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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