Biochemistry examines the chemistry of molecules involved in life. These range from small molecules such as carbohydrates to large molecules such as DNA. Much of the chemistry of biological molecules is organic reactions, and so its place within this book is logical.As might be expected, computational biochemists have applied the tools and methodologies of quantum chemistry to biological molecules. Many of the same techniques discussed in the previous chapters have been utilized to explicate reaction mechanisms, properties, and structures of a broad range of biomolecules, including proteins, DNA, and RNA. However, the scope of computational biochemistry is enormous, and a reasonable comprehensive coverage of this topic is beyond the scope of this book.To provide a flavor of how computational chemistry has been applied to biochemical problems, this chapter focuses on a small subset of computational biochemistry, namely, computational enzymology. Presented here are some examples of how quantum chemical computations have been used to understand the mechanism of catalysis provided by enzymes. The chapter ends with a look at one of the true "holy grails" of biochemistry: the ability to design an enzyme for a specific purpose, to catalyze a particular reaction where nature provides no such option.
MODELS FOR ENZYMATIC ACTIVITYIn 1948, Pauling proposed a model for understanding enzyme activity. 1 Pauling stated I think that enzymes are molecules that are complementary in structure to the activated complexes of the reactions they catalyze. The attraction of the enzyme molecule for the activated complex would thus lead to a decrease in its energy and hence to a decrease in the energy of activation of the reaction, and an increase in the rate of the reaction.