# 5.1: Prelude to Structure Determination I

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## Structural determination of organic structures

Paclitaxel, sold under the brand name Taxol® among others, is a chemotherapy medication used to treat a number of types of cancer. Paclitaxel was first isolated in 1971 from the Pacific yew and approved for medical use in 1993. Its chemical structure is quite complex, with several functional groups and a total of 11 stereogenic centers. How do chemists determine the structure of such complex molecules?

Chemical structure of Paclitaxel, sold under the brand name Taxol®. Image by Calvero., Public domain, via Wikimedia Commons

In the next two 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 begin to address, in the next two chapters, the question of how we get this knowledge in the first place. How are chemists able to draw with confidence the bonding arrangements in organic molecules, even simple ones such as acetone or ethanol? How was James Martin at Orion Analytical able to identify the chemical structure of the pigment compound responsible for the 'funky yellow color' in the forged William Aiken Walker painting?

This chapter is devoted to three very important techniques used by chemists to learn about the structures of organic molecules. First, we will learn how elemental analysis and mass spectrometry can provide us with information about the mass of a molecule as well as the mass of fragments into which the molecule has been broken. Then, we will begin our investigation of molecular spectroscopy, which is the study of how electromagnetic radiation at different wavelengths interacts in different ways with molecules - and how these interactions can be quantified, analyzed, and interpreted to gain information about molecular structure. After a brief overview of the properties of light and the elements of a molecular spectroscopy experiment, we will consider ultraviolet-visible (UV-vis) spectroscopy, with which chemists gain information about conjugated pi-bonding systems in organic molecules. Among other applications, we will see how information from UV-vis spectroscopy can be used to measure the concentration of biomolecules compounds in solution. Then we will move to a discussion of  infrared (IR) spectroscopy, the key technique to learn about functional groups present in an organic compound. T

Looking ahead, next chapter will be devoted to nuclear magnetic resonance (NMR) spectroscopy, where we use ultra-strong magnets and radiofrequency radiation to learn about the electronic environment of individual atoms in a molecule and use this information to determine the atom-to-atom bonding arrangement. For most organic chemists, NMR is one of the most powerful analytical tools available in terms of the wealth of detailed information it can provide about the structure of a molecule.