![]() The file chiral.dot fleshes out the branching and looping process a student of organic chemistry may use to identify and build all possible structures in set of stereoisomers. Just to be fancy, let’s denote the nodes that are questions as opposed to the ones that are statements by changing their shapes (see chiral-5.dot ):Ĭistrans[label="Are cis-/trans-\nisomers possible\n(rings orįigure 5: Denoting statements with ovals and questions with squares. Labeling links between nodes helps to clarify the nature of connections ( chiral-4.dot ).įigure 4: The beginnings of a flowchart/digraph. To make some connections explicit, we add following code within the brackets to give the file chiral-3.dot :Ĭompiling chiral-3.dot ( Ctrl-c, c, Enter ) finally yields a digraph:įigure 3: The beginnings of an algorithm. The power of digraphs is that they show connections. ![]() MoreĬistransįigure 2: Main nodes with more information. ![]() Because single words are not very descriptive, graphviz provides labels with proper descriptions (see file chiral-2.dot ). In the source code, each single word within the brackets becomes a node in the digraph. With the file chiral-1.dot open in the Emacs editor, typing Ctrl-c followed by c and Enter generates the image chiral-1.png :įigure 1: Visual pseudo-code for the algorithm. Compounds with carbon-carbon double bonds may exist as a set of cis- / trans- stereoisomers.Ring-containing compounds may exist as a set of cis- / trans- stereoisomers.If there is more than one chiral center, then the molecule exists as a set of chiral stereoisomers.If there is one chiral center, then the molecule exists as pair of chiral stereoisomers.If there are no chiral centers, the molecule is achiral.Start with some molecular structure represented by a three-dimensional model.The following snippet of text appears as the file chiral-1.dot, and it serves as a terse outline of the algorithm to search for stereoisomers: ![]() There are four overlapping possibilities: (i) no additional stereoisomers (ii) rings or carbon-carbon double bonds that give rise to cis-/ trans-isomers (iii) a single chiral center that gives rise to a pair of mirror-image stereoisomers, akin to a pair of hands (iv) or multiple chiral centers that allow stereoisomers to proliferate up to distinguishable structures, where n is the number of stereocenters.Īgain, the chemistry is not the point of this document-the programming is. As a result, the stereoisomers have different chemical and physical properties.Ī common method to torture students of organic chemistry is to require them to draw (or construct) all stereoisomers of a given molecule without duplication. Stereoisomers exhibit identical atom-to-atom connectivity, yet the atoms occupy three-dimensional space in different ways. It is not necessary to know organic chemistry to see how to program with graphviz, and of course many other example graphs with code exist online.īecause the element carbon is so versatile in its chemical behavior, many carbon-containing-organic-compounds exist as a set of distinguishable stereoisomers. To illustrate the power of graphviz, this document explains how to construct a digraph for a student of organic chemistry who wants to develop an algorithm or mental checklist for counting stereoisomers. In discrete mathematics, flowcharts are known as directed graphs or digraphs. There are graphical programs like ViewYourMind, Treesheets, and FreeMind, with similar functionality, but graphviz is smaller and more powerful …if you are willing to try a little programming. ![]() Graphviz is a program developed by AT
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