Analysis of Organic Substances

In short: Organic compounds are identified with chemical tests and instruments. Mass spectrometry gives the molar mass, infrared spectroscopy shows functional groups like O−H and C=O, and NMR spectroscopy shows the different carbon and hydrogen environments, which together reveal the structure.

Chemical tests for functional groups

Chemical tests are cheap and quick, but they use up the sample and only tell you about one group at a time.

Mass spectrometry (MS)

A mass spectrometer measures the mass of a molecule and its fragments.

1. Ionisation: a beam of high-energy electrons knocks an electron off each molecule, making a positive ion, ${\mathrm{M}}^{+}$.
2. Acceleration: the ions are sped up by an electric field.
3. Deflection: a magnetic field bends their paths. Lighter ions bend more.
4. Detection: ions are counted at each mass-to-charge ratio, $m/z$.

The sample is destroyed in the process.

Reading a mass spectrum:

• The molecular ion peak (${\mathrm{M}}^{+}$) is the peak with the highest $m/z$ (ignore tiny peaks at M+1 from carbon-13). It gives the molar mass.
• The base peak is the tallest peak, set to 100%. It is the most stable fragment.
• Other peaks are fragments. The difference from M tells you what broke off.

Chlorine and bromine show two molecular ion peaks, 2 apart, because of their isotopes: Cl gives M and M+2 in a 3 : 1 ratio; Br gives M and M+2 in a 1 : 1 ratio.

Infrared (IR) spectroscopy

Bonds vibrate (stretch and bend). Each type of bond absorbs infrared radiation at its own wavenumbers (in cm⁻¹). An IR spectrum shows troughs (low transmittance) where the sample absorbs.

The region below 1500 cm⁻¹ is the fingerprint region: complex, but unique to each molecule. It can confirm an identity by matching a known spectrum.

IR tells you which functional groups are present, but not how many or where.

Carbon-13 NMR

Some nuclei, including ${}^{13}\mathrm{C}$ and ${}^1\mathrm{H}$, behave like tiny magnets. In a strong magnetic field they absorb radio waves. The exact frequency depends on the atom's chemical environment (what it is bonded to). This is nuclear magnetic resonance.

In a ${}^{13}\mathrm{C}$ NMR spectrum:

• The number of peaks = the number of different carbon environments.
• The chemical shift $\delta$ (in ppm) shows what each carbon is near.
• Peak heights are not used for counting.

Carbons in symmetrical positions are equivalent. Propanone, $\mathrm{C}{\mathrm{H}}_3\mathrm{COC}{\mathrm{H}}_3$, has only 2 environments (both $\mathrm{C}{\mathrm{H}}_3$ are the same).

Proton (¹H) NMR

A ¹H NMR spectrum gives three pieces of information:

1. Number of peak sets = number of different hydrogen environments.
2. Area under each set (or the given ratio) = the number of H in that environment.
3. Splitting: a set of peaks is split by the H on neighbouring carbons. The n + 1 rule: $n$ neighbouring H atoms split a signal into $n+1$ peaks.

H on O−H or N−H is usually a singlet and does not split its neighbours.

Putting it together

No single technique is enough to be sure. Use them together:

1. Find the molar mass from MS (and the formula, if percentage composition is given).
2. Find the functional groups from IR and chemical tests.
3. Count environments with ¹³C and ¹H NMR.
4. Use splitting to join the pieces.
5. Check your final structure against every piece of data.

Quick summary

• Chemical tests: bromine water (C=C), dichromate (1° and 2° alcohols, aldehydes), carbonate (acids).
• MS: molecular ion gives molar mass; fragments show pieces. Sample is destroyed.
• IR: broad O−H at 3230 to 3550 (alcohol) or 2500 to 3000 (acid); C=O at 1680 to 1750 cm⁻¹.
• ¹³C NMR: number of peaks = number of carbon environments.
• ¹H NMR: number of sets, peak areas and n + 1 splitting.
• Combine all the data and check the structure fits every piece.

Quiz