Download Determining the Structure of an Organic Compound

7/27/16
Chapter 12- Structure Determination: Mass
Spectrometry and Infrared Spectroscopy
AshleyPiekarski,Ph.D.
Determining the Structure of an Organic
Compound
•  Theanalysisoftheoutcomeofareac=onrequiresthatwe
knowthefullstructureoftheproductsaswellasthe
reactants
•  Inthe19thandearly20thcenturies,structureswere
determinedbysynthesisandchemicaldegrada=onthat
relatedcompoundstoeachother
•  Physicalmethodsnowpermitstructurestobedetermined
directly.Wewillexamine:
• 
• 
• 
• 
mass spectrometry (MS)
infrared (IR) spectroscopy
nuclear magnetic resonance spectroscopy (NMR)
ultraviolet-visible spectroscopy (VIS)
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Why this Chapter?
•  Findingstructuresofnewmolecules
synthesizediscri=cal
•  Togetagoodideaoftherangeofstructural
techniquesavailableandhowtheyshouldbe
used
12.1 Mass Spectrometry of Small
Molecules:Magnetic-Sector Instruments
•  Measuresmolecularweight
•  Samplevaporizedandsubjectedtobombardmentby
electronsthatremoveanelectron
•  Creates a cation radical
•  Bondsinca=onradicalsbegintobreak(fragment)
•  Chargetomassra=oismeasured
hTp://
www.youtube.com/
watch?v=Jwao0O0_qM
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The Mass Spectrum
•  Plotmassofions(m/z)(x-axis)versustheintensityofthe
signal(roughlycorrespondingtothenumberofions)(y-axis)
•  Tallestpeakisbasepeak(100%)
•  Other peaks listed as the % of that peak
•  Peakthatcorrespondstotheunfragmentedradicalca=onis
parentpeakormolecularion(M+)
12.2 Interpreting Mass Spectra
•  Molecularweightfromthemassofthemolecularion
•  Double-focusinginstrumentsprovidehigh-resolu=on
“exactmass”
•  0.0001 atomic mass units – distinguishing specific
atoms
•  ExampleMW“72”isambiguous:C5H12andC4H8Obut:
•  C5H12 72.0939 amu exact mass C4H8O 72.0575 amu
exact mass
•  Result from fractional mass differences of atoms 16O =
15.99491, 12C = 12.0000, 1H = 1.00783
•  Instrumentsincludecomputa=onofformulasforeach
peak
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Other Mass Spectral Features
•  Ifparentionnotpresentduetoelectronbombardment
causingbreakdown,“soder”methodssuchaschemical
ioniza=onareused
•  Peaksabovethemolecularweightappearasaresultof
naturallyoccurringheavierisotopesinthesample
•  (M+1) from 13C that is randomly present
Interpreting Mass-Spectral Fragmentation
Patterns
•  Thewaymolecularionsbreakdowncanproduce
characteris=cfragmentsthathelpiniden=fica=on
•  Serves as a “fingerprint” for comparison with
known materials in analysis (used in forensics)
•  Positive charge goes to fragments that best can
stabilize it
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Mass Spectral Fragmentation of Hexane
•  Hexane(m/z=86forparent)haspeaksatm/z=71,57,
43,29
12.3 Mass Spectrometry of Some
Common Functional Groups
Alcohols:
•  Alcoholsundergoα-cleavage(atthebondnexttothe
C-OH)aswellaslossofH-OHtogiveC=C
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Mass Spectral Cleavage of Amines
•  Aminesundergoα-cleavage,genera=ng
radicals
Fragmentation of Carbonyl Compounds
•  AC-Hthatisthreeatomsawayleadstoaninternal
transferofaprotontotheC=O,calledtheMcLafferty
rearrangement
•  Carbonylcompoundscanalsoundergoαcleavage
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12.4 Mass Spectrometry in Biological
Chemistry: Time-of-Flight (TOF) Instruments
•  MostbiochemicalanalysesbyMSuse:
-  electrosprayioniza=on(ESI)
-  Matrix-assistedlaserdesorp=onioniza=on
(MALDI)
12.5 Spectroscopy and the
Electromagnetic Spectrum
•  Radiantenergyispropor=onaltoitsfrequency(cycles/s=
Hz)asawave(Amplitudeisitsheight)
•  Differenttypesareclassifiedbyfrequencyorwavelength
ranges
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Absorption Spectra
•  Organiccompoundexposedtoelectromagne=cradia=on,can
absorbenergyofonlycertainwavelengths(unitofenergy)
•  Transmits energy of other wavelengths.
•  Changingwavelengthstodeterminewhichareabsorbedand
whicharetransmiTedproducesanabsorp6onspectrum
•  Energyabsorbedisdistributedinternallyinadis=nctand
reproducibleway(SeeFigure12-12)
12.6 Infrared Spectroscopy
•  IRregionlowerenergythanvisiblelight(belowred–
produceshea=ngaswithaheatlamp)
•  2.5x10-6mto2.5x10-5mregionusedbyorganicchemists
forstructuralanalysis
•  IRenergyinaspectrumisusuallymeasuredaswavenumber
(cm-1),theinverseofwavelengthandpropor=onalto
frequency
•  SpecificIRabsorbedbyorganicmoleculerelatedtoits
structure
hTp://www.youtube.com/watch?v=DDTIJgIh86E
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Infrared Energy Modes
•  IRenergyabsorp=oncorrespondstospecificmodes,
correspondingtocombina=onsofatomicmovements,
suchasbendingandstretchingofbondsbetweengroups
ofatomscalled“normalmodes”
•  Energyischaracteris=coftheatomsinthegroupand
theirbonding
•  Correspondstovibra=onsandrota=ons
12.7 Interpreting Infrared Spectra
•  Mostfunc=onalgroupsabsorbataboutthesameenergyand
intensityindependentofthemoleculetheyarein
•  Characteris=chigherenergyIRabsorp=onsinTable12.1can
beusedtoconfirmtheexistenceofthepresenceofa
func=onalgroupinamolecule
•  IRspectrumhaslowerenergyregioncharacteris=cof
moleculeasawhole(“fingerprint”region)
•  SeesamplesinFigure12-14
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Regions of the Infrared Spectrum
•  4000-2500cm-1N-H,
C-H,O-H(stretching)
•  3300-3600 N-H, O-H
•  3000 C-H
•  2500-2000cm-1C-CandC-N
triplebonds(stretching)
•  2000-1500cm-1double
bonds(stretching)
–  C=O1680-1750
–  C=C1640-1680cm-1
•  Below1500cm-1
“fingerprint”region
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Differences in Infrared Absorptions
•  Moleculesvibrateandrotateinnormalmodes,whichare
combina=onsofmo=ons(relatestoforceconstants)
•  Bondstretchingdominateshigherenergymodes
•  Lightobjectsconnectedtoheavyobjectsvibratefastest:C-H,
N-H,O-H
•  Fortwoheavyatoms,strongerbondrequiresmoreenergy:
CCtriplebond,CNtriplebond>C=C,C=O,C=N>C-C,C-O,CN,C-halogen
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12.8 Infrared Spectra of Some Common
Functional Groups
IR: Aromatic Compounds
•  WeakC–Hstretchat3030cm-1
•  Weakabsorp=ons1660-2000cm-1range
•  Medium-intensityabsorp=ons1450to1600cm-1
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IR: Alcohols and Amines
•  O–H3400to3650cm-1
•  Usually broad and intense
•  N–H3300to3500cm-1
•  Sharper and less intense than an O–H
IR: Carbonyl Compounds
•  Strong,sharpC=Opeak1670to1780cm-1
•  Exactabsorp=oncharacteris=coftypeofcarbonyl
compound
•  1730 cm-1 in saturated aldehydes
•  1705 cm-1 in aldehydes next to double bond or
aromatic ring
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C=O in Ketones
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