Section 6.1: A first look at reaction mechanisms

1. acid-base (proton transfer) reaction
2. one-step nucleophilic substitution reaction (S_N2)
3. Two-step nucleophilic substitution reaction (S_N1)

Section 6.2: Describing the thermodynamics and kinetics of chemical reactions - energy diagrams

Section 6.3: Enzymatic catalysis - the basic ideas

Section 6.4: Protein structure

1. Amino acids and peptide bonds
2. Visualizing protein structure: X-ray crystallography
3. The four levels of protein structure
4. The molecular forces that hold proteins together

Section 6.5: How enzymes work

1. The active site
2. Transition state stabilization
3. Site-directed mutagenesis
4. Enzyme inhibition
5. Catalysts in the laboratory

Section 6.P Problems for Chapter 6

Up to this point, we have been focusing on the structure of organic molecules: essentially, how these molecule are put together.  The focus of the text will now shift to the study of their reactivity: what happens, in other words, when covalent bonds within a molecule break and new covalent bonds form, as molecule A is transformed into molecule B.

In your previous college general chemistry and high school chemistry courses  (and perhaps in biology courses as well), you have no doubt seen many different examples of chemical reactions.  Most likely, these reactions were depicted by chemical equations, showing the starting products (reactants) and the finished products connected by a 'reaction arrow'.  In most cases, the structures of reactants and products were not considered - they were defined only by molecular formula and perhaps by physical state (solid, liquid, gas, or solution).  The reaction below, showing the decomposition of dinitrogen pentoxide to nitrogen dioxide and oxygen, is a typical example of the 'equation' treatment of chemical reactivity.

N₂O₂  → 2NO₂ + ½O₂

More relevant to organic and biological chemistry, you probably at some point have also seen this chemical equation, showing how living cells break down glucose (a sugar) to form water and carbon dioxide:

C₆H₁₂O₆ + 6O₂  →  6CO₂  + 6H₂O

This way of talking about chemical reactions is perfectly adequate in introductory chemistry classes, when fundamental chemical concepts like stoichiometry, thermodynamics, and kinetics are being explained for the first time.  In organic chemistry, beginning with this chapter, we will go much further.  We will certainly review the important fundamental concepts of thermodynamics and kinetics that you learned previously.  But in our discussion of organic reactivity, we will bring our understanding of organic structure into the picture, and think about how reactions take place: which bonds break, which bonds form, why a particular bond breaks or forms, the order in which bond-breaking and bond-forming takes place, and the nature of any intermediate compounds that might form. Taken together, a description of a chemical reaction at this level is called a reaction mechanism.  Beginning here, and continuing throughout the rest of the text, our main job will be to understand the mechanisms of the most important types of reactions undergone by organic molecules.