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
Web-Based Interactive Animation of Organic Reactions Oliver Stueker, Ingo Brunberg, and Gregor Fels* Department of Organic Chemistry, University of Paderborn, D-33098 Paderborn, Germany,
[email protected] Hens Borkent and Jack van Rooij, Centre for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Organic reactions follow a limited number of rules defined by specific reaction mechanisms. Knowledge of these mechanisms is a unique and a desirable way of learning the multiple classes of reactions rather than memorizing each individual reaction. One of the major obstacles in learning organic chemistry is the need for a three-dimensional perspective of the molecules and the reaction pathways that they follow. Conventional two-dimensional drawings of reaction mechanisms may not be sufficient to foster a detailed understanding. Stereochemical aspects and sequences of multistep reactions can be difficult to visualize on the chalkboard or with hand-held model sets (1). In this respect, currently available molecular modeling software can be useful to model reaction mechanisms from the starting materials, via various transition states and intermediate stages, to the products. Using special software, modeled reaction mechanisms can be animated, and these animations can provide a better means of visualizing organic reactions. To overcome the current limitations of viewing organic reactions, we have developed a Web-based, interactive procedure that allows for the animation of an organic reaction, presented as an interactively viewable Chime object (2), on the basis of an approximate structure of the corresponding transition state. Only one-step reactions are supported at present; the results are based on solvent-free calculations. The procedure involves: •
•
Selection of a specific reaction from a list of precalculated organic reaction types, including Diels–Alderand SN2-reactions, Claisen- and Cope-rearrangements, cycloaddition, and cyclohexane inversion Editing the starting material by replacing any existing hydrogen with a substituent from a list of atoms or organic groups
•
Energy hypersurface calculation in the vicinity of the transition state for the new set of starting materials
•
Determination of the exact transition state
•
Calculation of the intrinsic reaction coordinate from transition state to the starting material and to the products, respectively
•
Selection of a given number of structures along the reaction coordinate for display in the final animation
•
Generation of a Web site that contains the animated reaction as an interactively viewable Chime object along with the corresponding energy curve of the reaction coordinate and atom coordinates of the transition state structure.
The resulting reactions can be controlled via buttons that start and stop the reaction and that allow a stepwise forward and backward animation of the reaction. The display can be altered from wireframe to stick, ball and stick, and spacefill, and the reaction can be viewed in three-dimensional space at any time. The only requirement for the animation of a given reaction is that the corresponding basic reaction type must be already available in the reaction database. The animation service is unique in the sense that it is entirely automated and allows investigation of the influence of substituents on a given organic reaction. Furthermore, utilizing the energy diagrams of a set of isomeric starting materials allows a direct comparison of the kinetic variation of the given reaction in relation to the position of substituents on the starting material as well as on the connectivity of the atoms in the substituents. The presented service provides a versatile tool for teaching and learning organic chemistry in introductory organic chemistry classes. It can be used by teachers to demonstrate and explain the three-dimensional course of organic reactions and it is useful for students to design and investigate their own reaction examples. Literature Cited 1. Fleming, S. A.; Hart, G. R.; Savage, P. B. J. Chem. Educ. 2000, 77, 790–793. 2. MDL Chime plugin is available at http://www.mdlchime.com (accessed Mar 2003).
JChemEd.chem.wisc.edu • Vol. 80 No. 5 May 2003 • Journal of Chemical Education
583
