Representing Structures of Organic Molecules

<?xml version="1.0" encoding="UTF-8"?>  <XholonWorkbook> <Notes> Khan Academy ------------ Title: Representing Structures of Organic Molecules Description: Representing Structures of Organic Molecules Url: http://www.khanacademy.org/video/representing-structures-of-organic-molecules?playlist=Organic Chemistry InternalName: representing-structures-of-organic-molecules YoutubeId: pMoA65Dj-zk Keywords: Organic, Chemistry, molecular, structure My Notes -------- naming, nomencature chains of carbon molecules Methane (1-carbon chain) - Carbon has 8 electrons, valence electrons, can bind with 4 Hydrogen molecules - the Carbon and Hydrogen share electrons Diagram of Methane H .. H :C: H .. H or H | H-C-H | H Propane 3-carbon chain 2:25 - same idea with 3C and 8H simpler notation for Propane 5:17 CH_3-CH_2-CH_3 (where _3 means subscripted 3 which I can't do here) simplest notation 6:00 /\ / \ I like what Sal says at 4:40 where he modularizes the Propane structure by drawing boxes around each Carbon and it's 3 or 3 Hydrogens. This would be a good way to represent it in Xholon. Possibly something like: <C><H multiplicity="3"/></C> <C><H multiplicity="2"/></C> <C><H multiplicity="3"/></C> I might use the JUNG network viewer to visualize the network structure? But this requires explicit ports. One visualization approach is to define the logical structure in Xholon, and then write scripts to output that in one or more chemical notations that can be read by other tools to do nice graphics. Ideally pass it off to other tools online. Maybe the Jmol applet? CML? SMILES (very simple) (used in many wikipedia chemistry articles) Methane C Propane CCC Ethanol CCO There are web sites that will display a graphic for a specified SMILES string. http://www.daylight.com/daycgi/depict </Notes> <script implName="lang:python:inline:"><![CDATA[ print "height = 12.34 m" ]]></script> <script implName="lang:javascript:inline:"><![CDATA[ print("height = 56.78 meters\n"); ]]></script> <_-.XholonClass>  <PhysicalSystem/> <Propane/> <C/> <H/> </_-.XholonClass> <xholonClassDetails/> <PhysicalSystem> <Propane> <C><H multiplicity="3"/></C> <C><H multiplicity="2"/></C> <C><H multiplicity="3"/></C> </Propane> </PhysicalSystem> <Blockbehavior implName="lang:python:inline:"><![CDATA[ # This works if pasted in as a last child of Block. height.incVal(0.02) print("Python wants something to do. Height:" + str(height)) ]]></Blockbehavior> <Blockbehavior implName="lang:javascript:inline:"><![CDATA[ // This works if pasted in as a last child of Block. height.incVal(0.02); print("JavaScript wants something to do. Height:" + height + "\n"); ]]></Blockbehavior> <Blockbehavior implName="lang:bsh:inline:"><![CDATA[ // This works if pasted in as a last child of Block. height.incVal(0.02); System.out.print("Java/Beanshell wants something to do. Height:" + height + "\n"); ]]></Blockbehavior> <Blockbehavior implName="lang:jruby:inline:"><![CDATA[ require 'java' # This works if pasted in as a last child of Block. $height.incVal(0.02) puts "Ruby wants something to do. Height: #{$height}" ]]></Blockbehavior> <Blockbehavior implName="lang:groovy:inline:"><![CDATA[ // This works if pasted in as a last child of Block. height.incVal(0.02); System.out.print("Groovy wants something to do. Height:" + height + "\n"); ]]></Blockbehavior> </XholonWorkbook>