IV.

The Mass Spectrum and Structural Analysis

C. Fragmentation Patterns of Groups
16. Halogens - Fragment Ions

a) Halogenated compounds often give good M+

b) Fluoro- and iodo-compounds do not have appreciable contribution from

isotopes

c) Chloro- and bromo-compounds are unique in that they will show

strong M+2 peaks for the contribution of higher isotopes

d) For chlorinated compounds, the ratio of M + to M+2 is about3:1

e) For brominated compounds, the ratio of M + to M+2 is 1:1

f) An appreciable M+4, 6, … peak is indicative of a combination of these

two halogens – use appropriate guide to discern number of each

g) Principle fragmentation mode is to lose halogen atom, leaving a

carbocation – the intensity of the peak will increase with cation stability

h) Leaving group ability contributes to the loss of halogen most

strongly for -I and -Br less so for -Cl, and least for –F

i) Loss of HX is the second most common mode of fragmentation – here the

conjugate basicity of the halogen contributes (HF > HCl > HBr > HI)

j) Aromatic halides give stronger M +, and typically lose the halogen

atom to form C6 H5 +
16. Example MS: chlorine –1-chloropropane

Study Question : Draw the curved arrows that describe this α-cleavage step.

Solution :

16. Example MS: chlorine –p-chlorotoluene

IV. The Mass Spectrum and Structural Analysis
C. Fragmentation Patterns of Groups
16. Example MS: bromine –1-bromobutane
16. Example MS: bromine –p-bromotoluene

17. Example MS: multiple bromines –3,4-dibromotoluene

IV. The Mass Spectrum and Structural Analysis
C. Fragmentation Patterns of Groups
18. Example MS: iodine –iodobenzene

B. Approach to analyzing a mass spectrum

 1. Get a general feel for the spectrum before you analyze anything –
is it simple, complex, groups of peaks, etc.

2. Once you’ve identified the M+ peak, ruminate and consider the following:
a. Strong or Weak?
b. Isotopes? M+1? M+2, 4, …
c. Apply the Nitrogen rule
d. Apply the Rule of Thirteen to generate possible formulas (you can
quickly dispose of possibilities based on the absence of isotopic
peaks or the inference of the nitrogen rule)
e. Use the IHD from the Rule of Thirteen to further
reduce the possibilities
f. Is there an M-1 peak?

3. When looking at the base peak, pay attention to the following:

a. What ions could give this peak? (m/z 43 doesn’t help much)

b. What was lost from M+ to give this peak?

c. When considering the base peak initially, only think of the
most common cleavages for each group

4. Look for the loss of small neutral molecules from M+

a. H2C=CH2, , H2O, HOR, HCN, HX

5. Now consider the possible diagnostic peaks on the

spectrum (e.g.: 29, 30, 31, 45, 59, 77, 91, 105 etc.)

6. Lastly, once you have a hypothetical molecule that explains the data, see
if you can verify it by use of other less intense peaks on the spectrum –
not 100% necessary (or accurate) but if this step works it can add to the
confidence level

LEARNING EXERCISES:
1. What is the major ion fragment expected in the mass spectrum of 3-methyloctane?
2. Show fragmentation pathways to arrive at the following peaks in the mass spectrum of
methylcyclopentane: m/z 84, 69, 56.
3. An organic compound gave a peak at m/z = 122 (W) and another peak of nearly equal
intensity at m/z= 124 in its mass spectrum. What is the likely molecular formula of the
compound?
4. Write out structures for the ions expected from a retro Diels-Alder reaction of each of the
following:
5. How will you distinguish 3-methylcyclohexene and 4-methylcyclohexene using mass
spectroscopy?
6. What are the species formed when 4-n-butyltoluene undergoes the following
fragmentations:
a) −cleavage
b) McLafferty rearrangement
7. The mass spectrum of o-CH3C6H4CH2OH shows an abundant fragment ion at m/z =104. What
is a feasible structure for this ion?
8. Calculate the mass of the fragment ion produced in the mass spectrum of 4-methyl-2-
cyclohexanol by simultaneous loss of water and alkene.
9. The mass spectrum of 3-butyn-2-ol shows the base peak at m/z= 55. Explain why the
fragment giving rise to this peak would be very stable.
10. When the molecular ion from n-butyl phenyl ether fragments through  hydrogen transfer,
what neutral (uncharged) fragment is extruded? What ion fragment results?
11. The mass spectrum of 3,3-dimethyl-2-butanone shows peaks at m/z 100, 85, 57 (base peak),
and 54. Interpret these.
12. Draw structures for the fragment due to McLafferty rearrangement resulting from butyric
acid and methyl butyrate.
13. Identify which of the two compounds in each set would be expected to show the individual
ion fragments in its mass spectrum. Justify your choice by showing fragmentation pathways.
a) m/z 91

or

b) m/z 58 and m/z 43

How will you distinguish 2-pentanone and 3-pentanone?

14. Outline the mode of fragmentation leading to the ions causing peaks at indicated m/e in the
mass spectra of the compounds:

(a) Pentanoic acid, at m/z = 60

(b) Ethyl phenyl ether, at m/z =94
(c) Diethylamine, at m/z = 30
15. The mass spectrum of benzamide is provided below. Account for the fragmentation ions
observed at m/z =105, 77,41, and 44.

16. The spectra provided below give the characteristic spectra of isomeric primary. secondary, and
tertiary 5 C alcohol. Provide the structures for the following fragments:

a) 1-pentanol – m/z =70, 55, 42, and 31

b) 2-pentanol – m/z = 71, 55, and 45
c) 2-methyl-2-butanol – m/z = 73, 59, 55 and 42
17. The MS spectrum of 4-chlorobenzophenone is shown below. Account for the fragment ions
at m/z =181, 139, 105, 77,and 51. Show the mechanism involved in generating these
fragments.
 Learning Resources:

https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Exercises%3A_Organic_Chem
istry/Exercises%3A_McMurry/12.E%3A_Structure_Determination%3A_Mass_Spectrometr
y_and_Infrared_Spectroscopy_(Exercises)

http://people.whitman.edu/~dunnivfm/C_MS_Ebook/CH6/6_9_5.htm

The Organic Chemistry Tutor Channel

(https://www.youtube.com/watch?v=8YKhiG25lcg&t=139s)

Mass Spectrometry Fragmentation Part 1

(https://www.youtube.com/watch?v=FCCFiyoDTaM&t=1090s)

Mass Spectrometry Fragmentation Part 2

(https://www.youtube.com/watch?v=mbXOP28W9z8&t=146s)

Lecture 6 Fragmentation in EIMS

(https://www.youtube.com/watch?v=e__PzYEmW7o&list=PLC86CC98DDF0CDDAC&index=8)

Lecture 6A Fragmentation in EIMS

(https://www.youtube.com/watch?v=e__PzYEmW7o&list=PLC86CC98DDF0CDDAC&index=8)

(https://chem.libretexts.org/Courses/Purdue/Purdue:_Chem_26200:_Organic_Chemistry_II
_(Wenthold)/Chapter_11:__IR_and_Mass_Spectrometry/11.08:_Fragmentation_Patterns_i
n_Mass_Spectrometry)

https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Exercises%3A_Organic_Chemis
try/Exercises%3A_McMurry/12.E%3A_Structure_Determination%3A_Mass_Spectrometry_a
nd_Infrared_Spectroscopy_(Exercises)