Molecular Model Building Instruction Manualharding/tutorials/models/models01.pdf · Molecular Model...
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Molecular Model Building Instruction Manual Molecular Model of Caffeine Based on a Chemistry 14C extra credit project, fall 2008 Models of organic molecules provide a physical representation of the three‐dimensional arrangement of atoms in space. Using a molecular model kit throughout your study of organic chemistry will enable you to better understand both the chemical and physical properties of the molecules you encounter. 1. The first step to successfully using your molecular model kit is to become acquainted with the contents of your kit and what each unit represents. • Your model kit contains several polyhedrons and spheres that will represent the atoms you work with. The Atom Table specifies the number of holes on each polyhedron and sphere and identifies which are used to form a specific hybridization. The Bond Table specifies the scaled bond length represented by each of the connectors in your kit along with a list of common bonds you will encounter throughout your study of organic chemistry and the corresponding connector that you should use. (for bonds in grey, more than one connector can be used) Atom Table Black Dark Blue Red Green Dark Grey Light Blue Light Grey Light Blue (Sphere) # of holes 4 4 4 4 5 5 14 2 sp 3 X X X X sp 2 X X sp X
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.
