Mass Spectrometry
Application of MS
• Characterization of compound
• Identification of unknown substance
MS Instrument
Mass Spectrum
MS Library Databases
Example: Orange Extract
Molecular Ion Peak
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Determination of molecular mass
Rule of Thirteen (Possible molecular formulae)
Odd vs. Even molecular mass
Isotopes
– M + 1 peaks
– M + 2 peaks
• Nominal Mass vs. Exact Mass
Empirical Formula and MS
• What is the MF of a compound with the
following data: M+= 110; %H = 12.72; %C =
87.27?
• Answer: C8H14
Rule of 13
• What if you are only given M+ data?
• Determine a range of possibilities using rule of
13
• Divide M+ by 13
– Quotient = #C
– Quotient + remainder = #H
– Replace CH4 with O, etc.
• Example: Give three MF for M+ = 110
Odd Mass
• Nitrogen rule
Isotopes
Remember: With MS, you are considering
individual molecules, not “average” molecules!
M+ + 1 Peak
• Arises from sum of all possible isotopes
• C-13 is most prevelant
• Therefore, we can use M+1 to determine the
likely number of carbon atoms in a molecule
Apply to CH4
• In a group of CH4:
– Most are 12C and 1H
– About 1% are 13C and 1H
– Small % are 12C and 2H
– VERY SMALL % are 13C and 2H
M+ = 16 amu
M+1 = 17 amu
M+1 = 17 amu
M+2 = 18 amu
• Application of M+ + 1 peak: determine #C
= (M++1 intensity/M+ intensity)/(1.1/98.9)
= (M+1 intesity/M intensity)/0.011
M+2 peak
Examples
MS Instrumentation
• Mass analyzer
– Magnetic sector
– Quadrupole mass
sorter
– Time of Flight
(TOF)
HRMS
• Nominal Mass
• “Exact” Mass
• Advantage of HRMS
– Unique mass
– Compare C8H14 with
C7H10O
– Nominal: 110 amu
– Exact: 110.10962 vs
110.07320
MS Instrumentation
• Ionization
– EI
– CI
– ESI
– FAB
– MALDI
Fragmentation
• Unstable
molecular ion:
radical cation
• Only cations
observed
– f+ (directly)
– f . (indirectly)
Mechanisms
• Draw Lewis
structure with
electron knocked
out of least
stable place
– Lone pair
– Pi bond
– Sigma bond
• Fishhook arrow
Example: Ethane
Inductive Cleavage
Example: Propane
Typical Aliphatic Fragments:
15, 29, 43, 57, 71…
Loss of Alkyl Fragments
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172-___=143
172-___=129
172-___=115
172-___=___
172-___=___
Functional Groups
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Benzylic group
Alkenes
Alcohols, amines, ethers, etc
Carbonyls: alpha fragemntation
Carbonyls: McLafferty fragmentation
Benzylic Group
• Weakest bond most stable ions/radicals
• Rearrangements
• Trypolium ion
Alkenes
• Allylic bond breaking
• Resonance stabilized cations/radicals
Amines/Alcohols/Ethers
• Inductive cleavage
• alpha bond fragmentation
• Stabilized cation!
Importance of alpha fragmentation
Carbonyls: Alpha Fragmentation
Carbonyls: McLafferty
• Gamma abstraction
• Even mass fragment
• How would McLafferty fragmentation
distinguish these ketones?
Applying MS
• What is the cause of the base peak? The
parent peak?
Identifying Fragments
• What are the most likely identities of the ions
that causes peaks at 41, 43, 69, and 84?
• What causes the little peak above 84?
• What is the molecular ion peak? Why is it not visible?
• Why is the peak at 59 bigger than the peak at 73?
• Draw a mechanism for the loss of neutral hydroxide
radical. What is the ion peak visible from this
fragmentation?
Case Study
• M+ = 114 and
C=O known to
be present
– Nitrogen?
– Cl/Br?
– 72 suggests…
• Strategy
– Rule of 13
– Table of mass
peaks and
fragments
Problem
• Provide structure that matches this spectrum:
Gas Chromatography/Mass Spec
• Identifying
components
in mixtures
• Separation
then
identification
• GC-MS