13.24: Mass Spectrometry

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Chapter 13: SpectroscopyMethods of structure determination Nuclear Magnetic Resonances (NMR) Spectroscopy(Sections 13.3-13.19) Infrared (IR) Spectroscopy (Sections 13.20-13.22) Ultraviolet-visible (UV-Vis) Spectroscopy (Section 13.23) Mass (MS) spectrometry (not really spectroscopy)(Section 13.24)Molecular Spectroscopy: the interaction of electromagneticradiation (light) with matter (organic compounds). Thisinteraction gives specific structural information.113.24: Mass Spectrometry:molecular weight of the sampleformulaThe mass spectrometer gives the mass to charge ratio (m/z),therefore the sample (analyte) must be an ion.Mass spectrometry is a gas phase technique- the sample mustbe “vaporized.”Electron-impactionizationSample Inlet10-7 - 10-8 torrionizationchamberR-HeR-H (M )electron beam70 eV(6700 KJ/mol)protonneutronelectronmassanalyzerm/z1.00728 u1.00866 u0.00055 u21

massm chargezB2 r22VB magnetic field strengthr radius of the analyzer tubeV voltage (accelerator plate)MagneticField, BoIons of selectedmass/charge ratioare detectedIons of non-selectedmass/charge ratioare not detectedIonizationchamber3The Mass SpectrometerDalton (Da) or mass unit (u) units for measuring molecular masses.One Da. 1/12 the mass of the 12C atomMonoisotopic (exact) mass – sum of the exact masses of the most abundantisotope of each element in a moleculeAverage mass – sum of the averaged masses of each element in a molecules,weighted according to isotopic abundance.Nominal mass – mass calculated using the integer mass of the most abundantisotope for each element (H 1, C 12, O 16, N 14, etc.)Exact Masses of Common Natural l 013.003398.8921.108 (1.11%)37Cl14.0030715.0001099.6340.366 (0.38%)81Br15.9949116.9991317.9991699.7630.037 (0.04%)0.200 (0.20%)massnatural abundance18.9984035Cl34.9688536.9659075.7724.23 (32.5%)78.9183980.9164250.6949.31 (98%)79Br127I126.90447100.00100.0042

Molecular Ion (parent ion, M) molecular mass of the analyte;sample minus an electron. (mass of an e– is 1/1836 that of aproton)Base peak- largest (most abundant) peak in a mass spectrum;arbitrarily assigned a relative abundance of 100%.m/z 78 (M )(100%)C6H6m/z 78.04695m/z 79 (M 1)( 6.6% of M )5The radical cation (M ) is unstable and will fragment intosmaller ionsm/z 15Relative abundance (%)m/z 16 (M )H HH C HHHHH C HHcharge neutralm/z 15 not detectedm/z 16 m/z 17(M 1)m/z 14H C H H H HH C C C Hm/z 29-e-em/z 43m/z 44(M) H H HH C C CH H H H H HH HH Hm/zcharge neutralnot detectedHchargeneutral notdetectedH H Hm/z 29H C C m/z 43H HH C C H H Hm/z 44H C C C Hm/z 45(M 1)H H HH C C CHH H HH H Hm/z 15Hcharge neutralnot detectedm/z 14m/zRelative abundance (%)-eH C H C HHcharge neutralnot detectedH C HH6m/z 153

Mass spectrum of halogenated organic compounds35Clm/z 112(M )Cl37Cl34.9688536.9659075.7724.23 (32.5%)m/z 114(M 2)m/z 77m/z 113(M 1)m/z 115(M 3)m/zBrm/z 7779Brm/z 156(M )m/z 157(M 1)m/z 158(M 2)81Br78.9183980.9164250.6949.31 (98%)m/z 159(M 3)m/z7Mass spectra can be quite complicated and interpretationdifficult.Some functional groups have characteristic fragmentationsIt is difficult to assign an entire structure based only on the massspectrum. However, the mass spectrum gives the mass andformula of the sample, which is very important information.To obtain the formula, the molecular ion must be observed.(Soft ionization techniques)Methods have been developed to get large molecules such aspolymers and biological macromolecules (proteins, peptides,nucleic acids) into the vapor phase84

13.25: Molecular Formula as a Clue to StructureNitrogen rule: In general, “small” organic molecules with anodd mass must have an odd number of nitrogens. Organicmolecules with an even mass have zero or an even number ofnitrogens.If the mass can be determined accurately enough, then themolecular formula can be determined (high-resolution massspectrometry).Information can be obtained from the molecular formula:Degrees of unsaturation: the number of rings and/or π-bondsin a molecule (Index of Hydrogen Deficiency).9Degrees of unsaturationsaturated hydrocarboncycloalkane (1 ring)alkene (1 π-bond)alkyne (2 π-bonds)CnH2n 2CnH2nCnH2nCnH2n-2For each ring or π-bond, –2H from the formula of the saturatedalkaneHH HHHHHHHH HHC6H14- C6H12H2122 1Hydrogen DeficiencyDegrees of UnsaturationC6H14- C6H6H812HHHHHH8 4105

Correction for other elements:For Group VII elements (halogens): subtract 1H from theH-deficiency for each halogen,For Group VI elements (O and S): No correction is neededFor Group V elements (N and P): add 1H to the H-deficiencyfor each N or PC10H14N2C12H4O2Cl41113.1: Principles of molecular spectroscopy:Electromagnetic radiationorganicmolecule(ground state)lighthνorganicrelaxation organic hνmoleculemolecule(excited state)(ground state)Electromagnetic radiation has the properties of a particle(photon) and a wave.λ distance of one waveν frequency: waves per unit time (sec-1, Hz)c speed of light (3.0 x 108 m sec-1)h Plank’s constant (6.63 x 10-34 J sec)126

Quantum: the energy of a photonE hνν E E α νγ Rays10 -910 -11shorthighhigh10 -7λh cλE α λ-1Ultraviolet VisX-Raysc10 -5ν α λ-1infrared10 -4microwaves10 -2radiowaves10Wavelength (λ)Frequency (ν)Energy (E)10 3λ (cm)longlowlow1313.2: Principles of Molecular Spectroscopy:Quantized Energy Levelsmolecules have discrete energy levels(no continuum between levels)A molecule absorbs electromagnetic radiation whenthe energy of photon corresponds to the difference inenergy between two states147

organicmolecule(ground state)lighthνorganicrelaxation organic hνmoleculemolecule(excited state)(ground state)UV-Vis: valance electron transitions- gives information about π-bonds and conjugated systemsInfrared: molecular vibrations (stretches, bends)- identify functional groupsRadiowaves: nuclear spin in a magnetic field (NMR)- gives a map of the H and C framework1513.23 Ultraviolet-Visible (UV-Vis) SpectroscopyUV400λ 200Recall bonding of a π-bondVis800 nm168

π-molecular orbitals of butadieneΨ4: 3 Nodes0 bonding interactions3 antibonding interactionsANTIBONDING MOΨ3: 2 Nodes1 bonding interactions2 antibonding interactionsANTIBONDING MOΨ2: 1 Nodes2 bonding interactions1 antibonding interactionsBONDING MOΨ1: 0 Nodes3 bonding interactions0 antibonding interactionsBONDING MOψ2 is the Highest Occupied Molecular Orbital (HOMO)17ψ3 is the Lowest Unoccupied Molecular Orbital (LUMO)UV-Vis light causes electrons in lower energy molecular orbitalsto be promoted to higher energy molecular orbitals.HOMOLUMOChromophore: light absorbing portion of a moleculeButadieneButadiene189

BondingEnergyAntibondingMolecular orbitals of conjugated polyenesH2C CH2180 nm258 nm217 nm290 nm19Molecules with extended conjugation move toward the visibleregion380 nm400 nmviolet-indigo450 nmblue500 nm550 nmgreenyellowColor ofabsorbed ed600 nmorangeλ400 nm450500530550600700700 nm780 lue-greengreen2010

Many natural pigments have conjugated systemsOHOHN OHON Mg carotenelycopene21Chromophore: light absorbing portion of a moleculeBeer’s Law: There is a linear relationship betweenabsorbance and concentrationA ε c lA absorbancec concentration (M, mol/L)l sample path length (cm)ε molar absorptivity (extinction coefficient)a proportionality constant for a specificabsorbance of an analyte2211

13.20: Introduction to Infrared SpectroscopyNearIRVis10-4FarIRInfrared (IR)2.5 x 10-4 cm2.5 µm4000 ν1.6 x 10-3 cm16 µm600 νmicrowave10-2λ (cm)1E αλλ is expressed as ν (wavenumber), reciprocal cm (cm-1)thereforeν 1E α νλIR radiation causes changes in a molecular vibrations23Stretch: change in bond mlSymmetric stretchAntisymmetric stretchBend: change in bond angle scissoringrockingin-plane bendwaggingtwistingout-of-plane bendAnimation of bond streches and mjm.html2412

Bond Stretch:Hooke’s Lawfν 12πcmx myX12Yν vibrational frequencyc speed of lightmx mass of Xmy mass of Ymx mymx my reduced mass (µ)mx myE α ν α ff spring constant; type ofbond between X and Y(single, double or triple)Hooke’s law mation.php?ani 57&cat tion.php?ani 56&cat chemistry2513.21 Infrared SpectraInterpretation of an Infrared Spectra:Organic molecules contain many atoms. As a result, thereare many stretching and bending modes and the IR spectrumhas many absorption bandsFour distinct regions of an IR spectraX-Hsingle bondregion4000 cm-1triplebondregion2500 cm-1C-HO-HN-HC CC Ndoublebondregionfingerprintregion2000 cm-1 1500 cm-1500cmcm-1-1600C CC O2613

Fingerprint region (500 - 1500 cm-1): low energy single bondstretching and bending modes. The fingerprint region isunique for any given organic compound. However, there arefew diagnostic absorptions.Double-bond regions (1600 - 1900 cm-1)C C1620 - 1680 cm-1C O1680 - 1850 cm-1Triple-bond region: (2100 - 2300 cm-1)C C2100 - 2200 cm-1 (weak, often not observed)C N2240 - 2280 cm-1X-H Single-bond region (2800 - 3600 cm-1)O-H3200 - 3600 cm-1 (broad)CO-OH 2500 - 3600 cm-1 (very broad)N-H3350 - 3500 cm-1C-H2800 - 3300 cm-1sp3 –C-H2850 - 2950 cm-1sp2 C-H3000 - 3100 cm-127sp C-H3310 - 3320 cm-113.22 Characteristic Absorption FrequenciesTable 13.3, p. 552Alkenes C-HC CAromatic C-HC CAlkynes C-HC CAlcoholsC-OO-HAminesC-NN-HCarbonylC OCarboxylic acidsO-HNitrileC N3000 - 3100 cm-11620 - 1680 cm-1medium - strongmedium3000 - 3100 cm-11450 - 1600 cm-1strongstrong3310 - 3320 cm-12100 - 2200 cm-1strongweak - medium1025 - 1200 cm-13200 - 3600 cm-1strongstrong and broad1030 - 1230 cm-13350 - 3500 cm-1mediummedium1680 - 1850 cm-1strong2500 - 3500 cm-1strong and very broad2240 - 2280 cm-1weak-medium2814

% transmittance% transmittanceC-HhexaneC C C-Hcm-1C-HH3CH2CH2CH2C C C H% transmittancecm-1 C-HC CH3CH2CH2CH2CHCCHHcm-1% transmittanceC C C-HH 3CH2CH2CC-HCHHC% transmittanceC-HC CC-HH3CH2CH2C C C CH3cm-1CH 329cm-1% transmittanceCH3(CH2)4CH2OHC NC-HH3C(H2C)4CH2C NO-HC-OCH3(CH2)4CH2NH-CH3CH3(CH2)4CH2NH2% transmittanceC-HN-HN-HC-HC-H3015

% HC O1705 cm-1% transmittanceH3C(H2C)3H2CHC-HOCC O1710 cm-1H3C(H2C)2H2CHOCCH3OCC O1730 cm-1C O1715 cm-1C-H31Typical IR Absorptions for Funtional Groups40003000X-H Regon(2500-4000 cm-1)20001000Triple Bond Double BondRegionRegion(2000-2500) (1500-2000)Fingerprint Region(600-1500 cm-1)C-HO-HN-H4000CCCN3000Functional GroupCCCCONdifficult to interpret2000cm-16001000600cm-1Functional GroupAlkanes, Alkyl groups2850-2950 (m-s)C-HAminesN-H3350-3500 (br, m)Alkenes C-HC C3000-3100 (m)1620-1680 (m-w)AmideN-HC O3180-3350 (br, m-w)1680-1700 (s)Alkynes C-HC C3310-3320 (s)2100-2260 (m-w)Carbonyl GroupC OC–O1650-1780 (s) 1200 (s)Alkyl HalidesC-ClC-BrC-I600-800500-600500Carboxylic Acids2500-3100 (br, s)O-H1700-1725 (s)C OAlcoholsO-HC–O3200-3600 (br, m-s)1025-1200 (s)NitrilesC N2240-2250 (w-m)3000-3100 (m-w)Nitro Group-NO21540Aromatics C-H1450-1600 em220b/IR.pdf16

13.3: Introduction to 1H NMRdirect observation of the H’s of a moleculesNuclei are positively charged and spin on an axis; they createa tiny magnetic field Not all nuclei are suitable for NMR.1H and 13C are the most important NMR active nuclei inorganic chemistryNatural Abundance1H 99.9%13C12C1.1%98.9% (not NMR active)33(a) Normally the nuclear magnetic fields are randomly oriented(b) When placed in an external magnetic field (Bo), the nuclearmagnetic field will either aligned with (lower energy) oroppose (higher energy) the external magnetic fieldFig 13.3, p. 5133417

The energy difference between aligned and opposed to the externalmagnetic field (Bo) is generally small and is dependent upon BoApplied EM radiation (radio waves) causes the spin to flip and thenuclei are said to be in resonance with Bo ΔE h νNote that h2πBo external magnetic field strengthγ gyromagnetic ratio1H 26.813C 6.7is a constant and is sometimes denoted as h35γB hΔE 2 oπNMR Active Nuclei: nuclear spin quantum number (I)atomic mass and atomic numberNumber of spin states 2I 1 (number of possible energy levels)Even mass nuclei that have even number of neutrons have I 0(NMR inactive)Even mass nuclei that have an odd number of neutrons have aninteger spin quantum number (I 1, 2, 3, etc)Odd mass nuclei have half-integer spin quantum number(I 1/2, 3/2, 5/2, etc)I 1/2: 1H, 13C, 19F, 31PI 1: 2H, 14NI 3/2: 15NI 0: 12C, 16O3618

Continuous wave (CW) NMRPulsed (FT) NMR37Fig. 13.5, p. 51513.4: Nuclear Shielding and 1H Chemical ShiftDifferent nuclei absorb EM radiation at different wavelength(energy required to bring about resonance)Nuclei of a given type, will resonate at different energiesdepending on their chemical and electronic environment.The position (chemical shift, δ) and pattern (splitting or multiplicity)of the NMR signals gives important information about thechemical environment of the nuclei. The integration of thesignal is proportional to the number of nuclei giving rise to thatsignalH OH HH C C O C C HHH H3819

Chemical shift: the exact field strength (in ppm) that a nuclei comesinto resonance relative to a reference standard (TMS)Electron clouds “shield” nuclei from the external magnetic field causingthem to resonate at slightly higher energyShielding: influence of neighboring functional groups on the electronicstructure around a nuclei and consequently the chemical shift of theirresonance.CH3ClHCH3C Si CH3ClCH3Cldownfieldlower magnetic fieldless shielded(deshielded)Tetramethylsilane (TMS);Reference standard δ 0for 1H NMRH–CCl3upfieldhigher magnetic fieldmore shieldedδ 7.28 ppmTMS39Chemical shift (δ, ppm)downfieldlower magnetic fieldless shielded(deshielded)N CCH2OCH3δ 4.20 ppm2Hδ 3.50 ppm3Hupfieldhigher magnetic fieldmore shieldedTMSChemical shift (δ, ppm)Vertical scale intensity of the signalHorizontal scale chemical shift (δ), dependent upon the field strengthof the external magnetic field; for 1H, d is usually from 1-10 ppmchemical shift in Hzδ ν – νTMS nooperating frequency in MHz14,100 gauss: 60 MHz for 1H (60 million hertz) ppm 60 Hz15 MHz for 13C140,000 gauss: 600 MHz for 1Hppm 600 Hz150 MHz for 13C4020

13.5: Effect of Molecular Structure on 1H Chemical ShiftElectronegative substituents deshield nearby protonsless shieldedmore shieldedH3C-F H3C-O-CH3 (H3C)3-N H3C-CH3 (H3C)4-Siδ 4.3δ 3.2δ 0.9δ 2.2δ 0.0The deshielding effect of a group drops off quickly with distance(number of bonds between the substituent and the proton)H3C-H2C-H2C-H2C-O-CH2-CH2-CH2-CH3δ 1.373.400.921.5541The influence of neighboring groups (deshielding) on 1Hchemical shifts is cumulativeHClClCCClH7.3OHδ OH2.1H5.3HCH3CH2OClHClδ ClCHH3.1 ppmOClHCH3CH2OH4.06ClClCH3CH2OH5.96 ppm4221

Typical 1H NMR chemical shifts ranges – additional substitutioncan move the resonances out of the range (Fig. 13.8, p. 518)121191087645312H1HRONMR Shift RangesORCO0HCR2R 2NR 2NHHCR2XCR2HHO CR2ArOHRC CR2X O, CR2HCR2PhOHNR C-HHX CR2 X F, Cl, Br, IHRCHOROHaromatics1211OC CvinylRCO 2H109876543sat. alkanesR-HH210δ em220b/NMR.pdfProtons attached to sp2 and sp hybridize carbons are deshieldedrelative to protons attached to sp3 hybridized carbonsHHOHHHCHHHHH C C HCHH3C CH3Hδ 9.77.35.32.10.9-1.5 ppmPlease read about ring current effects of π-bonds(Figs. 13.9-13.11, p. 519–522)CH3CH3COCCH3δ 2.3 - 2.81.5 - 2.62.1-2.5 ppm4422

13.6: Interpreting 1H NMR SpectraEquivalence (chemical-shift equivalence): chemically andmagnetically equivalent nuclei resonate at the same energy andgive a single signal or patternHHN C C O C HHHδ 4.20 ppm2Hδ 3.50 ppm3HTMS45H3CHC CH3CCH34623

Test of Equivalence:1. Do a mental substitution of the nuclei you are testing with anarbitrary label (–X)2. Ask what is the relationship of the compounds with thearbitrary label3. If the labeled compounds are identical (or enantiomers), then theoriginal nuclei are chemically equivalent and do not normallygive rise to separate resonances in the NMR spectraIf the labeled compounds are not identical (and not enantiomers),then the original nuclei are not chemically equivalent and cangive rise to different resonances in the NMR spectraHHHH CCH 3C CH 3CXXH CCH 3C CCH 3H 3CHHH CCH 3HX CC CH 3CCH 3CH 3C CCH 3H 3CCH 3Identical, so the protons are equivalentH 3CCH 3XC CH 3CCH 3H 3CC CCH 3H 3CXH 3CC CCH 3H 3CCH 3H 3CC CCH 3H 3CCH 3C CXXCH 3Identical, so the methyl groups are equivalentXHH 3CHC CH 3CH 3CCH 3XHHXH 3CCH 3HH 3CH 3CC CXH3CHC CCH 3H 3CCH 3H 3CC CC CH 3CC CXHC CCH 3H 3CX47These are geometricisomers (not identical andnot enantiomers). The threemethyl groups are thereforenot chemically equivalentand can give rise to differentresonancesHC CH3CCH34824

HHCH2CH3HHH49H ClH3C C C CH3H HHomotopic: equivalentEnantiotopic: equivalentDiastereotopic: non-equivalent5025

Integration of 1H NMR resonances: The area under an NMRresonance is proportional to the number of equivalent nuclei thatgive rise to that resonance.δ 4.20,2HHHN C C O C HHHδ 3.50,δ3HTMSThe relative area under the resonances at δ 4.20 and 3.50is 2:35113.7: Spin-Spin Splitting and 1H NMRprotons on adjacent carbons will interact and “split” each othersresonances into multiple peaks (multiplets)n 1 rule: equivalent protons that have n equivalent protons onthe adjacent carbon will be “split” into n 1 peaks.H Oδ 2.03HH HH C C O C C HHH Hδ 1.23Hδ 4.12HResonances always split each other. The resonance at δ 4.1splits the resonance at δ 1.2; therefore, the resonance atδ 1.2 must split the resonance at δ 4.2.5226

The multiplicity is defined by the number of peaks and the pattern(see Table 13.2 for common multiplicities patterns and relativeintensities)H Oδ 2.0s, 3HH HH C C O C C HHδ 1.2t, 3HH Hδ 4.1q, 2H-CH3--CH2-1 : 2 : 1531 : 3 : 3 : 1The resonance of a proton with n equivalent protons on theadjacent carbon will be “split” into n 1 peaks with a couplingconstant J.Coupling constant: distance between peaks of a split pattern; J isexpressed in Hz. Protons coupled to each other have the samecoupling constant J.H Oδ 2.0s, 3HH HH C C O C C HHH Hδ 1.2t, J 7.2 Hz, 3Hδ 4.1q, J 7.2 Hz, 2H3Jab3Jab3Jab3Jab543Jab27

13.8: Splitting Patterns: The Ethyl GroupTwo equivalent protons on an adjacent carbon will split a protona triplet (t), three peaks of 1:2:1 relative intensityThree equivalent protons on an adjacent carbon will split a protoninto a quartet (q), four peaks of 1:3:3:1 relative intensityHHHHO H HH HC C HHH HHHδ 7.4-7.1,m, 5HC C C HHδ 1.2, tJ 7.0, 3Hδ 2.6, q,J 7.0, 2HH HHHδ 3.0, qJ 7.2, 2Hδ 1.2, tJ 7.2, 3Hδ 8.0,2Hδ 7.6-7.3,m, 3H5513.9: Splitting Patterns: The Isopropyl GroupOne proton on an adjacent carbon will split a proton into adoublet (d), two peaks of 1:1 relative intensitySix equivalent protons on an adjacent carbon will split a protoninto a septet (s), seven peaks of 1:6:15:20:15:6:1 relativeintensityHHHHHHC CH 3CH 3δ 7.4-7.1,m, 5HHδ 1.2, dJ 6.9, 6HHO2NHδ 2.9, s,J 6.9, 1Hδ 8.1, d,J 6.1 Hz,2HHHC CH 3CH 3δ 7.4, dJ 6.1 Hz,2Hδ 1.2, dJ 6.9, 6Hδ 3.0, s,J 6.9, 1H5628

13.10: Splitting Patterns: Pairs of DoubletsHHH 3CCH 3C CH H3OCHδ 1.2, s, 9HOCH 3δ 8.0, d,J 9.0 2Hδ 7.4, d,J 9.0 2Hδ 3.9,s, 3HFig. 13.20,p. 5315713.11: Complex Splitting Patterns: when a protons is adjacentto more than one set of non-equivalent protons, they will splitindependentlyJ1-2 7.0J2-3 16.0J1-2 7.0J2-3 16.0HCOCCHHH2 splits H3 into a doublet with coupling constant J2-3 16.0H2 splits H1 into a doublet with coupling constant J1-2 7.0H1 splits H2 into a dou

Infrared (IR) Spectroscopy (Sections 13.20-13.22) Ultraviolet-visible (UV-Vis) Spectroscopy (Section 13.23) Mass (MS) spectrometry (not really spectroscopy) (Section 13.24) Molecular Spectroscopy: the interaction of electromagnetic radiation (light) with matter (organic compounds). This interaction gives specific structural information.

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