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Chemistry LibreTexts

12.S: Structure Determination - Mass Spectrometry and Infrared Spectroscopy (Summary)

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  • Concepts & Vocabulary

    12.1 Introduction

    • Spectroscopy describes several techniques used by chemists to understand chemical structures and bonds.

    12.2 Mass Spectrometry of Small Molecules - Magnetic Sector Instruments

    • Mass spectrometers consist of an ion source, mass analyzer and dectector.
    • There are several common ion sources including electron ionization and chemical ionization.
    • Upon ionization, a molecular ion is formed (the molecule after losing a single electron) which will break into smaller pieces (fragments).
    • Fragments that are charged will appear in the mass spectrum and are helpful in identifying the parent molecule.
    • The most abundant ion in a mass spectrum is called the base peak.
    • The ion with the same mass as the parent molecule is called the molecular ion.
    • Isotopes of carbon and hydrogen lead to common M+1 peaks.
    • The x-axis of a mass spectrum is m/z - the mass to charge ratio, which in practice equals the mass of the ion.

    12.3 Interpreting Mass Spectra

    • Uncharged particles do not appear in mass spectra.
    • The y-axis of a mass spectrum is the relative abundance, with the base peak set at 100 as the most abundant ion.
    • Abundance of ions is related to their stability.

    12.4 Mass Spectrometry of Some Common Functional Groups

    12.5 Mass Spectrometry in Biological - Time-of-flight (TOF) Instruments

    12.6 Spectroscopy and the Electromagnetic Spectrum

    • Electromagnetic radiation is composed of waves where shorter wavelengths correspond to higher energy radiation.
    • Electromagnetic radiation can also be thought of as a stream of particles called photons.
    • The electromagnetic spectrum is made up of many types of radiation including infrared, ultraviolet, and visible lights as well as x-rays, gamma rays, microwaves, and radio waves.
    • Molecular spectroscopy works by exposing a chemical sample to electromagnetic radiation. It will only absorb radiation with energy that corresponds to some excited state, while all other energies will pass through unabsorbed.

    12.7 Infrared Spectroscopy

    • When infrared radiation is absorbed, molecules will move to a higher vibrational energy state.
    • Examples of molecular vibrations include bending and stretching of bonds. These vibrations can be symmetric or asymmetric.
    • In general, more polar bonds have stronger IR absorption.
    • IR spectra typically use wavenumbers (cm-1) as units for the x-axis.
    • The y-axis for IR spectra is usually % transmittance, with 100% at the top of the spectrum and absorbances looking like valleys (or downward peaks).

    12.8 Interpreting Infrared Spectra

    • Functional groups have standard regions within the IR spectrum where they absorb.
    • The general regions include hydrogen bonding (O-H and N-H), carbon-hydrogen bonds, triple bonds, carbonyls, alkenes, and fingerprint region.

    12.9 Infrared Spectra of Some Common Functional Groups

    Skills to Master

    • Skill 12.1 Determine specific atoms from mass spectra based on molecular ion and M+2 peaks (N, Cl, Br).
    • Skill 12.2 Interpret mass spectra fragments - recognizing common fragments.
    • Skill 12.3 Interpret infrared spectra to determine functional groups that are present or absent.

    Memorization Tasks (MT)

    MT 12.1 Memorize common mass spectra fragments.

    MT 12.2 Memorize common functional group regions in infrared spectroscopy.


    • Layne Morsch (University of Illinois Springfield)