Molecular Model Building Instruction Manualharding/tutorials/models/models01.pdf · Molecular Model...
Transcript of Molecular Model Building Instruction Manualharding/tutorials/models/models01.pdf · Molecular Model...
Molecular Model Building Instruction Manual
Molecular Model of Caffeine
BasedonaChemistry14Cextracreditproject,fall2008Modelsoforganicmoleculesprovideaphysicalrepresentationofthethree‐dimensionalarrangementof atoms in space. Using a molecular model kit throughout your study of organic chemistry willenable you to better understand both the chemical and physical properties of themolecules youencounter.
1. Thefirststeptosuccessfullyusingyourmolecularmodelkitistobecomeacquaintedwiththecontentsofyourkitandwhateachunitrepresents.
• Yourmodelkitcontainsseveralpolyhedronsandspheresthatwillrepresenttheatomsyouworkwith.TheAtomTablespecifiesthenumberofholesoneachpolyhedronandsphereandidentifieswhichareusedtoformaspecifichybridization.
TheBondTablespecifiesthescaledbondlengthrepresentedbyeachoftheconnectorsinyourkitalongwithalistofcommonbondsyouwillencounterthroughoutyourstudyoforganicchemistryandthecorrespondingconnectorthatyoushoulduse.(forbondsingrey,morethanoneconnectorcanbeused)
AtomTable
Black
DarkBlue
Red
Green
DarkGrey
LightBlue
LightGrey
LightBlue(Sphere)
#ofholes 4 4 4 4 5 5 14 2
sp3 X X X X
sp2 X X
sp X
BondTable Orange1.10Å
H‐O
H‐N H‐C CΞC C=O CΞN O=N N=N NΞN
Green1.40Å
C=C C‐O C‐N C=N O‐N N‐N
White1.54Å
C‐C C‐N O‐O N‐N
Yellow1.80Å
C‐Cl C‐Br C‐l
Blue1.33Å
C=C CΞC C=O C=N CΞN O=N N=N NΞN
Electronlonepairscanberepresentedusingeitherthegreenorblueorbitalplatesinyourkit.
2. Nowthatyouarefamiliarwithwhatyourmodelkitcontains,thenextstepistolearnhowandwhentouseeachunit.
• Whenbuildingamolecularmodelitwillbehelpfultodesignatewhichpolyhedronyouwilluseforeachatominamolecularformula.Usingdifferentpolyhedronswithdifferentcolorsfordifferentatomswillmakeiteasierforyoutokeeptrackofatomswhencreatingandanalyzingisomers.Furthermore,usingtheappropriateconnectorstorepresentyourbonds(single,doubleortriple)willenableyoutobettervisualizewhichmoleculescandoresonance,whichmoleculesareconjugatedand/oraromatic,andwhichmoleculeshavebarrier(s)torotationandareorarenotplanar.Keepinmindthatwhilesomebondsmayberepresentedbymorethanoneconnector,itmaybeusefultopickconnectorsinawaythatwillmakeiteasiestforyoudorecognizesigma and pi bonds.
Alkanes:Singlebondsareconstructedbyconnectingtwopolyhedronsora
polyhedronandaspherewithasingleconnector(notincludingablueconnector)thatcorrespondstotheatomsyouarebonding.Example:ethane(CH3CH3)
Alkenes:Doublebonds(one sigma bond and one pi bond)canbeconstructedintwodifferentways.1) Twopolyhedrons(usuallyfour‐holed)areconnectedwithtwoblue
connectors.Thismethodofconstructionhighlightstheplanarityofamoleculeandthebarrier(s)torotationthatexistbecauseofthepibond.However,thismethodwillnotenableyoutodistinguishbetweenthesigmaandpibond.Example:ethene(CH2CH2)
2) Twopolyhedrons(usuallyfive‐holed)areconnectedwithasingleconnector(notincludingablueconnector)thatcorrespondstotheatomsyouarebonding.Thiswillrepresentthesigmabond.Oneorbitalplateofeachcolorisattachedtoeachpolyhedronwithsamecoloredorbitalplatesadjacent.Thiswillrepresentthepibond.Thismethodenablesyoutoclearlydistinguishbetweensigmaandpibonds,however,itwillmakeitmoredifficulttoseethebarrier(s)torotationthatexistbecauseofthepibond.Example:ethene(CH2CH2)
Alkynes:Triplebonds(one sigma bond and two pi bonds) canbeconstructedintwodifferentways.1) Twopolyhedrons(usuallyfive‐holed)areconnectedwiththreeblue
connectors.Thismethodofconstructionhighlightsthebarrier(s)torotationthatexistbecauseofthetwopibonds.However,thismethodwillnotenableyoutodistinguishbetweenthesigmaandpibonds.Example:ethyne(HC≡CH)
2) Twopolyhedrons(usuallyfourteen‐holed)areconnectedwithasingleconnector(notincludingablueconnector)thatcorrespondstotheatomsyouarebonding.Thiswillrepresentthesigmabond.Fourorbitalplates(twoofeachcolor)areattachedtoeachpolyhedronwithsamecoloredorbitalplatesadjacenttooneanotheranddifferentcoloredorbitalplatesoppositeoneanother.Thiswillrepresentthetwopibonds.Thismethodhighlightsthelinearityofamoleculeandclearlydistinguishesbetweensigmaandpibonds.However,itwillmakeitdifficulttoseethebarrier(s)torotationthatexistbecauseofthepibondsExample:ethyne(HC≡CH)
CyclicMolecules:Cyclicalkanes,alkenes,andalkynescanbeconstructedusingthesamemethodspreviouslymentioned.Example:Benzene(C6H6)isacommoncyclicmolecule(onethatyouwillrepeatedlyencounterinyourstudyoforganicchemistry)thatappliesmanyofthemodelbuildingruleslistedabove.
Furthermore,constructionofcyclicmoleculeswillenableyoutobettervisualizechairconformationsandaxialandequatorialinteractionsforcyclicmoleculeswithsubstituents.Masteryofthisskilliscriticallyimportantwhendealingwithcarbohydrates.
Example:1‐chlorocyclohexane
(Cl=axial)(Cl=equatorial)
*Whenbuildingamolecularmodel,youwilloftenencountermoleculesthatarenotonlycomposedofdifferentatoms,butalsoofsetsofthesameatomswithdifferenthybridizations.Becauseyourmodelkitcontainsalimitedsupplyofdifferentcoloredpolyhedrons,itisuptoyoutodecidewhetheryouwanttorepresentallthesameatomswiththesamecoloredpolyhedronsorwhetheryouwanttodisplaythedifferencesintheirhybridizationbyusingdifferentcoloredpolyhedrons.Ifyouchoosetorepresentsimilaratomsusingsamecoloredpolyhedrons,andthususepolyhedronsthatdonotnecessarilycorrespondtothecorrecthybridizationofanatom,makesureyoutakethisintoaccountwhenobserving/determiningthebondanglesofyourmodel.*C‐Hbondsdonotalwayshavetobeused/includedinyourmodelinorderforyoutounderstandamoleculesstructure.However,ifyouarehavingadifficulttimevisualizingtheformalcharges[ifany]orhybridizationoftheatomsinyourmolecule,itmaybeinyourbestinteresttoincludethem.
3. Nowthatyouknowhowtousethecontentsofyourmodelkittoconstructvariousmolecularstructures,thenextstepistolearnhowtousethestructuresyouconstructtohelpyoubetterunderstandthecharacteristicsofamolecule.
• Isomers:Isomersaremoleculeswiththesamechemicalformulabutdifferentspecialarrangementsofatoms.Usingthemodelsyouconstruct,youcanalterthestructureofyourmoleculetocreatedifferentisomers.
ConformationalIsomers:Tocreateaconformationalisomeryoucanrotatethe
substituent(s)ofyourmoleculearoundasinglebond.Rotatingthesubstituent(s)ofyourmoleculewillenableyoutovisualizeeclipsedandstaggered(gaucheandanti)conformationsaswellasdeterminewhetheryourmoleculeissisortrans.Thisinturnwillenhanceyourunderstandingofthevarioustypesofstrainandconsequentrelativeenergiesoftheisomersandconformationsofthevariousmoleculesyouwillencounterthroughoutyourstudyoforganicchemistry.Example:butane(CH3CH2CH2CH3)
(eclipsed)(gauche)(anti)
ConstitutionalIsomers:Tocreateaconstitutionalisomer,youcanaltertheconnectivityoftheatomsthatcompriseyourmoleculetocreatedifferentmolecules.Thesemoleculeswillhavedifferentstructuresandasaresultwillexhibitdifferentproperties.
Stereoisomers:Thereexisttwotypesofstereoisomers(enantiomersanddiastereomers).Tocreateanenantiomer(nonsuperposablemirrorimageofamolecule)invertallofyourmoleculesstereocentersbychangingthepositionofoneoftheatomsaroundeachstereocenter.Tocreateadiastereomerinvertatleastonebutnotallofyourmoleculesstereocentersbychangingthepositionofoneoftheatomsaroundthestereocenter.Thethree‐dimensionalstructureofyourmolecularmodelswillalsoenableyoutomoreeasilydeterminetheconfigurationsofthestereocenter(s)ofyourmolecule.Todeterminetheconfigurationofthestereocenter(s)ofyourmolecule,holdtheatomorgroupofatomswiththelowestpriorityinyourhandsothatthestereocenterisfacingyouandsothattheatomorgroupofatomswiththelowestpriorityisfacingawayfromyou.Iftheremainingatomsorgroupsofatomsfacingyoudecreaseclockwiseinpriority,theabsoluteconfigurationofyourstereocenterisR.Iftheremainingatomsorgroupsofatomsfacingyoudecreasecounterclockwiseinpriority,theabsoluteconfigurationofyourstereocenterisS.
Example:
(Br)
(Cl)(H)
(F)
(Sconfiguration)
• Resonance,Conjugation,&Aromaticity:Buildingthree‐dimensionalmodelsofamoleculesstructurebyusingthevariousunitsinyourmodelkittodepictnotonlythearrangementofatomsinspaceandtheirconnectivity’sbutalsothepresenceofporbitalsandlonepairelectrons,willenableyoutodeterminewhetheramoleculecandoresonance,hasconjugation,and/orisaromatic.Thisabilitywillgreatlyenhanceyourunderstandingofthepropertiesofthemoleculesyouencounterinorganicchemistry.