Chemical Education Today
NSF Highlights Projects Supported by the NSF Division of Undergraduate Education
Molecular Modeling and Computational Chemistry at Humboldt State University by Richard A. Paselk and Robert W. Zoellner
A multiyear project to integrate molecular modeling and computational chemistry (MM&CC) throughout the undergraduate chemistry curriculum at Humboldt State University (HSU) is currently nearing the end of the third and final year of funding. The program includes a new laboratory course, a targeted emphasis on improving and increasing undergraduate research projects, and enhancements to the joint undergraduate computational methods course taught as part of the chemistry and physics curricula. Faculty collaborative undergraduate research projects using computational chemistry methods are among the greatest initial successes of the project. In addition to the already established use of Mathematica (1) as a computational tool in the upper division chemistry and physics curricula, the improved availability of Mathematica has greatly enhanced and encouraged additional uses for this powerful tool in other departments. Facilities, Hardware, and Software In the initial proposal for this project, funds were requested to create a computer laboratory to enable the creation of two new courses in MM&CC and to integrate computational methods throughout the chemistry curriculum at HSU. Due to a campus reinterpretation of the Americans with Disabilities Act requirements, the originally proposed 24-seat computational chemistry laboratory was redesigned into what turned out to be a significantly more effective facility given the normal instructional methods and class sizes in the department of chemistry. Rather than site the computers in a single 24-seat facility, they were dispersed into a 15-seat instructional laboratory (14 student stations and one instructor station connected directly to a projector), a four-seat open access student and printer mini-laboratory, and a research laboratory for advanced students and faculty. Each of these facilities is in close proximity to the others and on the same floor. All labs are equipped with university-provided card locks enabling programmed student access and control. With such a system, students can be given access to the mini-laboratory 24 hours a day, 7 days a week, while access to the teaching lab can be restricted, thereby allowing the computers in that facility to be used as components of Linux Beowulf clusters during off hours and weekends. This arrangement also allows students to have access to the mini-laboratory computers when the main facility is used for instruction, and printer use does not interfere with teaching activities. The instructional facility computers are dual-boot Windows 2000/NT and Linux capable; the instructor’s station 1192
is connected directly to a ceiling-mounted projector.1 All of the computers in this facility and in the mini-laboratory are networked via a 40-port switch to independent Windows 2000/NT and Linux file servers, as are the high capacity black-and-white laser printer and the color laser printer. By using the Linux file server as a Linux controller, each of the computers in the two facilities can be linked into a Beowulf cluster parallel computer with up to 17 nodes. Currently, when booted as Windows 2000/NT computers, the workstations are equipped with PC Spartan Pro (2), Gaussian 98W and GaussViewW (3), and Mathematica; when booted as Linux systems, the workstations run Jaguar (4), GAMESS (5), and AIMPRO (6). The research laboratory is currently equipped with a Silicon Graphics, Inc. (SGI) dual processor Origin server running Insight II and Discover (7), enabling the modeling of bio- and macromolecules by advanced students and faculty, and Jaguar. Remote access to the SGI workstation from the instructional or mini-laboratory computers is possible when the machines are booted as Linux systems. When booted as Windows computers, access while using the machines as XWindows clients is currently under development. A dedicated Linux-based Beowulf parallel computer cluster is also under construction in this laboratory, and will run Jaguar, GAMESS, and AIMPRO. This system will also be accessible to students via the network from the other facilities. Courses The original vision for this project included a three-year planned implementation of hardware and software to accommodate development time and to allow modifications to be instituted based on early results. During the first full semester of the grant, a new course, Molecular Modeling, designed for intermediate level chemistry majors and students in allied sciences such as cellular and molecular biology, became a permanent part of the Chemistry curriculum. Molecular Modeling requires the completion of either the one-semester brief organic course or the first semester of the two-semester majors organic course, and some knowledge of how to use a Windows-based operating system is assumed. Theory is addressed only at a qualitative level, and the course focuses on the development of a practical, working knowledge of the programs and fostering an understanding of how to choose a computational method appropriate to the solution of a chemical problem. Students learn to treat the models as independent computational “universes” that only approximate reality. Most importantly, students learn to answer the question, “Given constraints of time and com-
Journal of Chemical Education • Vol. 79 No. 10 October 2002 • JChemEd.chem.wisc.edu
Chemical Education Today edited by
Susan H. Hixson National Science Foundation Arlington, VA 22230
Richard F. Jones Sinclair Community College Dayton, OH 45402-1460
putational equipment, which method will yield the data and results needed to solve the problem at hand?” Originally, Molecular Modeling was to be followed by an advanced course for chemistry majors with a physical chemistry prerequisite. However, this advanced course is impractical at present—there simply are not enough qualified and interested students at this point in the project timeline to produce a viable course. On the other hand, the advent of the computational facilities described above has resulted in an extraordinary response from students who desire to initiate independent undergraduate research projects or to take part in an already established project. Most of these students start with little or no modeling or computational chemistry background. Rather, the students learn how to use the programs and methods needed for their project under direct faculty and student mentoring. A capstone course is currently in development for these students to provide a venue for learning the theory and to “fill in the gaps” in their computational background so that they are able to successfully assess and critically evaluate their research results. The capstone course is envisioned as a fall semester offering with a spring semester follow-up during which the student will prepare a manuscript of their project for submission to a peer-reviewed journal. While MM&CC are being incorporated in many courses throughout the chemistry curriculum (described below), two courses, the new Molecular Modeling (described above) and the established Symbolic Computation in the Sciences (a course taught jointly by chemistry and physics faculty that uses Mathematica) use the computational facilities extensively. In addition, Biochemical Toxicology and other advanced courses use the facilities for preparing and presenting seminars. A breakdown of the majors of the students in these courses indicates that 47% were chemistry, 15% were physics, 9% were biology, 5% were environmental science, and the remainder (24%) were anthropology, nursing, or other fields. Undergraduate Research The most successful and gratifying aspect of the project thus far has been the enthusiastic response of students to independent projects involving computational chemistry. Most of these students have worked on purely computational projects under the direction of one of the PI’s (Zoellner), but a number of the projects are in support of experimental research pursued under the direction of other faculty. The two most recent faculty hires (Joshua R. Smith and William G. Golden) are already directing undergraduate MM&CC projects that use the facilities developed through this project. A particular advantage of MM&CC for undergraduate research is that a student can begin a real research project as early as the freshman year. All that is required on
a student’s part is enthusiasm and a willingness to work. If an interest in continuing undergraduate research develops, as is usually the case, the student can either continue to carry out the computational project or their faculty mentor can lead the student into experimental bench-work as the student develops the skills and knowledge necessary for a safe and productive laboratory experience. Some of the computational research projects in progress or that have been presented or published that use the facilities described above are described briefly in the list on p 1195. Applications throughout the Chemistry Curriculum The new instructional laboratory and the PC Spartan Pro software are also being used to progressively introduce MM&CC methods into the undergraduate Chemistry curriculum. As a first exercise in this initiative, the computers and software are used to illustrate molecular geometry in the General Chemistry laboratories. In this exercise, students first create Lewis structures of simple molecules, and then use Valence Shell Electron Pair Repulsion (VSEPR) theory to predict molecular geometries. These paper exercises are followed with hands-on molecular constructions using Styrofoam balls and toothpicks in a regular laboratory setting. The students are then taken to the computer laboratory where they use the computers and the PC Spartan Pro user interface to visualize and manipulate the same structures they built with Styrofoam balls and toothpicks. The students do not actually carry out the calculations to determine the geometric structures and properties (molecular surfaces, electrostatic potentials, polarity, vibrations), but simply access the pre-calculated output files for each of the molecules with PC Spartan Pro and employ the user interface as their visualization tool. The combination of hands-on construction with computer manipulation strongly reinforces students’ concepts of molecular shape and structure and is more effective than either technique alone.2 A slightly more advanced and focused exercise will be introduced into the organic chemistry laboratories next year, and a set of exercises supporting lecture materials (applications of symmetry and character tables, geometry optimizations) has also been used in the senior inorganic chemistry course and laboratory. The sophistication and extent of MM&CC in advanced courses will continue to increase as students move through the curriculum. Of course, MM&CC is not the only application of computation in chemistry. The computational facilities are already being used for computer data analysis of mass spectra using specialized software, supporting the use of the autosampler GC-MS in the major sequence organic course. Data analysis using spreadsheets has been implemented in the analytical chemistry course, and the computer facilities are also used in both the one-semester and majors sequence Biochemistry courses.
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Chemical Education Today
NSF Highlights Acknowledgments We thank the HSU Dean’s Office of the College of Natural Resources and Sciences, the Office of the Vice-President for Academic Affairs, and the Office for Research and Graduate Studies for their support and for matching funds for this project. This work was supported by the National Science Foundation Course, Curriculum, and Laboratory Improvement Program as grant number NSF-9950344, and by a grant from the California State University Program for Education and Research in Biotechnology (CSUPERB). Note 1. Each computer is equipped with a 600 MHz Pentium III processor with 384 Mbyte RAM and two hard drives (20 Gbyte for the Windows boot and 10 Gbyte for the Linux boot), as well as CD-ROM, 100 Mbyte Zip, and 3.5-in. floppy drives. Selected computers also have a CD-R/W drive installed as an additional data storage option. 2. For more details on this “hands-on building plus computation” experiment, contact the authors.
Literature Cited 1. Wolfram Research, Inc.; 100 Trade Center Drive; Champaign, IL 61820-7237; http://www.wolfram.com/ (accessed July 2002). 2. Wavefunction, Inc.; 18401 Von Karman Avenue; Suite 370; Irvine, CA 92612; http://www.wavefunction.com/ (accessed July 2002). 3. Gaussian, Inc.; Carnegie Office Park; Building 6; Suite 230; Pittsburgh, PA 15106; http://www.gaussian.com/ (accessed July 2002). 4. Schrödinger, Inc.; 1500 Southwest First Avenue; Suite 1180; Portland, OR 97201; http://www.schrodinger.com/ (accessed July 2002). 5. General Atomic and Molecular Electronic Structure System (GAMESS); http://www.msg.ameslab.gov/GAMESS/GAMESS.html (accessed July 2002).
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6. Ab Initio Modelling Program (AIMPRO); http:// aimpro.ncl.ac.uk/ and http://newton.ex.ac.uk/research/semiconductors/theory/jones/ (accessed July 2002). 7. Accelrys, Inc.; 9685 Scranton Road; San Diego, CA 921213752; http://www.accelrys.com/ (accessed July 2002). 8. Bennett, C. N.; Wanzong, B. L.; Golden, W. G.; Zoellner, R. W. Eleventh Annual American Chemical Society Undergraduate Research Conference; Santa Clara, CA; May 1999, #26 (poster). 9. Chervin, C. N.; Zoellner, R. W. in Yearout, R. D., Ed.; Proceedings of the Fourteenth National Conference on Undergraduate Research–NCUR 2000; Asheville, NC: The University of North Carolina at Asheville Press, 2000, CD file reference file:///E|/html/CS/p5CSJ07.pdf. 10. (a) Clark, I. T.; Zoellner, R. W.; Golden, W. G.; Proceedings of the Fifteenth National Conference on Undergraduate Research–NCUR 2001; Asheville, NC: The University of North Carolina at Asheville Press, 2001, CD file reference file:/// E|/html/CS/CSJ07.pdf. (b) Clark, I. T.; Smith, J. R. Sixteenth National Conference on Undergraduate Research (NCUR 2002); Whitewater, WI; April 2002, (poster). 11. Duckworth, L. A.; Van Horn, G. W.; Zoellner, R. W. Sixteenth National Conference on Undergraduate Research (NCUR 2002); Whitewater, WI; April 2002, (poster). 12. Higdon, M. A.; Zoellner, R. W. Sixteenth National Conference on Undergraduate Research (NCUR 2002); Whitewater, WI; April 2002, (poster). 13. Keller, T. A.; Zoellner, R. W. Sixteenth National Conference on Undergraduate Research (NCUR 2002); Whitewater, WI; April 2002, (poster). 14. Wanzong, B.; Zoellner, R. W.; Golden, W. G. 1999 California State University Computational Chemistry Council Conference; Arcata, California; July 1999; P-3 (poster).
Richard A. Paselk and Robert W. Zoellner are Professors in the Department of Chemistry, Humboldt State University, Arcata, CA 95521-8299;
[email protected] and
[email protected].
Journal of Chemical Education • Vol. 79 No. 10 October 2002 • JChemEd.chem.wisc.edu
Chemical Education Today
Undergraduate Computational Research Projectsa Cory N. Bennett fourth year A computational study of potential pre-adsorbate structures of simple hydrocarbon molecules and their perfluorocarbon analogs (8) Christopher N. Chervin third year Computational studies of thiocarbonyl derivatives of hypericin (9) Ian T. Clark third year A computational investigation of the structure and properties of monocarbonyliron (10a) and 1,2-dehydro-benzene, -cyclopentadienyl, and -cyclobutadiene metal complexes (10b) S. Bernadette Clueit second year Interactions of the simplest perfluorocarbon lubricant with the smallest metal surfaces: Computational studies of tetrafluoromethane with one, two, or three nickel atoms Laura A. Duckworth third year A computational investigation of the structures and properties of derivatives of methylphenidate and cocaine with comparisons to experimental activity data (11) Gregory Frankfurter first year Calculation of the structures and properties of paralytic and amnesiac shellfish toxins. Seth L. Griffin third year An evaluation of the energetics of Zaitsev’s (Saitzeff’s) Elimination Rule a
Year in college in which the student began the computational research.
Monica D. Higdon third year The computational determination of the relative anti-oxidant capabilities of selected phenolic compounds (12) Trish A. Keller first year A computational investigation of the structures and properties of Möbius-twisted molecules: Coronene and the kekulenes revisited (13) Andrew C. Malone fourth year Pseudohalogens, hydrogen pseudohalides, and pseudohalogen halides Travis Moe first year Computational investigations of molecules with unusually long bonds Jessica E. Momb first year The basicity of cyclo-aziridine and related azo-molecular belts Lehrin M. Morey first year Potentially aromatic molecular belts as analogs of “buckytubes” Jessica A. Nielson third year A re-investigation of the structures and properties of hypericin and its thiocarbonyl derivatives: Additional conformers and higher levels of theory Scott Stephansky third year The relationship of serotonin to selected psychoactive molecules Holly Sugrue first year Alkane molecular knots, catenanes, and rings Byron L. Wanzong third year Computationally-determined pre-adsorbate structures of simple hydrocarbon molecules and their perfluorocarbon analogs (14)
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