13.A: Structure Determination - Mass Spectrometry and Infrared Spectroscopy (Summary)

Concepts & Vocabulary

13.0 Introduction

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

13.1 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.

13.2 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).

13.3 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 the fingerprint region.

13.4 Infrared Spectra of Some Common Functional Groups

13.5 Mass Spectrometry of Small Molecules - Magnetic Sector Instruments

• Mass spectrometers consist of an ion source, mass analyzer and detector.
• 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.
• The x-axis of a mass spectrum is m/z - the mass to charge ratio, which in practice equals the mass of the ion.

13.6 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.
• The abundance of ions is related to their stability.

13.8 Mass Spectrometry and Natural Abundances of Isotopes

• Isotopes of carbon and hydrogen lead to common M+1 peaks.

  13.8 Mass Spectrometry of Some Common Functional Groups

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

  Skills to Master

  • Skill 13.1 Determine specific atoms from mass spectra based on molecular ion and M+2 peaks (N, Cl, Br).
  • Skill 13.2 Interpret mass spectra fragments - recognizing common fragments.
  • Skill 13.3 Interpret infrared spectra to determine functional groups that are present or absent.
  • Skill 13.4 Identify the presence of alcohols by IR, and MS.

  Memorization Tasks (MT)

  MT - Memorize common mass spectra fragments.

  MT - Memorize common functional group regions in infrared spectroscopy.