Transcript 12. Structure Determination: Mass Spectrometry and

12. Structure Determination: Mass
Spectrometry and Infrared
Spectroscopy
Based on
McMurry’s Organic Chemistry, 6th edition
©2003 Ronald Kluger
Department of Chemistry
University of Toronto
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
as the reactants
 In the 19th and early 20th centuries, structures were
determined by synthesis and chemical degradation
that related compounds to each other
 Physical methods now permit structures to be
determined directly. We will examine:
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mass spectrometry (MS)
infrared (IR) spectroscopy
nuclear magnetic resonance spectroscopy (NMR)
ultraviolet-visible spectroscopy (VIS)
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12.1 Mass Spectrometry (MS)
 Measures molecular weight
 Sample vaporized and subjected to bombardment by
electrons that remove an electron

Creates a cation-radical
 Bonds in cation radicals begin to break (fragment)
 Charge to mass ratio is measured (see Figure 12-1)
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The Mass Spectrum
 Plot mass of ions (m/z) (x-axis) versus the intensity of
the signal (roughly 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 unfragmented radical
cation is parent peak or molecular ion (M+)
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MS Examples: Methane and Propane
 Methane produces a parent peak (m/z = 16) and
fragments of 15 and 14 (See Figure 12-2 a)
 The MS of propane is more complex (Figure 12-2 b)
since the molecule can break down in several ways
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12.2 Interpreting Mass Spectra
 Molecular weight from the mass of the molecular ion
 Double-focusing instruments provide high-resolution
“exact mass”
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0.0001 atomic mass units – distinguishing specific
atoms
 Example MW “72” is ambiguous: C5H12 and C4H8O
but:
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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
 Instruments include computation of formulas for each
peak
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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 are used
 Peaks above the molecular weight appear as a result
of naturally occurring heavier isotopes in the sample
 (M+1) from 13C that is randomly present
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12.3 Interpreting Mass-Spectral
Fragmentation Patterns
 The way molecular ions break down can produce
characteristic 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 can
stabilize it
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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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12.4 Mass-Spectral Behavior of Some
Common Functional Groups
 Functional groups cause common patterns of
cleavage in their vicinity
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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 Amines
 Amines undergo -cleavage, generating
radicals
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Fragmentation of Ketones and
Aldehydes
 A C-H that is three atoms away leads to an internal
transfer of a proton to the C=O, called the McLafferty
rearrangement
 Carbonyl compounds can also undergo  cleavage
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12.5 Spectroscopy of the
Electromagnetic Spectrum
 Radiant energy is proportional to its frequency
(cycles/s = Hz) as a wave (Amplitude is its height)
 Different types are classified by frequency or
wavelength ranges
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Absorption Spectra
 Organic compound exposed to electromagnetic
radiation, can absorb energy of only certain
wavelengths (unit of energy)
 Transmits, energy of other wavelengths.
 Changing wavelengths to determine which are
absorbed and which are transmitted produces an
absorption spectrum
 Energy absorbed is distributed internally in a distinct
and reproducible way (See Figure 12-11)
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12.6 Infrared Spectroscopy of Organic
Molecules
 IR region lower energy than visible light (below red –
produces heating as with a heat lamp)
 2.5  106 m to 2.5  105 m region used by organic
chemists for structural analysis
 IR energy in a spectrum is usually measured as
wavenumber (cm-1), the inverse of wavelength and
proportional to frequency
 Specific IR absorbed by organic molecule related to
its structure
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Infrared Energy Modes
 IR energy absorption corresponds to specific modes,
corresponding to combinations of atomic movements,
such as bending and stretching of bonds between
groups of atoms called “normal modes”
 Energy is characteristic of the atoms in the group and
their bonding
 Corresponds to vibrations and rotations
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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 higher energy IR absorptions in Table
12.1 can be used to confirm the existence of the
presence of a functional group in a molecule
 IR spectrum has lower energy region characteristic of
molecule as a whole (“fingerprint” region)
 See samples in Figure 12-13
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Regions of the Infrared Spectrum
 4000-2500 cm-1 N-H, C-
 2000-1500 cm-1 double
H, O-H (stretching)
 3300-3600 N-H, O-H
 3000 C-H
 2500-2000 cm-1 CC
and C  N (stretching)
bonds (stretching)
 C=O 1680-1750
 C=C 1640-1680 cm-1
 Below 1500 cm-1
“fingerprint” region
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Differences in Infrared Absorptions
 Molecules vibrate and rotate in normal modes, which
are combinations of motions (relates to force
constants)
 Bond stretching dominates higher energy modes
 Light objects connected to heavy objects vibrate
fastest: C-H, N-H, O-H
 For two heavy atoms, stronger bond requires more
energy: 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 of Hydrocarbons
 C-H, C-C, C=C, C
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 C have characteristic peaks
absence helps rule out C=C or C  C
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12.9 Infrared Spectra of Some Common
Functional Groups
 Spectroscopic behavior of functional group is
discussed in later chapters
 Brief summaries presented here
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IR: Alcohols and Amines
 O–H 3400 to 3650 cm1
Usually broad and intense
 N–H 3300 to 3500 cm1
 Sharper and less intense than an O–H
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IR: Aromatic Compounds
 Weak C–H stretch at 3030 cm1
 Weak absorptions 1660 - 2000 cm1 range
 Medium-intensity absorptions 1450 to 1600 cm1
 See spectrum of phenylacetylene, Figure 12.15
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IR: Carbonyl Compounds
 Strong, sharp C=O peak 1670 to 1780 cm1
 Exact absorption characteristic of type of carbonyl
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
 1715 cm1 in six-membered ring and acyclic ketones
 1750 cm1 in 5-membered ring ketones
 1690 cm1 in ketones next to a double bond or an
aromatic ring
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C=O in Esters
 1735 cm1 in saturated esters
 1715 cm1 in esters next to aromatic ring or a
double bond
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Chromatography: Purifying Organic
Compounds
 Chromatography : a process that separates
compounds using adsorption and elution
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Mixture is dissolved in a solvent (mobile phase) and
placed into a glass column of adsorbent material
(stationary phase)
Solvent or mixtures of solvents passed through
Compounds adsorb to different extents and desorb
differently 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 Liquid Chromatography
 Stationary phase is alumina (Al2O3) or silica gel
(hydrated SiO2)
 Solvents of increasing polarity are used to elute more
and more strongly adsorbed species
 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 than ordinary
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LC
Coated silica microspheres (10-25 µm diameter) in
stationary phase
High-pressure pumps force solvent through tightly
packed HPLC column
Detector monitors eluting material
Figure 12.17: HPLC analysis of a mixture of 14
pesticides, using acetonitrile/water as the mobile
phase
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