Information • Textbooks • Media • Resources edited by
JCE WebWare
William F. Coleman
Web-Based Computations and Animations
Wellesley College Wellesley, MA 02481
W
Randall J. Wildman University of Wisconsin–Madison Madison, WI 53715
Mol4D: A Web-Based Computational Chemistry Interface for Educational Purposes Hens Borkent* and Jack van Rooij, Centre for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands;
[email protected]. Oliver Stueker, Ingo Brunberg, and Gregor Fels, Department of Organic Chemistry, University of Paderborn, D-33098 Paderborn, Germany
Mol4D (Molecules in Four Dimensions) is a Web-based molecule editor using the Chime browser plug-in linked to a MOPAC calculation engine that yields structural data (geometry parameters, transition states) as well as electronic data (orbitals, electrostatic potential). Visualization and interactivity are the predominant features. Students can submit and obtain computational results within seconds using their Internet browser. The structure and the keywords used as input for the computation can be chosen and amended using a menu interface. Among the options are the output of orbital information (in VRML format) and the selection of parameters for a linear or grid scan. Results from the computation are presented in a Web page that features an interactive energy plot and animation, when applicable. The MDL Chime plug-in (1) is widely used to display three-dimensional structures in Web pages. Use of Chime is generally confined to single structures, sometimes including buttons that offer shortcuts to Chime functions. Chime animations based on the multiple xyz-format, with control buttons to step through the animation, are not widely used. Apart from the commonly used xyz, pdb, and mol2 files, Chime also supports the MOPAC (2) input file format based on a z-matrix of internal coordinates (distances, angles, and dihedrals). This format allows for some molecule editing, in which a hydrogen or other monovalent atom can be replaced by a predefined group of atoms (for example, –CH3, –NO2, – C6H5), resulting in a new structure. Judicious use of this fea-
582
Figure 1. Result page for simple minimization.
ture allows the construction of almost any organic molecule. We have implemented this idea, taken from the MOLDEN (3) z-matrix editor, with a series of CGI scripts on our WWW server that also handle the input to MOPAC and the presentation of the results. The Web page returned to the user (Figure 1) includes the Chime structure, the calculated heat of formation, and buttons to allow geometrical measurements and control of the display of the electrostatic potential surface. If orbital information is requested, a link is included to our MOPAC-to-VRML service, which produces a Web page from which the orbital number and other relevant parameters can be selected. Another feature of Mol4D is the visualization of reactions and conformational changes. Starting with a predefined input file, students may add a group to a skeleton, run the calculation, and study the substituent effect on the reaction or conformational change. The Diels–Alder reaction is a typical example where this approach is useful to study directive effects of substituents in butadiene and ethylene, for instance. Comparison of the energy profiles and energy data from the output pages allows determination of the favored reaction.
Journal of Chemical Education • Vol. 80 No. 5 May 2003 • JChemEd.chem.wisc.edu
Information • Textbooks • Media • Resources
Figure 3. Starting point of the IRC calculation for a 2+3 cycloaddition of ethylnitrile oxide and ethylene. Figure 2. Result page for a one-dimensional reaction (conformational change), which provides for animation of the change.
The result of a one-dimensional reaction (e.g., a conformational change) coordinate calculation is presented with a number of features (Figure 2). The Chime display, based on a multiple-xyz file, is presented with buttons that control the animation through the respective structures. The energy values are translated into an interactive energy plot connected to the Chime display. This connection links the structure animation to a red ball that moves along the energy curve in the plot. In addition, clicking on a point in the graph displays the corresponding structure as a Chime object. A third display window includes the alphanumeric data (parameter value, energy). In the two-dimensional case the result is an interactive grid plot with energy contour lines (Figure 3). In practice the grid calculation is often applied to locate a transition state. Therefore, this feature has a couple of follow-up links: recalculation of the grid with different starting values, corresponding to zooming in on the transition state or shifting it; and continuation with an IRC calculation from a selected structure close to the saddle point (Figure 3). This latter link points
to an automated reaction animation service, described in detail in the following paper (4). A cross in the plot marks the position of a saddle point, and a line displays the direction of the reaction coordinate at this point. Supplemental Material Examples of exercises for use with Mol4D are included in the accompanying documentation. W
Literature Cited 1. Chime is a product of Molecular Design Ltd. See their Web site: http://www.mdlchime.com/chime (accessed Mar 2003). 2. MOPAC: Stewart, James J. P. J. Comput. Aided Mol. Design 1990, 4, 1–105. 3. MOLDEN: Schaftenaar, G.; Noordik, J. H. J. Comput. Aided Mol. Design 2000, 14, 123. http://www.cmbi.kun.nl/~schaft/ molden/molden.html (accessed Mar 2003). 4. Stueker, O.; Brunberg, I.; Fels, G.; Borkent, H.: van Rooij, J. J. Chem. Educ. 2003, 80, 583.
JChemEd.chem.wisc.edu • Vol. 80 No. 5 May 2003 • Journal of Chemical Education
583
