Chem 335 - Winter 1999 - Organic Chemistry II
Portland State University - Dr. Carl C. Wamser

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Chapter 12 - Mass Spectrometry

Determination of the Structure of Organic Compounds

• a variety of methods apply, mainly using specialized instruments
• spectroscopy - absorption of light of various wavelengths (Chaps 13 & 14)
• "wet" methods - inferences from specific chemical reactivity
• comparisons with known samples or databases

Mass Spectrometry

• sample converted to a beam of ions ( usually +, sometimes - )
• fragmentation of ionized molecules may take place
• fragments are collected by mass ( actually mass/charge ratio, but charge is usually +1 )
• original structure is deduced from
  • parent molecular ion (without fragmentation)
  • fragments and their abundance

Instrumental Operation

• various ways of generating ions from a sample
  • EI - electron ionization - high-energy beam of electrons knock electrons off the sample molecules
  • CI - chemical ionization - uses gas-phase reactions like protn transfer
  • FAB - fast atom bombardment - also knocks out electrons by impact
  • MALDI - matrix-assisted laser desorption ionization - laser blasts ions out of a matrix (solid)
• magnetic field causes deflection of the ions as they travel - bends them into a curve
  • light ions (low m/z) are defelected most
  • heavy ions are deflected less
• mass analyzer - the ions are spatially sorted by m/z and detected as an ion current

Mass Spectrum

• a plot of ion current observed as the detector scans over m/z values
• base peak - highest intensity peak (usually assigned intensity 100)
• parent molecular ion ( M+ or just M )
  • corresponds to the original molecule missing one electron
  • correlates with the molecular weight
• low-resolution MS - detects integer m/z values ( ± 1 )
• high-resolution MS - capable of identifying m/z to ± 0.0001
  • e.g., CO and N2 both have MW = 28 but differ at high resolution

Isotopes

• some elements have distinctive isotope patterns in their natural abundance
• C consists of 89.9% C-12 and 1.1 % C-13
  • a compound with 20 C would give an M+1 peak about 22% the size of M
• Br consists of about 50% each of Br-79 and Br-81 (atomic weight ~ 80)
  • a compound with one Br would have M and M+2 peaks about equal in size
• Cl consists of about 75% Cl-35 and 25% Cl-37
  • a compound with one Cl would have M and M+2 peaks in about 3:1 ratio

Fragmentation Patterns

• initial ionization generates a radical ion by loss of one electron
• loss of a bonding electron may lead to bond breakings
• different functional groups often have characteristic fragmentation patterns

Interpretation of Mass Spectra

• compounds containing C, H, O, S, halogen, will always have M even
• the nitrogen rule - compounds with one N (or an odd number of N) will have M odd
• a significant sized M+2 peak can indicate Br, Cl, or S (depending on intensity)
• alkanes tend to fragment C-C bonds that give more stable cations or radicals
• alkenes usually show a strong M+, fragment at allylic bonds
• alkynes usually show a strong M+, fragment at propargylic bonds
• alcohols fragment easily, losing H2O or breaking an alpha C-C bond
• PRACTICE with spectra to learn how to visualize the information they contain