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SDAS 2001 Vol 80 Proceedings of the South Dakota Academy of Science,Vol. 80 (2001) 151 IMPLEMENTING AND EXPLORING WebMO AS A WEB-BASED UNDERGRADUATE QUANTUM CHEMISTRY ENVIRONMENT Per Haakon Thrane-Nielsen and Arlen Viste Augustana College Sioux Falls, SD 57197 ABSTRACT WebMO is a web-based environment for working with such major quan- tum chemistry packages as Gaussian, GAMESS, and MOPAC (Hope 2000). Hope College generously encourages the free licensing of the WebMO software for installation elsewhere. This paper reports the process of installing, testing, adjusting, and applying the WebMO software package at Augustana College (WebMO Augustana 2001). Initial installation implemented work with Gaussian 94 through WebMO on an IBM RS/6000 computer under the Aix 4.3. Attention next turned to working with GAMESS through WebMO. We have not chosen to implement MOPAC thus far. In this environment, WebMO has been suc- cessfully applied to small organic molecules, such as ethene, C2H4 in GAMESS and allene, C3H4 in Gaussian 94.. Keywords WebMO, quantum chemistry, GAMESS, Gaussian INTRODUCTION Interesting Web-based tools related to quantum chemistry are beginning to appear. At an introductory level, The Simple Hückel Molecular Orbital Theory Calculator, implemented as a Java applet, is based at the University of Calgary (Hückel MO 2000). MolSurf, based at the University of Erlangen, provides vi- sualization of molecular surfaces in a VRML environment (Molsurf 2001). Web- MO is a web-based environment for working with such major quantum chem- istry packages as Gaussian, GAMESS, and MOPAC (Hope 2001). METHODS Hope College generously encourages the free licensing of the WebMO soft- ware for installation elsewhere. We have downloaded WebMO from the Hope College web site, and have installed the software package on an IBM RS/6000 computer under Aix 4.3.3 as the Unix operating system. Gaussian 94 has been installed on this computer for several years (Gaussian 2001). As part of the cur- 152 Proceedings of the South Dakota Academy of Science,Vol. 80 (2001) rent work, GAMESS was downloaded, compiled, and installed on the RS/6000 as well (Gordon 2001). In WebMO, building a molecule is with a visual editor, based on a Java applet. RESULTS AND DISCUSSION Installation of the WebMO software was relatively straightforward. (Web- MO Augustana 2001) Compilation of GAMESS is well documented and was successful. Installation of GAMESS under WebMO required more detailed at- tention than Gaussian 94. In both cases a template file needed to be convert- ed from Ascii DOS to Unix format. Using the Augustana installation of WebMO, quantum chemistry calcula- tions have been carried out on some small organic molecules, One example is ethene, C2H4. Using GAMESS an ab initio 6- 31G(d) MO calculation was done for geometry opti- mization and vibrational frequencies. The calculated infrared spectrum is shown as Figure 1. A WebMO Java applet displays the normal modes of vibration. An example is the strong band at 1095 cm- 1 shown in Figure 2. A second example is al- lene, C3H4 or H2C=C=CH2. Using Gaussian 94 an ab Figure 1. C2H4 GAMESS 6-31G(d) IR spectrum. initio 6- 31G(d) MO calcu- lation was done for geome- try optimization and vibra- tional frequencies. The cal- culated infrared spectrum is shown as Figure 3. The normal mode of vi- bration for the strong band at 2214 cm-1 shown in Fig- ure 4. WebMO currently does not include provision for graphical display of proba- bility density contour sur- faces for molecular orbitals Figure 2. C2H4 GAMESS 6-31G(d) normal mode cal- or total electron density. culated at 1095 cm-1. However with some further Proceedings of the South Dakota Academy of Science,Vol. 80 (2001) 153 effort, such surfaces can be displayed in separate visu- alization software such as Molekel or gOpenMol. (Molekel, 2001, Laaksonen, 2000) As an example, the electron density surface of allene, with electrostatic potential, in shown in Fig- ure 5, as rendered by Molekel. In WebMo, it is possible to add keywords such as POP=FULL to a Gaussian 94 run, so that Figure 3. Allene Gaussian 94 6-31G(d) IR spectrum. Molekel can produce such surfaces for molecular or- bitals, electron density, and electrostatic potential. CONCLUSION WebMO has been suc- cessfully installed on and IBM RS/6000 computer at Augustana College (SD). It has been tested and suc- cessfully applied to quan- tum chemistry calculations Figure 4. Allene Gaussian 94 6-31G(d) normal mode calculated at 2214 cm-1. on small organic molecules, such as ethene and allene, It is a useful tool, particu- larly for students in an un- dergraduate Chemistry aca- demic environment. The Hope College developers of this software have done a valuable service for the academic community. Figure 5. Allene electron density with electrostatic potential, from Gaussian 94 and Molekel. 154 Proceedings of the South Dakota Academy of Science,Vol. 80 (2001) LITERATURE CITED H¸ckel MO java applet. Simple H¸ckel Molecular Orbital Theory Calculator. 2000. http://www.chem.ucalgary.ca/SHMO/ Oellien, Frank. 2001. MolSurf. University of Erlangen, Germany. http://www2.chemie.uni-erlangen.de/services/molsurf/ Hope College. 2000. WebMO. Holland, MI. http://www.chem.hope.edu/web- mo/ Gaussian, Inc. 2001. Gaussian software. http://www.gaussian.com/ Gordon, Mark, research group. 2001. GAMESS software. Iowa State University, Ames, IA. http://www.msg.ameslab.gov/GAMESS/ Laaksonen, Leif. 2000. gOpenMol software. http://www.csc.fi/~laaksone/gopenmol/gopenmol.html Molekel. 2001. Advanced Interactive 3D-Graphics for Molecular Sciences. http://pobox.cscs.ch/molekel/home.html WebMO. 2001. Department of Chemistry, Augustana College, Sioux Falls, SD. http://inst.augie.edu/~spartan/ ACKNOWLEDGMENTS We thank Hope College for their public-spirited development provision of the WebMO software package. Thanks also to Augustana College and its De- partment of Chemistry for software and hardware support..
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