Computational Chemistry in Mineralogy
Introducing computational chemistry into mineralogy
was challenging partly because we had to learn some basic
mineralogy nomenclature and concepts, but also because
there actually exist too many possible applications of computational chemistry to that discipline. Also, because this is
a course in geology, not chemistry, we had to meet the needs
of the geology department; that is, we were not going to tell
them what they should do. Rather, we read their textbook,
evaluated their syllabus, and then made some recommendations
for them to consider.
Our initially agreed-upon project was to use the facilities
only for visualization. Their students, like ours, have a difficult
time seeing chemical structures in three dimensions, especially when complex lattices are involved, and the possibility
of using molecular graphics to assist in their teaching endeavors
was as appealing to them as it is to us. (This is a sophomorelevel course, so their students understanding of chemistry is
comparable to that of a typical sophomore organic chemistry
student.) The big advantage of computer graphics over hand-

Journal of Chemical Education Vol. 76 No. 5 May 1999 JChemEd.chem.wisc.edu

Information Textbooks Media Resources

held mechanical models was, for the geologists, that the

mechanical models they were using could be done away with
(they are prone to damage and are exceedingly expensive).
Additionally, we convinced them that other types of structural
features such as molecular electrostatic potential surfaces and
polygon representations for rendering could be implemented
in a way not possible with mechanical models. Eventually,
more than simple viewing was embedded into the course, but
much of what the students do involves generating lattices
from unit cells, visualizing the nanocrystallites, and then
making measurements and formulating arguments about
minerals based on those structures being viewed.
To help direct our efforts we focused our attention on
the laboratory part of the course (we also have routine homework assignments, but those are not described here). Four
lab exercises were developed and integrated into the mineralogy curriculum. Each experiment is scheduled for two hours
per week as are the other mineralogy experiments, but the
modeling facility is available during off-hours as well. Two of
the computational chemistry labs are instructed by a chemist
along with a geology professor who also serves as a teaching
assistant. The remaining labs and homework assignments are
taught completely by the geologists. The experiments we
developed for our curriculum are described below and they
are available from the authors upon request. The computers
we use are Silicon Graphics workstations (a mixture of models
but typically containing MIPS R4000 chips); the software
we use is Cerius2 from MSI (8). Almost any major researchgrade molecular modeling package would suffice. This just
happens to be the software we have in the chemistry department, but it is especially good for this mineralogy course
because of its many advanced features for inorganic systems
(lattice generators; complete databases of minerals, ceramics, and
other relevant materials) and because of its reasonable cost
and ease of operation.
Laboratory 1. Introduction to Molecular Modeling

The exercises focus on halite (NaCl) because of its simplicity but also because it is a material that the geology
students had just finished working with. In a previous lab
they collected X-ray diffraction data (the XRD above) and
had computed the unit cell dimensions of this mineral and
estimated the Na+ radius on the basis of symmetry arguments.
The connection between crystallography and diffractometry
commonly used in mineralogy is thus made. Other options such
as viewing Miller planes are also introduced here, but most
of the laboratory assignments are made so as to reconnect
the geology students with many of the topics they had in
freshman chemistry. This was also a crucial exercise because
it reinforces concepts of scale that are important to geologists
(see below). Here, students crush macroscopic halite crystals,
measure unit cell dimensions, and view the cell with its constituent atoms with molecular graphics on a microscopic level.
Laboratory 2. Polyhedral Models of Silicates
Two goals are achieved in this laboratory experiment.
First, students are made aware that various representations
of molecular structures exist (e.g., wire-frame, ball-and-stick,
and space-filling presentations of atomic connectivity) and
also that one can present surfaces such as van der Waals and
molecular electrostatic potential surfaces and map out properties like lipophilicity. More important for this course,
though, is that students become accustomed to working with
polyhedral representations, especially tetrahedral and octahedral clusterings of atoms. Without this simplification of
the lattice, mineral structures can be both difficult to see and
intellectually prohibitive to comprehend for most novices
(these structures are usually more complex than those a typical
organic chemistry student would struggle with). An example
of this is depicted in Figure 1.
The second goal is to remind students about the various
kinds of intermolecular forces that exist in nature and to recall
for them the relative strengths and characteristics of those

This is the beginning molecular modeling exercise. Here

the various types of molecular modeling techniques used in
different disciplines throughout science and technology are
brought to light, the computational tools used for those
purposes are mentioned, and the students learn how to use
the Cerius software. This lecture is comparable to what we
teach our undergraduate organic chemistry students, but with
an emphasis on inorganic solid-state systems. In this course we
do not train students about the UNIX platform; the machines
are simply made available to them and the software pops up
upon login to that course number.
Some representative elementary exercises taken directly
from the first lab handout are listed below.

Use CERIUS to pull up the unit cell of HALITE.

Rotate, translate, and zoom into and out of the unit cell.
Turn on atom labels.
Measure the Na+ Na + distances. How many different
distances exist?
Measure the Na+ Cl{ distances.
Measure the Na+ Cl{ Na+ angles.
Compare the measured distances and angles with your
XRD values. Are they the same?
Make a graphics plot of that structure.

Figure 1. The tremolite lattice, a typical complex structure students

work with. Opposing chains comprised 6-membered rings of polymerized SiO4 tetrahedra, linked by octahedra and cross linked
by distorted cubic Ca2+ sites. The ability to zoom in, expand, rotate, and highlight atoms and symmetry-related groupings and to
visualize such complex structures in stereo is a compelling reason
for using computer models rather than hand-held mechanical models. (This figure appears in color on the cover of this issue.)

JChemEd.chem.wisc.edu Vol. 76 No. 5 May 1999 Journal of Chemical Education

685

Information Textbooks Media Resources

interactions. With this knowledge students are then expected

to make predictions concerning properties of minerals. An
example is to predict cleavage planes in crystals that are
subjected to shear-induced stresses. How minerals cleave,
together with influences of weathering described later in the
course, affect things like oceans and climates. A connection
between atomic and global views of the world is thus made.
(The dynamic range of scale that a geology student must be
cognizant of is much greater than that for most chemistry
students; we find these computational chemistry exercises a
good way to make the connection between macroscopic objects
like rocks, boulders, and continents and the microscopic
atomic world that is otherwise difficult for students to
comprehend.) Learning how to concisely describe a visual
image of such complex solid solutions containing multiple
ions and varying types of interplanar bonding is a difficult
but important task. Because of our commitment to writing
across the curriculum, laboratory reports contain brief (less
than 1 page) written descriptions comparing the structures
and bonding motifs of the minerals being studied (fayallite
and almandine, in our case).
Laboratory 3. Double- and Single-Chain Silicates
This laboratory is an extension of the second laboratory
experiment. In it students examine far more complex minerals
and then compare and contrast minerals containing double
and single polymeric strands of siloxanes. Again, predictions
concerning cleavage planes are made. In this experiment, though,
students return to the geology laboratory with their predictions.
There they carry out fracture experiments to verify that the
predicted and observed cleavage planes are the same. They also
make measurements of the angles between such planes for
comparison with their modeling studies. An example of a
predicted cleavage plane is presented in Figure 2. Figure 3
illustrates the interplanar bonding of micas; it is clear that only
van der Waals forces hold the planes together, making the
formation of atomically smooth surfaces possible.
Finally, based on (i) the types and number of interplanar
forces, (ii) the kinds of interatomic interactions in those
planes, and (iii) the spatial placement of ions in minerals,
our students are asked to rank-order the hardness of several
minerals. They then compare their predictions with the Mohs
hardness test (a standard measure of hardness in geology) and
defend their findings, both in written form and orally in front
of their peers.

placement of cations in mineral matrices, how this arises in

nature, the relationships between classes of minerals related
by these small differences and the relative stabilities (heats of
formation) of these classes of minerals. The systems we direct
our attention to are classified under the superfamily of feldspars.
In the albite crystal 1/4 of the Si 4+ atoms have been replaced
by Al3+. To maintain a charge balance, nature inserts an alkali
metal atom of suitable size (Na + in this case) into holes near
the Al3+. The high-temperature form of this mineral has the
alkali cations centered in the cubic holes, but in this lowtemperature structure the cations are snuggled up close to
the aluminum. This type of replacement is represented by
the following equation: Na+Al3+ Si4+ , where the square
refers to the square vacancy of the lattice. Albite and anorthite
form the two end points of a range of minerals found in nature.
At the one extreme (albite) the Si 4+ atoms are replaced by
Al3+ atoms along with a charge-compensating M+ alkali metal
atom to maintain charge neutrality. At the other extreme
(anorthite), half of the silicons are replaced by aluminum,
making the crystal negatively charged, and to compensate for
this, calcium ions (Ca2+) are inserted. The corresponding
equation here is Na+ Si 4+ Ca2+ Al3+. These idealized end
points (albite and anorthite) can be made in pure form in a
laboratory but they cannot be found in nature. There exists a
range of minerals between these end points and taken together
these minerals show a gradient of mole ratios of metal and
oxygen. Each mineral has its characteristic mole ratio; some
of these species have common names such as labradorite and

Laboratory 4. Cationic Ordering in Framework

Silicates
This experiment contains two parts. The first extends
the ideas of previous labs (where isolated tetrahedra and linked
tetrahedra of silicates were studied). It may be perceived as somewhat trivial, but searching for and analyzing networks of
chains in silicates completes a theme of [SiOSiO]n bonding
patterns we have our students focus on. In this experiment
nanocrystallites of minerals containing cross-linked silicates
are generated and studied. The emphasis is on and forms
of quartz along with spessartine. The nature of the crosslinking is evaluated and predictions of mineral durability
under stress and of ordering of melting points are made.
The second part of this laboratory experiment involves
solid solutions. In particular we stress here the relative
686

Figure 2. A nanocrystallite of hornblende depicted with a ball-andstick presentation for clarity. In this figure we note that some areas
have spaces and gaps in addition to regions that are inherently less
well bonded to neighboring atoms than others. These regions in
turn correspond to places where stress-induced fracture and parting will appear. Students locate those regions and predict where
macroscopic cleavage will occur. In this case the smaller, vertical
lines are highlighting the microscopic fracture zones while the
larger diagonal line highlights the predicted cleavage plane. Students then verify these predictions with appropriate laboratory experiments.

Journal of Chemical Education Vol. 76 No. 5 May 1999 JChemEd.chem.wisc.edu

Information Textbooks Media Resources

andesine (from Labrador and the Andes, respectively), while

others have more exotic names.
We initially wanted our students to calculate the heats
of formation of these systems quantum mechanically. The
idea here was that the relative stabilities of minerals would
be compared with tabulated experimental values and students
would again be asked to make arguments concerning mineral
durability, the influence of weathering, and so on. The logical
quantum-based approach would be to implement a semiempirical Hamiltonian. Unfortunately the computed results were
poor at best (the geometry of the lattice is poorly reproduced
when energy is minimized), and this part of the experiment
was not implemented.
This laboratory experiment is followed by one in the
mineralogy laboratory, where students select pure starting
materials (magnesium oxides, carbon, silica, etc.) and then
mix them in mole ratios that would lead to the formation of
a desired mineral upon heating in a furnace (mineralogical
synthesis). Upon synthesis the students verify their products
with X-ray diffraction spectrometry.
Discussion
The laboratory experiments described above are part of
Mineralogy 221. This is a sophomore-level geology course
and the laboratory experiments we codeveloped constitute
33% of the entire laboratory syllabus. The experiments are
interspersed among other mineralogy experiments, so while

Figure 3. A ball-and-stick representation of talc showing layers of

SiO4 tetrahedral groups sandwiching MgO6 octahedral groups
bonded only by weak van der Waals forces. Visualizing this mineral allows students to bridge the gap between the microscopic
world depicted here, and the macroscopic world in which talc is
known to be a soft, lubricant-like material. Another example of
layers held together exclusively by weak van der Waals forces is
the micas. Again, the macroscopic world of peeling mica layers
to make atomically smooth surfaces can be connected to the microscopic underpinning of what gives rise to that phenomenon.

they follow the order presented here, they are not concatenated. Rather, they are offered when that part of the lecture
covers those topics.
The experiments we have developed maintain a theme of
silicate chemistry, but this is just our local preference; other ideas
would no doubt be welcomed by geology instructors. The
computational laboratories bring basic concepts in structural
chemistry together with real-world mineralogy. In particular,
we strive to make the connection between chemists microscopic, atomic-level views and macroscopic (sometimes global) scales that geologists work with. Students build, measure, and predict the properties of nanocrystallites and then
make predictions about mineral durability, stress fracturing,
weathering, and so on.
We have attempted to use the available force fields of
Cerius to optimize mineral lattices, but we have found these
force fields to be uniformly incapable of reproducing known
mineral lattices with a suitable root-mean-square deviation.
Similarly, geometry optimizations with the semiempirical
Hamiltonians have failed, so we do not predict lattice geometries in this course. We do find, however, that ion replacement
calculations (e.g., Mg2+ for Ca2+) do predict the correct trends
in stability and students can use these computational tools
to begin thinking about thermodynamic implications of minerals in high- vs low-temperature phases as well as to foster
an understanding of why minerals deposit as they do in nature.
This aspect of the laboratory is still under development.
Most of these laboratory experiments are based on
relatively simple computational techniques, relying heavily
on visualization. Molecular graphics allows us to use, relatively cheaply, a greater number of models than we could ever
purchase from our limited budget. (MSI now supplies hundreds of minerals and ceramics in their materials database,
along with numerous other polymers and organics.) Moreover it allows us to see things such as electrostatic fields, Miller
planes, and the like that are not otherwise possible to see from
mechanical models.
Several other aspects of this interdisciplinary curriculum
also need to be highlighted. First, we have focused on bridging
the size gap where the connections between macroscopic
and microscopic worlds are made. In contrast to chemists,
geologists have a far greater range of scales to think about.
For example, they need to make the connections between
atomic-level details and how these affect weathering of
minerals, which in turn affects oceans and climates. Computational chemistry has proved capable of helping students
make those connections. Second, we were taken aback by the
eagerness of our students for manipulating and viewing the
models computationally in comparison to using the handheld mechanical models. Students seemed apprehensive about
using the mechanical models, perhaps for fear of breaking
them or maybe because they hadnt seen such models before.
In contrast, they were very eager to use the computer models
(and clearly expressed their opinions of this), perhaps because
they felt comfortable using a computer and knew they
couldnt damage the models. Third, we reiterate that the
students in this course are at a similar level of comprehension
of molecular structure as first-semester organic chemistry
students, so one cannot raise the level of computational
difficulty beyond what would be presented in an organic
chemistry class. Finally, we point out that this collaboration
is interdisciplinary and forces students in geology to make

JChemEd.chem.wisc.edu Vol. 76 No. 5 May 1999 Journal of Chemical Education

687

Information Textbooks Media Resources

use of the chemistry they have had. We notice that students

tend to compartmentalize their knowledge, in part as a defense
mechanism when being overwhelmed by class work, and this
combined geology-chemistry experience helps shed those
shackles. In our opinion, the earlier we begin to remove the
barriers between disciplines (in this case in the sophomore
year) the easier it will become for students to understand how
the sciences are all interconnected, and especially for them
to see the commonalties rather than the differences.
Summary
If chemistry is the central science, one would expect
to see more interdisciplinary learning partnerships between
chemistry and cognate disciplines of science and technology.
Computational chemistry is inherently multidisciplinary and
capable of conveying important pedagogical messages to
students of chemistry as well as to students of other disciplines
where knowledge at an atomic or molecular level is desired. In
this paper we have documented how we used computational
chemistry in a collaborative effort with a geology department.
Specifically, we have developed a set of tutorials, homework

688

assignments, and laboratory experiments for use in a mineralogy course. If we, as a group of chemists, intend to make the
claim that chemistry is the central science, we need to reach
out to other disciplines to provide guidance for those who
wish to learn about what we already know. There are many
pathways for achieving such an intellectual collaboration and
we have demonstrated one such way here. We encourage
others to do likewise.
Literature Cited
1. See for example Brown, T. L; LeMay, H. E. Jr.; Bursten, B. E.
Chemistry The Central Science, 5th ed.; Prentice Hall: Englewood
Cliffs, NJ, 1991.
2. Boyd, D. B.; Lipkowitz, K. B. J. Chem. Educ. 1982, 59, 269.
3. Lipkowitz, K. B. J. Chem. Educ. 1982, 59, 595; 1984, 61, 1051.
4. Lipkowitz, K. B. J. Chem. Educ. 1989, 66, 275.
5. Lipkowitz, K. B. J. Chem. Educ. 1995, 72, 1070.
6. Lipkowitz, K. B.; Robertson, D.; Pearl, G.; Schultz, F. A. J. Chem.
Educ. 1996, 73, 105.
7. Klein, C.; Hurlbut, C. S. Jr.; Manual of Mineralogy, 21st ed.;
Wiley: New York, 1993.
8. MSI Inc., 9685 Scranton Road, San Diego, CA 92121-3752.

Journal of Chemical Education Vol. 76 No. 5 May 1999 JChemEd.chem.wisc.edu

Information Textbooks Media Resources

Figure 1.

JChemEd.chem.wisc.edu Vol. 76 No. 5 May 1999 Journal of Chemical Education

689

Information Textbooks Media Resources

Figure 2.

690

Journal of Chemical Education Vol. 76 No. 5 May 1999 JChemEd.chem.wisc.edu

Information Textbooks Media Resources

Figure 3.

JChemEd.chem.wisc.edu Vol. 76 No. 5 May 1999 Journal of Chemical Education

691