This thesis was a study of the molecular recognition process of chloramphenicol acetyltransferase (CAT). In an approach, which is complementary to site-directed mutagenesis, the substrate, acetyl Coenzyme A (AcCoA), has been modified in a variety of ways to allow quantitative evaluations of the energetics of individual enzyme-ligand interactions to be made. A series of CoA analogues have been prepared and their kinetic parameters for binding to CAT determined. These compounds had modifications in both the base and pantethrine regions of the CoA molecule.;The synthesis of CoA analogues with alternative bases involved coupling activated nucleotides with D-pantetheine-4'-phosphate which had been prepared from D-pantethine using a cyanoethyl phosphate and DCC coupling method. CoA analogues with modified pantetheine moieties were prepared by coupling pantetheine analogues with an activated adenine nucleotide.;From the kinetic studies of the CAT reaction with the modified ligands the apparent binding energies, Gapp, of some of the substituents of AcCoA have been evaluated. Analogues in which the adenine nucleotide were substituted with alternative bases were found to be relatively poor substrates for the CAT reaction. This suggests that the adenine moiety is important in the recognition process of AcCoA binding by the enzyme. AcCoA analogues with modified pantetheine moieties were found to bind relatively well. These results suggest that the pantetheine moiety may not substantially be involved in the specificity of CoA for the enzyme, but instead contribute to the binding strength of AcCoA to CAT. Examination of analogues in which the acetyl group of AcCoA was replaced by alkyl groups suggested that they bound within the chloramphenicol binding pocket in a region eight times less hydrophobic than n-octanol.