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