Chemical Education Today
Letters Interactive 3D Phase Diagrams Using Jmol Three-dimensional (3D) pVT phase diagrams for CO2 and H2O have been published previously in this Journal (1, 2) with discussion of the benefits of using 3D diagrams over the more common separate projections onto 2D planes. Such static 3D images suffer, though, from inherent limitations for detailed use, which may be overcome by the use of a virtual 3D representation that can be manipulated at will, for example, rotated, expanded to focus in a certain area, projected onto one of the three planes, labeled, and so forth. Prompted by this idea, we have developed a 3D representation of the data forming the above-mentioned diagrams, by using the new capabilities recently added to Jmol. Jmol (3–5) is Javabased open-source software for displaying molecular structures but has, in recent years, been greatly expanded to manage data in 3-coordinate orthogonal space, among other features. The phase diagrams presented here are an example of what can now be achieved with this tool. The Jmol applet permits placement of such interactive 3D graphs within a Web page, without separate browser plug-ins (other than the Java Virtual Machine), and so maximizes their accessibility by users. The data for phase diagrams of H2O and CO2 (1, 2) were extracted as a series of points and were manually organized according to the molfile format from MDL (6), one of the many molecular formats that Jmol can read. These data are interpreted by Jmol as dummy atoms and bonds, which constitute the lines of the phase diagram graph. Additional features, such as captions, pointers, tie-lines, axes, and labels, were added using the new drawing capabilities of Jmol. Many of these elements can be displayed and hidden at will by the user, interactively and reversibly, thus assisting when a simplification is needed, or to focus on certain aspects or details of the diagram. Furthermore, emulating a feature of the static graphs previously published, the three projections of the phase diagram onto the pV, pT, and VT planes were generated from the 3D data using Jmol capabilities (so called “molecular math”) and added to the graph. The resulting virtual 3D, highly-interactive, phase diagrams are offered freely for online use and linked as online material from the original articles (1, 2). Author Contribution L.G. conceived the idea of using Jmol for a 3D graph, prepared the data from the sources described in the previously mentioned papers, and adapted them to be read by Jmol. A.H.
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implemented the 3D graph under Jmol and designed the Web page and user interface. R.M.H. implemented the commands into Jmol that have allowed the display of generalized graphic data. Literature Cited 1. Glasser, Leslie. J. Chem. Educ. 2002, 79, 874–876. 2. Glasser, Leslie. J. Chem. Educ. 2004, 81, 414–418. 3. Jmol: An Open-Source Java Viewer for Chemical Structures in 3D. http://www.jmol.org/ (accessed Dec 2008). 4. Herráez, Angel. Biochem. Mol. Biol. Educ. 2006, 34, 255–261. 5. Herráez, Angel. How To Use Jmol To Study and Present Molecular Structures, Vol. 1; Lulu Enterprises: Morrisville, NC, 2007. 6. Symyx Technologies, Inc. CTFile formats. http://www.mdl.com/ downloads/public/ctfile/ctfile.pdf (accessed Mar 2009).
Supporting JCE Online Material
http://www.jce.divched.org/Journal/Issues/2009/May/abs566.html Keywords Full text (HTML and PDF) Links to cited URLs and JCE articles Supplement Virtual 3D, highly-interactive phase diagrams Angel Herráez Department of Biochemistry and Molecular Biology University of Alcalá 28871 Alcalá de Henares Spain
[email protected] Robert M. Hanson Department of Chemistry St. Olaf College Northfield, MN 55057
[email protected] Leslie Glasser Nanochemistry Research Institute Curtin University Perth 6845 Western Australia
[email protected] Journal of Chemical Education • Vol. 86 No. 5 May 2009 • www.JCE.DivCHED.org • © Division of Chemical Education
