Mass spectrometry (MS) is not true “spectroscopy” because it does not involve the absorption of...

• 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 spectrometer1. A compound is vaporized in a vacuum and then ionized.2. The masses of the ions are detected and graphed.

Mass Spectrometry

Copyright 2012 John Wiley & Sons, Inc. Klein, Organic Chemistry 1e 15-1

• 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.

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.

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.

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?

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.

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

Mass Spectrometry


• In the mass spectrum for benzene, the M+• peak is the base peak.

• The M+• peak does not easily fragment.

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.



• 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)



N

NH2 NN

CH3NH2

N

N

HO

Chemical Formula: C5H11NMolecular Weight: 85

Chemical Formula: C5H11NOMolecular Weight: 101

Chemical Formula: CH5NMolecular Weight: 31



Chemical Formula: C4H4N2Molecular Weight: 80

• 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.

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?



• 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 =

112.56)



• 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)



• Analysis of the fragment peaks can often yield structural information.

• Consider pentane.

– Remember, MS only detects charged fragments.

15.12 Analyzing the Fragments


• What type of fragmenting is responsible for the “groupings” of peaks observed?



• 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.



• 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.



• 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.



• Amines generally undergo alpha cleavage:

• Carbonyls generally undergo McLafferty rearrangement:



• High resolution (high-res) MS allows m/z values to be measured to 4 decimal places. “Exact Mass”

• 12C weights exactly 12.0000 amu. Why?• All other atoms have known exact masses.

15.13 High Res MS


• Why are the values in the table different from those on the periodic table?

• Imagine you want to use MS to distinguish betweenthe molecules below.

• Why can’t you use low resolution (low-res) MS?

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.

15.13 High Resolution Mass Spectrometry


• 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.

15.14 GC/MS


• GC-MS gives two main forms of information:1. The chromatogram gives

the retention time.

2. The Mass Spectrum 3. GC-MS is a great

technique for detecting compounds such as drugs in solutions such as blood or urine and for analyzing reaction products.

15.14 GC/MS


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