Preprint submitted to the Internet Journal of Chemistry and archived as a PRE-REFEREED PREPRINT under the Journal's ROMEO-GREEN policy. The manuscsript is an HTML + SVG hyperdocument of many components. The main paper is deposited but the hyperlinks have not been added so will appear broken. A major theme of the article is the animation of reactions using SVG and for this the reader should view the individual document components. (As a last resort they may download the ZIP file, unpack it, and view it in a modern browser). If they do not have SVG they should install a plugin, e.g. from http://www.adobe.com/svg.The MAIN PAPER is paper.htmlTHE MATERIAL IS COPYRIGHT AND MAY NOT CURRENTLY BE ALTERED OR REDISTRIBUTED. For more information, and animated demos, see http://wwmm.ch.cam.ac.uk/moin/CmlSnap
Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language1 representation of all components is given. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions.
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