Transcript 12. Structure Determination: Mass Spectrometry and

12. Structure Determination:
Mass Spectrometry and
Infrared Spectroscopy
Based on McMurry’s Organic Chemistry, 7th edition
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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Why this Chapter?
 Finding structures of new molecules
synthesized is critical
 To get a good idea of the range of structural
techniques available and how they should be
used
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12.1 Mass Spectrometry of Small
Molecules:Magnetic-Sector Instruments
 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
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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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12.2 Interpreting Mass Spectra
 Molecular weight from the mass of the molecular ion
 Double-focusing instruments provide high-resolution
“exact mass”

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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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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12.3 Mass Spectrometry of Some
Common Functional Groups
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 Carbonyl
Compounds
 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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12.4 Mass Spectrometry in Biological
Chemistry: Time-of-Flight (TOF)
Instruments
 Most biochemical analyses by MS use:
- electrospray ionization (ESI)
- Matrix-assisted laser desorption ionization
(MALDI)
• Linked to a time-of-flight mass analyzer
(See figure 12.9)
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12.5 Spectroscopy and 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 12-12)
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12.6 Infrared Spectroscopy
 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 12-14
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Regions of the Infrared Spectrum
 4000-2500 cm-1 N-H,
C-H, O-H (stretching)
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3300-3600 N-H, O-H
3000 C-H
 2500-2000 cm-1 CC and C
 N (stretching)
 2000-1500 cm-1 double
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 Some
Common Functional Groups
Alkanes, Alkenes, Alkynes
 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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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: 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: 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
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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