Experiment 8A
Mass Spectrometry and Structural Analysis
1. The Mass Selective Detector (MSD).
When a neutral substance mass spectrometer, it is bombarded with an
electron, which causes the substance to ionize as illustrated in Equation 1.
-
e + M
. +
[M] +
-
2e
Equation 1: Electron Impact Ionization
The species [M]+. is both a carbocation and a free radical (has an unpaired
electron) and is referred to as a radical cation. The mass of this first
formed radical cation is equal to that of the original molecule entering the
mass spectrometer and is referred to as the molecular ion.
The molecular ion, because it has one fewer electron than is needed to be
neutral and stable, will break down (fragment) into smaller and more stable
components. These fragments can be neutral, cationic, and/or free radicals.
Only those fragments that are cationic will be observed by the detector. A
detailed description of the detection process is given in McMurry,
Section 12.1-12.4. You should also consult
http://www.chem.uic.edu/web1/OCOL-II/WIN/SPEC/MS/MSF.HTM
For our purposes in this Worksheet it is important to know the following:
• The mass spectrometer detects only positive ions and disperses them on
the according to their mass to charge ratio, m/z.
• Most ions produced on ionization in the electron beam are uni-positive so
numerically, m/z =mass.
• The mass of the molecular ion can usually be taken as the molecular
weight of the substance.
• The MSD can separate ions that have different isotopes of their atoms.
• The most intense peak in the spectrum is called the base peak and
represents the ion of highest abundance and therefore the highest intensity
• Knowledge of the isotope composition of the more common elements is
essential to the interpretation of mass spectral data. See Figure 1
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Figure 1: Table of Isotope Composition of Some Common Elements
From this table we can conclude:
•• The presence of bromine in a compound leads to an M+2 peak that is
nearly equal to that of the molecular ion.
•• The presence of chlorine is detected by a M+2 peak about one third the
intensity of the molecular ion.
•• A single nitrogen in a molecule will give the molecule an odd number for
the molecular ion.
2. Fragmentation Patterns in Mass Spectrometry
a. Hydrocarbons
Figure 2. illustrates the mass spectrum of 2,3-dimethylpentane
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Figure 2: Mass Spectrum of 2,3-Dimethylpentane
1. Draw a Lewis structure for 2,3-dimethylpentane and number the carbon
atoms in the chain.
2. What is the molecular weight in whole number mass units of
2,3-dimethylpentane?
3. Can you detect the molecular ion in the mass spectrum of
2,3-dimethylpentane? If so, what is the numerical value?
4. What is the mass of the base beak in the mass spectrum of
2,3-dimethylpentane?
5. What is the m/z of the peak of second highest mass in the spectrum?
How can it be accounted for? What was lost as a fragment from the
molecular ion to generate this species?
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6. How can the peak at m/z=71 be accounted for?
7. How can the peak at m/z=57 be accounted for?
8. How can the peak at m/z=43 be accounted for?
9. In the boxes below, draw the structures for the substances with masses
of 43 and 57 and 71.
Mass of 43
Mass of 57
Mass of 71
2. Fragmentation Patterns in Mass Spectrometry
b. Molecules with Hetero Atoms
1. Alkyl Halides
Remember to look for the M+2 peaks
Molecular ions from alkyl halides (and from alcohols) undergo fragmentation
by cleavage of the bond (alpha) to the carbon-halogen bond in a process
called alpha cleavage and which is represented in Figure 3. The process is
more common in alkyl chlorides than in alkyl bromides. It is not seen in aryl
halides.
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 cleavage
H
C
CH3
CH3
C CH3
: Cl: CH3
..
CH3
H
C+
: Cl :
..
CH3
CH3
. C CH
3
CH3
H
C
: Cl +
..
Figure 3: Alpha Cleavage of Alkyl Chlorides
The cleavage produces a resonance stabilized cation (non-bonded electrons
from chlorine are shared with electron deficient carbon) and a very stable
alkyl free radical. Often this phenomenon occurs so quickly that there is no
or little evidence of a molecular ion in the mass spectrum.
To fully understand this phenomenon you need to recall the relative
stabilities of carbocations (ChemActivity 11D) and alkyl free radicals
(ChemActivity 11E). (Tertiary is more stable than secondary is more
stable than primary is more stable than methyl). The sequence of stability is
the same for alkyl carbocations and alkyl free radicals.
QUESTIONS:
A
Figure 4 shows the mass spectrum of 3-chloro-3-methylpentane.
*
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Figure 4: Mass spectrum of 3-chloro-3-methylpentane
1. What is the molecular weight of C6H13Cl? Can you find the molecular ion
in the mass spectrum of 3-chloro-3-methylpentane? What is its numerical
value?
2. In the boxes below, draw the structures for the fragments responsible for
the peaks at m/z=91 and 93?
Mass of 91
Mass of 93
3. What is the fragment responsible for the peak at m/z=55? Does it
contain chlorine? Explain your answer. Draw its structure.
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Complete the Following Exercises for Homework:
1. Figure 5 shows several alkyl halides, which on ionizations produce
molecular ions of the formula ([RCl]+.. Show how each can undergo alpha
cleavage. Draw all products. If there is more than one opportunity for a
substance to undergo alpha cleavage draw the products from each cleavage.
CH 3 H
CH 3 C
C
CH 3
CH 3 Cl
H
CH 3
C CH 3
CH 3 C
CH 3 Cl
CH 3
CH 3
C
CH 2 CH 2 CH 3
Cl
CH 3
CH 3
C
CH 2 CH 2 CH3
Cl
CH 3
H
CH 3
C
CHCH 2 CH 3
Cl
CH 3
H
Cl
C
CHCH 2 CH 3
CH 3
Figure 5: Alkyl Chlorides
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2. Figure 6 shows the spectrum of bromobenzene, C6H5
Br
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
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Figure 6: Mass Spectrum of Bromobenzene
2a. What are the molecular weights for bromobenzene?
2b. Can you find the molecular ions in the mass spectrum of
bromobenzene?
2c. Draw the structure of the fragment responsible for the peak at m/z=77?
3. Figure 7 shows the mass spectrum of bromocyclohexane.
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Figure 7. Mass Spectrum of Bromocyclohexane
3a. What is the molecular formula for bromocyclohexane?
3b. What are the molecular weights for bromocyclohexane?
3c. Can you find the molecular ions in the mass spectrum of
bromocyclohexane?
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3d. Draw the structure of the fragment responsible for the peak at m/z=83?
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USING SPECTRABOOK
We will use the SpectraBook program to look at the MS of a series of
compounds in order to get a feel for how and hopefully why the radical
cations initially produced in GC-MS analyses fragment the way they do. The
intent is to use this latter information to become more fully informed on the
ways by which electrons become more stable.
1. Examine the MS of 2-butanol (SpectraBook #1) and 3-pentanol
(SpectraBook #2) and compare the fragmentation patterns.
1a. What is the molecular ion for each and is it visible? What are the
numerical values for each?
1b. What is the base peak for each?
1c. Are they the same?
1d. Draw the structure of the species responsible for the base peak?
1e. Account for the differences and similarities in the two spectra.
2. Examine the MS of 3,3-dimethyl-2-butanone (SpectraBook #1) and 4heptanone (SpectraBook #1) and compare the fragmentation patterns.
2a. What is the molecular ion for each and is it visible? What are their
numerical values?
2b. What is the base peak for each?
2c. Are they the same?
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2d. Draw the structure of the species responsible for the base peak?
2e. Account for the differences and similarities in the two spectra.
3. Examine the MS of ethyl acetate (SpectraBook #2) and acetophenone
(SpectraBook #2)
3a. What is the molecular ion for each and is it visible? What are their
numerical values?
3b. What is the base peak for each?
3c. Are they the same?
3d. Draw the structure of the species responsible for the base peak?
3e. Account for the differences and similarities in the two spectra.