determining the structure of an organic compound · determining the structure of an organic...
TRANSCRIPT
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Chapter 12- Structure Determination: Mass Spectrometry and Infrared Spectroscopy
AshleyPiekarski,Ph.D.
Determining the Structure of an Organic Compound
• Theanalysisoftheoutcomeofareac=onrequiresthatweknowthefullstructureoftheproductsaswellasthereactants
• Inthe19thandearly20thcenturies,structuresweredeterminedbysynthesisandchemicaldegrada=onthatrelatedcompoundstoeachother
• Physicalmethodsnowpermitstructurestobedetermineddirectly.Wewillexamine:• mass spectrometry (MS) • infrared (IR) spectroscopy • nuclear magnetic resonance spectroscopy (NMR) • ultraviolet-visible spectroscopy (VIS)
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Why this Chapter?
• Findingstructuresofnewmoleculessynthesizediscri=cal
• Togetagoodideaoftherangeofstructuraltechniquesavailableandhowtheyshouldbeused
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=J-wao0O0_qM
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The Mass Spectrum
• Plotmassofions(m/z)(x-axis)versustheintensityofthesignal(roughlycorrespondingtothenumberofions)(y-axis)
• Tallestpeakisbasepeak(100%)• Other peaks listed as the % of that peak
• Peakthatcorrespondstotheunfragmentedradicalca=onisparentpeakormolecularion(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=onofformulasforeachpeak
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Other Mass Spectral Features
• Ifparentionnotpresentduetoelectronbombardmentcausingbreakdown,“soder”methodssuchaschemicalioniza=onareused
• Peaksabovethemolecularweightappearasaresultofnaturallyoccurringheavierisotopesinthesample• (M+1) from 13C that is randomly present
Interpreting Mass-Spectral Fragmentation Patterns
• Thewaymolecularionsbreakdowncanproducecharacteris=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=ngradicals
Fragmentation of Carbonyl Compounds
• AC-HthatisthreeatomsawayleadstoaninternaltransferofaprotontotheC=O,calledtheMcLaffertyrearrangement
• 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)
• Differenttypesareclassifiedbyfrequencyorwavelengthranges
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Absorption Spectra
• Organiccompoundexposedtoelectromagne=cradia=on,canabsorbenergyofonlycertainwavelengths(unitofenergy)• Transmits energy of other wavelengths.
• ChangingwavelengthstodeterminewhichareabsorbedandwhicharetransmiTedproducesanabsorp6onspectrum
• Energyabsorbedisdistributedinternallyinadis=nctandreproducibleway(SeeFigure12-12)
12.6 Infrared Spectroscopy
• IRregionlowerenergythanvisiblelight(belowred–produceshea=ngaswithaheatlamp)
• 2.5x10-6mto2.5x10-5mregionusedbyorganicchemistsforstructuralanalysis
• IRenergyinaspectrumisusuallymeasuredaswavenumber(cm-1),theinverseofwavelengthandpropor=onaltofrequency
• SpecificIRabsorbedbyorganicmoleculerelatedtoitsstructure
hTp://www.youtube.com/watch?v=DDTIJgIh86E
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Infrared Energy Modes
• IRenergyabsorp=oncorrespondstospecificmodes,correspondingtocombina=onsofatomicmovements,suchasbendingandstretchingofbondsbetweengroupsofatomscalled“normalmodes”
• Energyischaracteris=coftheatomsinthegroupandtheirbonding
• Correspondstovibra=onsandrota=ons
12.7 Interpreting Infrared Spectra
• Mostfunc=onalgroupsabsorbataboutthesameenergyandintensityindependentofthemoleculetheyarein
• Characteris=chigherenergyIRabsorp=onsinTable12.1canbeusedtoconfirmtheexistenceofthepresenceofafunc=onalgroupinamolecule
• IRspectrumhaslowerenergyregioncharacteris=cofmoleculeasawhole(“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-Ntriplebonds(stretching)
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• 2000-1500cm-1doublebonds(stretching)– C=O1680-1750– C=C1640-1680cm-1
• Below1500cm-1“fingerprint”region
Differences in Infrared Absorptions
• Moleculesvibrateandrotateinnormalmodes,whicharecombina=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,C-N,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=coftypeofcarbonylcompound• 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