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CHEM1021 Lecture 7 PDF
CHEM1021 Lecture 7 PDF
CHEM1021 Lecture 7 PDF
groupsarethesame.
NOTa
stereocentre!
Onlyhas3
different
groups,not4
limonene
Howmanyisomersdoesthisstructuralisomerof
limonenehave?
Only1!Moleculehasno
stereocentres.
145
Inorganic Stereoisomers
Geometrical Isomers
Same chemical composition, different
ligand arrangement
Have different chemical properties
Found for square planar and octahedral
complexes
Square planar
cisplatin
http://pubs.acs.org/cen/coverstory/83/8325
/8325cisplatin.html
LearningObjectives
(Stereochemistry)
Understandconceptofisomerism.
Recallconceptsofstructureandbondingfromlast
semester.
Distinguishbetweenthedifferenttypesofisomers:
structuralisomers(differentconnectivity)
stereoisomers (sameconnectivity)
configurationalisomers(bondsneedtobebrokento
interconvert)
enantiomers (nonsuperimposablemirrorimages)
diastereoisomers (asappliedtoE/Zisomers)
conformational isomers(rotationofsinglebondsonly)
Systematicallydescribestereochemistry(E/Z,R/S).
148
Appreciatetherelevanceofallthisinbiologyandmedicine.
Youshouldbeableto
Identifyanddefinestructuralisomersandstereoisomers
Defineandgiveexamplesofthefollowingconcepts:
Stereocentre
Enantiomer
Diastereomer
Chiral
Achiral
Conformationalisomers
Determinewhetheranobjectoramoleculeischiral.
Identifystereocentres inamoleculegiventhemolecularstructure.
Definetherelationshipbetweenstereoisomersaseitherenantiomericordiastereomeric.
Applysequencerulestodeterminetheabsoluteconfigurationofastereocentre (R/S)
Applysequencerulestodeterminetheconfigurationofanalkene(E/Z).
Identifyconformationalisomers.
Appreciatetherelevanceofallthisinbiologyandmedicine
ThisisNOTarotelearningexercise!Youneedtobeabletothinkcriticallyabout
molecules,identifyiftherecouldbeisomers,seehowtheyrelatetoeachotherand
whattheimplicationswouldbe!
149
CHEM1021
Chemistry B:
Elements, Compounds and Life
Dr Jon Beves
TextBookReferences
Thissection:
BlackmanChemistry 2nd Ed.
Chapter3.4 Empericalformulae
Chapter7.5 Xraydiffraction
Chapter20.1 Toolsfordeterminingstructure
Chapter20.2 Massspectrometry
Chapter20.3 Infraredspectroscopy
Chapter20.4 Interpretinginfraredspectra
Chapter20.5 Nuclearmagneticresonancespectroscopy
Chapter20.6 InterpretingNMRspectroscopy
Chapter20.7 Othertoolsfordeterminingstructure
LearningObjectives
(structuredetermination)
Knowthecommontoolsusedtodeterminethestructureof
compounds.
Massspectrometry(MS)
UVVisspectroscopy
Infraredspectroscopy(IR)
Nuclearmagneticresonancespectroscopy(NMR)
Structuraldetermination
Howcanwefigureoutwhatasubstanceis?
Thiscouldbeasuspiciouswhitepowder,anoilysmear
4
Image:kootation.com/csilasvegasallsphoto.html
Structuraldetermination
Howcanwefigureoutwhatasubstanceis?
Thiscouldbeasuspiciouswhitepowder,anoilysmear
oranewmaterialforelectronicsorapharmaceutical.
AlthoughCSIiscrazyfiction,withmoderntechniques
(andapuresample!)itisoftenpossibletoidentifyan
unknowncompoundinamatterofminutesorhours
usingscienceinsteadofscifi
Structuraldetermination
Thereareessentiallytwoprincipalmethodsfor
determiningmolecularstructure:
Directmethods(e.g.Xraycrystallography)
Indirectmethods(e.g.spectroscopicmethods)
Inallcasesweuseorreleasesomeenergyto
interrogate thechemicalstructure.
3.4
Elementalanalysis
Thisliterallyiswhatitsoundslike itis
determinationoftheelementspresentandtheir
ratio.Thisisusuallydonebycombustionanalysis.
3.4
Elementalanalysis
Notethatthedataprovidedistheempirical
formula thesimplestintegralratiobetween
theelementspresent.
Thisdoesnotalwaysmatchthemolecular
formula,whichshowsthenumberofeach
typeofatompresent.Forbutane
C4H10
molecularformula
C2 H 5
empiricalformula
3.4
Elementalanalysis
Q. Howdoyougettheempiricalformula?
A. Youstartwiththepercentagecomposition.
%element=
massofelement
x100%
massofwholesample
Thisisproperlyreferredtoasamassfraction.
Soacompoundmightbereportedas
havingamassfractionofCof92.3%andamass
fractionofHof7.7%,or
havingmassfractionsofC,H,NandOof67.3%,
6.98%,4.62%and21.1%.
Example1
Whatistheempiricalformulaofacompoundwhich
hasamassfractionofCof92.3%andamass
fractionofHof7.7%?
Startbyconsideringtheratiobymass:
C:H=92.3:7.7
Thenconvertittoratioofatomsbydividingbythe
averageatomicmassesofeachspecies.
C:H=(92.3/12.01):(7.7/1.008)
=7.69:7.64
=1:1
(note:roundingoftenneeded)
SotheempiricalformulaisC1H1.
3.4
10
Example2
3.4
Whatistheempiricalformulaofacompoundwhichhas
amassfractionsofC,H,NandOof67.3%,6.98%,4.62%
and21.1%,respectively?
Ratiobymass:
C:H:N:O=67.3:6.98:4.62:21.1
Ratiobyamount:
C:H:N:O=5.60:6.92:0.33:1.32
=17:20.97:1:4 Thisiscocaine!
=17:21:1:4
SotheempiricalformulaisC17H21NO4.
11
Howcanweuseenergysourcesto
revealmolecularinformation?
Theinformationgatheredvarieswiththeenergysource.
ScatteringusinghighenergyXray photons
providesinformationoncrystalstructure
Ionisationbybombardmentwithelectrons
providesions(M+)formassanalysis
Excitationofamoleculebyelectromagnetic
radiation providesspectroscopicinformation.
Theemphasisherewillbeonspectroscopic methods.
12
Somedefinitions
Spectroscopy:
theactoftakingaspectrum,
whichinvolvesresolving
electromagneticradiationinto
componentwavelengths.
Spectra:
Plotsofradiant
intensityvs wavelength.
Itistheabsorptionofparticularwavelengthsof
electromagneticradiationwhichwillbecomecrucial. 13
Electromagneticspectrum
E = hv =
hc
E=Energy,=frequency,l=wavelength
h=Plank'sconstant 6.626x1034 Js,c=2.998x108 ms1
14
Energy
Theenergyscale
XrayCrystallography:
Xrays1.5or8500eV or775,000kJmol1
Massspectrometry:
electronsupto70eV or6700kJmol1
(n.b. electronsarenotpartoftheelectromagneticspectrum)
UVVisspectroscopy:
700200nmor16eVor150600kJmol1
Infraredspectroscopy:
10004000cm1 or0.10.5eV or1040kJmol1
Nuclearmagneticresonancespectroscopy:
60700MHzor0.22meV or0.020.3Jmol1
15
Electromagneticspectrum
Xraycrystallography
(12)
16
7.5
Directstructuraldetermination:
XrayCrystallography
Thiscanbeusedtodeterminethearrangementof
atoms,ionsormoleculesinacrystallinestructure.
WhenthecrystalisexposedtoXrays,diffractedbeams
duetoconstructiveinterferenceappearonlyinspecific
directionsleadingtoadiffractionpattern.
NB:ThisisNOTXrayabsorption!
17
7.5
XrayCrystallography
TheBraggequation(notexaminable)relates, and
thedistancebetweentheplanesofatoms,d:
n =2dsin
18
7.5
XrayCrystallography
Whatdoyouneed?
a) ahighqualitycrystal
b) computationalmethodstosolvethediffraction
pattern.
Corresponding
Threedimensionalstructure
twodimensionalcartoon
representation
19
XrayCrystallography
Threedimensionalstructure
Corresponding
twodimensionalcartoon
representation
cyclodextrin
Whatifitsnotanicecrystal?
Incaseswherethematerialisnotcrystalline,therearea
numberofindirectmethods.
Massspectrometry: Molecularformula.
UVVisspectroscopy:Conjugation(doublebonds).
Infraredspectroscopy:Keyfunctionalgroups.
Nuclearmagneticresonancespectroscopy:
Detailedstructuralinformation.
Thesearetypicallyusedincombination.
21
20.2
Gettingthemolecularformula:
Massspectrometry
Thisreliesongeneratingachargedmolecularion (M+
orMH+)whichisdeflectedbyamagneticfield
22
One typeofMScalledElectronImpactMassSpectrometry usesabeamofelectronstogenerateions
20.2
Massspectrometry
InEIMS:
M+ =86
C6H14 =86
hexane
M+
=84
C6H12 =84
Molecularion
cyclohexane
Whatisthatlittlepeakjustto
rightoftheM+peakatM+1?It
comesfromthe13Cisotopein
thesamplewellcomebackto
23
this
Example3
3.4
Ifyouhavethemolecularmassandtheempiricalformula,itis
quitestraightforward.Again,anexample.
Whatisthemolecularformulaofacompoundwithan
empiricalformulaC1H1 andamolecularmass of
(a)26u;
(b)78u?
FirstastheempiricalformulaisC1H1 thenthemolecular
formulawillbe(C1H1)n.Asaresultthemolecularmasswillbe
(12.01+1.008)n=13.018n
(a) 13.018n=26thereforen=26/13.018=2
(b)(noterounding!)
somolecularformulais(C1H1)2=C2H2
(c) 13.018n=78thereforen=78/13.018=6(noterounding!)
24
somolecularformulais(C1H1)6=C6H6
Example4
3.4
Ifyouhavethemolecularmassandthemassfraction,youcan
skiptheempiricalformulastage.
Whatisthemolecularformulaofacompoundwithmass
fractionsofC,H,NandOof67.3%,6.98%,4.62%and21.1%,
respectively,andamolecularmassof303.5u?
Foreachelement,youcancalculatethemasspermolecule
andhencethenumberofatomsofthatelement.
C 67.3%of303.5=204.2u
H 6.98%of303.5=21.17u
N 4.62%of303.5=14.01u
O 21.1%of303.5=64.01u
No.ofatomsC=(204.2/12.01)=17
No.ofatomsH=(21.17/1.008)=21
No.ofatomsN=(14.01/14.01)=1
No.ofatomsO=(64.01/16.00)=4
SothemolecularformulaisC17H21NO4
(Notethathereitisthesameastheempiricalformula!)
25
20.1
Usingthemolecularformula
Bylookingatthenumberofeachtypeofelements
present,thenumberofmultiplebondsandringscan
bedetermined.
Note: Theoldtermforthisisdegreesof
unsaturation youwillstillseethisaround.Butwell
talkaboutthenewtermforthis
26
20.1
IndexofHydrogenDeficiency(IHD)
Notethatthereferenceisdependentontypeof
molecule forhydrocarbons,thereferenceisCnH2n+2
27
20.1
IndexofHydrogenDeficiency(IHD)
28
forhydrocarbons,thereferenceisCnH2n+2
20.1
Whenotherelementsareabout
ForcompoundscontainingelementsotherthanCandH
adjustHinreferencehydrocarbon:
Group17 (F,Cl,Br,I):subtract1Hfromthe
reference
e.g.acyclicmonochloroalkane CnH2n+1Cl
Group16 (O,S,Se):Nocorrectionisnecessaryfor
theadditionofe.g.CnH2n+2
Group15(NandP):add1H
e.g.acyclicalkylamine CnH2n+3N
29
forhydrocarbons,thereferenceisCnH2n+2
WorkedExample20.1,20.2
20.1
Example5
Calculatetheindexofhydrogendeficiencyforaspirin
(C9H8O4)fromthemolecularformula.Doesthismatch
thestructure.
2x9+2 - 8
IHD =
2
= 6 multiple bonds/rings
Fromthestructure 1ring,5doublebonds(3inthe
ring,2outside)whichmatches.
TutorialQ#1
forhydrocarbons,thereferenceisCnH2n+2
30
20.2
Otherinfofrommassspectrometry
Becausemassspectrometry
observesindividualmolecules,
thepresenceofdifferent
isotopesgivesdifferent
signals.
Rememberthe13Cpeaksfrom
previously
31
20.2
Otherinfofrommassspectrometry
Theisotopeabundancehelpsdeterminethepresenceof
particularelements
e.g.Brmassdifferenceis2,equalintensity
e.g.Clmassdifferenceis2,ratiois3:1
32
20.2
Otherinfofrommassspectrometry
Theisotopeabundancehelpsdeterminethepresenceof
particularelements
e.g.Brmassdifferenceis2,equalintensity
e.g.Clmassdifferenceis2,ratiois3:1
35ClC
3H5
37ClC
3H5
33
TutorialQ#2
Example6
20.2
CompoundBhasamolecularformulaC6H5Xandgives
thefollowingmassspectra.WhatisX?
Thereisamolecularion(M+)peakaround112with
peakatM+2thatis1/3oftheintensityoftheM+ peak.
Thisischaracteristicofthe35Cl/37Clisotopepattern.
C6H535Cl=12x6+5x1+35=112 and
XisCl
C6H537Cl=12x6+5x1+37=114
34
Example6
TutorialQ#2
20.2
Someelementshaveverycomplexnaturalisotope
patterns,egruthenium(atomicnumber44,atomicweight
101.07):
35%
30%
% Abundance
25%
20%
15%
10%
5%
0%
95.9
96.9
97.9
98.9
99.9
mass
100.9
101.9
102.9
103.9
35
RealWorldExample1
MarionJones(USA)wongoldmedalsatthe
Sydney2000Olympics.
TestingrevealedtheuseofthesteroidTHG
(admittedin2007)andshewasstrippedofall
medals.Thiswasdeterminedusingmass
spectrometrywhichcouldtellbetweennatural Tetrahydrogestrinone
(THG)
andsyntheticTHG.
STEROID SOURCES
Human Body
Synthesised (from plant material)
13C
1.1%
1.0%
12C
98.9%
99.0%
36
More 13C
Less 13C
graphics8.nytimes.com/images/2007/10/05/sports/medals600.jpg,seattletimes.com/ABPub/2007/12/14/2003929187.jpg
20
Spectroscopictechniques
Rememberthatthisinvolvesabsorptionofspecific
wavelengthsofelectromagneticradiation.The
moleculesmovetoanexcitedstate.
37
20
Spectroscopictechniques
Thenatureoftransitionandexcitedstatedependson
thefrequency(andthereforeenergy)oftheradiation
absorbed.
Electronic
transitions
Molecular
vibrations
Nuclearspin
transitions
38
20.2
UVVisiblespectroscopy
Correspondstotransitionsbetweendifferentelectronic
energylevelsinamolecules.
39
20.7
UVVisiblespectroscopy
Rememberthatspectroscopyinvolvesabsorptionof
specificwavelengthsofelectromagneticradiation.The
moleculesmovetoanexcitedstate.
40
20.7
UVVisiblespectroscopy
Theenergygapbetweenstatesisstronglydependenton
theextentofconjugation thatis,thepresenceof
alternatingdoubleandsinglebonds.
max 258nm
max 254nm
41
20.7
UVVisiblespectroscopy
AbsorptionofUVVisradiationusuallyindicatesa
conjugatedsystem thegreaterthedegreeof
conjugation,thelongerthewavelengthabsorbed.
max 258nm
max 254nm
42
Image:www.fitho.in/wpcontent/uploads/2010/08/CarrotVegetable.jpg
20.7
UVVisiblespectroscopy
Andthesecancontainheteroatoms
max 219nm
max 257nm
43
20.7
RealWorldExample2
Conjugatedcompoundscontainingheteroatomsare
importantbecauseofthewavelengthofradiation
absorbed.
max 310nm
max 299nm
ThesecompoundsabsorbharmfulUVB (290320
nm)radiationfromthesunandareused
extensivelyinsunscreens.
http://www.dumpaday.com/wpcontent/uploads/2013/06/sunburnpicturesdumpaday2.jpg
44
20.7
Sowhatinfodoyouget?
DoesthecompoundhaveanabsorptionintheUV
visibleregionoftheelectromagneticspectrum?
Yes indicatesthatthemoleculecontainsconjugation.
No indicatesthatthemoleculedoesnotcontain
conjugation.
45