Organic Analysis

• Mass spectrometry


  Can be used to determine the molecular formula of a compound from the accurate mass of the molecular ion
• Molecular ion


  • The peak with the highest mass/charge ratio is normally due to the original molecule that hasn't fragmented
  • As the charge of the ion is +1 the mass/charge ratio is equal to Mr
• Molecular ion formation


  Molecule M → [M]+. + e–
• Molecular ion


  The molecule with one electron knocked off (It is both an ion and a free radical)
• High resolution mass spectroscopy


  • Can measure the mass to 5 d.p. to help differentiate between compounds that appear to have similar Mr (to the nearest whole number)
• Accurate masses of atoms: H = 1.0078, C = 12.0000, O = 15.9949, N = 14.0031
• Molecular formulas with Mr of 60

  • C2H4O2
  • C3H8O
  • CH4N2O
• Example 1: Determining molecular formula from accurate Mr

  1. Calculated Mr for CH3CH2OH = 46.0417

  2. Calculated Mr for H2NCH2NH2 = 46.0530

  3. Therefore the compound has molecular formula CH3CH2OH
• M+2 peak


  • If a compound contains a chlorine or bromine atom, two molecular ion peaks will occur: M and M+2 due to the two naturally occurring isotopes
  • Ratio of M:M+2 peaks is 3:1 for chlorine, 1:1 for bromine
• M+2 and M+4 peaks

  • If a compound contains two chlorine or bromine atoms, M+2 and M+4 peaks will occur
  • Ratio of M:M+2:M+4 peaks is 9:6:1 for C2H4Cl2, 1:2:1 for C2H4Br2
• M+2, M+4, M+6 peaks


  • If a compound contains three chlorine atoms, M+2, M+4, M+6 peaks will occur
  • Ratio of M:M+2:M+4:M+6 peaks is 27:27:9:1 for C2H3Cl3
• Infrared spectroscopy


  • Certain groups in a molecule absorb infra-red radiation at characteristic frequencies
  • Complicated spectra can be obtained that provide information about the types of bonds present in a molecule
• Infrared spectroscopy regions


  • Below 1500 cm-1 - "Fingerprinting" region, unique for every compound
  • Above 1500 cm-1 - "Functional group identification" region, use IR absorption table to deduce presence/absence of particular bonds/functional groups
• Infrared spectra interpretation


  • Absorption in 1680-1750 cm-1 range indicates presence of C=O bond
  • Absorption in 2500-3000 cm-1 range indicates presence of O-H bond in an acid
• Functional group identification by test-tube reactions

  • Bromine water decolourises for alkenes
  • Fehling's solution gives red precipitate for aldehydes
  • Tollens' reagent forms silver mirror for aldehydes
  • Sodium carbonate effervesces for carboxylic acids
  • Orange to green colour change for 1o, 2o alcohols and aldehydes with sodium dichromate and sulfuric acid
  • Slow white precipitate of AgCl for chloroalkanes with warm silver nitrate
• Mechanism of greenhouse effect

  1. UV radiation passes through atmosphere to heat Earth's surface

  2. Earth radiates out infrared radiation

  3. CO2 C=O bonds absorb infrared radiation, preventing it from escaping atmosphere

  4. Absorbed energy is transferred to other atmospheric molecules, warming the atmosphere