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Mass Spectrometry

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

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Mass Spectrometry

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  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. 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. 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. 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. 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? 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. 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 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. 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. 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) 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. 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? 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 = 112.56) 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) 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. Klein, Organic Chemistry 1e

  16. 15.12 Analyzing the Fragments • What type of fragmenting is responsible for the “groupings” of peaks observed? 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. 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. 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. Klein, Organic Chemistry 1e

  20. 15.12 Analyzing the Fragments • Amines generally undergo alpha cleavage: • Carbonyls generally undergo McLafferty rearrangement: 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 12.0000 amu. Why? • All other atoms have known exact masses. 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? 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. 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. 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. Klein, Organic Chemistry 1e

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