1. Mass Spectrometry
Mass spectrometry (MS) is not true “spectroscopy” because it does not involve the absorption of electromagnetic radiation to form an excited state.
MS is very useful for
Determining a compound’s molecular weight
Detecting the presence of Br, Cl, and N atoms in a molecule
Structure determination
Two things happen in a mass spectrometer
A compound is vaporized in a vacuum and then ionized.
The masses of the ions are detected and graphed.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

2. Mass Spectrometry
The most common method of ionizing molecules is by electron impact (EI). The sample is bombarded with a beam of high energy electrons (1600 kcal or 70 eV).
EI causes an electron to be ejected from the molecule.
A radical cation is the result.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

3. Mass Spectrometry
The initially formed radical cation is known as the molecular ion (M+•).
The mass of the M+• is the same as the mass of the original molecule.
The M+• is generally very unstable and usually undergoes a variety of fragmentation reactions.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

4. Mass Spectrometry
The resulting fragments may undergo even further fragmentation often to form radicals and cations.
The cations are accelerated toward an analyzer, which separates them based on the mass to charge ratio, m/z.
Separation Methods include using a magnetic field, time-of-flight, ion trapping, and quadrapole.
Neutral fragments are not detected.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

5. Mass Spectrometry Here is the MS of methane (MW = 16)
The base peak is the tallest peak in the spectrum.
For methane, the base peak is M+•.
For some molecules, the M+• peak is not observed in the spectrum. Why?
What is the small peak at m/z = 17?
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

6. Mass Spectrometry
Peaks with a mass of less than M+• represent fragments:
Subsequent H radicals can be fragmented to give the ions with a mass/charge = 12, 13 and 14.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

7. Mass Spectrometry MS is a very sensitive analytical method.
Many organic compounds can be identified:
Pharmaceutical: drug discovery and drug metabolism,
Organic Synthesis: reaction monitoring, product characterization
Biotech: amino acid sequencing, analysis of macromolecules
Clinical: neonatal screening, hemoglobin analysis
Environmental: water quality, food contamination testing
Geological: evaluating oil composition
Forensic: explosives, illegal drugs
Many More
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

8. 15.9 Analyzing the M+• Peak
In the mass spectrum for benzene, the M+• peak is the base peak.
The M+• peak does not easily fragment.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

9. 15.9 Analyzing the M+• Peak
Like most compounds, the M+• peak for pentane (MW = 72) is NOT the base peak. This is because the molecular ion fragments easily.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

10. 15.9 Analyzing the M+• Peak
The first step in analyzing a mass spec is to identify the M+• peak:
Tells you the MW of the compound.
The Nitrogen Rule
If m/z for the M+• peak is odd, this usually means that there is a nitrogen atom in the molecule. (Or an odd # of Ns)
If m/z for the M+• peak is even, then there are no nitrogens. (Or an even # of Ns)
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

11. 15.10 Analyzing the (M+1)+• Peak
Recall that the (M+1)+• peak in methane was about 1% as abundant as the M+• peak.
The (M+1)+• peak results from the presence of 13C in the sample. The natural abundance of 13C is 1.1%. Thus approx 1% of the molecules will have a MW of M+1.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

12. 15.10 Analyzing the (M+1)+• Peak
For every 100 molecules of decane, how many of them will contain one C-13 atom.
Comparing the heights of the (M+1)+• peak and the M+• peak can allow you to estimate how many carbons are in the molecule.
The natural abundance of deuterium is 0.015%. Will that affect the mass spectrum analysis?
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

13. 15.11 Analyzing the (M+2)+• Peak
Chlorine has two abundant isotopes:
35Cl=76% and 37Cl=24%
Molecules with one Cl have strong (M+2)+• peaks.
Below is the spectrum of chlorobenzene, C6H5Cl (MW = )
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

14. 15.11 Analyzing the (M+2)+• Peak
79Br=51% and 81Br=49%, so molecules that contain a bromine atom show equally strong (M)+• and (M+2)+• peaks. See spectrum of C6H5Br below (MW = 157.0)
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

15. 15.12 Analyzing the Fragments
Analysis of the fragment peaks can often yield structural information.
Consider pentane.
Remember, MS only detects charged fragments.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

16. 15.12 Analyzing the Fragments
What type of fragmenting is responsible for the “groupings” of peaks observed?
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

17. 15.12 Analyzing the Fragments
In general, fragmentation will be more prevalent when more stable fragments are produced.
Correlate the relative stability of the fragments here with their abundances on the previous slide.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

18. 15.12 Analyzing the Fragments
Consider the fragmentation below.
All possible fragmentations are generally observed under the high energy conditions employed in EI-MS.
The most abundant fragments can often be predicted.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

19. 15.12 Analyzing the Fragments
Alcohols generally undergo two main types of fragmentation: alpha cleavage and dehydration.
They often do not display an M+ peak. Instead the highest m/z is at M – 18.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

20. 15.12 Analyzing the Fragments
Amines generally undergo alpha cleavage:
Carbonyls generally undergo McLafferty rearrangement:
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

21. 15.13 High Res MS
High resolution (high-res) MS allows m/z values to be measured to 4 decimal places. “Exact Mass”
12C weights exactly amu. Why?
All other atoms have known exact masses.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

22. 15.13 High Resolution Mass Spectrometry
Why are the values in the table different from those on the periodic table?
Imagine you want to use MS to distinguish between
the molecules below.
Why can’t you use low resolution (low-res) MS?
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

23. 15.13 High Resolution Mass Spectrometry
Using the exact masses and natural abundances for each element, we can see the difference high-res makes.
The molecular ion results from the molecule with the highest natural abundance.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

24. 15.14 GC/MS MS is suited for the identification of pure substances.
However, MS instruments are often connected to a gas chromatograph (GC) so mixtures can be analyzed.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e

25. 15.14 GC/MS GC-MS gives two main forms of information:
The chromatogram gives the retention time.
The Mass Spectrum
GC-MS is a great technique for detecting compounds such as drugs in solutions such as blood or urine and for analyzing reaction products.
Copyright 2012 John Wiley & Sons, Inc.
Klein, Organic Chemistry 1e