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ChemWiki: The Dynamic Chemistry Hypertext > Core > Organic Chemistry > Organic Chemistry With a Biological Emphasis > Chapter 4: Structure Determination I: UV-Vis and Infrared Spectroscopy, Mass Spectrometry

Chapter 4: Structure Determination I: UV-Vis and Infrared Spectroscopy, Mass Spectrometry

Organic Chemistry With a Biological Emphasis has been updated to a 2016 edition.  It will take some time to incorporate all of the revisions to the chemwiki, but the new edition is now available here as a free PDF download.

Section 4.1: Introduction to molecular spectroscopy

  1. The electromagnetic spectrum
  2. Molecular spectroscopy – the basic idea

Section 4.3: Ultraviolet and visible spectroscopy

  1. Electronic transitions
  2. Looking at UV-vis spectra
  3. Applications of UV spectroscopy in organic and biological chemistry

Section 4.4: Mass Spectrometry

  1. The basics of mass spectrometry
  2. Looking at mass spectra
  3. Gas Chromatography - Mass Spectrometry
  4. Mass spectrometry of proteins - applications in proteomics

Section 4.5: Problems for Chapter 4


In the first three chapters of this text, we have focused our efforts on learning about the structure of organic compounds.  Now that we know what organic molecules look like, we can start to address the question of how chemists are able to elucidate organic structures. The individual atoms and functional groups in organic compounds are far too small to be directly observed or photographed, even with the best electron microscope.   How, then, are chemists able to draw with confidence the bonding arrangements in organic molecules, even simple ones such as acetone or ethanol?

The answer lies, for the most part, in a field of chemistry called molecular spectroscopy.  Spectroscopy is the study of how electromagnetic radiation, across a spectrum of different wavelengths, interacts with molecules - and how these interactions can be quantified, analyzed, and ultimately interpreted to gain information about molecular structure.

After first reviewing some basic information about the properties of light and introducing the basic ideas behind spectroscopy, we will move to a discussion of infrared (IR) spectroscopy, a technique which is used in organic chemistry to detect the presence or absence of common functional groups.  Next, we will look at ultraviolet-visible (UV-vis) spectroscopy, in which light of a shorter wavelength is employed to provide information about organic molecules containing conjugated p-bonding systems.  

In the final section of this chapter, we will change tack slightly and consider another analytical technique called mass spectrometry (MS).   Here, we learn about the structure of a molecule by, in a sense, taking a hammer to it and smashing it into small pieces, then measuring the mass of each piece.  Although this metaphorical description makes mass spectrometry sound somewhat crude, it is in fact an extremely powerful and sensitive technique, one which has in recent years become central to the study of life at the molecular level.

Looking ahead, Chapter 5 will be devoted to the study of nuclear magnetic resonance (NMR) spectroscopy, where we use ultra-strong magnets and radio frequency radiation to learn about the electronic environment of individual atoms in a molecule.  For most organic chemists, NMR is the single most powerful analytical tool available in terms of the wealth of detailed information it can provide about the structure of a molecule.  It is the closest thing we have to a ‘molecular camera’.

In summary, the analytical techniques we will be studying in this chapter and the next primarily attempt to address the following questions about an organic molecule:

  • Infrared (IR) spectroscopy: What functional groups does  the molecule contain?
  • Ultraviolet-visible (UV-vis) spectroscopy:To what extent does the molecule contain a system of  conjugated pi bonds?
  • Mass spectrometry (MS): What is the atomic weight of the molecule and its common fragments?
  • Nuclear magnetic resonance spectroscopy (NMR): What is the overall  bonding framework of the molecule?


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Last modified
16:03, 14 Feb 2016



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This material is based upon work supported by the National Science Foundation under Grant Numbers 1246120, 1525057, and 1413739.

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