MolecularStructure

Valence
Carbon4bonds Nitrogen3bonds Oxygen2bonds Halogens1bond

FormalCharge=(Group#)(#nonbondingelectrons)(1/2#bondingelectrons)

IndexofHydrogenDeficiency
TheNUMBEROFPAIRSofHYDROGENSrequiredtobecomeaSATURATEDALKANE
ForResonanceStructuresAtomsmustnotbemoved,onlyELECTRONSMOVE
AromaticMolecules (4n+2)electrons
HydrogenBondingoccurswhenHYDROGENisbondedtoaHIGHLYELECTRONEGATIVEATOM

ConformationalIsomers
NotTRUEisomersdifferentspatialorientationsofthesamemolecule

ChiralityAchiralcarbonisbondedtoFOURDIFFERENTSUBSTITUENTS
AbsoluteConfiguration
Rectus(totheright)&Sinister(totheleft)accordingtopriority
TheLARGESTMOLECULARWEIGHTistheHIGHESTPRIORITY(1)
Hydrogenisalwaysthelowestpriority(4)andshouldbeorientedoutthebackofthepage
RelativeConfiguration
TwomoleculeshavetheSAMErelativeconfigurationaboutacarboniftheydifferbyonlyONE
SUBSTITUENTandtheothersubstituentsareorientedidenticallyaboutthecarbon
OpticalActivity&ObservedRotation
Opticallyinactivecompoundsmayhave
Nochiralcenters & Equalamountofbothstereoisomers(aracemicmixture)
OpticallyActivecompoundscanbe
1) +/drotateslightCLOCKWISE
2) /lrotateslightCOUNTERCLOCKWISE
StructuralIsomers
1) Samemolecularformula
2) DIFFERENTBONDTOBONDCONNECTIVITY
3) Isobutane(C
4
H
10
) vs. nbutane(C
4
H
10
)
4) AreNOTTHESAMEMOLECULE

StereoisomerSUBTYPEEnantiomers
1) Samemolecularformula
2) Samebondtobondconnectivity
3) MIRRORIMAGESOFEACHOTHER
4) AreNOTTHESAMEMOLECULEoppositeabsoluteconfigurationsatchiralcenters
Samechemicalandphysicalcharacteristicsexceptfor
1) Reactionswithotherchiralcompounds
2) Reactionswithpolarizedlight
StereoisomerSUBTYPEDiastereomers
1) Samemolecularformula
2) Samebondtobondconnectivity
3) AreNOTMIRRORIMAGESOFEACHOTHER
4) AreNOTTHESAMEMOLECULE
GeometricIsomers(aspecialtypeofdiastereomer)
Cisisomers&Transisomers
MesoCompounds
1) WhenTWOchiralcentersOFFSETEACHOTHER
2) OpticallyInactive
3) PLANEofSYMMETRYdividescompoundintotwohalvesthataremirrorimages
StrongerDipoleMoment
StrongerIntermolecularForces
HigherBoilingPoints

HigherEnergyLevelHigherHeatofCombustion
FunctionalGroups
Alkane H
3
CCH
3
Alcohol ROH
Alkene H
2
C=CH
2
Ether ROR
Alkyne HCCH Amine RNH
2
R
2
NH R
3
N

Aldehyde Ketone CarboxylicAcid Ester Amide

Alkyl R Halogen[X] F/Cl/Br/I
Hydroxyl OH Geminaldihalide
Alkoxy OR Vicinaldihalide

Hemiketal R|R|OR|OH
Ketal R|R|OR|OR

Hemiacetal H|R|OR|OH
Acetal H|R|OR|OR

MesylGroup(Ms) TosylGroup(Ts)
H|R|OR|OH

Carbonyl Acyl Anhydride

Aryl Benzyl Hydrazine Hydrazone

Vinyl Allyl Nitrile Epoxide

Enamine Imine Oxime Nitro Nitroso

Hybridization BondAngles Shape
sp 180 Linear
sp
2
120 TrigonalPlanar
sp
3
109.5 Tetrahedral,Pyramidal,orBent

Hydrocarbons,Alcohols,&Substitutions
Alkanes
MethylCH
3
PrimaryCRH
2
SecondaryCR
2
H TertiaryCR
3

LowestDensityofallgroupsoforganiccompounds
Methane,Ethane,Propane,andButanearegasesatroomtemperature
INCREASEDMolecularWeight|INCREASEDBoilingPoint|INCREASEDMeltingPoint
INCREASEDBranching|DECREASEDBoilingPoint|INCREASEDMeltingPoint
CycloAlkanes
CHAIRandBOATconformations
LargeSubstituentsareMORESTABLEintheEQUATORIALPOSITION

Combustion(radical&exothermicreaction)
CH
4
+ 2O
2
+ energy CO
2
+ 2H
2
O+ heat
COMBUSTIONisaRADICALREACTION
HEATOFCOMBUSTIONchangeinenthalpyofacombustionreaction

Halogenation(radical&exothermicreaction)
AlkaneswillreactwithHALOGENSinthepresenceofheatorlighttoformaFREERADICAL
HOMOLYTICCLEAVAGEbondisbrokenwithoneelectrongoingwitheachatom
1) INITIATION
a. Halogenisdiatomicmolecule,andHOMOLYTICCLEAVAGEresultsin2freeradicals
2) PROPAGATION
a. HALOGENRADICALremoveshydrogenfromalkane,creatinganALKYLRADICAL
b. ALKYLRADICALreactswithdiatomicmoleculecreatingALKYLHALIDEandaNEWHALOGEN
RADICAL
3) TERMINATION
a. TWORADICALSBONDorRADICALbondstothewallofthecontainertoendthechainreaction
StabilityofALKYLRADICALS: 3>2>1>methyl
FluorineVERYREACTIVE,majorproductisPRIMARY
ChlorineREACTIVE,majorproductiswhateverisLEASTSTERICALLYHINDERED
BromineSELECTIVE,majorproductisTERTIARY
Dehydrationofanalcohol(E1Reaction)
Alcohol+ hotconcentratedH
2
SO
4
Alkene+ H
2
O+ HSO
4

SaytzeffRuleMAJORproductofELIMINATIONistheMOSTSUBSTITUTEDALKENE

Dehydrohalogenation(E1orE2Reaction)
E1MechanismWITHOUTastrongbase2stepsunimolecular(substrateonly)
1) HalogendropsoffformingaCARBOCATION
2) Hydrogenisremovedleavingalkene

E2MechanismSTRONGBULKYBASE1stepbimolecular(substrate&nucleophile)
1) BaseREMOVESahydrogenadjacenttothehalogen
2) Halogendropsoffleavingalkene

InELIMINATION,basepullsoffahydrogen
InSUBSTITUTION,nucleophileattackscarbon

CatalyticHydrogenation(additionreaction)
Heterogeneouscatalyst(Ni/Pd/Pt)promotesSYNaddition
HydrogenationisEXOTHERMICwithhighenergyofactivation

OxidationOfAlkenes
OZONOLYSISozoneisVERYreactive,breakingrightthroughalkenesandalkynes

AlkenesINTOtwoCARBONYLGROUPS
AlkynesINTOtwoCARBOXYLICACIDS

ElectrophilicAddition
ElectrophilesattractedtoelectronsPOSITIVELYCHARGED & AlkenesareELECTRONRICH

WhenHF/HCl/HBr/HIareaddedtoanalkene:
MarkovnikovsrulethehydrogenwilladdtothecarbonwiththeMOSTHYDROGENS

HBr&Peroxides(ROOR)addtoalkenesANTIMARKOVNIKOV

HydrationofanAlkene
Alkene+ colddiluteH
2
SO
4
+ H
2
O Alcohol

Oxymercuration/Demercuration
1) Oxymercurialionattacksalkene,formingtriangularmercurycomplex
2) H2OattacksANTItoformanALCOHOL,losingthemercurygroup
3) IfROHisusedinsteadofwater,anETHERisformed

Hydroboration
Alkene+ BH3+ peroxide Alcohol(antimarkovnikov)

HalogenationOfAnAlkene
Br
2
andCl
2
addANTItoalkenestoformVICDIHALIDES

Benzene
UndergoesSUBSTITUTION,notaddition
Flatmolecule,stabilizedbyRESONANCE
Ortho/Meta/Para

ElectronDonatingGroups(ACTIVATEStheRing)
STRONGLYdonating(ortho/paradirecting)
O

OH NR
2

MODERATELYdonating(ortho/paradirecting)
OR
WEAKLYdonating(ortho/paradirecting)
R

ElectronWithdrawingGroups(DEACTIVATEStheRing)
STRONGLYwithdrawing(metadirecting)
NO
2
NR
3
+
CCl
3

MODERATELYwithdrawing(metadirecting)
Carbonyls SO
3
H CN
WEAKLYwithdrawing(ortho/paradirecting)
Halogens

SN1(substitution/nucleophilic/unimolecular)
1) HydrogendropsoffformingaCARBOCATIONratedeterminingstep
2) Nucleophileattacksthecarbocation

SN2(substitution/nucleophilic/bimolecular)
1) Nucleophileattackssubstratefrombehindknocksleavinggroupfreewhilebindingtosubstrate

Nucleophilicity
ABASEisastrongerNUCLEOPHILEthanitsconjugateacid,butaBASEisNOTNECESSARILYaNUCLEOPHILE

IfaNUCLEOPHILEbehavesasaBASE,ELIMINATIONRESULTS

LESSBULKYNUCLEOPHILE,withNEGATIVECHARGE&POLARIZABILITYaddto
nucleophilicity
Solvents
POLARPROTICSOLVENTSstabilizethenucleophileandanycarbocationthatforms
INCREASES
N
1SPEED DECREASES
N
2SPEED

POLARAPROTICSOLVENTScannotformhydrogenbonds
INCREASES
N
2SPEED DECREASES
N
1SPEED

LeavingGroups
ThebestleavinggroupsarethosethatareSTABLEWHENTHEYLEAVE
TheWEAKERtheBASE,theBETTERtheLEAVINGGROUP

SN1vs.SN2
SN1 SN2
Nucleophile N/A StrongNucleophile
Substrate 2/3 Methyl/1/2(unhindered)
Solvent Polarsolventincreasesrate PolarsolventDECREASESrate
Speed [Substrate] [substrate][nucleophile]
Stereochemistry CreatesRACEMICmixture INVERTSaroundchiralcenter
Skeleton Maybeskeletalrearrangement NOrearrangement

Alcohols
BPgoesupwithincreasingMolecularWeight
ROHhydrogenbonds,dramaticallyraisingMPandBP
AlcoholscanbehaveasACIDS,withmethylOHbeingtheSTRONGESTACID

GrignardSynthesisofAlcohols

OxidationOfAlcohols
OxygenHydrogenratioINCREASESOxidationoccurred
OxygenHydrogenratioDECREASESreductionoccurred

ThePinacolRearrangement
InVICINALDIOLS,DEHYDRATIONproductisaKETONEorALDEHYDE

Ethers
ALMOSTALWAYSTHEANSWERtoSOLVENTQUESTIONSontheMCAT
ROR+ HBr ROH+ RBr

AciditiesOfFunctionalGroups

Alkane Alkene Hydrogen Ammonia Alkyne

ALDEHYDE
Alcohol Water
CARBOXYLIC
ACID

Carbonyls&Amines
TheCarbonyl
CarbonDOUBLEBONDEDtooxygen PLANARStereochemistry PARTIALPOSITIVEonthecarbon

Aldehydes&Ketones
ALDEHYDE R(C=O)H KETONE R(C=O)R
FORMALDEHYDE H(C=O)H ACETONE CH3(C=O)CH3
LowerBoilingPointthanALCOHOL

carbonisVERYACIDIClosesaprotontobecomeanENOLATEION(stabilizedbyresonance)
Indicarbonyls,theENOLATEIONICformismoreprevalent
KETOENOLTautomerization

FormationofAcetals
KETONE+ALCOHOL HEMIKETAL+ALCOHOL KETAL

ALDEHYDE+ALCOHOL HEMIACETAL+ALCOHOL ACETAL

Acetals/KetalscanactasBLOCKINGGROUPS
toPRESERVEaCARBONYLGROUP

AldolCondensation
Aldehyde+Aldehyde Ketone+Ketone Aldehyde+Ketone

hydrogenisabstracted,forminganENOLATEION
carbonofENOLATEattackscarbonylcarbonofothermolecule,formingALKOXIDEION
ALKOXIDEIONgrabsahydrogentobecomeanALDOL(aldehyde&alcohol)

Halogenation&HaloformReaction
HALOGENSaddtoKETONESatthecarboninpresenceofacidorbase
METHYLKETONEwithBASE,thecarbonisCOMPLETELYHALOGENATED
HALOFORMbreaksoff(CHCl3/CHBr3/CHF3)leavingCARBOXYLATEION

WittigReaction
Ketone/Aldehyde+ Ylide(carbanion) ALKENE

UnsaturatedCarbonyls
Alsocalled1,4additionaddingHXformsENOLTAUTOMERandthenKETO

CarboxylicAcids
CarboxylicAcid RCOOH FormicAcid HCOOH
BenzoicAcid C6H5COOH AceticAcid CH3COOH
Ifthenameendsinate RCOO

MakeSTRONGHYDROGENBONDStoformdimmers
ThiseffectivelydoublesM.W.significantlyincreasingB.P.

Decarboxylation
CARBOXYLATEIONLOSESCO2tobecomeKETOENOLTAUTOMERS

CarboxylicAcidDerivativesACYLCHLORIDES
MOSTREACTIVEOFALLCARBOXYLICACIDDERIVATIVES
ACIDCHLORIDE+ H2O CARBOXYLICACID+ HCl
ACIDCHLORIDE+ ROH ESTER+ HCl
ACIDCHLORIDE+ RNH2 AMIDE+ HCl
ACIDCHLORIDE+ RCOOH ANHYDRIDE+ HCl

ACIDCHLORIDE+ H2O CARBOXYLICACID+ HCl

ESTER+ H2O CARBOXYLICACID+ ROH
AMIDE+ H2O CARBOXYLICACID+ RNH2
ANHYDRIDE+ H2O CARBOXYLICACID+ RCOOH

ALDEHYDES/KETONES NucleophilicADDITION

CARBOXYLICACIDS/DERIVATIVES NucleophilicSUBSTITUTION

CarboxylicAcidDerivativesESTERIFICATION

CarboxylicAcidDerivativesTRANSESTERIFICATION

CarboxylicAcidDerivativesACETOACETICESTERSYNTHESIS
ACETOACETICESTER+ RX+ H+/HEAT KETONE+ CO2

CarboxylicAcidDerivativesREACTIVITIES
Amide Ester CarboxylicAcid AcidAnhydride AcylChloride

Amines
Ammonia NH3
AmineDegreedependsonnumberofATTACHEDRGROUPS
1) ActasLEWISBASEDONATINGLONEPAIROFELECTRONS
2) ActasaNUCLEOPHILEwhereLONEPAIRofELECTRONSattacksPOSITIVECHARGE
3) NitrogencantakeonaFOURTHBOND(+)
4) NitrogencanHYDROGENBONDincreasingBOILINGPOINTandSOLUBILITY

CondensationwithKetones
AMINE+ ALDEHYDE/KETONE WATER+ IMINE/ENAMINE

WolffKishnerReduction
HYDRAZINE+ALDEHYDE/KETONE ALKANE+WATER+N2

AlkylationofAmine

HofmannElimination

Amines&NitrousAcid
NITROUSACID+1AROMATICAMINE DIAZONIUMION

TheDiazoniumGroupisEASILYREPLACED

Amides
Acetamide Nethylacetamide

Lactams(CYCLICAMIDES)

HofmannDegradation

PhosphoricAcid

Whenheated,phosphoricacidformsPHOSPHORICANHYDRIDES
Triphosphatesexistasnegativeions,suchasATP

Biochemistry&LabTechniques
FattyAcids
LONGCARBONCHAINWITHCOOHontheend

AminoAcids
ZwitterionDIPOLARION(onesideandoneside+)

BASICAMINOACIDS
Histidine
Arginine
Lysine

ISOELECTRICPOINTthepHwhere100%oftheaminoacidsareZWITTERIONS

Carbohydrates
1) GENERALFORMULAC
n
(H
2
O)
n

2) CanhaveeitherALDEHYDEorKETONEgroupstobecalledALDOSEorKETOSE
3) ANOMERICCARBONtheONLYCARBONattachedtoTWOOXYGENS

LabTechniques
SPECTROSCOPY
NuclearMagneticResonance(NMR)
InfraredSpectroscopy(IR)
UltravioletSpectroscopy(UV)
SPECTROMETRY
MassSpectrometry
SEPARATIONTECHNIQUES
Chromatography
Distillation
Crystallization
Extraction

NMR
1) EachpeakisaCHEMICALLYEQUIVALENTHYDROGEN
2) SPLITTINGPEAKSiscreatedbyNEIGHBORINGHYDROGENSasbyn+1(n=#ofneighboringcarbons)
3) TotheLEFTisDOWNFIELD(unshieldedbyelectronegativeatoms)

IRSpectroscopy
CARBONYLGROUP 1700
OHGROUP 32003600

UltravioletSpectroscopy
UVstartsaround220nm(butadiene)
1) EachadditionalCONJUGATEDBONDadds3040nmtothewavelengthABSORBEDMOST

VisibleSpectrum
Ifcompoundhas8+CONJUGATEDDOUBLEBONDS,itsabsorbanceenterstheVISIBLESPECTRUM
Carotenehas11CONJUGATEDDOUBLEBONDS,withanabsorbanceofabout500nm
CaroteneabsorbstheBLUEGREENcolorof500nm,anddisplaystheCOMPLEMENTARYCOLORofred
orange

MassSpectrometry
MassSpectrometrygivestheMOLECULARWEIGHT
Samplemoleculesarebombardedbyelectrons,causingthemtobreakapartandIONIZE
Ionsareacceleratedthroughamagneticfield,mostare+1
RADIUSOFCURVATUREdependsupontheMASStoCHARGERATIO(m/z)
BASEPEAKthelargestpeak
PARENTPEAKthepeakmadebythemolecularion(sameasORIGINALMOLECULEbutwithoutONE
ELECTRONsoithasa+1charge)

Chromatography
SeparationofamixturebypassingitoverorthroughamatrixthatADSORBSdifferentcompoundswith
DIFFERENTAFFINITIES
MOBILEPHASE/STATIONARYPHASE
TheMOREPOLARcompoundmovesmoreSLOWLYbecauseitbindstothePOLARSTATIONARYPHASE

Distillation
SeparationbaseduponVAPORPRESSURE
SeparatesasolutionoftwovolatileliquidswithaBOILINGDIFFERENCEofatleast20C
ThecompoundwiththeLOWERBOILINGPOINT(HIGHERVAPORPRESSURE)willboiloffandcanbe
captured

Crystallization
WorksontheprinciplethatPURESUBSTANCESFORMCRYSTALSmoreeasilythanimpuresubstances
CrystallizationisVERYINEFFICIENT

Extraction
BasedonSOLUBILITYDUETOSIMILARPOLARITIES
LIKEDISSOLVESLIKE