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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
Physical methods now permit structures to be
determined directly. We will examine:
mass spectrometry (MS)
infrared (IR) spectroscopy
nuclear magnetic resonance spectroscopy (NMR)
ultraviolet-visible spectroscopy (VIS)
2
Why this Chapter?
Finding structures of new molecules
synthesized is critical
3
12.1 Mass Spectrometry of Small
Molecules:Magnetic-Sector Instruments
Bonds in cation radicals
begin to break (fragment)
Sample
vaporized and
subjected to
bombardment
by electrons
that remove an
electron
creating a Mass to charge (m/z)
cation radical ratio is measured
Molecular ion (M+)
shows molecular weight
4
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+)
H H H
Propane H C C C H
MW = M+ = 44 H H H
5
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
Instruments include computation of formulas for each
peak
If parent ion not present due to electron bombardment causing
breakdown, softer methods such as chemical ionization are used
6
M+ peak Example:
Possible formulas can be determined from the mass. (M+)
7
M+ peak Example:
Possible formulas can be predicted from the mass. (M+)
8
M+ peak :
Peaks above the molecular weight appear as a result
of naturally occurring heavier isotopes in the sample
(M+1) from 1.1% 13C in nature
(M and M+2) in 75.8%/24.2% ratio = 35Cl and 37Cl
(M and M+2) in 50.7%/49.3% ratio = 79Br and 81Br
H H H
Propane
H C C C H
MW = M+ = 44
H H H
M+1 = 45
From 1.1% 13C
9
Click on image to enlarge
M+ peak: Halides
M+ and M+2 in
75.8%:24.2% CH3Cl
(~ 3:1) ratio
= 35Cl and 37Cl
M+ and M+2 in Br
50.7%:49.3%
(~ 1:1) ratio
= 79Br and 81Br
10
Mass-Spec Fragmentation Patterns
Molecular ions break into characteristic fragments that can be
identifed
Serves as a fingerprint for comparison with known materials in
analysis (used in forensics)
Positive charge goes to fragments that best can stabilize it
11
Mass-Spec Fragmentation Patterns
M -15 = 57
CH3=15
MW=72;
M+ peak not seen
12
Mass Spec: Fragmentation of Hexane
Hexane (m/z = 86 for parent) has peaks at
m/z = 71, 57, 43, 29
13
CH3
Learning Check:
MW=98 MW=98
Identify the following MS as that of methylcyclohexane or ethylcyclopentane.
14
CH3
Solution:
MW=98 MW=98
Identify the following MS as that of methylcyclohexane or ethylcyclopentane.
M+ =98
15
CH3
Learning Check:
MW=98 MW=98
Identify the following MS as that of methylcyclohexane or ethylcyclopentane.
16
CH3
Solution:
MW=98 MW=98
Identify the following MS as that of methylcyclohexane or ethylcyclopentane.
M+ =98
17
12.3 Mass Spec: Common Functional Groups
Alcohols:
Alcohols undergo -cleavage (at bond next to the C-OH)
as well as loss of H-OH (18) to give C=C
Loss of 18
18
Mass Spec: Alcohols
CH3
CH
H3C
19
Mass Spec: Amines
Nitrogen Rule: Amines with odd # of Ns have Odd M+
Amines undergo -cleavage, generating radicals
20
Mass Spec: 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
Loss of 28
21
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
MALDI-TOF MS of chicken
eg-white lysozyme
22
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
23
Electromagnetic Spectrum
24
Absorption Spectra
Organic compound exposed to electromagnetic radiation, can
absorb energy of certain wavelengths.
Changing wavelengths to determine which are absorbed and
which are transmitted produces an absorption spectrum
Energy absorbed is shown as dips in spectrum
25
12.6 Infrared Spectroscopy
IR region lower energy than visible light (< 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
Specific IR absorbed by organic molecule related to its structure
26
Infrared Spectroscopy
IR energy absorption corresponds to atomic movements, such as
vibrations and rotations from bending and stretching of bonds
between groups of atoms
Energy is characteristic of the bonding of atoms in a functional group
2500-2000 cm-1
CC and C N
(stretching)
28
Infrared Spectra: Functional Grps
Characteristic higher energy IR absorptions used to confirm the
existence of the presence of functional groups
29
12.8 IR Spectra: Functional Grps
Alkane C-C
-C-H
Alkene
Alkyne
30
IR: Aromatic Compounds
CC
31
IR: Alcohols and Amines
CH3CH2OH
C-O
C-O
34
IR: Amines
Primary and secondary
amines exhibit a
characteristic broad IR N-H
stretching absorption between
3250 and 3500 cm-1.
Primary amines show two
strong peaks in this range,
whereas secondary amines
show only one.
Primary amines also show a
band near 1600 cm-1 due to a
scissoring motion of the NH2
group.
Tertiary amines do not show
any of these signals since
they do not have a hydrogen
bound to nitrogen. Amines similar to OH
N-H broadens with Hydrogen bonding
35
IR: Amines Examples
36
IR: Carbonyls: C=O Aldehydes
Carbonyls in general:
Strong, sharp C=O peak 1670 to 1780 cm1
Conjugation lowers stretching frequency
37
IR: C=O: Aldehydes
38
IR: C=O: Ketones
39
IR: C=O: Ketones
Ring strain increases frequency:
Incorporation of the carbonyl group in
a small ring (5, 4 or 3-membered),
raises the stretching frequency.
40
IR: C=O: Esters
1735 cm1 in saturated esters
Electron donating O increased the frequency
1715 cm1 in esters next to aromatic ring or a double bond
Conjugation decreases the frequency
41
IR: Carboxylic Acids
42
Learning Check:
32. Which of the following represents cyclohexane and which cyclohexene?
43
Solution:
32. Which of the following represents cyclohexane and which cyclohexene?
=C- H -C-H
-C=C-
44
Learning Check:
41.Propose a structure for the following unknown hydrocarbon:
45
Solution: 68-53 =15
loss of CH3
M-1=67 C5H8
2 deg of unsat
M=68
C- H -CC-
-C-H
46
Learning Check:
42. Propose a structure for the following unknown hydrocarbon:
47
Solution:
42. Propose a structure for the following unknown hydrocarbon:
70-55 =15
C5H10
loss of CH3
M=70
=C-H -C-H
-C=C-
48
In mass spectrometry, what term is used to describe the ion
that results from the ejection of one electron from a
molecule?
20% 20% 20% 20% 20%
1. base peak
2. parent peak
3. fragment
4. analyte
5. none of these
1 2 3 4 5
What quantity is detected by mass spectrometry?
1. the energy of a 20% 20% 20% 20% 20%
molecule
2. the number of electrons
ejected from a molecule
3. the number of ions of a
particular mass to
charge ratio
4. the number of electrons
needed to ionize a
molecule
5. the number of hydrogen
atoms in a molecule
1 2 3 4 5
High-resolution mass spectrometry enables one
to determine the molecular formula of a
molecule.
50% 50%
1. True
2. False
1 2
High-resolution mass spectrometry would allow one to
distinguish between the following molecules.
50% 50%
Br
Br
1. True
2. False
1 2
Which of the given C6H12O isomers would be expected
to produce an m/z peak at M+-18?
25% 25% 25% 25%
1. 2.
O O
4.
3.
OH
O
1 2 3 4
Which of the following reasons explains why some
mass spectrum peaks are larger than others?
3.
O
4. 5.
OH OH
1 2 3 4 5
Frequency is commonly reported in units of:
1. Joules
2. nm
3. amu
4. Hz
5. m/z
1 2 3 4 5
The higher the wavenumber of a molecular vibration, the lower
the energy of the infrared radiation needed to stimulate it.
50% 50%
1. True
2. False
1 2
Which type of electromagnetic radiation
possesses the highest energy?
20% 20% 20% 20% 20%
1. IR light
2. UV light
3. microwaves
4. visible light
5. FM radio waves
1 2 3 4 5
Infrared spectroscopy is based on _____
excitation.
25% 25% 25% 25%
1. electronic
2. rotational
3. nuclear
4. vibrational
1 2 3 4
What functional groups are most likely present in a compound
whose IR spectrum shows absorbances at 2217 and 1648 cm-1?
1 2 3 4 5
(R)-2-pentanol and (S)-2-pentanol give
identical IR spectra.
50% 50%
1. True
2. False
1 2
Which of the following compounds will have its
carbonyl absorb at the lowest frequency in IR
spectroscopy?
20% 20% 20% 20% 20%
1. 2.
O O
3.
O
4. 5.
O O
O
1 2 3 4 5
What approximate frequency range is considered
the fingerprint region in infrared spectroscopy?
20% 20% 20% 20% 20%
1 2 3 4 5
(E)-2-Butene and (Z)-2-butene give
identical IR spectra.
50% 50%
1. True
2. False
1 2