interdisciplinary learning with computational chemistry: a collaboration between chemistry and...

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

Chemistry is often touted as “the central science” (1).While this claim may be true, in part because many scientistsin other disciplines are now beginning to focus their studiesat a molecular level (a domain that has traditionally belongedto chemists), such a proclamation rings somewhat hollowparticularly in the area of chemical education. In fact, aperusal of this Journal reveals that, with the exception ofbiochemistry (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 reachout to other disciplines, especially in these times when somany scientists and educators in those other disciplines havea desire to carry out their research and to begin teaching froman atomic and molecular level? One reason is that it takes alot of work to learn about another discipline and, so, themomentum required to get started can be enormous. Anotherreason for our lack of reaching out from chemistry to otherareas of education is that many subdisciplines in chemistryare not really geared for such an adventure. Perhaps if therewere more overlap between the subdisciplines of chemistry anddisciplines outside of chemistry we would be more willing asa group to make the connection.

Computational chemistry is inherently a multidisci-plinary area of study that transcends the traditional barriersseparating biology, chemistry, physics, and mathematics.Accordingly, computational chemistry is a perfect tool formaking the interconnections between chemistry and othersciences. In this paper we describe how we have integratedcomputational chemistry into a mineralogy course taught byour geology department.

The Departments

At IUPUI the chemistry department offers a varietyof degree options including an ACS-certified B.S. degree; thegeology department offers B.S. and B.A. degrees. Thechemistry department (17 faculty) neither has a geochemiston its staff nor does anyone carry out research in geologicalor environmental sciences. The geology department (10faculty) has no faculty members with a degree in chemistry.While the chemistry department does not require its studentsto take a course in geology, geology students are required totake two semesters of freshman chemistry to prepare themfor courses in geochemistry, mineralogy, and petrology. Thechemistry department has already integrated computationalchemistry into its curriculum, in part from the efforts of two

of the coauthors of this paper (2–6 ). The geology depart-ment makes some use of computing for statistics and wordprocessing, for classes on the Internet, for map making,and in some instances for running and manipulating datafrom instrumentation, but no compuational chemistry ex-isted before this collaboration began.

The geochemistry course taught at this institution is nottypical of what might be found in a chemistry departmentor even in most geology departments where the emphasis ison chemistry. Rather, the course offered here focuses on globaland environmental aspects of geochemistry, foregoing theatomic-scale view of things. A more appropriate course forour collaboration thus became Mineralogy 221, a sophomore-level course required of all geology students. The book usedin that course is Manual of Mineralogy by Klein and Hurlbut,in its 21st printing (7 ).

Our institution is fairly well endowed when it comes totechnology because we have instituted a “technology fee”. Theschool of science maintains several student clusters containingPC and Macintosh computers and the chemistry departmentuses those machines for molecular modeling, especially fororganic chemistry classes and their associated labs. We alsomaintain a high-end research laboratory that is used fordepartmental research activities but also for upper-divisioncomputational chemistry projects in our curriculum. This isthe facility we use for the mineralogy classes simply becauseit is configured for in-lab tutorials and also because it hasthe equipment and software we need (see below).

Computational Chemistry in Mineralogy

Introducing computational chemistry into mineralogywas challenging partly because we had to learn some basicmineralogy nomenclature and concepts, but also becausethere actually exist too many possible applications of com-putational chemistry to that discipline. Also, because this isa course in geology, not chemistry, we had to meet the needsof the geology department; that is, we were not going to tellthem what they should do. Rather, we read their textbook,evaluated their syllabus, and then made some recommendationsfor them to consider.

Our initially agreed-upon project was to use the facilitiesonly for visualization. Their students, like ours, have a difficulttime seeing chemical structures in three dimensions, espe-cially when complex lattices are involved, and the possibilityof using molecular graphics to assist in their teaching endeavorswas as appealing to them as it is to us. (This is a sophomore-level course, so their students’ understanding of chemistry iscomparable to that of a typical sophomore organic chemistrystudent.) The big advantage of computer graphics over hand-

Interdisciplinary Learning with Computational Chemistry:A Collaboration between Chemistry and Geology

Kenny B. Lipkowitz,*† Mehran Jalaie, Daniel RobertsonDepartment of Chemistry, Indiana University-Purdue University at Indianapolis (IUPUI), Indianapolis, IN 46202-3274;*[email protected]

Andrew BarthDepartment of Geology, Indiana University-Purdue University at Indianapolis (IUPUI), Indianapolis, IN 46202

†Mailing address: 402 North Blackford Street, Indianapolis,IN 46202.


JChemEd.chem.wisc.edu • Vol. 76 No. 5 May 1999 • Journal of Chemical Education 685

held mechanical models was, for the geologists, that themechanical 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 structuralfeatures such as molecular electrostatic potential surfaces andpolygon representations for rendering could be implementedin a way not possible with mechanical models. Eventually,more than simple viewing was embedded into the course, butmuch of what the students do involves generating latticesfrom unit cells, visualizing the nanocrystallites, and thenmaking measurements and formulating arguments aboutminerals based on those structures being viewed.

To help direct our efforts we focused our attention onthe laboratory part of the course (we also have routine home-work assignments, but those are not described here). Fourlab exercises were developed and integrated into the miner-alogy curriculum. Each experiment is scheduled for two hoursper week as are the other mineralogy experiments, but themodeling facility is available during off-hours as well. Two ofthe computational chemistry labs are instructed by a chemistalong with a geology professor who also serves as a teachingassistant. The remaining labs and homework assignments aretaught completely by the geologists. The experiments wedeveloped for our curriculum are described below and theyare available from the authors upon request. The computerswe use are Silicon Graphics workstations (a mixture of modelsbut typically containing MIPS R4000 chips); the softwarewe use is Cerius2 from MSI (8). Almost any major research-grade molecular modeling package would suffice. This justhappens to be the software we have in the chemistry depart-ment, but it is especially good for this mineralogy coursebecause of its many advanced features for inorganic systems(lattice generators; complete databases of minerals, ceramics, andother relevant materials) and because of its reasonable costand ease of operation.

Laboratory 1. Introduction to Molecular Modeling

This is the beginning molecular modeling exercise. Herethe various types of molecular modeling techniques used indifferent disciplines throughout science and technology arebrought to light, the computational tools used for thosepurposes are mentioned, and the students learn how to usethe Cerius software. This lecture is comparable to what weteach our undergraduate organic chemistry students, but withan emphasis on inorganic solid-state systems. In this course wedo not train students about the UNIX platform; the machinesare simply made available to them and the software pops upupon login to that course number.

Some representative elementary exercises taken directlyfrom 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.

The exercises focus on halite (NaCl) because of its sim-plicity but also because it is a material that the geologystudents had just finished working with. In a previous labthey collected X-ray diffraction data (the “XRD” above) andhad computed the unit cell dimensions of this mineral andestimated the Na+ radius on the basis of symmetry arguments.The connection between crystallography and diffractometrycommonly used in mineralogy is thus made. Other options suchas viewing Miller planes are also introduced here, but mostof the laboratory assignments are made so as to reconnectthe geology students with many of the topics they had infreshman chemistry. This was also a crucial exercise becauseit 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 con-stituent 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 representationsof molecular structures exist (e.g., wire-frame, ball-and-stick,and space-filling presentations of atomic connectivity) andalso that one can present surfaces such as van der Waals’ andmolecular electrostatic potential surfaces and map out prop-erties like lipophilicity. More important for this course,though, is that students become accustomed to working withpolyhedral representations, especially tetrahedral and octa-hedral clusterings of atoms. Without this simplification ofthe lattice, mineral structures can be both difficult to see andintellectually prohibitive to comprehend for most novices(these structures are usually more complex than those a typicalorganic chemistry student would struggle with). An exampleof this is depicted in Figure 1.

The second goal is to remind students about the variouskinds of intermolecular forces that exist in nature and to recallfor them the relative strengths and characteristics of those

Figure 1. The tremolite lattice, a typical complex structure studentswork with. Opposing chains comprised 6-membered rings of po-lymerized SiO4 tetrahedra, linked by octahedra and cross linkedby distorted cubic Ca2+ sites. The ability to zoom in, expand, ro-tate, and highlight atoms and symmetry-related groupings and tovisualize such complex structures in stereo is a compelling reasonfor using computer models rather than hand-held mechanical mod-els. (This figure appears in color on the cover of this issue.)



interactions. With this knowledge students are then expectedto make predictions concerning properties of minerals. Anexample is to predict cleavage planes in crystals that aresubjected to shear-induced stresses. How minerals cleave,together with influences of “weathering” described later in thecourse, affect things like oceans and climates. A connectionbetween atomic and global views of the world is thus made.(The dynamic range of scale that a geology student must becognizant of is much greater than that for most chemistrystudents; we find these computational chemistry exercises agood way to make the connection between macroscopic objectslike rocks, boulders, and continents and the microscopicatomic world that is otherwise difficult for students tocomprehend.) Learning how to concisely describe a visualimage of such complex solid solutions containing multipleions and varying types of interplanar bonding is a difficultbut important task. Because of our commitment to “writingacross the curriculum”, laboratory reports contain brief (lessthan 1 page) written descriptions comparing the structuresand bonding motifs of the minerals being studied (fayalliteand almandine, in our case).

Laboratory 3. Double- and Single-Chain Silicates

This laboratory is an extension of the second laboratoryexperiment. In it students examine far more complex mineralsand then compare and contrast minerals containing doubleand single polymeric strands of siloxanes. Again, predictionsconcerning 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 thepredicted and observed cleavage planes are the same. They alsomake measurements of the angles between such planes forcomparison with their modeling studies. An example of apredicted cleavage plane is presented in Figure 2. Figure 3illustrates the interplanar bonding of micas; it is clear that onlyvan der Waals’ forces hold the planes together, making theformation of atomically smooth surfaces possible.

Finally, based on (i) the types and number of interplanarforces, (ii) the kinds of interatomic interactions in thoseplanes, and (iii) the spatial placement of ions in minerals,our students are asked to rank-order the “hardness” of severalminerals. They then compare their predictions with the Mohshardness test (a standard measure of hardness in geology) anddefend their findings, both in written form and orally in frontof their peers.

Laboratory 4. Cationic Ordering in FrameworkSilicates

This experiment contains two parts. The first extendsthe ideas of previous labs (where isolated tetrahedra and linkedtetrahedra of silicates were studied). It may be perceived as some-what trivial, but searching for and analyzing networks ofchains in silicates completes a theme of [Si–O–Si–O]n bondingpatterns we have our students focus on. In this experimentnanocrystallites of minerals containing cross-linked silicatesare generated and studied. The emphasis is on α and β formsof quartz along with spessartine. The nature of the cross-linking is evaluated and predictions of mineral durabilityunder stress and of ordering of melting points are made.

The second part of this laboratory experiment involvessolid solutions. In particular we stress here the relative

placement of cations in mineral matrices, how this arises innature, the relationships between classes of minerals relatedby these small differences and the relative stabilities (heats offormation) of these classes of minerals. The systems we directour attention to are classified under the superfamily of feldspars.In the albite crystal 1/4 of the Si4+ atoms have been replacedby Al3+. To maintain a charge balance, nature inserts an alkalimetal atom of suitable size (Na+ in this case) into holes nearthe Al3+. The high-temperature form of this mineral has thealkali cations centered in the cubic holes, but in this low-temperature structure the cations are snuggled up close tothe aluminum. This type of replacement is represented bythe following equation: Na+Al3+ Si4+ ❒, where the squarerefers to the square vacancy of the lattice. Albite and anorthiteform the two end points of a range of minerals found in nature.At the one extreme (albite) the Si4+ atoms are replaced byAl3+ atoms along with a charge-compensating M+ alkali metalatom 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 forthis, calcium ions (Ca2+) are inserted. The correspondingequation here is Na+ Si4+ Ca2+ Al3+. These idealized endpoints (albite and anorthite) can be made in pure form in alaboratory but they cannot be found in nature. There exists arange of minerals between these end points and taken togetherthese minerals show a gradient of mole ratios of metal andoxygen. Each mineral has its characteristic mole ratio; someof these species have common names such as labradorite and

Figure 2. A nanocrystallite of hornblende depicted with a ball-and-stick presentation for clarity. In this figure we note that some areashave spaces and gaps in addition to regions that are inherently lesswell bonded to neighboring atoms than others. These regions inturn correspond to places where stress-induced fracture and part-ing will appear. Students locate those regions and predict wheremacroscopic cleavage will occur. In this case the smaller, verticallines are highlighting the microscopic fracture zones while thelarger diagonal line highlights the predicted cleavage plane. Stu-dents then verify these predictions with appropriate laboratory ex-periments.



andesine (from Labrador and the Andes, respectively), whileothers have more exotic names.

We initially wanted our students to calculate the heatsof formation of these systems quantum mechanically. Theidea here was that the relative stabilities of minerals wouldbe compared with tabulated experimental values and studentswould again be asked to make arguments concerning mineraldurability, the influence of weathering, and so on. The logicalquantum-based approach would be to implement a semiem-pirical Hamiltonian. Unfortunately the computed results werepoor at best (the geometry of the lattice is poorly reproducedwhen energy is minimized), and this part of the experimentwas not implemented.

This laboratory experiment is followed by one in themineralogy laboratory, where students select pure startingmaterials (magnesium oxides, carbon, silica, etc.) and thenmix them in mole ratios that would lead to the formation ofa desired mineral upon heating in a furnace (mineralogicalsynthesis). Upon synthesis the students verify their productswith X-ray diffraction spectrometry.

Discussion

The laboratory experiments described above are part ofMineralogy 221. This is a sophomore-level geology courseand the laboratory experiments we codeveloped constitute33% of the entire laboratory syllabus. The experiments areinterspersed among other mineralogy experiments, so while

they follow the order presented here, they are not concat-enated. Rather, they are offered when that part of the lecturecovers those topics.

The experiments we have developed maintain a theme ofsilicate chemistry, but this is just our local preference; other ideaswould no doubt be welcomed by geology instructors. Thecomputational laboratories bring basic concepts in structuralchemistry together with real-world mineralogy. In particular,we strive to make the connection between chemists’ micro-scopic, atomic-level views and macroscopic (sometimes glo-bal) scales that geologists work with. Students build, mea-sure, and predict the properties of nanocrystallites and thenmake predictions about mineral durability, stress fracturing,weathering, and so on.

We have attempted to use the available force fields ofCerius to optimize mineral lattices, but we have found theseforce fields to be uniformly incapable of reproducing knownmineral lattices with a suitable root-mean-square deviation.Similarly, geometry optimizations with the semiempiricalHamiltonians have failed, so we do not predict lattice geom-etries in this course. We do find, however, that ion replacementcalculations (e.g., Mg2+ for Ca2+) do predict the correct trendsin stability and students can use these computational toolsto begin thinking about thermodynamic implications of min-erals in high- vs low-temperature phases as well as to fosteran 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 onrelatively simple computational techniques, relying heavilyon visualization. Molecular graphics allows us to use, rela-tively cheaply, a greater number of models than we could everpurchase from our limited budget. (MSI now supplies hun-dreds of minerals and ceramics in their materials database,along with numerous other polymers and organics.) More-over it allows us to see things such as electrostatic fields, Millerplanes, and the like that are not otherwise possible to see frommechanical models.

Several other aspects of this interdisciplinary curriculumalso need to be highlighted. First, we have focused on bridgingthe “size” gap where the connections between macroscopicand 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 betweenatomic-level details and how these affect weathering ofminerals, which in turn affects oceans and climates. Com-putational chemistry has proved capable of helping studentsmake those connections. Second, we were taken aback by theeagerness of our students for manipulating and viewing themodels computationally in comparison to using the hand-held mechanical models. Students seemed apprehensive aboutusing the mechanical models, perhaps for fear of breakingthem or maybe because they hadn’t seen such models before.In contrast, they were very eager to use the computer models(and clearly expressed their opinions of this), perhaps becausethey felt comfortable using a computer and knew theycouldn’t damage the models. Third, we reiterate that thestudents in this course are at a similar level of comprehensionof molecular structure as first-semester organic chemistrystudents, so one cannot raise the level of computationaldifficulty beyond what would be presented in an organicchemistry class. Finally, we point out that this collaborationis interdisciplinary and forces students in geology to make

Figure 3. A ball-and-stick representation of talc showing layers ofSiO4 tetrahedral groups sandwiching MgO6 octahedral groupsbonded only by weak van der Waals’ forces. Visualizing this min-eral allows students to bridge the gap between the microscopicworld depicted here, and the macroscopic world in which talc isknown to be a soft, lubricant-like material. Another example oflayers held together exclusively by weak van der Waals’ forces isthe micas. Again, the macroscopic world of peeling mica layersto make atomically smooth surfaces can be connected to the mi-croscopic underpinning of what gives rise to that phenomenon.



use of the chemistry they have had. We notice that studentstend to compartmentalize their knowledge, in part as a defensemechanism when being overwhelmed by class work, and thiscombined geology-chemistry experience helps shed thoseshackles. In our opinion, the earlier we begin to remove thebarriers between disciplines (in this case in the sophomoreyear) the easier it will become for students to understand howthe sciences are all interconnected, and especially for themto see the commonalties rather than the differences.

Summary

If chemistry is “the central science”, one would expectto see more interdisciplinary learning partnerships betweenchemistry and cognate disciplines of science and technology.Computational chemistry is inherently multidisciplinary andcapable of conveying important pedagogical messages tostudents of chemistry as well as to students of other disciplineswhere knowledge at an atomic or molecular level is desired. Inthis paper we have documented how we used computationalchemistry in a collaborative effort with a geology department.Specifically, we have developed a set of tutorials, homework

assignments, and laboratory experiments for use in a miner-alogy course. If we, as a group of chemists, intend to make theclaim that chemistry is the central science, we need to reachout to other disciplines to provide guidance for those whowish to learn about what we already know. There are manypathways for achieving such an intellectual collaboration andwe have demonstrated one such way here. We encourageothers 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: EnglewoodCliffs, 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.



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