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Chemistry · 11. Spectroscopy and structure determination

Infrared (IR) and mass spectrometry (MS) in structural elucidation

Interpret characteristic wavenumbers on IR spectra and molecular ion fragments on MS to deduce molecular structures.

40 minutesContent version: 2.1
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Driving question

How can scientists deduce invisible molecular structures using only infrared absorption peaks and mass spectrometry charts?

Curriculum coverage

Vietnam 2018 Chemistry 11 (Organic chemistry); Cambridge A-Level Chemistry 9701 (Analytical chemistry); AP Chemistry.

Model scope and limitations

Focuses on mid-IR (4000–400 cm⁻¹) and electron ionisation MS for foundational organic families.

Learning objectives

  • Identify organic functional groups using characteristic wavenumber absorption bands on IR spectra.
  • Determine molecular mass from the molecular ion peak [M]+ and analyse fragment peaks on MS.
  • Combine elemental analysis, IR, and MS data to establish molecular and structural formulas.

Prerequisite knowledge

  • Molecular formulas and organic functional groups (alcohols, aldehydes, carboxylic acids, esters).
  • Conservation of mass and molecular mass calculations.

Core knowledge

Infrared spectroscopy principle

Bonds absorb IR radiation matching their natural vibrational frequencies (stretching or bending), producing diagnostic absorption peaks indexed by wavenumber (cm⁻¹).

Diagnostic IR absorption bands

Alcohol O–H: broad band at 3200–3600 cm⁻¹; Carbonyl C=O: intense sharp peak at 1680–1750 cm⁻¹; Carboxylic acid O–H: very broad band spanning 2500–3300 cm⁻¹.

Molecular ion peak in MS

High-energy electron bombardment strips one electron to form the molecular radical cation [M]+; its m/z directly indicates the compound’s molar mass.

Worked example

Compound X displays a molecular ion peak at m/z = 60. Its IR spectrum exhibits an intense sharp peak at 1715 cm⁻¹ (C=O) and a broad band from 2500 to 3300 cm⁻¹ (acidic O–H). This identifies a carboxyl group –COOH; with M = 60, X is acetic acid CH₃COOH.

Misconceptions to avoid

  • Alcohol O–H and carboxylic O–H differ distinctly: alcohol O–H is smooth around 3300 cm⁻¹, while carboxylic O–H is extremely broad (2500–3300 cm⁻¹), overlapping C–H stretches.
  • The highest peak in MS is the base peak (abundance 100%), which is often a stable fragment rather than the molecular ion peak [M]+.

Virtual experiment procedure: Ester synthesis and spectral analysis

  1. Place pure liquid or pellet sample onto the diamond/ZnSe crystal of an FTIR spectrometer.
  2. Record the transmittance spectrum (%T vs wavenumber) and identify hallmark peaks for C=O, O–H, and N–H bonds.
  3. Inject sample into the mass spectrometer ionization chamber, observing fragmentation and locating the [M]+ m/z peak.

Safety and cautions

  • Volatile organic solvents are flammable; prepare samples in a ventilated fume hood away from heat sources.

Evidence to collect

  • Lookup table pairing diagnostic absorption wavenumbers with corresponding functional groups.
  • MS fragmentation scheme matching loss peaks (loss of 15 for –CH₃, 18 for H₂O) to deduce structure.
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Diagnostic check

1. An intense, sharp absorption band around 1715 cm⁻¹ on an IR spectrum signals which bond?

  1. C=O double bond
  2. C–C single bond
  3. Alcohol O–H bond
Show answer and explanation

Correct answer: C=O double bond

The polar C=O bond exhibits a strong dipole change, producing characteristic absorption at 1680–1750 cm⁻¹.

2. On a mass spectrum (MS), what quantity is plotted along the horizontal axis?

  1. Mass-to-charge ratio (m/z)
  2. Density
  3. Light frequency
Show answer and explanation

Correct answer: Mass-to-charge ratio (m/z)

Mass spectrometers separate charged fragments by their mass-to-charge ratio m/z (for z = +1, m/z equals fragment mass).

Application practice

1. An MS of acyclic ester X shows [M]+ at m/z = 88. For C_n H_{2n} O₂, what is its molecular formula?

  1. C₄H₈O₂
  2. C₃H₆O₂
  3. C₅H₁₀O₂
Show answer and explanation

Correct answer: C₄H₈O₂

14n + 32 = 88 yields 14n = 56, so n = 4, giving C₄H₈O₂.

2. A compound has formula C₂H₆O. Its IR spectrum lacks any broad band at 3200–3600 cm⁻¹. The compound is?

  1. Dimethyl ether (CH₃–O–CH₃)
  2. Ethanol (C₂H₅OH)
  3. Acetic acid (CH₃COOH)
Show answer and explanation

Correct answer: Dimethyl ether (CH₃–O–CH₃)

Lack of the characteristic O–H stretch rules out ethanol, leaving dimethyl ether as the correct structural isomer.

3. In the mass spectrum of ethanol CH₃CH₂OH, the major fragment peak at m/z = 31 corresponds to which ion?

  1. [CH₂OH]+
  2. [CH₃]+
  3. [C₂H₅]+
Show answer and explanation

Correct answer: [CH₂OH]+

Cleavage of the central C–C bond loses a methyl radical (15), yielding resonance-stabilized [CH₂OH]+ at m/z = 31.

Academic references

  1. Cambridge IGCSE Chemistry 0620 — official syllabus and resources
  2. Cambridge AS & A Level Chemistry 9701 — official syllabus
  3. OpenStax Chemistry 2e — peer-reviewed general chemistry
  4. IUPAC Color Books — authoritative chemical terminology and nomenclature
  5. BIPM — SI Brochure, 9th edition

This lesson is maintained against the cited sources below. Simulations are learning models and do not replace supervised physical-laboratory safety procedures.

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