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Mass Spectrometry

Mass Spectrometry. Mass Spectrometry. Used to identify organic compounds mainly through molar mass and identification of major fragments. A mass spectrometer is often used as the “detector” for a gas chromatograph (GC-MS)

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Mass Spectrometry

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  1. Mass Spectrometry

  2. Mass Spectrometry • Used to identify organic compounds • mainly through molar mass and identification of major fragments. • A mass spectrometer is often used as the “detector” for a gas chromatograph (GC-MS) • A mixture is separated and a total ion chromatogram (TIC) obtained. A TIC is the GC-MS equivalent of a gas chromatogram. • The MS then allows identification of the components without having to rely on a comparison of retention times.

  3. Mass Spectrometers

  4. Mass Spectrometry • Analysis time once the GC has been set up (column chosen, gas flow set, oven program finalized) is about 20 minutes. • Not too expensive • Our benchtop model was $30K. • Compounds that can be analyzed are those that can be analyzed on a GC: • Low to moderate boiling liquids (and, of course, gases)

  5. Mass Spectrometers • analyze particles…cations!, not photons. • Impact from a high-energy electron knocks an electron from the organic compound and creates the Molecular ion (aka parent ion) • a cation with an unpaired electron M+• • It has the m/z of the molecule, so the value of m/z in most cases is the value of the molar mass (provided z, the charge of the cation, is +1)

  6. Mass Spectrometers • analyze cations, not photons • Impact from a high-energy electron also causes fragmentation. • Base peak • is the most intense m/z peak • is the most stable fragment • Other fragments form as well, some from complex rearrangements

  7. Mass Spectrometers • The MS detects the m/z of each fragment by directing the ionized particles through a magnetic quadrupole • The trajectory of the ions in the magnetic field bends as a function of the mass of the particle and its charge:

  8. Mass Spectrometers • The magnetic quadrupole thus acts as a mass filter. • For a given magnetic field strength, light particles are bent more and heavier particles less. • By changing the magnetic field strength, m/z can be focused on the detector (an electron multiplier) in succession and yield a mass spectrum • A plot of signal vs m/z

  9. OCCC’s GC-MS • Shimadzu • GC • GC-17A version 3 • RestekRtx-XLB 30 meter fused silica capillary column with 0.25 mm inner diameter and a 0.25μm coating (the liquid phase is low polarity…and proprietary) for a column volume of 1.5 mL • Column operates from 30° - 340°C

  10. OCCC’s GC-MS • Shimadzu • MS parameters • GCMS-QP5000 • requires an operating pressure of approximately 2 Pa • quadruple mass filter • electron multiplier detector • turns on after 2 min to clear solvent • set up for 2 scans of 35-300 m/z per second

  11. Fragmentation Patterns - Benzene Ring Odd m/z suggests N may be present. Peaks at 51 and 77 are very typical of the benzene ring.

  12. Fragmentation Patterns - the benzyliccation, the allyliccation Extraneous peaks happen.

  13. Fragmentation Patterns - Amines

  14. Fragmentation Patterns - alcohols Alcohols can fragment so easily that the M+ peak may be missing altogether.

  15. Fragmentation Patterns - aldehydes and ketones

  16. Fragmentation Patterns - halogens • Chlorine has 3:1 ratio of 35Cl : 37Cl • Look for peaks at 35 and 37 • Look for a gap of 35. • Look for M:M+2 ratio of 3:1. • Bromine has 1:1 ratio of 79Br : 81Br • Look for peaks at 79 and 81 • Look for a gap of 79. • Look for M:M+2 ratio of 1:1. • Iodine • Look for peak at 127. • Look for a gap of 127.

  17. Rule of Thirteen • Once you have the molecular weight (MW)… • Divide MW by 13 and express the result as an integer (n) and a remainder (r). • If your compound is a hydrocarbon, its formula is approximated as CnHn+r. • You may then find elements of unsaturation from the molecular formula.

  18. Rule of Thirteen • If you have hetero atoms in your compound, adjust the formula to accommodate: • For O, add O and subtract CH4. • For N, add N and subtract CH2. • For Cl, add Cl and subtract either C2H11 or C3H-1. • Again, calculate elements of unsaturation from the formula.

  19. How to Analyze a Mass Spectrum • Identify the molecular ion peak, if present. Note if the MW is odd. • Mark the base peak and show the fragment which gives rise to it. • Mark significant fragment peaks and identify the fragments giving rise to them. • Mark peaks or gaps that indicate the halogens, Cl (M : M+2 peaks = 3:1), Br (M : M+2 peaks = 1:1), I (M or gap = 127). • The mass of the compound with Br will be M+1.

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