12.

Structure Determination:
Mass Spectrometry and Infrared
Spectroscopy
Based on
McMurry’s Organic Chemistry, 7
th
edition
2
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 19
th
and early 20
th
centuries,
structures were determined by
synthesis and chemical degradation
that related compounds to each other
3
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) spectroscopy—this chapter
– nuclear magnetic resonance spectroscopy
(NMR)—Chapter 13
– ultraviolet-visible spectroscopy (VIS)—
Chapter 14
4
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)
Mass Spectrometer
5
6
Mass Spectrometer
7
The Mass Spectrum
 Plot mass of ions (m/z) (x-axis) versus the
intensity 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 unfragmented
radical cation is parent peak or molecular
ion (M
+
)
8
MS Examples: Methane
and Propane
 Methane produces a parent peak (m/z = 16)
and fragments of 15 and 14
9
MS Examples: Methane
and Propane
 The Mass Spectrum of propane is
more complex (Figure 12-2 )
since the molecule can break
down in several ways
Mass spectrum of propane
10
11
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: C
5
H
12
and
C
4
H
8
O but:
– C
5
H
12
72.0939 amu exact mass C
4
H
8
O 72.0575 amu
exact mass
– Result from fractional mass differences of atoms
16
O
= 15.99491,
12
C = 12.0000,
1
H = 1.00783
12
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
13
C that is randomly present
13
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
2,2-Dimethylpropane:
MM = 72 (C
5
H
12
)
14
15
Mass Spectral Fragmentation of Hexane
Hexane (m/z = 86 for parent) has peaks at m/z
= 71, 57, 43, 29
Hexane
16
Worked example 12.1: methylcyclohexane or
ethylcyclopentane?
17
18
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
19
Mass Spectral Cleavage of
Amines
 Amines undergo -cleavage,
generating radicals
20
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
21
Fragmentation of
Ketones and Aldehydes
12.4 Mass Spec. in
Biochemistry: TOF
 ESI and MALDI are techniques to
produce charged molecules at
relatively low energy, to minimize
fragmentation.
 The large biological molecules are
separated by Time of Flight analysis
(TOF) in a drift tube without a
magnetic field imposed.
22
MALDI-TOF spectrum of
chicken egg-white lysozyme
23
24
12.5 The Electromagnetic
Spectrum
Wavelength and Frequency
25
26
Absorption Spectra
 Organic compounds exposed to electromagnetic
radiation can absorb photons of specific energies
(wavelengths or frequencies)
 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)
Infrared Absorption
Spectrum of Ethanol
27
28
12.6 Infrared Spectroscopy
of Organic Molecules
 IR region is lower in photon 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:
 Wavenumber (cm
-1
) = 1/l(cm)
 Specific IR absorbed by organic molecule is
related to its structure
IR region and vicinity
29
30
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 molecular vibrations
Infrared Energy Modes
31
32
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 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)
33
34
35
36
Regions of the Infrared
Spectrum
 4000-2500 cm
-1
N-H, C-H, O-H (stretching)
– 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


Regions of the Infrared
Spectrum
37
38
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 (frequency)
modes
39
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 (higher
frequency): C  C, C  N > C=C, C=O,
C=N > C-C, C-O, C-N, C-halogen
12.8 Infrared Spectra of
Hydrocarbons
40
 C-H, C-C, C=C, C  C have characteristic
peaks
Hexane
41
Alkenes
42
1-Hexene
43
Alkynes
44
45
12.8 Infrared Spectra of Some
Common Functional Groups
Spectroscopic behavior of
functional groups is
discussed in later chapters
Brief summaries presented
here
Aromatic compounds:
46
47
Phenylacetylene
48
IR: Alcohols
Cyclohexanol
49
Amines
50
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
51
Practice problem 12.7:
52
Phenylacetaldehyde
53
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
54
C=O in Esters
 1735 cm
1
in saturated esters
 1715 cm
1
in esters next to aromatic ring
or a double bond
55
Chromatography: Purifying
Organic Compounds
 Chromatography : a process that separates
compounds using adsorption and elution
– 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
56
Principles of Liquid
Chromatography
 Stationary phase is alumina (Al
2
O
3
) or silica
gel (hydrated SiO
2
)
 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
57
High-Pressure (or High-Performance)
Liquid Chromatography (HPLC)
 More efficient and complete separation than
ordinary 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 12.18: HPLC analysis of a mixture of
ten fat-soluble vitamins, using acetonitrile
as the mobile phase

HPLC of
Fat
Soluble
Vitamins
58
59
Prob. 12.32: Cyclohexane or
Cyclohexene?
60
Problem 12.41: Unknown
hydrocarbon
61
Problem 12.42: Unknown
hydrocarbon
2
62
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/t
utorial.html
 NIST Chemistry WebBook:
http://webbook.nist.gov/chemistry/
 SDBS Data Base:
http://www.aist.go.jp/RIODB/SDBS/menu-
e.html