Organic Chemistry Molecular Models: Structure and Nomenclature

You should use the odd-colored flexible pieces in your model kit to form small (3- and 4-membered) rings, as the strain is likely to break the normal, less flexible pieces. See your kit manual for guidance.

Notice, from the models you have built with your model kit, how the rings get "floppier" as they get larger. The molecules are shown below as line drawings, in which each vertex represents a carbon atom, and hydrogens are automatically assumed to exist at unfilled carbon valences. You will see that your Molecular Visions kit works very much like a line drawing.

Jmol._Canvas2D (Jmol) "jmolApplet0"[x] loading... ../JmolFolder/j2s/core/corescript.z.js starting QueueThread0_2 script 1 started loading... ../JmolFolder/j2s/core/corestate.z.js   FileManager.getAtomSetCollectionFromFile(structures/Cycpro.pdb) starting HoverWatcher_3 FileManager opening 1 https://homepages.bluffton.edu/~bergerd/Models/structures/Cycpro.pdb The Resolver thinks Pdb loading... ../JmolFolder/j2s/core/corebio.z.js loading... ../JmolFolder/j2s/J/render/MeshRenderer.js -- required by J.renderbio.BioShapeRenderer loading... ../JmolFolder/j2s/J/shape/Mesh.js loading... ../JmolFolder/j2s/J/util/Hermite.js Time for openFile(structures/Cycpro.pdb): 193 ms reading 9 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 9 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation spinX = 20 spinY = 40 spinFPS = 30 Script completed Jmol script terminated Jmol JavaScript applet jmolApplet1_object__9233788567841614__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet1_object__9233788567841614__) viewerOptions: { "name":"jmolApplet1_object","applet":true,"documentBase":"https://homepages.bluffton.edu/~bergerd/Models/struc3.html","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1_object__9233788567841614__","codePath":"https://homepages.bluffton.edu/~bergerd/Models/../JmolFolder/j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"9233788567841614","bgcolor":"#FFFFFF" } setting document base to "https://homepages.bluffton.edu/~bergerd/Models/struc3.html" (C) 2012 Jmol Development Jmol Version: 14.1.6_dev_2014.01.13 2014-01-13 20:50: java.vendor: j2s java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM os.name: j2s Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet1_object (signed) starting HoverWatcher_4 Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #FFFFFF backgroundColor = "#FFFFFF" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet1_object__9233788567841614__ ready	Jmol._Canvas2D (Jmol) "jmolApplet1"[x] starting QueueThread0_5 script 1 started   FileManager.getAtomSetCollectionFromFile(structures/Cybut.pdb) starting HoverWatcher_6 FileManager opening 1 https://homepages.bluffton.edu/~bergerd/Models/structures/Cybut.pdb The Resolver thinks Pdb Time for openFile(structures/Cybut.pdb): 18 ms reading 12 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 12 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation spinX = 20 spinY = 40 spinFPS = 30 Script completed Jmol script terminated Jmol JavaScript applet jmolApplet2_object__9233788567841614__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet2_object__9233788567841614__) viewerOptions: { "name":"jmolApplet2_object","applet":true,"documentBase":"https://homepages.bluffton.edu/~bergerd/Models/struc3.html","platform":"J.awtjs2d.Platform","fullName":"jmolApplet2_object__9233788567841614__","codePath":"https://homepages.bluffton.edu/~bergerd/Models/../JmolFolder/j2s/","display":"jmolApplet2_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"9233788567841614","bgcolor":"#FFFFFF" } setting document base to "https://homepages.bluffton.edu/~bergerd/Models/struc3.html" (C) 2012 Jmol Development Jmol Version: 14.1.6_dev_2014.01.13 2014-01-13 20:50: java.vendor: j2s java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM os.name: j2s Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet2_object (signed) starting HoverWatcher_7 Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #FFFFFF backgroundColor = "#FFFFFF" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet2_object__9233788567841614__ ready	Jmol._Canvas2D (Jmol) "jmolApplet2"[x] starting QueueThread0_8 script 1 started   FileManager.getAtomSetCollectionFromFile(structures/cypent.pdb) starting HoverWatcher_9 FileManager opening 1 https://homepages.bluffton.edu/~bergerd/Models/structures/cypent.pdb The Resolver thinks Pdb Time for openFile(structures/cypent.pdb): 19 ms reading 15 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 15 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation spinX = 20 spinY = 40 spinFPS = 30 Script completed Jmol script terminated Jmol JavaScript applet jmolApplet3_object__9233788567841614__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet3_object__9233788567841614__) viewerOptions: { "name":"jmolApplet3_object","applet":true,"documentBase":"https://homepages.bluffton.edu/~bergerd/Models/struc3.html","platform":"J.awtjs2d.Platform","fullName":"jmolApplet3_object__9233788567841614__","codePath":"https://homepages.bluffton.edu/~bergerd/Models/../JmolFolder/j2s/","display":"jmolApplet3_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"9233788567841614","bgcolor":"#FFFFFF" } setting document base to "https://homepages.bluffton.edu/~bergerd/Models/struc3.html" (C) 2012 Jmol Development Jmol Version: 14.1.6_dev_2014.01.13 2014-01-13 20:50: java.vendor: j2s java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM os.name: j2s Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet3_object (signed) starting HoverWatcher_10 Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #FFFFFF backgroundColor = "#FFFFFF" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet3_object__9233788567841614__ ready	Jmol._Canvas2D (Jmol) "jmolApplet3"[x] loading... ../JmolFolder/j2s/core/package.js loading... ../JmolFolder/j2s/core/core.z.js -- required by ClazzNode Jmol JavaScript applet jmolApplet0_object__9233788567841614__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet0_object__9233788567841614__) viewerOptions: { "name":"jmolApplet0_object","applet":true,"documentBase":"https://homepages.bluffton.edu/~bergerd/Models/struc3.html","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0_object__9233788567841614__","codePath":"https://homepages.bluffton.edu/~bergerd/Models/../JmolFolder/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"9233788567841614","bgcolor":"#FFFFFF" } setting document base to "https://homepages.bluffton.edu/~bergerd/Models/struc3.html" (C) 2012 Jmol Development Jmol Version: 14.1.6_dev_2014.01.13 2014-01-13 20:50: java.vendor: j2s java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM os.name: j2s Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet0_object (signed) starting HoverWatcher_1 Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #FFFFFF backgroundColor = "#FFFFFF" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet0_object__9233788567841614__ ready starting QueueThread0_11 script 1 started   FileManager.getAtomSetCollectionFromFile(structures/Chair.pdb) starting HoverWatcher_12 FileManager opening 1 https://homepages.bluffton.edu/~bergerd/Models/structures/Chair.pdb The Resolver thinks Pdb Time for openFile(structures/Chair.pdb): 17 ms reading 18 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 18 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation spinX = 20 spinY = 40 spinFPS = 30 Script completed Jmol script terminated

Dan Berger's home page

Dan Berger's chemistry pages

Bluffton organic chemistry pages

Copyright © 1998, 1999, 2000, 2003, 2007 by Daniel J. Berger. This work may be copied without limit if its use is to be for non-profit educational purposes. Such copies may be by any method, present or future. The author requests only that this statement accompany all such copies. All rights to publication for profit are retained by the author.