12.

Structure Determination: Mass

Spectrometry and Infrared Spectroscopy
 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

2
 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

3
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)

4
Mass Spectrometer

5
 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+)

6
 MS Examples: Methane and
Propane
Methane produces a parent peak (m/z = 16) and
fragments of 15 and 14 (See Figure 12-2 a)

7
 MS Examples: Methane and
Propane
The Mass Spectrum of propane is more
complex (Figure 12-2 b) since the molecule
can break down in several ways

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9
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:
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
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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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2,2-Dimethylpropane:
MM = 72 (C5H12)

13
Mass Spectral Fragmentation of
Hexane
Hexane (m/z = 86 for parent) has peaks at
m/z = 71, 57, 43, 29

14
Hexane

15
Practice Problem 12.2: methylcyclohexane
or ethylcyclopentane?

16
 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

17
 Mass Spectral Cleavage of
Amines
Amines undergo -cleavage,
generating radicals

18
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

19
Fragmentation of Ketones and
Aldehydes

20
12.5 The Electromagnetic Spectrum

21
Wavelength and Frequency

22
 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)

23
Infrared Absorption Spectrum of
Ethanol

24
 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)
2.5 106 m to 2.5 105 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 25
IR region and vicinity

26
 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
27
Infrared Energy Modes

28
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)
29
30
31
32
 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

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Regions of the Infrared
Spectrum

34
 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

35
 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

36
 12.8 Infrared Spectra of
Hydrocarbons
C-H, C-C, C=C, C C have characteristic
peaks

37
Hexane

38
Alkenes

39
1-Hexene

40
Alkynes

41
 12.9 Infrared Spectra of Some
Common Functional Groups

Spectroscopic behavior of
functional groups is discussed
in later chapters
Brief summaries presented
here

42
IR: Alcohols

43
Amines

44
 IR: Aromatic Compounds
Weak CH stretch at 3030 cm1
Weak absorptions 1660 - 2000 cm1 range
Medium-intensity absorptions 1450 to 1600 cm1

45
Phenylacetylene

46
 IR: Carbonyl Compounds
Strong, sharp C=O peak 1670 to 1780 cm1
Exact absorption characteristic of type of carbonyl
compound
1730 cm1 in saturated aldehydes
1705 cm1 in aldehydes next to double bond or
aromatic ring

47
Practice problem 12.7:

48
Phenylacetaldehyde

49
 C=O in Ketones
1715 cm1 in six-membered ring and
acyclic ketones
1750 cm1 in 5-membered ring ketones
1690 cm1 in ketones next to a double
bond or an aromatic ring

50
 C=O in Esters
1735 cm1 in saturated esters
1715 cm1 in esters next to aromatic ring or a
double bond

51
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

52
 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

53
 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 12.17: HPLC analysis of a mixture of 14
pesticides, using acetonitrile/water as the mobile
phase

54
HPLC of Pesticide Mixture

55
Prob. 12.39: Cyclohexane or
Cyclohexene?

56
Problem 12.48: Unknown
hydrocarbon

57
Problem 12.49: Unknown
hydrocarbon2

58
 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

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