12.

Structure Determination:
Mass Spectrometry and Infrared
Spectroscopy
Based on
McMurrys 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) spectroscopythis 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
CC 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 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 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