CH 09

Chapter 9
Nuclear Magnetic
Resonance and Mass
Spectrometry
Created by
Professor William Tam & Dr. Phillis Chang
Copyright © 2014 by John Wiley & Sons, Inc. All rights reserved.
About The Authors
These PowerPoint Lecture Slides were created and prepared by Professor
William Tam and his wife Dr. Phillis Chang.
Professor William Tam received his B.Sc. at the University of Hong Kong in
1990 and his Ph.D. at the University of Toronto (Canada) in 1995. He was an
NSERC postdoctoral fellow at the Imperial College (UK) and at Harvard
University (USA). He joined the Department of Chemistry at the University of
Guelph (Ontario, Canada) in 1998 and is currently a Full Professor and
Associate Chair in the department. Professor Tam has received several awards
in research and teaching, and according to Essential Science Indicators, he is
currently ranked as the Top 1% most cited Chemists worldwide. He has
published four books and over 80 scientific papers in top international journals
such as J. Am. Chem. Soc., Angew. Chem., Org. Lett., and J. Org. Chem.
Dr. Phillis Chang received her B.Sc. at New York University (USA) in 1994, her
M.Sc. and Ph.D. in 1997 and 2001 at the University of Guelph (Canada). She
lives in Guelph with her husband, William, and their son, Matthew.
© 2014 by John Wiley & Sons, Inc. All rights reserved.

Table of Contents (hyperlinked)
1. Introduction
2. Nuclear Magnetic Resonance (NMR) Spectroscopy
3. How to Interpret Proton NMR Spectra
4. Nuclear Spin: The Origin of the Signal
5. Detecting the Signal: Fourier Transform NMR Spectrometers
6. The Chemical Shift
7. Shielding & Deshielding of Protons
8. Chemical Shift Equivalent and Nonequivalent Protons
9. Signal Splitting: Spin–Spin Coupling
10. Proton NMR Spectra and Rate Processes
11. Carbon-13 NMR Spectroscopy
12. Two-Dimensional (2D) NMR Techniques
13. An Introduction to Mass Spectrometry
14. Formation of Ions: Electron Impact Ionization
15. Depicting the Molecular Ion
16. Fragmentation
17. Isotopes in Mass Spectra
18. GC/MS Analysis
19. Mass Spectrometry of Biomolecules
Table of Contents
1. Introduction
2. Nuclear Magnetic Resonance (NMR) Spectroscopy
3. How to Interpret Proton NMR Spectra
4. Nuclear Spin: The Origin of the Signal
5. Detecting the Signal: Fourier Transform NMR Spectrometers
7. Shielding & Deshielding of Protons
8. Chemical Shift Equivalent and Nonequivalent Protons
9. Signal Splitting: Spin–Spin Coupling
10. Proton NMR Spectra and Rate Processes
12. Two-Dimensional (2D) NMR Techniques
13. An Introduction to Mass Spectrometry
14. Formation of Ions: Electron Impact Ionization
16. Fragmentation
18. GC/MS Analysis
19. Mass Spectrometry of Biomolecules
In this chapter we will consider:
❖ Nuclear magnetic resonance (NMR), a
form of spectroscopy that is one of the
most powerful tools for the
identification of functional groups and
for the determination of connections
between the atoms in molecules
❖ Mass spectroscopy (MS), which allows
the determination of exact molecular
formulas of molecules both large and
small
1. Introduction
❖ Classic methods for organic structure
determination
● Boiling point
● Refractive index
● Solubility tests
● Functional group tests
● Derivative preparation
● Sodium fusion (to identify N, Cl, Br, I & S)
● Mixture melting point
● Combustion analysis
● Degradation
❖ Classic methods for organic structure
determination
● Require large quantities of

sample and are time consuming

❖ Spectroscopic methods for organic
structure determination
a) Mass Spectroscopy (MS)
● Molecular Mass & characteristic
fragmentation pattern
b) Infrared Spectroscopy (IR)
● Characteristic functional groups
c) Ultraviolet Spectroscopy (UV)
● Characteristic chromophore
d) Nuclear Magnetic Resonance (NMR)

❖ Spectroscopic methods for organic
structure determination
● Combination of these
spectroscopic techniques provides
a rapid, accurate, and powerful
tool for Identification and
Structure Elucidation of organic
compounds
● Effective in mg and microgram
quantities

❖ General steps for structure elucidation
1. Elemental analysis
● Empirical formula
● e.g. C2H4O
2. Mass spectrometry
● Molecular weight
● Molecular formula
● e.g. C4H8O2, C6H12O3 … etc.
● Characteristic fragmentation
pattern for certain functional
groups
3. From molecular formula
● Double bond equivalent (DBE)
4. Infrared spectroscopy (IR)

● Identify some specific
functional groups
● e.g. C=O, C–O, O–H, COOH,
NH2 … etc.

5. UV (Ultraviolet) Spectroscopy
● Sometimes useful especially for
conjugated systems
● e.g. dienes, aromatics, enones
6. 1H, 13CNMR and other advanced

NMR techniques
● Full structure determination

❖ Electromagnetic spectrum
cosmic micro- radio-

X-rays ultraviolet visible infrared
& -rays wave wave
 0.1nm 200nm 400nm 800nm 50m
UV IR NMR
X-Ray
Crystallography
1Å = 10-10m
1nm = 10-9m
1m = 10-6m

2. Nuclear Magnetic Resonance
(NMR) Spectroscopy
❖ A graph that shows the characteristic
energy absorption frequencies and
intensities for a sample in a magnetic
field is called a nuclear magnetic
resonance (NMR) spectrum

1. The number of signals in the
spectrum tells us how many different
sets of protons there are in the
molecule
2. The position of the signals in the

spectrum along the x-axis tells us
about the magnetic environment of
each set of protons arising largely
from the electron density in their
environment
3. The area under the signal tells us
about how many protons there are in
the set being measured
4. The multiplicity (or splitting pattern)

of each signal tells us about the
number of protons on atoms adjacent
to the one whose signal is being
measured

❖ Typical 1H NMR spectrum
● Chemical Shift ()
● Integration (areas of peaks  no.

of H)
● Multiplicity (spin-spin splitting) and

coupling constant

❖ Typical 1H NMR spectrum
1
Record as: H NMR (300 MHz, CDCl3):
 4.35 (2H, t, J = 7.2 Hz, Hc)

b
2.05 (2H, sextet, J = 7.2 Hz, H )
1.02 (3H, t, J = 7.2 Hz, Ha)
chemical coupling
shift () constant
no. of H
in ppm
(integration) multiplicity in Hz

2A. Chemical Shift
❖ The position of a signal along the x-axis of
an NMR spectrum is called its chemical
shift
❖ The chemical shift of each signal gives
information about the structural
environment of the nuclei producing that
signal
❖ Counting the number of signals in a 1H NMR
spectrum indicates, at a first approximation,
the number of distinct proton environments
in a molecule
❖ Normal range of 1H NMR
"upfield" (more shielded)

"downfield" (deshielded)
15 -10
(low field  ppm (high field
strength) strength)

❖ Reference compound Me
● TMS = tetramethylsilane Me Si Me
Me
as a reference standard (0 ppm)
● Reasons for the choice of TMS as
reference
⧫ Resonance position at higher field
than other organic compounds
⧫ Unreactive and stable, not toxic
⧫ Volatile and easily removed
(B.P. = 28oC)
❖ NMR solvent
● Normal NMR solvents should not
contain hydrogen
● Common solvents
⧫ CDCl3
⧫ C6D6
⧫ CD3OD
⧫ CD3COCD3 (d6-acetone)

❖ The 300-MHz 1H NMR spectrum of
1,4-dimethylbenzene

2B. Integration of Signal Areas
Integral Step Heights

❖ The area under each signal in a 1H
NMR spectrum is proportional to the
number of hydrogen atoms producing
that signal
❖ It is signal area (integration), not
signal height, that gives information
about the number of hydrogen atoms
Ha Ha
Hb
R O Hb
Hb 3H b
a
2H
b a
H H
2C. Coupling (Signal Splitting)
❖ Coupling is caused by the magnetic
effect of nonequivalent hydrogen
atoms that are within 2 or 3 bonds of
the hydrogens producing the signal
❖ The n+1 rule
● Rule of Multiplicity:
If a proton (or a set of magnetically
equivalent nuclei) has n neighbors
of magnetically equivalent protons,
its multiplicity is n + 1
❖ Examples
(1) H b
H a
Ha: multiplicity = 3 + 1 = 4 (a quartet)
Hb C C Cl
Hb: multiplicity = 2 + 1 = 3 (a triplet)
H b Ha
(2) Ha Hb
Ha: multiplicity = 2 + 1 = 3 (a triplet)
Cl C C Cl
Hb: multiplicity = 1 + 1 = 2 (a doublet)
Cl Hb

❖ Examples
(3) Hb H a
Ha: multiplicity = 6 + 1 = 7 (a septet)
Hb C C Br
b
H Hb Hb: multiplicity = 1 + 1 = 2 (a doublet)
Hb
Hb
Note: All Hb’s are chemically and

magnetically equivalent.

❖ Pascal’s Triangle
● Use to predict relative intensity of
various peaks in multiplet
● Given by the coefficient of
binomial expansion (a + b)n
singlet (s) 1
doublet (d) 11
triplet (t) 121
quartet (q) 1331
quintet 14641
sextet 1 5 10 10 5 1
H a
H b Due to
symmetry, Ha
● For Br C C Br
and Hb are
Cl Cl identical
 a singlet
Ha Hb
Ha ≠ Hb
● For Cl C C Br
 two doublets
Cl Br

3. How to Interpret Proton NMR
Spectra
1. Count the number of signals to
determine how many distinct proton
environments are in the molecule
(neglecting, for the time being, the
possibility of overlapping signals)
2. Use chemical shift tables or charts to
correlate chemical shifts with possible
structural environments
3. Determine the relative area of each signal,
as compared with the area of other
signals, as an indication of the relative
number of protons producing the signal
4. Interpret the splitting pattern for each
signal to determine how many hydrogen
atoms are present on carbon atoms
adjacent to those producing the signal and
sketch possible molecular fragments
5. Join the fragments to make a molecule in
a fashion that is consistent with the data
❖ Example: 1H NMR (300 MHz) of an
unknown compound with molecular
formula C3H7Br

❖ Three distinct signals at ~ 3.4, 1.8
and 1.1 ppm
 3.4 ppm: likely to be near an
electronegative group (Br)
 (ppm): 3.4 1.8 1.1
Integral: 2 2 3

 (ppm): 3.4 1.8 1.1
Multiplicity: triplet sextet triplet
2 H's on 5 H's on 2 H's on

adjacent C adjacent C adjacent C
Complete structure:
most upfield signal
most downfield
signal CH2 CH3
Br CH2
• 2 H's from • 2 H's from • 3 H's from

integration integration integration
• triplet • sextet • triplet
4. Nuclear Spin:
The Origin of the Signal
The magnetic The spinning
field associated proton
with a spinning resembles a tiny
proton bar magnet

❖ Spin quantum number (I)
1H: I = ½ (two spin states: +½ or -½)
 (similar for 13C, 19F, 31P)
12C, 16O, 32S:

I=0
 These nuclei do not give an NMR
spectrum

5. Detecting the Signal: Fourier
Transform NMR Spectrometers

❖ Reference compound Me
● TMS = tetramethylsilane Me Si Me
Me
as a reference standard (0 ppm)
● Reasons for the choice of TMS as
reference
⧫ Resonance position at higher field
than other organic compounds
⧫ Unreactive and stable, not toxic
⧫ Volatile and easily removed
(B.P. = 28oC)
6A. PPM and the  Scale
❖ The chemical shift of a proton, when
expressed in hertz (Hz), is
proportional to the strength of the
external magnetic field
❖ Since spectrometers with different
magnetic field strengths are commonly
used, it is desirable to express
chemical shifts in a form that is
independent of the strength of the
external field
❖ Since chemical shifts are always very small
(typically 5000 Hz) compared with the total
field strength (commonly the equivalent of
60, 300, or 600 million hertz), it is
convenient to express these fractions in
units of parts per million (ppm)
❖ This is the origin of the delta scale for the

expression of chemical shifts relative to TMS
(observed shift from TMS in hertz) x 106
=
(operating frequency of the instrument in hertz)

❖ For example, the chemical shift for benzene
protons is 2181 Hz when the instrument is
operating at 300 MHz. Therefore
2181 Hz x 106
= = 7.27 ppm
300 x 106 Hz
❖ The chemical shift of benzene protons in a
60 MHz instrument is 436 Hz:
436 Hz x 106
= = 7.27 ppm
60 x 106 Hz
❖ Thus, the chemical shift expressed in ppm is
the same whether measured with an
instrument operating at 300 or 60 MHz (or
any other field strength)
7. Shielding & Deshielding of
Protons
❖ Protons absorb at different NMR frequencies
depending on the electron density around
them and the effects of local induced
magnetic fields
❖ All protons do not absorb energy at the same
frequency in a given external magnetic field
❖ Lower chemical shift values correspond with
lower frequency
❖ Higher chemical shift values correspond with
higher frequency
"upfield" (more shielded)
"downfield" (deshielded)
15 -10
(low field  ppm (high field
strength) strength)

❖ Protons of Hydrogen Atoms in Alkyl
C–H Groups
● The chemical shift for hydrogens of
unsubstituted alkanes is typically in the
range of  0.8–1.8
❖ Protons of Hydrogens Near Electro-

negative Groups
● The chemical shift of hydrogens bonded
to a carbon bearing oxygen or a halogen
is typically in the range of  3.1–4.0

❖ Deshielding by electronegative groups
CH3X
X= F OH Cl Br I H
Electro-
4.0 3.5 3.1 2.8 2.5 2.1
negativity
 (ppm) 4.26 3.40 3.05 2.68 2.16 0.23
● Greater electronegativity
⧫ Deshielding of the proton
⧫ Larger 
❖ Protons of Hydrogen Atoms p Electrons
● The hydrogens of benzene absorb at 
7.27. Hydrogens bonded to substituted
benzene rings have chemical shifts in
the range of  6.0–8.5, depending on
the electron-donating or electron-
withdrawing effect of the substituents
● The chemical shift of alkene hydrogens
is typically in the range of  4.0–6.0
● The chemical shift of an alkyne
hydrogen is typically in the range of 
2.5–3.1
❖ Shielding and deshielding by circulation
of p electrons
● If we were to consider only the
relative electronegativities of carbon
in its three hybridization states, we
might expect the following order of
protons attached to each type of
carbon:
(higher (lower
sp < sp < sp
2 3
frequency) frequency)
● In fact, protons of terminal alkynes
absorb between  2.0 and  3.0,
and the order is
(higher (lower
sp < sp < sp
2 3
frequency) frequency)

● This upfield shift (lower frequency)
of the absorption of protons of
terminal alkynes is a result of
shielding produced by the
circulating p electrons of the triple
bond
Shielded
( 2 – 3 ppm)
● Aromatic system
Shielded region
Deshielded region

● e.g.
Hc
Hd
Hb
a
H
 (ppm)
a b
H & H : 7.9 & 7.4 (deshielded)
c d
H & H : 0.91 – 1.2 (shielded)
● Alkenes
Deshielded
( 4.5 – 7 ppm)

● Aldehydes
R
O
H
Electronegativity effect + Anisotropy effect

  = 8.5 – 10 ppm (deshielded)

8. Chemical Shift Equivalent and
Nonequivalent Protons
❖ Two or more protons that are in
identical environments have the same
chemical shift and, therefore, give only
one 1H NMR signal
❖ Chemically equivalent protons are

chemical shift equivalent in 1H NMR
spectra
8A. Homotopic and Heterotopic Atoms
❖ If replacing the hydrogens by a
different atom gives the same
compound, the hydrogens are said to
be homotopic
❖ Homotopic hydrogens have identical

environments and will have the same
chemical shift. They are said to be
chemical shift equivalent

Br H H Br
H C C H H C C H
same compounds
same compounds
H H H H
H H H H H H
Br C C H H C C H H C C Br
H H H H H H
Ethane
H H H H
H C C H H C C H
Br H H Br
❖ The six hydrogens of ethane are homotopic
and are, therefore, chemical shift equivalent
❖ Ethane, consequently, gives only one
signal in its 1H NMR spectrum
❖ If replacing hydrogens by a different
atom gives different compounds,
the hydrogens are said to be
heterotopic
❖ Heterotopic atoms have different

chemical shifts and are not
chemical shift equivalent

same Cl Br
compounds H C C H
 these 3 These 2 H’s
H H
H’s of the are also
H Br H Br
CH3 group homotopic
are Cl C C H H C C H
to each
homotopic H H H H other
 the CH3 H Br
group gives H C C H
only one 1H H Br H Br
Cl H
NMR signal H C C H H C C H
Cl H H Cl
different compounds
 heterotopic
H Br
H C C H
H H
❖ CH3CH2Br
● two sets of hydrogens that are
heterotopic with respect to each
other
● two 1H NMR signals

❖ Other examples
H CH3
(1) C C  2 1H NMR signals
H CH3
H CH3
(2) H H  4 1H NMR signals
H CH3

❖ Other examples
H
H H
(3) CH3
H3C
H H
H
 3 1H NMR signals

❖ Application to 13C NMR spectroscopy
● Examples
(1) H3C CH3 1 13C NMR signal
CH3
(2) 4 13C NMR signals

CH3

(3) 5 13C NMR signals
HO OH
4 13C NMR signals

8B. Enantiotopic and Diastereotopic
Hydrogen Atoms
❖ If replacement of each of two

hydrogen atoms by the same group
yields compounds that are
enantiomers, the two hydrogen atoms
are said to be enantiotopic

❖ Enantiotopic hydrogen atoms have the
same chemical shift and give only one
1H NMR signal:
H G
enantiotopic H3C Br
H H
enantiomer
H3C Br
G H
H3C Br

H OH
chirality H3C
center CH3
diastereomers
Hb G
H OH
H3C
CH3
Hb Ha
H OH
diastereotopic H3C
CH3
G Ha

G
Br
Hb
diastereomers
Ha H
Br
Hb
H Ha
diastereotopic Br
G
H

9. Signal Splitting:
Spin–Spin Coupling
❖ Vicinal coupling is coupling between
hydrogen atoms on adjacent carbons
(vicinal hydrogens), where separation
between the hydrogens is by three s
bonds
H a Hb
3
J or vicinal coupling

9A. Vicinal Coupling
❖ Vicinal coupling between heterotopic
protons generally follows the n + 1 rule.
Exceptions to the n + 1 rule can occur
when diastereotopic hydrogens or
conformationally restricted systems are
involved
❖ Signal splitting is not observed for
protons that are homotopic
(chemical shift equivalent) or
enantiotopic
9B. Splitting Tree Diagrams and the
Origin of Signal Splitting
❖ Splitting analysis for a doublet
H b Ha
C C

❖ Splitting analysis for a triplet
Hb Ha
C C
Hb
Hb Ha Hb
C C C

❖ Splitting analysis for a quartet
b a
H H
Hb C C
Hb

● Use to predict relative intensity of
various peaks in multiplet
● Given by the coefficient of
binomial expansion (a + b)n
singlet (s) 1
doublet (d) 11
triplet (t) 121
quartet (q) 1331
quintet 14641
sextet 1 5 10 10 5 1
9C. Coupling Constants – Recognizing
Splitting Patterns
Ha Hb
X C C Hb
Ha Hb

9D. The Dependence of Coupling
Constants on Dihedral Angle
❖ 3Jvalues are related to the dihedral
angle ()
H 
H

❖ Karplus curve
❖  ~0o or 180o
 Maximum
3J value
❖  ~90o
 3J ~0 Hz

❖ Karplus curve
● Examples
b
H
b
H
Ha
Ha
(axial, axial) (equatorial, equatorial)
Hb
Ha
a
Hb
H
 = 180º  = 60º
Ja,b = 10-14 Hz Ja,b = 4-5 Hz
❖ Karplus curve
● Examples b
H
a
H
(equatorial, axial)
b
H
a
H
 = 60º
Ja,b = 4-5 Hz
9E. Complicating Features
❖ The 60 MHz 1H NMR spectrum of ethyl
chloroacetate

❖ The 300 MHz 1H NMR spectrum of
ethyl chloroacetate

9F. Analysis of Complex Interactions

❖ The 300 MHz 1H NMR spectrum of
1-nitropropane

10. Proton NMR Spectra and Rate
Processes
❖ Protons of alcohols (ROH) and amines (RNH2)
may appear over a wide range from 0.5 – 5.0
ppm
● Hydrogen-bonding is the reason for this
range

❖ Why don’t we see coupling with the
O–H proton, e.g. –CH2–OH (triplet?)
● Because the acidic protons are
exchangeable about 105 protons
per second (residence time 10-5
sec), but the NMR experiment
requires a time of 10-2 – 10-3 sec.
to “take” a spectrum, usually we
just see an average. Thus, OH
protons are usually a broad
singlet.
Trick:
● Run NMR in d6-DMSO where H-

bonding with DMSO’s oxygen
prevents H’s from exchanging and
we may be able to see the coupling

❖ Deuterium Exchange
● To determine which signal in the

NMR spectrum is the OH proton,
shake the NMR sample with a drop
of D2O and whichever peak
disappears that is the OH peak
(note: a new peak of HOD appears)
D2O
R O H R O D + HOD

❖ Phenols
● Phenol protons appear downfield at
4-7 ppm
● They are more “acidic” - more H+
character
● More dilute solutions - peak
appears upfield: towards 4 ppm
OH O H

❖ Phenols
● Intramolecular H-bonding causes
downfield shift
12.1 ppm
O
H
O

11A. Interpretation of 13C NMR
Spectra
❖ Unlike 1H with natural abundance
~99.98%, only 1.1% of carbon,
namely 13C, is NMR active

11B. One Peak for Each Magnetically
Distinct Carbon Atom
❖ 13C NMR spectra have only become
commonplace more recently with the
introduction of the Fourier Transform
(FT) technique, where averaging of
many scans is possible (note 13C
spectra are 6000 times weaker than 1H
spectra, thus requiring a lot more
scans for a good spectrum)

❖ Note for a 200 MHz NMR (field strength
4.70 Tesla)
● 1H NMR  Frequency = 200 MHz
● 13C NMR  Frequency = 50 MHz

H
❖ Example:
● 2-Butanol CH3 C CH2 CH3
OH
Proton-coupled
13C NMR spectrum

H
❖ Example:
● 2-Butanol CH3 C CH2 CH3
OH
Proton-decoupled
13C NMR spectrum

11C. 13C Chemical Shifts
❖ Decreased electron density around an
atom deshields the atom from the
magnetic field and causes its signal to
occur further downfield (higher ppm, to
the left) in the NMR spectrum
❖ Relatively higher electron density around
an atom shields the atom from the
magnetic field and causes the signal to
occur upfield (lower ppm, to the right)
in the NMR spectrum
❖ Factors affecting chemical shift
i. Diamagnetic shielding due to bonding
electrons
ii. Paramagnetic shielding due to low-lying
electronic excited state
iii. Magnetic Anisotropy – through space
due to the near-by group (especially p
electrons)
In 1H NMR, (i) and (iii) most significant;
in 13C NMR, (ii) most significant (since
chemical shift range >> 1H NMR)
❖ Electronegative substituents cause
downfield shift
❖ Increase in relative atomic mass of

substituent causes upfield shift
13
X Electronegativity Atomic Mass C NMR: CH3X
Cl 2.8 35.5 23.9 ppm
Br 2.7 79.9 9.0 ppm
I 2.2 126.9 -21.7 ppm

❖ Hybridization of carbon
● sp2 > sp > sp3
e.g.
H2C CH2 HC CH H3C CH3
123.3 ppm 71.9 ppm 5.7 ppm

❖ Anisotropy effect
● Shows shifts similar to the effect

in 1H NMR
e.g.
C C C
shows large
upfield shift

(a) (b) (c)
Cl CH2 CH CH3
OH
1-Chloro-2-propanol
(c)
(b) (a)

11D. DEPT 13C Spectra
❖ DEPT 13C NMR spectra indicate how
many hydrogen atoms are bonded to
each carbon, while also providing the
chemical shift information contained in
a broadband proton-decoupled 13C
NMR spectrum. The carbon signals in a
DEPT spectrum are classified as CH3,
CH2, CH, or C accordingly

(a) (c)
(b)
(a) (b) (c)
Cl CH2 CH CH3
OH
1-Chloro-2-propanol

❖ The broadband proton-decoupled 13C
NMR spectrum of methyl methacrylate

12. Two-Dimensional (2D) NMR
Techniques
❖ HCOSY
● 1H–1H correlation spectroscopy
❖ HETCOR
● Heteronuclear correlation
spectroscopy

12A. 1H–1H COSY Cross-Peak Correlations
H1 H4
H3
H2
❖ HCOSY of
2-chloro-
H4
butane
H1
H3
H2

12B. 1H–13C Heteronuclear Corre-lation
Cross-Peak Correlations
HETCOR of
C3 C1 C4
❖
C2
2-chloro-
butane
H4
H1
H3
H2

13. An Introduction to Mass
Spectrometry
❖ Partial MS of octane (C8H18, M = 114)
14 (CH2)
29 (CH3CH2)
57
85 M+
71 114

❖ The M+ peak at 114 is referred to as
the parent peak or molecular ion
-
e
C8H18 [C8H18] + 2 e-
70 eV
(M+)
❖ The largest or most abundant peak is

called the base peak and is assigned
an intensity of 100%, other peaks are
then fractions of that e.g. 114(M+,40),
85(80), 71(60), 57(100) etc.
❖ Masses are usually rounded off to
whole numbers assuming:
H = 1, C = 12, N = 14, O = 16, F = 19 etc.
Daughter
fragmentation ions
[C8H18] [C6H13]
(M+, 114) -CH3CH2 (29) (85)
-CH3CH2CH2 (29+14) [C5H11]

Molecular ion (parent peak) (71)

14. Formation of Ions: Electron
Impact Ionization
❖ In the mass spectrometer, a molecule in the
gaseous phase under low pressure is
bombarded with a beam of high-energy
electrons (70 eV or ~ 1600 kcal/mol)
❖ This beam can dislodge an electron from a
molecule to give a radical cation which is
called the molecular ion, M+ or more
accurately
70 eV e-
M M
❖ This molecular ion has considerable
surplus energy so it can fly apart or
fragment to give specific ions which
may be diagnostic for a particular
compound
- m1º - m2º - m3º
M A B C etc.
mº = neutral fragment radical

CH3CH2 CH3
Radical cations from ionization

of nonbonding on p electron
H3C OH H3C N CH3 H2C CHCH 2CH3

CH3
Methanol Trimethylamine 1-Butene

❖ Ionization potentials of selected
molecules
Ionization
Compound Potential (eV)
CH3(CH2)3NH2 8.7
C6H6 (benzene) 9.2
C2H4 10.5
CH3OH 10.8
C2H6 11.5
CH4 12.7
16. Fragmentation
1. The reactions that take place in a mass
spectrometer are unimolecular, that is, they
do not involve collisions between molecules
or ions. This is true because the pressure is
kept so low (10-6 torr) that reactions
involving bimolecular collisions do not occur
2. We use single-barbed arrows to depict
mechanisms involving single electron
movements
3. The relative ion abundances, as indicated by
peak intensities, are very important
16A. Fragmentation by Cleavage at a
Single Bond
❖ When a molecular ion fragments, it will
yield a neutral radical (not detected) and
a carbocation (detected) with an even
number of electrons
❖ The fragmentation will be dictated to
some extent by the fragmentation of the
more stable carbocation:
+ + +
ArCH2 > CH2=CHCH2 > 3o > 2o > 1o > CH3

❖ e.g.
R+ + CH3
R CH
X +
R + CH3
● Site of ionization: n>p>s
non-bonding

❖ As the carbon skeleton becomes more
highly branched, the intensity of the
molecular ion peak decreases
❖ Butane vs. isobutane
a + CH3
a (43)
70eV
e-
b+ b + CH2CH3
M (58)
(29)
70eV
+ CH3
e- (43)
+
M (58)
16B. Fragmentation of Longer Chain
and Branched Alkanes
❖ Octane vs. isooctane
(85) +
(71) +
(57) +
+
M (114)
(43) +
+
+ (57)
M (114)
16C. Fragmentation to Form
Resonance-Stabilized Cations
❖ Alkenes
● Important fragmentation of terminal
alkenes
⧫ Allyl carbocation (m/e = 41)
R +
(41)
❖ Carbon–carbon bonds next to an atom
with an unshared electron pair usually
break readily because the resulting
carbocation is resonance stabilized
❖ Ethers
● Cleavage a (to ether oxygen) C–C bonds
CH3 O O
+
(m/e = 59)
❖ Alcohols
● Most common fragmentation: loss of
alkyl groups
a OH b
M+(74) b OH OH
CH3CH2 +
(m/e = 45)
❖ Carbon–carbon bonds next to the
carbonyl group of an aldehyde or
ketone break readily because
resonance-stabilized ions called
acylium ions are produced

❖ Aldehydes
● M+ peak usually observed but may
be fairly weak
● Common fragmentation pattern

⧫ a-cleavage
H + R C O
O acylium ion
R H
R + H C O
(m/e = 29)
❖ Ketones
● a-cleavage
b O a

❖ Alkyl-substituted benzenes ionize by
loss of a π electron and undergo loss of
a hydrogen atom or methyl group to
yield the relatively stable tropylium ion
(see Section 14.7C). This
fragmentation gives a prominent peak
(sometimes the base peak) at m/z 91

❖ Aromatic hydrocarbons
● very intense M+ peaks
● characteristic fragmentation pattern
(when an alkyl group attached to
the benzene ring): tropylium cation
CH2 rearrangement
CH3
CH3 +
benzyl cation tropylium cation

(m/e = 91)

16D. Fragmentation by Cleavage of
Two Bonds
❖ Alcohols frequently
+
show a prominent
peak at M - 18. This corresponds to
●
the loss of a molecule of water
● May lose H2O by 1,2- or 1,4-

elimination

OH
1,2-elimination: + H2O
M (M - 18)
1,4-elimination:
OH + CH3CH2
OH H
M
(M - 18) + H2O
❖ Cycloalkenes show a characteristic
fragmentation pattern which corresponds
to a reverse Diels-Alder reaction
retro Diels-Alder
+
❖ e.g.

❖ Aromatic hydrocarbons
● e.g.
McLafferty Rearrangement
CH2
H +
H
(m/e = 92)

❖ Ketones
● McLafferty rearrangement
H
O OH OH
+
1st McL. Rearr. H

O OH
(m/e = 86)
2nd McL. Rearr.
OH
+
(m/e = 58)
OH OH
i 2º radical (m/e = 86)

H H
O observed
ii i
OH
ii OH
1º radical (m/e = 114)

NOT observed

❖ Characteristics of McLafferty
rearrangements
1. No alkyl migrations to C=O, only H
migrates
H R
O
H R
O
X R
O
H

❖ Characteristics of McLafferty
rearrangements
2. 2o is preferred over 1o
H H OH
O
ii i
2º radical
OH
not
1º radical

❖ 13C and 12C
About 1.1% of all carbon atoms are
the 13C isotope
❖ About 98.9% of the methane

molecules in the sample will contain
12C, and the other 1.1% will contain
13C

❖ Example
● Consider 100 molecules of CH4
H 1
H 1
H1
1 12 1 1 13 1 1 12 2
H C H H C H H C H
H 1
H 1 H1
M : 16 M + 1 = 17
C12: 100 C13: 1.11
H1: 100 H2: 0.016

H1 H1 H1
1
H C12 H1 H 1 C13 H1 1
H C12 H2
H1 H1 H1
M : 16 M + 1 = 17
1.11 molecules 4x0.016 = 0.064 molecules

contain a 13C atom contain a 2H atom
+
Intensity of M + 1 peak:+ ●
1.11+0.064=1.174% of the M● peak

+
M
●
relative ion abundance
100
+
M +1
●
≈ 1.17
m/z
❖ 35Cl and 37Cl; 79Br and 81Br
Some elements that are common in
organic molecules have isotopes that
differ by two atomic mass units. These
include 16O and 18O, 32S and 34S, 35Cl
and 37Cl, and 79Br and 81Br. It is
particularly easy to identify the
presence of chlorine or bromine using
mass spectrometry because the
isotopes of chlorine and bromine are
relatively abundant
• The natural abundance of 35Cl is
75.5% and that of 37Cl is 24.5%
• In the mass spectrum for a sample

containing chlorine, we would
expect to find peaks separated by
two mass units, in an approximately
3 : 1 (75.5% : 24.5%) ratio for the
molecular ion or any fragments that
contain chlorine

• The natural abundance of 79Br is
51.5%, and that of 81Br is 49.5%
• In the mass spectrum for a sample

containing bromine we would expect
to find peaks separated by two mass
units in an approximately 1 : 1 ratio
(49.5% : 51.5%)

❖ Example 1
● O2, N2H4 and CH3OH all have M.W. of 32

(by MS), but accurate masses are
different
⧫ O2 = 2(15.9949) = 31.9898
⧫ N2H4 = 2(14.0031) + 4(1.00783) =

32.0375
⧫ CH4O = 12.00000 + 4(1.00783) +

15.9949 = 32.0262
❖ Example 2
● Both C3H8O and C2H4O2 have M.W. of 60

(by MS), but accurate masses are
different
⧫ C3H8O = 60.05754
⧫ C2H4O2 = 60.02112

18. GC/MS Analysis

19. Mass Spectrometry of
Biomolecules
❖ Advances in mass spectrometry have
made it a tool of exceptional power for
analysis of large biomolecules

❖ Electrospray ionization, MALDI (matrix-
assisted laser desorption ionization),
and other “soft ionization” techniques
for nonvolatile compounds and
macromolecules make possible
analyses of proteins, nucleic acids, and
other biologically relevant compounds
with molecular weights up to and in
excess of 100,000 daltons

❖ Electrospray ionization with quadruple
mass analysis is now routine for
biomolecule analysis as is analysis
using MALDI–TOF (time of flight)
instruments

 END OF CHAPTER 9 

CH 09

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CH 09

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Chapter 9

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● Require large quantities of

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4. Infrared spectroscopy (IR)

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6. 1H, 13CNMR and other advanced

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cosmic micro- radio-

 0.1nm 200nm 400nm 800nm 50m

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2. The position of the signals in the

4. The multiplicity (or splitting pattern)

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● Integration (areas of peaks  no.

● Multiplicity (spin-spin splitting) and

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 4.35 (2H, t, J = 7.2 Hz, Hc)

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"upfield" (more shielded)

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Integral Step Heights

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Note: All Hb’s are chemically and

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2 H's on 5 H's on 2 H's on

• 2 H's from • 2 H's from • 3 H's from

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12C, 16O, 32S:

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❖ This is the origin of the delta scale for the

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❖ Protons of Hydrogens Near Electro-

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Electronegativity effect + Anisotropy effect

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❖ Chemically equivalent protons are

❖ Homotopic hydrogens have identical

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❖ Heterotopic atoms have different

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(2) H H  4 1H NMR signals

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(1) H3C CH3 1 13C NMR signal

(2) 4 13C NMR signals

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4 13C NMR signals

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