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

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  • 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?

    • 4.1: Prelude to Structure Determination I
      William Aiken Walker was a 19th-century 'genre' painter, known for his small scenes of sharecroppers working the fields in the post-Civil War south. For much of his career, he traveled extensively, throughout the southern states but also to New York City and even as far as Cuba. He earned a decent living wherever he went by setting up shop on the sidewalk and selling his paintings to tourists, usually for a few dollars each.
    • 4.2: Introduction to molecular spectroscopy
      In a spectroscopy experiment, electromagnetic radiation of a specified range of wavelengths is allowed to pass through a sample containing a compound of interest. The sample molecules absorb energy from some of the wavelengths, and as a result jump from a low energy ‘ground state’ to some higher energy ‘excited state’. Other wavelengths are not absorbed by the sample molecule, so they pass on through.
    • 4.3: Mass Spectrometry
      Our third and final analytical technique for discussion in this chapter does not fall under the definition of spectroscopy, as it does not involve the absorbance of light by a molecule. In mass spectrometry (MS), we are interested in the mass - and therefore the molecular weight - of our compound of interest, and often the mass of fragments that are produced when the molecule is caused to break apart.
    • 4.4: Infrared spectroscopy
      Covalent bonds in organic molecules are not rigid sticks – rather, they behave more like springs. At room temperature, organic molecules are always in motion, as their bonds stretch, bend, and twist. These complex vibrations can be broken down mathematically into individual vibrational modes.
    • 4.5: Ultraviolet and visible spectroscopy
      While interaction with infrared light causes molecules to undergo vibrational transitions, the shorter wavelength, higher energy radiation in the UV (200-400 nm) and visible (400-700 nm) range of the electromagnetic spectrum causes many organic molecules to undergo electronic transitions. What this means is that when the energy from UV or visible light is absorbed by a molecule, one of its electrons jumps from a lower energy to a higher energy molecular orbital.
    • 4.P: Problems for Chapter 4