Paper No. : 06 Atomic Spectroscopy
Module : 34 Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
Principal Investigator: Dr. Nutan Kaushik, Senior Fellow
The Energy and Resouurces Institute (TERI), New Delhi Co-Principal Investigator: Dr. Mohammad Amir, Professor of Pharm. Chemistry,
Jamia Hamdard University, New Delhi
Paper Coordinator: Dr. Mymoona Akhtar, Associate professor, Dept. of Pharm.
Chemistry, Jamia Hamdard, New Delhi.
Content Writer: Dr. S.K.Raza, Former Director,Institute of Pesticide formulation Technology, Gurugram
Content Reviwer: Dr. Nutan Kaushik, Senior Fellow , The Energy and Resouurces Institute (TERI), New Delhi
Analytical Chemistry / Instrumentation
Atomic Spectroscopy
Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
FRAGMENTATIUON PATTERN OF ORGANIC MOLECULES UNDER ELECTRON IONIZATION MASS SPECTROMETRY (EI MS)–PART II
1. Aim of the Module
To give an account of the Fragmentation of Organic Molecules under Electron Ionization Mass Spectrometry.
To discuss the fragmentation patterns of different classes of organic molecules under EIMS
To understand the role of fragment ions as diagnostic tool for various classes of organic compounds.
2. Objectives of the Module
At the end of this module one should be able to :
a) Understand the role of fragmentation in structure elucidation of organic molecules under EI MS.
b) Diagnose characteristic fragment ions for various classes of organic compounds and thus helping in the identification of such molecules.
3. Introduction
Description of Module
Subject Name Analytical Chemistry / Instrumentation Paper Name Atomic Spectroscopy
Module Name/Title Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
Module Id 34
Pre-requisites Objectives Keywords
The general guidelines for fragmentation and some basic principles of mass spectrometric fragmentation such as Nitrogen rule, role of isotopes in mass spectrometry, high resolution mass spectrometry & accurate mass measurements and rearrangements taking place in the ion source of the mass spectrometer have already been discussed in Module 4. The fragmentation patterns observed in Hydrocarbons, Branched Hydrocarbons, Cyclic Hydrocarbons, Alkenes, Aromatic Hydrocarbons, Alcohols and Phenols have already been discussed in Module 4. In this Module we are going to discuss the fragmentation of the remaining classes of molecules, namely, alkyl halides, ethers,
4. Mass Spectra of Various Classes of Organic Compounds
4.1 Alkyl Halides: Most alkyl halides fragment by i-cleavage to lose the halogen radical. Fluorine and Iodine containing compounds are not very interesting as they have single isotope as compared with their Chlorine and Bromine analogues which give two molecular ion peaks due to isotopic abundance. The presence of Chlorine and Bromine can thus be detected easily due to characteristic isotopic ratios. Chlorine and Bromine contain two isotopes and this is reflected in compounds containing these elements.
4.2 Ethers : Alkyl ethers fragment in two principal ways:
M+156/158 M - Br
M+140/142
Analytical Chemistry / Instrumentation
Atomic Spectroscopy
Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
i) -Bond Cleavage: An electron of Oxygen of ether is lost under EI to give an oxonium radical which undergoes fragmentation. It is expected that the larger R group of ether will be lost preferentially.
ii) C-O bond cleavage with the charge on the C fragment.
OCH3 OCH+ 3
m/z = 73 m/z = 88
m/z = 59 A
OCH3
+
M+ 88
+
OCH3 O CH3
m/z = 88 m/z = 57
m/z = 73 M – CH3
Analytical Chemistry / Instrumentation
Atomic Spectroscopy
Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
O
In aromatic ethers the molecular ion is usually strong. The fragmentation pattern in aromatic ether is similar to phenols – both form phenoxyl cation (m/z 93) and associated fragment ions.
4.3 Ketones : Ketones usually give strong molecular ion peaks. Ketones undergo a major fragmentation pathway involving -cleavage to give an acylium ion. The carbonyl-
containing fragment can also take the radical to give m/z 43 and m/z 29.
A very characteristic fragmentation in ketones with longer chains having γ-hydrogen is due to the McLafferty rearrangement which often leads to strong peaks.
m/z = 43 O
m/z = 29
In aromatic ketones, the molecular ion peak is quite strong. Primary cleavage is to the carbonyl to give a strong ArCO+
peak (m/z 105 when Ar = Ph). This will lose CO to give the phenyl cation (m/z 77).
+
Analytical Chemistry / Instrumentation
Atomic Spectroscopy
Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
M+ m/z = 88 COOH
m/z = 71(M+ - OH) m/z = 43
m/z = 60 OH
4.4 Aldehydes: Aldehydes undergo fragmentation giving rise toan M+–H and M+–R peaks due to -cleavage. Aldehydes having a γ-hydrogen undergo McLafferty Rearrangement.
Aromatic aldehydes are similar to aromatic ketones. The molecular ion peak is quite strong
and M-1 (-cleavage to carbonyl) is also strong to give the ArCO+ion (m/z 105 for Ar = Ph).
Loss of CO from this ion is common to give m/z 77 phenyl cation.
4.5 Carboxylic Acids: In carboxylic acids, the molecular ion peak is weak, and not always visible. A characteristic m/z 60 peak is often present due to the McLafferty Rearrangement. Bonds to carbonyl group also frequently break to give M–OH and M–CO2H peak.
The molecular ion peak in aromatic acids is very prominent. Common fragmentation is due to loss of OH (M–17) and COOH (M–45) from the molecular ion.
m/z =44
•+
OH
CO
OH
+•
OH + OH
4.6 Aliphatic Esters: Aliphatic esters show distinct molecular ion peak. The most characteristic fragmentation takes place due to the McLafferty Rearrangement. Acetate esters are characterized by the presence of a strong peak at m/.z 43 (CH3CO+) and a peak corresponding to loss of 60 amu (acetic acid) which occurs most probably, by 1,2 elimination.
H3C OH H3C + H3C
M+ m/z = 136
M-17 m/z = 119 M-45 m/z = 91
+ H +•
O
+
M+ m/z = 144 m/z = 88
+
Analytical Chemistry / Instrumentation
Atomic Spectroscopy
Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
In aromatic esters, the molecular ion peak is usually prominent, unless RO chain is long. The base peak is due to the loss of RO•. The McLafferty rearrangement gives the corresponding acid. A more complicated rearrangement often gives a prominent acid+1 peak.
4.7 Amines: Aliphatic monoamines have odd numbered and weak molecular ion peaks. Most important cleavage is usually breakage of the C–C bond next to the C–
+
+
M+ m/z = 164 m/z = 105
+ + CO
m/z = 77
+ O
O H
M+ = 164
+ O
OH m/z 122
OH OH + m/z 123
+•
NH2
NH2
+ +
H m/z = 72 m/z = 58 m/z = 44
N bond. The base peak in nearly all primary amines comes at m/z 30. Amines with longer alkyl chains are capable of undergoing McLafferty rearrangement once a carbon nitrogen double bond is created after initial loss of an alkyl group.
In aromatic amines, the molecular ion peak is intense. An N–H bond can be broken to give a moderately intense M–1 peak. A common fragmentation is loss of HCN and H2CN to give peaks at 65 and 66 m/z. Alkyl substituted aromatic amines typically show breakage of the C–C bond next to the C–N to give a strong peak at 106 when Ar = Ph.
M+ m/z = 73 +•
NH2 NH2
+
•NH2
+
NH2
M+ 101 m/z = 30
Analytical Chemistry / Instrumentation
Atomic Spectroscopy
Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
O+
O
+
NH2 NH2
M+ m/z = 115 m/z = 44
4.8 Amides: In amides, both carbonyl and amino groups are available and hence one expects the fragmentation triggered by both these functional groups. Primary amides give a strong peak at m/z 44 due to breakage of the R-CONH2 bond. In liphatic amides the molecular ion peak is weak but discernible. In straight chain amides having more than three carbons, McLafferty gives rise to the base peak at m/z 59. In aromatic amides the molecular ion peak is strong. The loss of NH2 to gives rise to PhCO+at m/z 105 followed by loss of CO to give the phenyl cation (m/z 77).
H N+
H
N +
M+ m/z = 121 m/z = 106
M+ - H2CN m/z = 66 M+ - HCN m/z = 65
+
4.9 Nitriles: In nitriles the Molecular ion peaks are weak or absent for aliphatic nitriles. Loss of the -hydrogen gives a weak M–1 peak. The base peak is usually observed at m/z 41 due to a rearrangement like the McLafferty rearrangement. This has limited diagnostic value since (C3H5)+ has the same mass.
NH2 M+ 115
NH2 +•
m/z = 59 +
O
NH2 +
+
M+ 121 m/z = 105 m/z = 77
O+•
C
m/z 29 CH3CH2+
M+ 69
m/z 41 CH2=C=NH+
m/z = 68
N C
H C
C C
Analytical Chemistry / Instrumentation
Atomic Spectroscopy
Fragmentatiuon Pattern Of Organic Molecules Under Electron Ionization Mass Spectrometry (Ei Ms) Part 2
+
+m/z = M-46 m/z =
M-30 m/z =
+
•NM+ 123 M-46 m/z = 77
M-30 m/z = 93 4.10 Nitro Compounds: Aliphatic nitro compounds have weak odd molecular ion peak. The main peaks are hydrocarbon fragments up to M–
NO2. In aromatic nitro compounds the molecular ion peak (M+) is strong.
The other prominent peaks result from loss of NO2 radical to give an M–46 peak and an M–30 due to loss of NO.
5. Conclusion
This Module on fragmentation of organic compounds has discussed the fragmentation pattern of various classes of organic compounds namely alkyl halides, ethers, ketones, aldehydes, carboxylic acids and their esters, amines, amides, nitriles and nitro compounds. The fragmentation pattern for both aliphatic and aromatic compounds
NO2
m/z = 71
M+ 131
m/z = 57 m/z = 43 m/z = 29 m/z = 85
+• +
+ + + +
O
O
has been discussed with specific examples. The fragmentation pattern clearly shows that different classes of organic compounds undergo fragmentation in a characteristic fashion. Some of the fragment ions formed are of diagnostic Value and help in identifying the molecule/class of molecule.
6. Bibliography
Scott E. Van Bramer, An Introduction to Mass Spectrometry (1998) http://science.widener.edu/~svanbram
Fred W. McLafferty (1 January 1993). Interpretation of Mass Spectra (https://
books.google.com/books?id=x QWk5WQfMQAC). University Science Books. ISBN 978-0-935702-25-5.
Dass, Chhabil (2007). Fundamentals of contemporary mass spectrometry ([Online- Ausg.]. ed.). Hoboken, NJ [u.a.]: Wiley. ISBN 978-0-471-68229-5.
Tandem Mass Spectrometry for Sequencing Proanthocyanidins. Hui-Jing Li and Max L.
Deinzer, Anal. Chem., 2007, volume 79, pages 1739-1748, doi:10.1021/ac061823v (https://dx.doi.org/10.1021%2Fac061823v)
