ORGANIC CHEMISTRY CHAPTER 2

Organicstructures
Learnthediagramsusedinfuture
Aim whyweusetheseparticulardiagrams
Howtoname
moleculesinwritingandinspeech
whatistheskeletonofanorganic
molecule
Functionalgroup
Abbreviations
Drawingorganicmoleculesrealistically

andfunctionalgroups
Hydrocarbonframeworks

organicchemistryisthestudy ofcompoundsthatcontaincarbon

iscarbon incarbon cacarbon achainofatoms cringsincluded

chainisbranched1
t

callatomsinasingle
chain chain ringby
forms itself
Aminoacids
allsoluableinwater ay
sharesimilarproperties allbothacidicandbasiccamphoteric
IcanjoinwithotheraAsforformingprotein
Theorganiccompounds chemistrydependsmuchlessonnumbersorarrangementof Cor H Moreontheothertypesofatoms
suchas 0 n s p si
I
of of
Functionalgroupsparts themoleculescontainsmallcollation theseatoms
t
anartscontainafunctionalgroups anaminoinHrorNitgroup
acarboxylicacidgroup
organicskeletons
chainsand
of
rings carbonatomsinmolecules
crudeoil literallycarbonskeletons
Nofunctionalgroups
coal containslittleelsebutcarbon
themoleculesincoalandoildifferwidelyinchemistrystructurehere
Although
onethingincommonno Groups
Functional

areveryunreactive
Many

BERealisticEconomicalandCLEAR
Drawingmolecules
zizig
Guideline l Drawchainsofatomsaszigzags

linoleicacid
Atattyacidcannotbesynthesizedinthehumanbody
but
must beancomponentofahealthydiet
found
out
Guideline2Miss theHsattachedtocarbonatomsalongwiththeCHbondsunlessthere is agoodreasonnotto
3 outthecapitalCsrepresentingcarbonatoms1unlessthere'sagoodreasonnotto
Guideline Miss
 Thenewversionofdrawinglinoleicacidisshownbelow

o whenthecarbonatomisnotpartofadoublebond
Theangleofthezigzagsisabouttgo

go
Tetrahedralanger to di
Ib
1090

1200whenit ispart
ofthedoublebond
ywo
c c

structuraldiagramscanbemodifiedtosuit theoccation
Forexample AAscanartasacidorbase
when itactsasanacid abaseremovesHt
fromcarboxylicacidgroupin a reaction
Mtv
fit foot 1 00 two Both t 0 areokay
leucine

whenitactsas abasetheaminoIN
Hisgroupisinvolved
H H
l a H Oit
H n
H l H
N
6TH W cony Huo Alonepairis apairofelectronsthatisnotinvolved
at inachemicalbond
Also not
haslonepairbut
relevantso draw
don't

threedimensionalinformationontwo dimensionalpage
structuraldiagramscanshow

Mtv mn
k N w p
leucine
r 4 way d cont
About stereochemistryofAAs mostnaturallyoccurringaminoacidsarecs attheircarbonwithcysteinebeing R andglycinenonchiral
frameworks
Hydrocarbon

of
names carbonchains

Rememberthatthesesymbolsandnamescanbe
onlyforterminalchainsofatoms
 carbonrings

phenylgroupCph when a benzeneringisattachedto a

molecule
byonlyoneofitscarbonatoms
war nun
OH H
ph
phenylalanine

Aryllar Anycompoundcontaininga benzeneringor arelatedringsystemisknownas aromatic

Arcanmeananysubstitutedphenylring inotherwordsphenylwithanynumberofhydrogenatomsreplacedby
othergroups
a
9
150 phot YY or HN ArOH
phenol
a
paracetamol
2 4btrichlorophenol
Buckminsterfullerene Cbo

Othercyclorings

LIK T grit som

Hoy
oI h
avid cyclamate
Chrysanthemum grandisol
cyclopropane cyclobutanel cyclohexane

Branches

TheisopropylgroupLipm I i pr ipr Pri

e.g yi
N
YY
Lithiumdiisopropylamideupa
Astrongbase
LiniPra
The n alkyl group forexample n PrmBuforstraightchainalkylgroupsnfornormal
N n Pr
Butylgroups
isobutylgroupCiBu Sevbutylgroup sbutylor 5But
it
r l
Atm
Tt Nti rip
theisobutylgroup
l thesebutylgroup
diisobutylaluminumhydridecruzan i Bu s Buli SBn
reducingreagent
antiBu
tertbutylgroup ltbutylortB.nl

yykIBhqyjtBn if
He tertbutylgroup
the
BHT tBu
anantioxidant
 primarysecondaryand
tertiary
A atomisattachedtoonlyoneotherCatom asecondarytoothertwocatomsandSoon
carbon
primary

of
Thereare btypes carbonatoms

methylinoattachedc Primary secondary

µ loneattached c twoattachedC
Me OH 1
methanol on Wtop
butan l ol butan 2 01
n butanol seebutanol

tertiary quaternary
battauhedl 4attachedC
It
Xor Xeon
2 methypropan 201 2 2dimethylpropan101
tertbutanol
ORGANIC CHEMISTRY CHAPTER 2

Functional groups
Alkanescontainnofunctionalgroups
extremelyunreactive
L.mn rr
beusedassolventsuchaspentaneandhexane
could
alkenes sometimescaned
olefinscontain cdoublebonds
cdoublebondsimpartreactivitytoanorganicmolecule
coloredorganiccompoundsoftencontainchainsorrings
of a c
alkynescontain c ctriple bonds

saturatedandunsaturated
atomsattachedtofour
Ingeneralcarbon otheratomsaresaturated
thoseattachedtothreetwooroneareunsaturated
CR containahydroxylcorngroup
Alcohols
on
contain
molecules
torn
oftensolubleinwater
Ethers crio r4containanoak
oxygroupcor
Etheranycompoundhas two alkyi linked
groups throughanoxygenatom
Aminesormancontain the cmin
a mino group
Basic
Formedasmeat decays
Nitrocompoundsornow groupinon
thenitro
contain
nitro
several groupinone can
molecule makeitquiteunstableandevenexplosive
n
n 00 Me
ow no me
nitro
the group Ey n
o L
nor I
TNT nitrazepam
is pin
leering
explosive

halides
alkyl fluoridesRFchlorides r u bromidesRBr oriodidesr IIcontainthe
fluorochlorobromooriodo
groups
fourhave propertiesalkyl
these similar iodides the
are most andalkyl
reactive areleast
fluorides
alsoknownasnaval
Kanes cnn.ro alkanesor
alkaneschiotomicanesbromo iodoakanes

crewand crewrn
aldehydes ketones contain carbonyl group o
o beformed oxidizingalcohols
can
aldehydes by
yaio µ
represents

acids contcontainthecarboxyl
carboxylic cr group cont
canr eact baseslosingaprotonto
with formcarboxylatesalts
Esterser comecontainacarboxylgroupwithanextraalkylgroupcw.rs
Fatareesterssaturatedfat Rgroupsaresaturatedcno c
unsaturated
fat rgroupscontainc c
Amidescrcomn riconureorr con rare
amidesformed
are
proteins betweencarboxylic groupofanother anamide
acidgroupofoneaminoacidwiththeamino linkages

Nitritesorcyanidescrew containthecyanogroup w
beintroducedintomoleculesbyrentingpotassiumcyanidewithalkanehalides
nitrilegroupscan
achlorides rwa
Acylchloridescan
o Too tobe
active foundinnature
11
me a
chloride
acetyl
acetals Roi or
anacetal
Carbonatoms carryingfunctionalgroupscanbeclassified oxidation level
by
Thecarboxylicoxidationlevel 3bonds

Rion R OR R wHv R EN R a
acids
carboxylic esters amides nitriles acylchlorides
beeasilyconvertedintonitriles
Amidescan bydehydration removalofwater sotheyaresameoxidationlevel
Thecarbonatomhas 3bondstoneteroatomsandoniyonetocorri
TanatomthatisnotCorti
leveldetermined
oxidation bythenumberofhetero
atomsbondedtocarbon
oxidationstatedetermined
bythenumberofbondsoncarbon inaudingthosetocandH
Inallthesecompoundscarbonhasfourbondsandisinoxidationstate14
Thealdehydeoxidationlevel12bonds
012
k 14 Riders Roy Uncle
aldehydes ketones
R2 dichloromethane
Racetals H t
Contains acarbon twobonds
atomwith toheteroatom
Thealcoholoxidationlevel cibond
Kray R o R2 Kru R Br
alcohols ethers alkylhalides
contains acarbonatomswithonlyonebondto aheteroatom
fromalcoholswithoutoxidationorreduction
Alleasilymade
Thealkaneoxidationleveltobond
Hugh
H
methane
H
wobondtoheteroatoms
Thecarbondioxideoxidationlevelcabonds
i u a F
c c c c it
Eto ret ai a ai a
y carbontetrachloride CFC au
carbon diethylcarbonate gg yy
dioxide usetuteagentfor formerlyusedasa theaerosolpropellants
oneof
addingestergroups drydeaningfinia totheozonelayer En
causingdamage

summary
ORGANIC CHEMISTRY CHAPTER 2
Namingcompounds
Epseth
systematic nomenclature
describesthehydrocarbon
framework
systematicnamescanbedividedinto3Parts describes functional
the group
indicateswherethefunctionalgroupattachedtotheskeleton

Names forthehydrocarbonframework

NameoffunctionalgroupsThename
Has Fass ofafunctionalgroupcanbeaddedtothenameofhydrocarbonframework
eitherasasuffixor as aprefix
countallofthecarbonatomsinthechainevenifoneofthemispartof afunctionalgroup

Buon
c
Ey
do
To benzene

functionalgroupattachedto a benzene
ringisnamedsimilarly
Numbersareusedtolocate
functionalgroups
whennumbersareusedthecarbonatomsarecountedfromoneend
Inmostcases bothendscouldbeusedforcountingtheonechosen isalwaystheloweroneoftwo
Functionalgroupnamescouldbesuffixor prefixthenumber
alwaysgoesdirectlybeforetheFGnames

Formorethanonefunctionalgroups
 Forcycliccompoundswithoutends usenumberstoshowthedistancebetweentwogroups Istartfromthe C
carryingoneoftheFG Thisrulealsoworksforchainsor ringswithbranchedskeleton

ioftenabbreviatedasomandpi
orthometaand
para
workswithbenzenerings

for
thomeanstwogroupsarenexttoeachotheronthe ringeventhoughtheatomsmaynothappentobenumbered1and

whatdochemistsreallycallcompounds
Namesforwellknownandwidelyusedsimplecompounds
REMEMBER They'recommonlyusedinIab

chemistsusespecial
name forfourfragmentsbecausetheyhavemechanisticaswellasstructuralsignificance

O
f v t I
quitereactive
unreactivetypically
oftenreactive
fairly
fairlyunreactive

namesforcomplicatedbutstillwellknownmolecules

poison

TNT
 compoundsnamed as acronymsk1347347Bog

forwhichchemistsusesystematicnames
compounds

Hath
tellsyoutheframeworksize
thesenamescontain asyllablethat
PentaforCs octaforCsrnona forCgundeeaforcmanddo decaforGv

Howshouldyounamecompounds
structurefirstandworryaboutthenameafterwards
sixpointsinorderofimportance Drawa
Learnthenamesofthefunctional groupscesternitrile etcI
Learnanduse thenamesofafewsimplecompoundsusedbyallchemists
Inspeechrefertocompoundsas thatacid eorwhatever1whilepointingtoa diagram
Grasptheprinciplesofsystematicnomenclatureanduseitformediumsizecompounds
keepanotebooktorecordacronymstrivialnames structuresetcthatyoumayneedlater

Importantstructurestolearn
ORGANIC CHEMISTRY CHAPTER 4 structureofmolecules
Howweknowthatelectronshavedifferentenergies
Aim
Howelectrons fit intoatomic orbitals
Howatomicorbitalscombine tomakemolecularorbitals
tetrahedralstructures
Whyorganicmoleculesadoptlinearplanarand
Connection betweenshapeandelectronicstructure

Picturingtheshapeandenergyofmolecularorbitals insimplemolecules
of
Predictingthelocations lonepairsandemptyorbitals

Electronsoccupy atomicorbitals

canneverknowexactlyboth
Heisenberg's uncertainty principle we thelocationandthemomentumofanyparticle

Thehydrogenatom ThehydrideCHIion The heliumatom

also3Dandareknowasorbitalsoratomorbitals
Thevibrationanalogy vibration canadoptare
functionsknownas wavefunctions
Theshapeoftheseorbitalsare determined
bymathematical

Thenextorbitalhasonenode
zsorbital 2 becauseit'sanorbitalwithanode
s becausetheorbitalisstillspherical

Sandp orbitalshavedifferent shapes

turnsout thatforanorbitalwithonenodesuchasthevsorbitalthenodedoes notneedtobespherical
node
The can alternativelybeaplane
This
a lternative arrangementforanorbitalwithasingleplanarnodegivesusanewtypeoforbitalthezporbital

axis
unlikeis or2sorbitalstheZporbitalisdirectional itpointsalongthe Inthreedimensionstherearethreepossibleorientations
theaxiseach whichgiveriseto anewzp
for of orbital 2Paspy 2Pa
electronsarenegativelychargedandrepeloneanother
at of
thereis achoice equalenergyorbitalsthey untilthey
occupydifferentorbitalssingly
are to
f orced start
p up
airing

theboronatom thecarbonatom thenitrogenatomtheoxygenatom thefluorineatom Theneonatom

Theentiresetoforbitalsisgoingdowninenergybecausethenucleus isattractingtheelectronsmorestrongly
Thephaseofanorbital

Thereis a changeofphase ateachnode

Anodesplanecaporbitalforexample dividestheorbitalintotwopartswithdifferentphasesonewherethephase
functionispositive
andonewhereitisnegative
ofthewave
Thephasesareusuallyrepresentedbyshading

Furtherorbitalnames spdf
Fourshortclarificationsaboutorbitalsbeforewegoon
orbitalsdonotneedelectronsinthem
Electrons befoundanywhere in a orbitalexceptin anode
may say
A theseorbitalsofanatomaresuperimposed oneachotherTheisorbitalisnotthemiddlepartofasorbitalTheisandas
ownrightsbuttheasorbitaldoesoccupysomeof
orbitalsareseparateorbitalsintheir thesamespaceasthe isorbital

Aswemoveacrosssubsequentrowsoftheperoidictablestartingfromsodium theis as2porbitalsarealreadyfilledwithelectrons

sowemuststartputtingelectronsintothe35and3Porbitalsthenthe4S3DandAPorbitals
 ORGANIC CHEMISTRY CHAPTER 4 structureofmolecules

Molecularorbitals diatomicmolecules

wethinkofmolecularorbitalsasbeingbuildupfromacombinationofatomicorbitals
Thecombinationofwavescasatomicorbitalsarewavefunctions1 couldbeeitherconstructivelyCinphase ordestructively1outof
phaserTheatomicorbitalsarecombinedinthesameway

Theresultingorbitalsbelongtobothatoms theyaremolecularratherthanatomicorbitals
Forexamplethecombinationofatomicisorbitalsi
ahigherin
energy

put2e
Inuclei
inenergy
glower the
than
constituent
is
orbitals

MolecularorbitaltheoryCMOtheory ForthecaseofH
TwoatomicorbitalsCAoscombinetogivetwomolecularorbitalsCmos you thesamenumberofMosoutasyou
alwaysget
putAosin
Addingthewavefunctions combininginphase
ofthetwoAosmakesthebindingorbitalsubstitutingthemcombiningthem
outofphasemakestheantibondingorbital
thetwoatomsarethesameibothH eachAocontributesthesameamounttoMosnotalwaysthecase
Since
ThebindingMoislowerinenergythantheAOs
Theanti bindingMoishigherinenergy thantheAos
EachHatomhadinitiallyone thespinoftheseelectronsis unimportant
electron
ThezeendupintheMolowestinenergy thebindingMo
Anyorbitalmaycontainnomore than2electrons
Theze betweentwonucleiinthebondingmoholdthemoleculetogethertheyarethechemicalbond
Thesearearelowerinenergyinthemo moleculeismorestable thanitsconstituentatoms energyisgivenoutwhentheatoms
the
combine

wemustputinenergytoseparatethetwoatomsagainandtobreakthebond
Breakingbonds
promotinganelectronfromthebondingmototheantibondingMobreaksthechemicalbond
whyhydrogen is diatomicbutheliumisnot

camelout

heliumatomicorbital

Bondorder
onlyifthere'remore e inbondingMosthanantibondingMoswilltherebeanybondingbetween2atoms

FbndantibTf
fbondorde.ve tnofe inndingM0s

9 bondordert.HN i singlebond
bondorderHeu o nobond

Formingbondsusingzsandzpatomicorbitals Gand Norbitals

combining 25orbitalsaresameas is orbitals buthigherenergies Becausethe25orbitalsarehigherin

energy it'salsobiggerthan isorbitals

Thebondingorbitalsfrom is is and2525haveimportantfeatureincommon cylindricallysymmetrical

Bondingorbitalswithcylindricalsymmetrylike
thisareknownas Gsigmaorbitals
ThebondswhichresultfromputtingZeintotheseorbitalsareknowas 6bonds
TheantibondingorbitalswhichresultfromcombiningtheseHosarealsocylindricallysymmetricalandarecalled
6orbitalswith donatingtheirantibondingcharacter
Foruporbitals
Endon overlap
combinethetwo217orbitalsout phase aswiththe25 orbitals wehave a nodebetweenatoms
of
an antibondingorbital

If wecombinein phase wegetbondingorbital

6bondcanbemadefrom s or patomicorbitals providedtheyforma cylindrically symmetrical

molecularorbital

side onoverlapEachatompresentsitsother2porbitalsforside on overlap

Foroutofphasecombination

Forinphasecombination

TheseMDsdonothavecylindricalsymmetry needtorotate180abouttheaxisbetweenthenuclei
startbutwithoppositephase
beforegettingbacksthlookinglikethe
Asaresult thissymmetrywasnamedas a thebondingorbitalis aorbitalandtheantibondingorbitalis at
orbital Bondsformedbyfillingaorbitalsarecalled 2bonds
Moreoverlapispossiblewhen heAosoverlapendonthanwhen theyoverlapsideon Asaresulttheupup
orbitalislowerinenergythantheupupaorbitals
 For Nv Eachnitrogen atomcontributes7 e tothemolecule sowehavetofillthisstackof
orbitalswith14er

nitrogen atom
energyleveldiagram

Theelectrons inthe 6 bond lie between 2 nucleiwhilethe electronsinthe 2 Nbonds lie

Ekins ARITAAFG
intwoperpendicular cloudsflankingthecentral6bond

Bondorder 10 4
CNN
2 3
wecan'tignorethe e that are notinvolved inbonding 8ofthemtogetherTheycanbethought
asbeinglocalized oneachofthe Natoms

Thefour e on is orbitalsarelowenergyinnershelle that are

notinvolved inthechemistry of Nz
providethenonbonded lonepairslocatedone on

µ.foueach N atom
ORGANIC CHEMISTRY CHAPTER 4 structureofmolecules

Bondsbetween differentatoms
whathasbeenchanged
atomisdifferent
Thenumberofelectronscontributedbyeach
TherelativeenergiesoftheAosbeingcombined thegreaterthenumberofprotonsinthenucleus thegreater
theattractionandhencethemoretightlyholdmorestableandlowerinenergytheelectronbecomes

1 uronegativityThemoreelectronegativityanatomis themore itattractselectronsthelowerinenergyareitsAOs

e
increases This is
Itincreasesacrosseachrowanddecreasesdownearncolumneventhoughthenuclearcharge
becauseonceelectronsstart fillinganewsheertheyareshieldedfromthenucleusbyallthee inthelowerenergy
fieldshells contributiontonitrogenAos
havegreater
bondingorbitals

anyti
overrane distributionisskewed polarized
towards 0

Qaiaiten Ination

tooxygenAos

gofnitricoxideNo
Molecularorbitaldiagram

BondorderNo 242

wecan'teasilyrepresenthalfabondinvalencebondtermssoweusuallydraw
radical NOwithdoublebondrepresenting4bonding e
Theremaining 7 e canbeshown as 3lonepairsandoneunpairede
unpairede occupiedanorbitalclosertoN soputit onN

Fortwoatomsforming a bonddifferhugelyinelectronegativity
AOsforsodium

IIItats MeTAHITI
up 3s Nata
Endupwith
AOs forchloride

FETE HIP IEIFHEET

TheseHosaretoo
farapartinenergytocombine
toformnewMosandno covalentbond isformed
1
Molecularorbital forNau
diagram

TheionicbondinginNauisduesimplytotheattractionbetweentwooppositechargedions there'snooverlap
Summary

otherfactorsaffectingdegreeoforbitalinteraction
Aos
similarenergiesforgoodinteractionbetweentwo
Howtheorbitalsoverlap
thanitdoeswith3Pand orbitals
sizeoftheAoscaporbitaloverlapsmuchbetterwithanother zporbital

Thesymmetryoftheorbitals

ofmoleculeswithmorethantwoatoms
Molecularorbitals

pµ Amoleculeofmethane
enclosedin a cube f2sAocan
Thecarbon overlap
Thehydrogen isorbitalscanoverlap
withthethreesporbitals
withallfourhydrogenisAos
atonce

4bonds C cangiveus 25 and 3 217 while 4xHgive us 44Is

ORGANIC CHEMISTRY CHAPTER 4 structureofmolecules
Hybrization
ofatomicorbitals
Methane

Forgetting apictureofmethanewithA with4equivalent

i equivalentpairsofelectrons weneedtostart
Aos on c which we have
don't

Butwecangetifwecombinethecarbonasandzpfirsttomakefourneworbitals

0
Eachsp 3orbitaltakesthreequartersofitscharacterfroma porbitalandonequarterfroman sorbital
Ithasa planarnodethroughthenucleuslikea porbitalbutonelobeislargerthantheotherbecause theextra
of
contribution
ofthe zsorbital

Theelectronsarespatiallydistributedexactlyastheywereinourpreviousmodelbutnowwecanthink themasbeing
locatedin 4bonds
of
Ethane
3Aos orientatedtowardsthethreehydrogenatoms leavingonesp3
Eachcarbonuses3 sp orbitaloneachcarbonforthe
c cbond

Ethene ethylene
Aplanarmoleculewithbondanglescloseto1200
Inthiscaseweneed3equivalentbondsfromeachcarbonatom1onetomake a c cbondandtwotomake c Hbonds

O_O
tomakeallAosintheplane

2pm 2Pa

Thefactthatthesidewaysoverlapoftheporbitalstoform a abondisnoteffectiveastheheadonoverlapofthe
orbitalstoforma 6bondmeans ittakeslessenergytobreak a c c abondthana c c obond about200KSmoi i
comparedto350 KJmoi 1

Ethyne
Has a c cbond Eachcarbon bondstoonlytwootheratomstoform a linearskeleton
onlythecarbon and2pmhavetherightsymmetrytobondtothetwoatoms atonce leavingspyand2pztoform
aMoswiththezporbitals ontheothercarbonatom
wecanhybridizeanyatoms

Thecarbonylgroup

oxygenismoreelectronegativethancarbonhas no consequencesforthisdiagram
Firstly itmakestheenergyoftheorbitalsofa G obondlowerthan abond
thereactivityofalkenesandcarbonylcompounds
secondly polarization It receivesgreatercontributionfromtheporbitalon0thanfromtheporbitalonc

7 orbitaliscloserinenergytothe p
of
orbital ethano
a beingempty noeffectonthestructure

Irbital
ofo_0bondbutwitheffectonreactivity
iseasiertoputelectronsintotheat
orbitalat hecendthanat 0end
a ismoresimilarinenergyto
theporbitalon0than porbitalonc