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.