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12. Structure Determination:Mass Spectrometry and Infrared
Spectroscopy
Based onMcMurrysOrganic Chemistry, 7thedition
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Determining the Structure
of an Organic Compound The analysis of the outcome of a
reaction requires that we know the full
structure of the products as well asthe reactants
In the 19thand early 20thcenturies,structures were determined bysynthesis and chemical degradationthat related compounds to each other
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Determining the Structure
of an Organic Compound Physical methods now permit
structures to be determined directly.We will examine: mass spectrometry (MS)this chapter infrared (IR) spectroscopythis chapter nuclear magnetic resonance spectroscopy
(NMR)Chapter 13 ultraviolet-visible spectroscopy (VIS)Chapter 14
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12.1 Mass Spectrometry
(MS) Sample vaporized and bombarded by
energetic electrons that remove an electron,creating a cation-radical
Bonds in cation radicals begin to break(fragment)
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Mass Spectrometer
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Mass Spectrometer
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The Mass Spectrum
Plot mass of ions (m/z) (x-axis) versus theintensity of the signal (corresponding to the
number of ions) (y-axis) Tallest peak is base peak(100%)
Other peaks listed as the % of that peak
Peak that corresponds to the unfragmentedradical cation is parent peakor molecularion (M+)
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MS Examples: Methane
and Propane Methane produces a parent peak (m/z = 16)
and fragments of 15 and 14
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MS Examples: Methane
and Propane The Mass Spectrum of propane is
more complex (Figure 12-2 )
since the molecule can breakdown in several ways
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Mass spectrum of propane
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12.2 Interpreting Mass
Spectra Molecular weight from the mass of the molecular
ion Double-focusinginstruments provide high-
resolution exact mass 0.0001 atomic mass unitsdistinguishing specific
atoms
Example MW 72 is ambiguous: C5H12and
C4H8O but: C5H1272.0939 amu exact mass C4H8O 72.0575 amuexact mass
Result from fractional mass differences of atoms 16O= 15.99491, 12C = 12.0000, 1H = 1.00783
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Other Mass Spectral
Features If parent ion not present due to electron
bombardment causing breakdown, softer
methods such as chemical ionization areused
Peaks above the molecular weight appear asa result of naturally occurring heavier
isotopes in the sample (M+1) from 13C that is randomly present
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Interpreting Mass-SpectralFragmentation Patterns
The way molecular ions break down can producecharacteristic fragments that help in identification
Serves as a fingerprint for comparison with known
materials in analysis (used in forensics)
Positive charge goes to fragments that best canstabilize it
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2,2-Dimethylpropane:
MM = 72 (C5H12)
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Mass Spectral Fragmentation of Hexane
Hexane (m/z = 86 for parent) has peaks at m/z
= 71, 57, 43, 29
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Hexane
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Worked example 12.1: methylcyclohexane orethylcyclopentane?
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Mass Spectral Cleavage
Reactions of Alcohols Alcohols undergo -cleavage (at the bond
next to the C-OH) as well as loss of H-OH to
give C=C
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Mass Spectral Cleavage of
AminesAmines undergo -cleavage,
generating radicals
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Fragmentation of
Ketones and Aldehydes
A C-H that is three atoms awayleads to an internal transfer of aproton to the C=O, called theMcLafferty rearrangement
Carbonyl compounds can alsoundergo cleavage
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Fragmentation of
Ketones and Aldehydes
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12.4 Mass Spec. in
Biochemistry: TOF ESI and MALDI are techniques to
produce charged molecules at
relatively low energy, to minimizefragmentation.
The large biological molecules are
separated by Time of Flight analysis(TOF) in a drift tube without amagnetic field imposed.
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MALDI-TOF spectrum ofchicken egg-white lysozyme
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12.5 The ElectromagneticSpectrum
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Wavelength and Frequency
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Absorption Spectra
Organic compounds exposed to electromagneticradiation can absorb photons of specific energies(wavelengths or frequencies)
Changing wavelengths to determine which areabsorbed and which are transmitted produces anabsorption spectrum
Energy absorbed is distributed internally in adistinct and reproducible way (See Figure 12-11)
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Infrared AbsorptionSpectrum of Ethanol
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12.6 Infrared Spectroscopyof Organic Molecules
IR region is lower in photon energy than visiblelight (below redproduces heating as with aheat lamp)
2.5 106m to 2.5 105m region used byorganic chemists for structural analysis
IR energy in a spectrum is usually measured aswavenumber (cm-1), the inverse of wavelengthand proportional to frequency:
Wavenumber (cm-1) = 1/l(cm)
Specific IR absorbed by organic molecule is
related to its structure
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IR region and vicinity
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Infrared Energy Modes
IR energy absorption corresponds tospecific modes, corresponding to
combinations of atomic movements,such as bending and stretching ofbonds between groups of atoms called
normal modes
Energy is characteristic of the atoms inthe group and their bonding
Corresponds to molecular vibrations
http://www.columbia.edu/cu/chemistry/edison/IRTutor.htmlhttp://www.columbia.edu/cu/chemistry/edison/IRTutor.html8/12/2019 Mcmurry 12
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Infrared Energy Modes
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12.7 Interpreting
Infrared Spectra Most functional groups absorb at about
the same energy and intensity
independent of the molecule they are in Characteristic IR absorptions in Table
12.1 can be used to confirm theexistence of the presence of a functional
group in a molecule IR spectrum has lower energy region
characteristic of molecule as a whole(fingerprint region)
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Regions of the Infrared
Spectrum 4000-2500 cm-1N-H, C-H, O-H (stretching)
3300-3600 N-H, O-H
3000 C-H
2500-2000 cm-1CC and C N (stretching)
2000-1500 cm-1double bonds(stretching)
C=O 1680-1750
C=C 1640-1680 cm-1
Below 1500 cm-1fingerprint region
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Regions of the Infrared
Spectrum
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Differences in Infrared
AbsorptionsMolecules vibrate and rotate in
normal modes, which are
combinations of motions(relates to force constants)
Bond stretching dominateshigher energy (frequency)modes
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Differences in Infrared
Absorptions Light objects connected to heavy
objects vibrate fastest (at higher
frequencies): C-H, N-H, O-H For two heavy atoms, stronger bond
requires more energy (higherfrequency): C C, C N > C=C, C=O,C=N > C-C, C-O, C-N, C-halogen
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12.8 Infrared Spectra ofHydrocarbons
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C-H, C-C, C=C, C C have characteristicpeaks
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Hexane
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Alkenes
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1-Hexene
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12.8 Infrared Spectra of SomeCommon Functional Groups
Spectroscopic behavior offunctional groups isdiscussed in later chapters
Brief summaries presentedhere
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Phenylacetylene
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Amines
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IR: Carbonyl Compounds
Strong, sharp C=O peak 1670 to 1780 cm1 Exact absorption characteristic of type of
carbonyl compound 1730 cm1in saturated aldehydes 1705 cm1in aldehydes next to double bond or
aromatic ring
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Practice problem 12.7:
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Phenylacetaldehyde
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C=O in Ketones
1715 cm1in six-membered ring andacyclic ketones
1750 cm1in 5-membered ring ketones 1690 cm1in ketones next to a double
bond or an aromatic ring
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C=O in Esters
1735 cm1
in saturated esters 1715 cm1in esters next to aromatic ring
or a double bond
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Chromatography: PurifyingOrganic Compounds
Chromatography : a process that separatescompounds using adsorption and elution
Mixture is dissolved in a solvent (mobile phase) and placed
into a glass column of adsorbent material (stationaryphase)
Solvent or mixtures of solvents passed through
Compounds adsorb to different extents and desorbdifferently in response to appropriate solvent (elution)
Purified sample in solvent is collected from end of column
Can be done in liquid or gas mobile phase
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Principles of LiquidChromatography
Stationary phase is alumina (Al2O3) or silicagel (hydrated SiO2)
Solvents of increasing polarity are used toelute more and more strongly adsorbedspecies
Polar species adsorb most strongly to
stationary phase For examples, alcohols adsorb more strongly
than alkenes
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High-Pressure (or High-Performance)Liquid Chromatography (HPLC)
More efficient and complete separation thanordinary LC
Coated silica microspheres (10-25 m
diameter) in stationary phase High-pressure pumps force solvent through
tightly packed HPLC column Detector monitors eluting material
Figure 12.18: HPLC analysis of a mixture often fat-soluble vitamins, using acetonitrileas the mobile phase
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HPLC ofFatSolubleVitamins
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Prob. 12.32: Cyclohexane orCyclohexene?
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Problem 12.41: Unknownhydrocarbon
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Problem 12.42: Unknownhydrocarbon2
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Some Useful Websites:
Interpretation of IR spectra (CSU Stanislaus):http://wwwchem.csustan.edu/Tutorials/INFRARED.HTM
IR Spectroscopy Tutorial (CU Boulder):http://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.html
NIST Chemistry WebBook:
http://webbook.nist.gov/chemistry/
SDBS Data Base:http://www.aist.go.jp/RIODB/SDBS/menu-e.html
http://wwwchem.csustan.edu/Tutorials/INFRARED.HTMhttp://wwwchem.csustan.edu/Tutorials/INFRARED.HTMhttp://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://webbook.nist.gov/chemistry/http://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://webbook.nist.gov/chemistry/http://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://wwwchem.csustan.edu/Tutorials/INFRARED.HTMhttp://wwwchem.csustan.edu/Tutorials/INFRARED.HTM